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96. Srimanta Pakhira, Benjamin S. Lengeling, Olayinka Olatunji-Ojo, Michel Caffarel, Michael Frenklach, and William A. Lester, Jr. . A Quantum Monte Carlo Study of the Reactions of CH with Acrolein. The Journal of Physical Chemistry A 2015, 119 (18) , 4214-4223. https://doi.org/10.1021/acs.jpca.5b00919
97. Joanna Lipinski-Kruszka, Jacob Stewart-Ornstein, Michael W. Chevalier, and Hana El-Samad . Using Dynamic Noise Propagation to Infer Causal Regulatory Relationships in Biochemical Networks. ACS Synthetic Biology 2015, 4 (3) , 258-264. https://doi.org/10.1021/sb5000059
98. Zachary A. Morseth, Li Wang, Egle Puodziukynaite, Gyu Leem, Alexander T. Gilligan, Thomas J. Meyer, Kirk S. Schanze, John R. Reynolds, and John M. Papanikolas . Ultrafast Dynamics in Multifunctional Ru(II)-Loaded Polymers for Solar Energy Conversion. Accounts of Chemical Research 2015, 48 (3) , 818-827. https://doi.org/10.1021/ar500382u
99. Diego A. Oyarzún, Jean-Baptiste Lugagne, and Guy-Bart V. Stan . Noise Propagation in Synthetic Gene Circuits for Metabolic Control. ACS Synthetic Biology 2015, 4 (2) , 116-125. https://doi.org/10.1021/sb400126a
100. Daven Sanassy, Paweł Widera, and Natalio Krasnogor . Meta-Stochastic Simulation of Biochemical Models for Systems and Synthetic Biology. ACS Synthetic Biology 2015, 4 (1) , 39-47. https://doi.org/10.1021/sb5001406
101. Robert S. Weber, Mariefel V. Olarte, and Huamin Wang . Modeling the Kinetics of Deactivation of Catalysts during the Upgrading of Bio-oil. Energy & Fuels 2015, 29 (1) , 273-277. https://doi.org/10.1021/ef502483t
102. Amit K. Tripathi, John G. Tsavalas, and Donald C. Sundberg . Monte Carlo Simulations of Free Radical Polymerizations with Divinyl Cross-Linker: Pre- and Postgel Simulations of Reaction Kinetics and Molecular Structure. Macromolecules 2015, 48 (1) , 184-197. https://doi.org/10.1021/ma502085x
103. Daniel A. Nissley and Edward P. O’Brien . Timing Is Everything: Unifying Codon Translation Rates and Nascent Proteome Behavior. Journal of the American Chemical Society 2014, 136 (52) , 17892-17898. https://doi.org/10.1021/ja510082j
104. Doraiswami Ramkrishna, Che-Chi Shu, and Vu Tran . New “Tau-Leap” Strategy for Accelerated Stochastic Simulation. Industrial & Engineering Chemistry Research 2014, 53 (49) , 18975-18981. https://doi.org/10.1021/ie502929q
105. Safa Shoaee, Shafigh Mehraeen, John G. Labram, Jean-Luc Brédas, Donal D. C. Bradley, Veaceslav Coropceanu, Thomas D. Anthopoulos, and James R. Durrant . Correlating Non-Geminate Recombination with Film Structure: A Comparison of Polythiophene: Fullerene Bilayer and Blend Films. The Journal of Physical Chemistry Letters 2014, 5 (21) , 3669-3676. https://doi.org/10.1021/jz5018575
106. Xin Guo, Daisuke Minakata, and John Crittenden . Computer-Based First-Principles Kinetic Monte Carlo Simulation of Polyethylene Glycol Degradation in Aqueous Phase UV/H2O2 Advanced Oxidation Process. Environmental Science & Technology 2014, 48 (18) , 10813-10820. https://doi.org/10.1021/es5029553
107. Shaghayegh Hamzehlou, Yuri Reyes, and Jose R. Leiza . Modeling the Mini-Emulsion Copolymerization of N-Butyl Acrylate with a Water-Soluble Monomer: A Monte Carlo Approach. Industrial & Engineering Chemistry Research 2014, 53 (22) , 8996-9003. https://doi.org/10.1021/ie403182t
108. Dimitrios Meimaroglou and Costas Kiparissides . Review of Monte Carlo Methods for the Prediction of Distributed Molecular and Morphological Polymer Properties. Industrial & Engineering Chemistry Research 2014, 53 (22) , 8963-8979. https://doi.org/10.1021/ie4033044
109. Edward M. Nelson, Volker Kurz, Nicolas Perry, Douglas Kyrouac, and Gregory Timp . Biological Noise Abatement: Coordinating the Responses of Autonomous Bacteria in a Synthetic Biofilm to a Fluctuating Environment Using a Stochastic Bistable Switch. ACS Synthetic Biology 2014, 3 (5) , 286-297. https://doi.org/10.1021/sb400052f
110. Eisa Zarepour, Adesoji A. Adesina, Mahbub Hassan, and Chun Tung Chou . Innovative Approach to Improving Gas-to-Liquid Fuel Catalysis via Nanosensor Network Modulation. Industrial & Engineering Chemistry Research 2014, 53 (14) , 5728-5736. https://doi.org/10.1021/ie403931x
111. Joseph Sang-II Kwon, Michael Nayhouse, Panagiotis D. Christofides, and Gerassimos Orkoulas . Protein Crystal Shape and Size Control in Batch Crystallization: Comparing Model Predictive Control with Conventional Operating Policies. Industrial & Engineering Chemistry Research 2014, 53 (13) , 5002-5014. https://doi.org/10.1021/ie400584g
112. Max B. Scheible, Günther Pardatscher, Anton Kuzyk, and Friedrich C. Simmel . Single Molecule Characterization of DNA Binding and Strand Displacement Reactions on Lithographic DNA Origami Microarrays. Nano Letters 2014, 14 (3) , 1627-1633. https://doi.org/10.1021/nl500092j
113. Adam D. Hill, Matthew C. Zoerb, Son C. Nguyen, Justin P. Lomont, Miriam A. Bowring, and Charles B. Harris . Determining Equilibrium Fluctuations Using Temperature-Dependent 2D-IR. The Journal of Physical Chemistry B 2013, 117 (49) , 15346-15355. https://doi.org/10.1021/jp403791k
114. Shaghayegh Hamzehlou, Yuri Reyes, and Jose R. Leiza . A New Insight into the Formation of Polymer Networks: A Kinetic Monte Carlo Simulation of the Cross-Linking Polymerization of S/DVB. Macromolecules 2013, 46 (22) , 9064-9073. https://doi.org/10.1021/ma4016054
115. Chen Liao and Ting Lu . A Minimal Transcriptional Controlling Network of Regulatory T Cell Development. The Journal of Physical Chemistry B 2013, 117 (42) , 12995-13004. https://doi.org/10.1021/jp402306g
116. Thierry Mora and Aleksandra M. Walczak . Effect of Phenotypic Selection on Stochastic Gene Expression. The Journal of Physical Chemistry B 2013, 117 (42) , 13194-13205. https://doi.org/10.1021/jp403231f
117. Ishtiaq Maqsood, Lance D Cundy, Matt Biesecker, Jung-Han Kimn, Dustin Johnson, Rachel Williams, and Venkat Bommisetty . Monte Carlo Simulation of Förster Resonance Energy Transfer in 3D Nanoscale Organic Bulk Heterojunction Morphologies. The Journal of Physical Chemistry C 2013, 117 (41) , 21086-21095. https://doi.org/10.1021/jp406073y
118. Junchao Xia, Nan-jie Deng, and Ronald M. Levy . NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations. The Journal of Physical Chemistry B 2013, 117 (22) , 6625-6634. https://doi.org/10.1021/jp400797y
119. Anna Synak, Piotr Bojarski, Beata Grobelna, Leszek Kułak, and Aneta Lewkowicz . Determination of Local Dye Concentration in Hybrid Porous Silica Thin Films. The Journal of Physical Chemistry C 2013, 117 (21) , 11385-11392. https://doi.org/10.1021/jp401839j
120. Kevin A. Payne, Dagmar R. D’hooge, Paul H. M. Van Steenberge, Marie-Françoise Reyniers, Michael F. Cunningham, Robin A. Hutchinson, and Guy B. Marin . ARGET ATRP of Butyl Methacrylate: Utilizing Kinetic Modeling To Understand Experimental Trends. Macromolecules 2013, 46 (10) , 3828-3840. https://doi.org/10.1021/ma400388t
121. Theodore S. Sabir, Leah K. Rowland, Jamie R. Milligan, Dong Yan, A. Wilson Aruni, Qiao Chen, Danilo S. Boskovic, R. Steven Kurti, and Christopher C. Perry . Mechanistic Investigation of Seeded Growth in Triblock Copolymer Stabilized Gold Nanoparticles. Langmuir 2013, 29 (12) , 3903-3911. https://doi.org/10.1021/la400387h
122. Ralph E. Weston, Jr., Thanh Lam Nguyen, John F. Stanton, and John R. Barker . HO + CO Reaction Rates and H/D Kinetic Isotope Effects: Master Equation Models with ab Initio SCTST Rate Constants. The Journal of Physical Chemistry A 2013, 117 (5) , 821-835. https://doi.org/10.1021/jp311928w
123. Kevin Leu, Eric Kervio, Benedikt Obermayer, Rebecca M. Turk-MacLeod, Caterina Yuan, Jesus-Mario Luevano, Jr., Eric Chen, Ulrich Gerland, Clemens Richert, and Irene A. Chen . Cascade of Reduced Speed and Accuracy after Errors in Enzyme-Free Copying of Nucleic Acid Sequences. Journal of the American Chemical Society 2013, 135 (1) , 354-366. https://doi.org/10.1021/ja3095558
124. Ginusha M. Perera, Yogendra Narayan Pandey, Abhijit A. Patil, Gila E. Stein, and Manolis Doxastakis . Reaction Kinetics in Acid-Catalyzed Deprotection of Polymer Films. The Journal of Physical Chemistry C 2012, 116 (46) , 24706-24716. https://doi.org/10.1021/jp308997g
125. Paul H. M. Van Steenberge, Dagmar R. D’hooge, Yu Wang, Mingjiang Zhong, Marie-Françoise Reyniers, Dominik Konkolewicz, Krzysztof Matyjaszewski, and Guy B. Marin . Linear Gradient Quality of ATRP Copolymers. Macromolecules 2012, 45 (21) , 8519-8531. https://doi.org/10.1021/ma3017597
126. Ishutesh Jain, David Lacoste, Dulal Panda, and Ranjith Padinhateeri . History-Dependent Depolymerization of Actin Filaments. Biochemistry 2012, 51 (38) , 7580-7587. https://doi.org/10.1021/bi300629f
127. Alex Dickson and Charles L. Brooks, III . Quantifying Hub-like Behavior in Protein Folding Networks. Journal of Chemical Theory and Computation 2012, 8 (9) , 3044-3052. https://doi.org/10.1021/ct300537s
128. Seunghee S. Jang, Kevin T. Oishi, Robert G. Egbert, and Eric Klavins . Specification and Simulation of Synthetic Multicelled Behaviors. ACS Synthetic Biology 2012, 1 (8) , 365-374. https://doi.org/10.1021/sb300034m
129. E. A. Ustinov and D. D. Do . Thermodynamic Analysis of Ordered and Disordered Monolayer of Argon Adsorption on Graphite. Langmuir 2012, 28 (25) , 9543-9553. https://doi.org/10.1021/la301328x
130. Erich D. Bain, Keith Dawes, A. Evren Özçam, Xinfang Hu, Christopher B. Gorman, Jiří Šrogl, and Jan Genzer . Surface-Initiated Polymerization by Means of Novel, Stable, Non-Ester-Based Radical Initiator. Macromolecules 2012, 45 (9) , 3802-3815. https://doi.org/10.1021/ma300491e
131. Yu Rim Lim, Seong Jun Park, Bo Jung Park, Jianshu Cao, Robert J. Silbey, and Jaeyoung Sung . Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity. Journal of Chemical Theory and Computation 2012, 8 (4) , 1415-1425. https://doi.org/10.1021/ct200785q
132. Dezső Boda and Dirk Gillespie . Steady-State Electrodiffusion from the Nernst–Planck Equation Coupled to Local Equilibrium Monte Carlo Simulations. Journal of Chemical Theory and Computation 2012, 8 (3) , 824-829. https://doi.org/10.1021/ct2007988
133. Paul H. M. Van Steenberge, Joke Vandenbergh, Dagmar R. D’hooge, Marie-Françoise Reyniers, Peter J. Adriaensens, Laurence Lutsen, Dirk J. M. Vanderzande, and Guy B. Marin . Kinetic Monte Carlo Modeling of the Sulfinyl Precursor Route for Poly(p-phenylene vinylene) Synthesis. Macromolecules 2011, 44 (22) , 8716-8726. https://doi.org/10.1021/ma201617r
134. Dominik Konkolewicz, Stanislaw Sosnowski, Dagmar R. D’hooge, Ryszard Szymanski, Marie-Françoise Reyniers, Guy B. Marin, and Krzysztof Matyjaszewski . Origin of the Difference between Branching in Acrylates Polymerization under Controlled and Free Radical Conditions: A Computational Study of Competitive Processes. Macromolecules 2011, 44 (21) , 8361-8373. https://doi.org/10.1021/ma201704w
135. Tobias J. Pflock, Silke Oellerich, June Southall, Richard J. Cogdell, G. Matthias Ullmann, and Jürgen Köhler . The Electronically Excited States of LH2 Complexes from Rhodopseudomonas acidophila Strain 10050 Studied by Time-Resolved Spectroscopy and Dynamic Monte Carlo Simulations. I. Isolated, Non-Interacting LH2 Complexes. The Journal of Physical Chemistry B 2011, 115 (28) , 8813-8820. https://doi.org/10.1021/jp202353c
136. S. Pressé, K. Ghosh, and K. A. Dill . Modeling Stochastic Dynamics in Biochemical Systems with Feedback Using Maximum Caliber. The Journal of Physical Chemistry B 2011, 115 (19) , 6202-6212. https://doi.org/10.1021/jp111112s
137. Weihua Zheng, Emilio Gallicchio, Nanjie Deng, Michael Andrec, and Ronald M. Levy . Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations. The Journal of Physical Chemistry B 2011, 115 (6) , 1512-1523. https://doi.org/10.1021/jp1089596
138. Andrew B. Goryachev. Understanding Bacterial Cell−Cell Communication with Computational Modeling. Chemical Reviews 2011, 111 (1) , 238-250. https://doi.org/10.1021/cr100286z
139. Song Cao, Boris Fürtig, Harald Schwalbe, and Shi-Jie Chen . Folding Kinetics for the Conformational Switch between Alternative RNA Structures. The Journal of Physical Chemistry B 2010, 114 (42) , 13609-13615. https://doi.org/10.1021/jp107912s
140. Peter D. Drummond, Timothy G. Vaughan, and Alexei J. Drummond. Extinction Times in Autocatalytic Systems. The Journal of Physical Chemistry A 2010, 114 (39) , 10481-10491. https://doi.org/10.1021/jp104471e
141. Won Jung, Seongeun Yang and Jaeyoung Sung. Novel Chemical Kinetics for a Single Enzyme Reaction: Relationship between Substrate Concentration and the Second Moment of Enzyme Reaction Time. The Journal of Physical Chemistry B 2010, 114 (30) , 9840-9847. https://doi.org/10.1021/jp1001868
142. Dimitrios Meimaroglou and Costas Kiparissides. A Novel Stochastic Approach for the Prediction of the Exact Topological Characteristics and Rheological Properties of Highly-Branched Polymer Chains. Macromolecules 2010, 43 (13) , 5820-5832. https://doi.org/10.1021/ma1005233
143. G. Dumazer, A. Smith and A. Lemarchand . Master Equation Approach to Gypsum Needle Crystallization. The Journal of Physical Chemistry C 2010, 114 (9) , 3830-3836. https://doi.org/10.1021/jp910775w
144. Rob D. Coalson and Mary Hongying Cheng. Discrete-State Representation of Ion Permeation Coupled to Fast Gating in a Model of ClC Chloride Channels: Comparison to Multi-ion Continuous Space Brownian Dynamics Simulations. The Journal of Physical Chemistry B 2010, 114 (3) , 1424-1433. https://doi.org/10.1021/jp907965b
145. Russell Whitesides and Michael Frenklach. Detailed Kinetic Monte Carlo Simulations of Graphene-Edge Growth. The Journal of Physical Chemistry A 2010, 114 (2) , 689-703. https://doi.org/10.1021/jp906541a
146. Zhanghan Wu, Vlad Elgart, Hong Qian and Jianhua Xing. Amplification and Detection of Single-Molecule Conformational Fluctuation through a Protein Interaction Network with Bimodal Distributions. The Journal of Physical Chemistry B 2009, 113 (36) , 12375-12381. https://doi.org/10.1021/jp903548d
147. Tiejun Xiao, Zhonghuai Hou and Houwen Xin . Stochastic Thermodynamics in Mesoscopic Chemical Oscillation Systems. The Journal of Physical Chemistry B 2009, 113 (27) , 9316-9320. https://doi.org/10.1021/jp901610x
148. Ying Li, Xiaohui Qu, Ao Ma, Glenna J. Smith, Norbert F. Scherer and Aaron R. Dinner . Models of Single-Molecule Experiments with Periodic Perturbations Reveal Hidden Dynamics in RNA Folding. The Journal of Physical Chemistry B 2009, 113 (21) , 7579-7590. https://doi.org/10.1021/jp900225q
149. Dieter Armbruster, John D. Nagy, E. A. F. van de Rijt and J. E. Rooda. Dynamic Simulations of Single-Molecule Enzyme Networks. The Journal of Physical Chemistry B 2009, 113 (16) , 5537-5544. https://doi.org/10.1021/jp807520f
150. Hong Jin, Daniel A. Heller, Jong-Ho Kim and Michael S. Strano. Stochastic Analysis of Stepwise Fluorescence Quenching Reactions on Single-Walled Carbon Nanotubes: Single Molecule Sensors. Nano Letters 2008, 8 (12) , 4299-4304. https://doi.org/10.1021/nl802010z
151. Mirco S. Till, Timm Essigke, Torsten Becker and G. Matthias Ullmann. Simulating the Proton Transfer in Gramicidin A by a Sequential Dynamical Monte Carlo Method. The Journal of Physical Chemistry B 2008, 112 (42) , 13401-13410. https://doi.org/10.1021/jp801477b
152. Nikolaos Bentenitis . A Convenient Tool for the Stochastic Simulation of Reaction Mechanisms. Journal of Chemical Education 2008, 85 (8) , 1146. https://doi.org/10.1021/ed085p1146
153. Javad R. Shahrouzi, Denis Guillaume, Pierre Rouchon and Patrick Da Costa . Stochastic Simulation and Single Events Kinetic Modeling: Application to Olefin Oligomerization. Industrial & Engineering Chemistry Research 2008, 47 (13) , 4308-4316. https://doi.org/10.1021/ie071215l
154. Jiří Horský. Semiflexible Oligomer−Polymer Binding: Combinatorial and Conditional Probability Analyses and Stochastic Simulation. Macromolecules 2008, 41 (13) , 5014-5023. https://doi.org/10.1021/ma702493w
155. Andrea Maranzana,, John R. Barker, and, Glauco Tonachini. Oxidation of Ethyne and But-2-yne. 2. Master Equation Simulations. The Journal of Physical Chemistry A 2008, 112 (16) , 3666-3675. https://doi.org/10.1021/jp077180k
156. Jin Qian,, Jizeng Wang, and, Huajian Gao. Lifetime and Strength of Adhesive Molecular Bond Clusters between Elastic Media. Langmuir 2008, 24 (4) , 1262-1270. https://doi.org/10.1021/la702401b
157. Hyonseok Hwang, , George C. Schatz and, Mark A. Ratner. Incorporation of Inhomogeneous Ion Diffusion Coefficients into Kinetic Lattice Grand Canonical Monte Carlo Simulations and Application to Ion Current Calculations in a Simple Model Ion Channel. The Journal of Physical Chemistry A 2007, 111 (49) , 12506-12512. https://doi.org/10.1021/jp075838o
158. G. Vidali,, V. Pirronello,, L. Li,, J. Roser,, G. Manicó,, E. Congiu,, H. Mehl,, A. Lederhendler,, H. B. Perets,, J. R. Brucato, and, O. Biham. Analysis of Molecular Hydrogen Formation on Low-Temperature Surfaces in Temperature Programmed Desorption Experiments. The Journal of Physical Chemistry A 2007, 111 (49) , 12611-12619. https://doi.org/10.1021/jp0760657
159. Ma Juan,, Zhonghuai Hou, and, Houwen Xin. Theoretical Study on the Effects of Internal Noise for Rate Oscillations during CO Oxidation on Platinum(110) Surfaces. The Journal of Physical Chemistry A 2007, 111 (45) , 11500-11505. https://doi.org/10.1021/jp073890e
160. David Lepzelter,, Keun-Young Kim, and, Jin Wang. Dynamics and Intrinsic Statistical Fluctuations of a Gene Switch. The Journal of Physical Chemistry B 2007, 111 (34) , 10239-10247. https://doi.org/10.1021/jp071735u
161. Thanh Lam Nguyen,, Shaun A. Carl,, Minh Tho Nguyen, and, Jozef Peeters. Quantum Chemical and Statistical Rate Investigation of the CF2(a3B1) + NO(X2Π) Reaction:  A Fast Chemical Quenching Process. The Journal of Physical Chemistry A 2007, 111 (29) , 6628-6636. https://doi.org/10.1021/jp068284i
162. Thanh Lam Nguyen,, Jozef Peeters, and, Luc Vereecken. Theoretical Reinvestigation of the O(3P) + C6H6 Reaction:  Quantum Chemical and Statistical Rate Calculations. The Journal of Physical Chemistry A 2007, 111 (19) , 3836-3849. https://doi.org/10.1021/jp0660886
163. Antonio M. Puertas, , Gerardo Odriozola. Linking Phase Behavior and Reversible Colloidal Aggregation at Low Concentrations:  Simulations and Stochastic Mean Field Theory. The Journal of Physical Chemistry B 2007, 111 (20) , 5564-5572. https://doi.org/10.1021/jp068698b
164. Kyungchan Chae and, Angela Violi. Thermal Decomposition of Decalin:  An Ab Initio Study. The Journal of Organic Chemistry 2007, 72 (9) , 3179-3185. https://doi.org/10.1021/jo062324x
165. Yonghua Wang,, Yan Li, and, Bin Wang. Stochastic Simulations of the Cytochrome P450 Catalytic Cycle. The Journal of Physical Chemistry B 2007, 111 (16) , 4251-4260. https://doi.org/10.1021/jp071222n
166. Dimitrios Meimaroglou,, Apostolos Krallis,, Vassilis Saliakas, and, Costas Kiparissides. Prediction of the Bivariate Molecular Weight - Long Chain Branching Distribution in Highly Branched Polymerization Systems Using Monte Carlo and Sectional Grid Methods. Macromolecules 2007, 40 (6) , 2224-2234. https://doi.org/10.1021/ma0623439
167. Hongli Wang,, Zhengping Fu,, Xinhang Xu, and, Qi Ouyang. Pattern Formation Induced by Internal Microscopic Fluctuations. The Journal of Physical Chemistry A 2007, 111 (7) , 1265-1270. https://doi.org/10.1021/jp0674064
168. Marco A. J. Iafolla and, David R. McMillen. Extracting Biochemical Parameters for Cellular Modeling:  A Mean-Field Approach. The Journal of Physical Chemistry B 2006, 110 (43) , 22019-22028. https://doi.org/10.1021/jp062739m
169. Thanh Lam Nguyen,, Jozef Peeters, and, Luc Vereecken. Quantum Chemical and Statistical Rate Study of the Reaction of O(3P) with Allene:  O-Addition and H-Abstraction Channels. The Journal of Physical Chemistry A 2006, 110 (44) , 12166-12176. https://doi.org/10.1021/jp0639905
170. Harpreet S. Juneja,, Asad Iqbal,, Junpin Yao, and, Farhang Shadman. Mechanism and Kinetics of Nonequilibrium and Multilayer Adsorption and Desorption of Gases on Solids. Industrial & Engineering Chemistry Research 2006, 45 (19) , 6585-6593. https://doi.org/10.1021/ie060475k
171. Ian J. Laurenzi, , John D. Bartels, , Scott L. Diamond. Regression of Multicomponent Sticking Probabilities Using a Genetic Algorithm. Industrial & Engineering Chemistry Research 2006, 45 (16) , 5482-5488. https://doi.org/10.1021/ie051159t
172. M. Ethayaraja,, Kanchan Dutta, and, Rajdip Bandyopadhyaya. Mechanism of Nanoparticle Formation in Self-Assembled Colloidal Templates:  Population Balance Model and Monte Carlo Simulation. The Journal of Physical Chemistry B 2006, 110 (33) , 16471-16481. https://doi.org/10.1021/jp0623645
173. Thanh Lam Nguyen,, Luc Vereecken, and, Jozef Peeters. Quantum Chemical and Theoretical Kinetics Study of the O(3P) + C2H2 Reaction:  A Multistate Process. The Journal of Physical Chemistry A 2006, 110 (21) , 6696-6706. https://doi.org/10.1021/jp055961k
174. Dennis C. Wylie,, Yuko Hori,, Aaron R. Dinner, and, Arup K. Chakraborty. A Hybrid Deterministic−Stochastic Algorithm for Modeling Cell Signaling Dynamics in Spatially Inhomogeneous Environments and under the Influence of External Fields. The Journal of Physical Chemistry B 2006, 110 (25) , 12749-12765. https://doi.org/10.1021/jp056231f
175. Thanh Lam Nguyen,, Bart Dils,, Shaun Avondale Carl,, Luc Vereecken, and, Jozef Peeters. Experimental and Theoretical Studies of the C2F4 + O Reaction:  Nonadiabatic Reaction Mechanism. The Journal of Physical Chemistry A 2005, 109 (43) , 9786-9794. https://doi.org/10.1021/jp053585y
176. Ravi Radhakrishnan and, Tamar Schlick. Fidelity Discrimination in DNA Polymerase β:  Differing Closing Profiles for a Mismatched (G:A) versus Matched (G:C) Base Pair. Journal of the American Chemical Society 2005, 127 (38) , 13245-13252. https://doi.org/10.1021/ja052623o
177. Thanh Lam Nguyen,, Luc Vereecken,, Xin Juan Hou,, Minh Tho Nguyen, and, Jozef Peeters. Potential Energy Surfaces, Product Distributions and Thermal Rate Coefficients of the Reaction of O(3P) with C2H4(XAg):  A Comprehensive Theoretical Study. The Journal of Physical Chemistry A 2005, 109 (33) , 7489-7499. https://doi.org/10.1021/jp052970k
178. Christopher Fockenberg,, Ralph E. Weston, Jr., and, James T. Muckerman. Product Study of the Reaction of CH3 with OH Radicals at Low Pressures and Temperatures of 300 and 612 K†. The Journal of Physical Chemistry B 2005, 109 (17) , 8415-8427. https://doi.org/10.1021/jp045792o
179. Patrick B. Warren and, Pieter Rein ten Wolde. Chemical Models of Genetic Toggle Switches. The Journal of Physical Chemistry B 2005, 109 (14) , 6812-6823. https://doi.org/10.1021/jp045523y
180. Bogdan Nowakowski and, Andrzej L. Kawczyński. Master Equation Simulations of Bistable and Excitable Dynamics in a Model of a Thermochemical System. The Journal of Physical Chemistry A 2005, 109 (14) , 3134-3138. https://doi.org/10.1021/jp047747m
181. Viktor Chikan,, Boris Nizamov, and, Stephen R. Leone. Product State Distributions of Vibrationally Excited CO(v) for the CH(X2Π) and CH(A2Δ) Channels of the C2H + O(3P) Reaction. The Journal of Physical Chemistry A 2004, 108 (49) , 10770-10782. https://doi.org/10.1021/jp040317b
182. G. Cota-Sanchez,, G. Soucy,, A. Huczko,, J. Beauvais, and, D. Drouin. Effect of Iron Catalyst on the Synthesis of Fullerenes and Carbon Nanotubes in Induction Plasma. The Journal of Physical Chemistry B 2004, 108 (50) , 19210-19217. https://doi.org/10.1021/jp047629z
183. Winnie Chien, Victor Anbalagan, Melvin Zandler, Michael Van Stipdonk, Dorothy Hanna, Garold Gresham, Gary Groenewold. Intrinsic hydration of monopositive uranyl hydroxide, nitrate, and acetate cations. Journal of the American Society for Mass Spectrometry 2004, 15 (6) , 777-783. https://doi.org/10.1021/jasms.8b02183
184. J. H. Miners,, P. Gardner,, A. M. Bradshaw, and, D. P. Woodruff. A Real-Time Vibrational Spectroscopic Investigation of the Low-Temperature Oscillatory Regime of the Reaction of NO with CO on Pt{100}. The Journal of Physical Chemistry B 2004, 108 (5) , 1708-1718. https://doi.org/10.1021/jp036487q
185. Wolfgang R. Plass, R. Graham Cooks. A model for energy transfer in inelastic molecular collisions applicable at steady state or non-steady state and for an arbitrary distribution of collision energies. Journal of the American Society for Mass Spectrometry 2003, 14 (12) , 1348-1359. https://doi.org/10.1021/jasms.8b01902
186. Garold L. Gresham,, Anita K. Gianotto,, Peter de B. Harrington,, Libo Cao,, Jill R. Scott,, John E. Olson,, Anthony D. Appelhans,, Michael J. Van Stipdonk, and, Gary. S. Groenewold. Gas-Phase Hydration of U(IV), U(V), and U(VI) Dioxo Monocations. The Journal of Physical Chemistry A 2003, 107 (41) , 8530-8538. https://doi.org/10.1021/jp035443e
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1038. Francisco Merino-Casallo, Maria J. Gomez-Benito, Yago Juste-Lanas, Ruben Martinez-Cantin, Jose M. Garcia-Aznar. Integration of in vitro and in silico Models Using Bayesian Optimization With an Application to Stochastic Modeling of Mesenchymal 3D Cell Migration. Frontiers in Physiology 2018, 9 https://doi.org/10.3389/fphys.2018.01246
1039. Qiang Zhang, Jin Li, Alistair Middleton, Sudin Bhattacharya, Rory B. Conolly. Bridging the Data Gap From in vitro Toxicity Testing to Chemical Safety Assessment Through Computational Modeling. Frontiers in Public Health 2018, 6 https://doi.org/10.3389/fpubh.2018.00261
1040. Ryszard Szymanski, Stanislaw Sosnowski. Evolution of Chain Length Distribution and Microstructure of Macromolecules in Irreversible Copolymerization Proceeding with Segmental Exchange Investigated with a New Monte Carlo Algorithm. Macromolecular Theory and Simulations 2018, 27 (5) , 1800015. https://doi.org/10.1002/mats.201800015
1041. Hidetaka Tobita. Hyperbranched Polymers Formed Through Self-Condensing Vinyl Polymerization in a Continuous Stirred-Tank Reactor (CSTR): 1. Molecular Weight Distribution. Macromolecular Theory and Simulations 2018, 27 (6) , 1800027. https://doi.org/10.1002/mats.201800027
1042. Julio C. Hernández-Ortiz, Paul H. M. Van Steenberge, Jan N. E. Duchateau, Carolina Toloza, Fons Schreurs, Marie-Françoise Reyniers, Guy B. Marin, Dagmar R. D’hooge. Sensitivity Analysis of Single-Phase Isothermal Free Radical-Induced Grafting of Polyethylene. Macromolecular Theory and Simulations 2018, 27 (6) , 1800036. https://doi.org/10.1002/mats.201800036
1043. Matthias Rank, Erwin Frey. Crowding and Pausing Strongly Affect Dynamics of Kinesin-1 Motors along Microtubules. Biophysical Journal 2018, 115 (6) , 1068-1081. https://doi.org/10.1016/j.bpj.2018.07.017
1044. Ada W.C. Yan, Andrew J. Black, James M. McCaw, Nicolas Rebuli, Joshua V. Ross, Annalisa J. Swan, Roslyn I. Hickson. The distribution of the time taken for an epidemic to spread between two communities. Mathematical Biosciences 2018, 303 , 139-147. https://doi.org/10.1016/j.mbs.2018.07.004
1045. Yao Li, Lingchen Bu. From billiards to thermodynamic laws: Stochastic energy exchange model. Chaos: An Interdisciplinary Journal of Nonlinear Science 2018, 28 (9) , 093105. https://doi.org/10.1063/1.5040296
1046. Lisa Weber, William Raymond, Brian Munsky. Identification of gene regulation models from single-cell data. Physical Biology 2018, 15 (5) , 055001. https://doi.org/10.1088/1478-3975/aabc31
1047. Benedikt von Bronk, Alexandra Götz, Madeleine Opitz. Complex microbial systems across different levels of description. Physical Biology 2018, 15 (5) , 051002. https://doi.org/10.1088/1478-3975/aac473
1048. Joëlle Barido-Sottani, Timothy G. Vaughan, Tanja Stadler. Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth–death model. Journal of The Royal Society Interface 2018, 15 (146) , 20180512. https://doi.org/10.1098/rsif.2018.0512
1049. M. López-García, M. Nowicka, C. Bendtsen, G. Lythe, S. Ponnambalam, C. Molina-París. Quantifying the phosphorylation timescales of receptor–ligand complexes: a Markovian matrix-analytic approach. Open Biology 2018, 8 (9) , 180126. https://doi.org/10.1098/rsob.180126
1050. Chapin S. Korosec, Martin J. Zuckermann, Nancy R. Forde. Dimensionality-dependent crossover in motility of polyvalent burnt-bridges ratchets. Physical Review E 2018, 98 (3) https://doi.org/10.1103/PhysRevE.98.032114
1051. Spencer G. Farrell, Arnold B. Mitnitski, Olga Theou, Kenneth Rockwood, Andrew D. Rutenberg. Probing the network structure of health deficits in human aging. Physical Review E 2018, 98 (3) https://doi.org/10.1103/PhysRevE.98.032302
1052. Yoshiya J. Matsubara, Kunihiko Kaneko. Kinetic Selection of Template Polymer with Complex Sequences. Physical Review Letters 2018, 121 (11) https://doi.org/10.1103/PhysRevLett.121.118101
1053. Tim Herpich, Juzar Thingna, Massimiliano Esposito. Collective Power: Minimal Model for Thermodynamics of Nonequilibrium Phase Transitions. Physical Review X 2018, 8 (3) https://doi.org/10.1103/PhysRevX.8.031056
1054. Emilio Incerto, Annalisa Napolitano, Mirco Tribastone. Moving Horizon Estimation of Service Demands in Queuing Networks. 2018,,, 348-354. https://doi.org/10.1109/MASCOTS.2018.00040
1055. Albert C. J. Luo, Siyu Guo. Analytical Solutions of Period-1 to Period-2 Motions in a Periodically Diffused Brusselator. Journal of Computational and Nonlinear Dynamics 2018, 13 (9) https://doi.org/10.1115/1.4038204
1056. Vladimir P. Zhdanov. Initial Phase of Replication of Plus-Stranded RNA Viruses. Biophysical Reviews and Letters 2018, 13 (03) , 93-108. https://doi.org/10.1142/S1793048018500078
1057. Karen Whitworth, Sarah Leupen, Chistopher Rakes, Mauricio Bustos, . Interactive Computer Simulations as Pedagogical Tools in Biology Labs. CBE—Life Sciences Education 2018, 17 (3) , ar46. https://doi.org/10.1187/cbe.17-09-0208
1058. Wim Hordijk, Jonathan Naylor, Natalio Krasnogor, Harold Fellermann. Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World. Life 2018, 8 (3) , 33. https://doi.org/10.3390/life8030033
1059. Mariano Asteasuain. Deterministic Approaches for Simulation of Nitroxide-Mediated Radical Polymerization. International Journal of Polymer Science 2018, 2018 , 1-16. https://doi.org/10.1155/2018/7803702
1060. Li Xu, Jin Wang, . Landscape and flux for quantifying global stability and dynamics of game theory. PLOS ONE 2018, 13 (8) , e0201130. https://doi.org/10.1371/journal.pone.0201130
1061. Margaret J. Tse, Brian K. Chu, Cameron P. Gallivan, Elizabeth L. Read, . Rare-event sampling of epigenetic landscapes and phenotype transitions. PLOS Computational Biology 2018, 14 (8) , e1006336. https://doi.org/10.1371/journal.pcbi.1006336
1062. Bradley D. Buren, Yutian R. Zhao, Judit E. Puskas, Kimberley B. McAuley. Predicting Average Molecular Weights and Branching Level for Self-Condensing Vinyl Copolymerization in a CSTR. Macromolecular Reaction Engineering 2018, 12 (4) , 1700074. https://doi.org/10.1002/mren.201700074
1063. Frits Veerman, Carsten Marr, Nikola Popović. Time-dependent propagators for stochastic models of gene expression: an analytical method. Journal of Mathematical Biology 2018, 77 (2) , 261-312. https://doi.org/10.1007/s00285-017-1196-4
1064. Matthias Reis, Justus A. Kromer, Edda Klipp. General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks. Journal of Mathematical Biology 2018, 77 (2) , 377-419. https://doi.org/10.1007/s00285-018-1205-2
1065. David Doty, David Soloveichik. Stable leader election in population protocols requires linear time. Distributed Computing 2018, 31 (4) , 257-271. https://doi.org/10.1007/s00446-016-0281-z
1066. Leonid Rubinovich, Micha Polak. Remarkable NanoConfinement Effects on Equilibrated Reactions: Statistical-Mechanics Modeling Focused on Ir Dimerization Beneath Surface Sites in Pd–Ir Nanoparticles. Topics in Catalysis 2018, 61 (12-13) , 1237-1246. https://doi.org/10.1007/s11244-018-0978-2
1067. David Borland, Hong Yi, Gavin D. Grant, Katarzyna M. Kedziora, Hui Xiao Chao, Rachel A. Haggerty, Jayashree Kumar, Samuel C. Wolff, Jeanette G. Cook, Jeremy E. Purvis. The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression. Cell Systems 2018, 7 (2) , 180-184.e4. https://doi.org/10.1016/j.cels.2018.06.004
1068. David J. Warne, Ruth E. Baker, Matthew J. Simpson. Multilevel rejection sampling for approximate Bayesian computation. Computational Statistics & Data Analysis 2018, 124 , 71-86. https://doi.org/10.1016/j.csda.2018.02.009
1069. Mario Banuelos, Suzanne Sindi. Modeling transposable element dynamics with fragmentation equations. Mathematical Biosciences 2018, 302 , 46-66. https://doi.org/10.1016/j.mbs.2018.05.009
1070. Zongmao Gao, Haoyuan Sun, Shanshan Qin, Xiaojing Yang, Chao Tang. A systematic study of the determinants of protein abundance memory in cell lineage. Science Bulletin 2018, 63 (16) , 1051-1058. https://doi.org/10.1016/j.scib.2018.07.010
1071. Jieming Li, Alexander Johnson-Buck, Yuhe Renee Yang, William M. Shih, Hao Yan, Nils G. Walter. Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat. Nature Nanotechnology 2018, 13 (8) , 723-729. https://doi.org/10.1038/s41565-018-0130-2
1072. Monjur Morshed, Brian Ingalls, Silvana Ilie. Effective implicit finite-difference method for sensitivity analysis of stiff stochastic discrete biochemical systems. IET Systems Biology 2018, 12 (4) , 123-130. https://doi.org/10.1049/iet-syb.2017.0048
1073. David M. Bianchi, Joseph R. Peterson, Tyler M. Earnest, Michael J. Hallock, Zaida Luthey-Schulten. Hybrid CME–ODE method for efficient simulation of the galactose switch in yeast. IET Systems Biology 2018, 12 (4) , 170-176. https://doi.org/10.1049/iet-syb.2017.0070
1074. Niall Murphy, Rasmus Petersen, Andrew Phillips, Boyan Yordanov, Neil Dalchau. Synthesizing and tuning stochastic chemical reaction networks with specified behaviours. Journal of The Royal Society Interface 2018, 15 (145) , 20180283. https://doi.org/10.1098/rsif.2018.0283
1075. Cameron A. Smith, Christian A. Yates. The auxiliary region method: a hybrid method for coupling PDE- and Brownian-based dynamics for reaction–diffusion systems. Royal Society Open Science 2018, 5 (8) , 180920. https://doi.org/10.1098/rsos.180920
1076. Spencer G. Farrell, Andrew D. Rutenberg. Anomalously slow transport in single-file diffusion with slow binding kinetics. Physical Review E 2018, 98 (2) https://doi.org/10.1103/PhysRevE.98.022114
1077. Pawel J. Zuk, Marek Kochańczyk, Tomasz Lipniacki. Sampling rare events in stochastic reaction-diffusion systems within trajectory looping. Physical Review E 2018, 98 (2) https://doi.org/10.1103/PhysRevE.98.022401
1078. Xiaokang Liu, Liangsuo Shu, Shiping Jin. Model of osmosis in a single-file pore. Physical Review E 2018, 98 (2) https://doi.org/10.1103/PhysRevE.98.022406
1079. P. Zimmer, K. Kruse, J. Nagler. Anomalous percolation features in molecular evolution. Physical Review E 2018, 98 (2) https://doi.org/10.1103/PhysRevE.98.022408
1080. Michele Monti, David K. Lubensky, Pieter Rein ten Wolde. Robustness of Clocks to Input Noise. Physical Review Letters 2018, 121 (7) https://doi.org/10.1103/PhysRevLett.121.078101
1081. Enrique Martínez, Laurent Capolungo, Carlos N. Tomé. Atomistic analysis of the {101¯2} twin stability and growth in α -Ti. Physical Review Materials 2018, 2 (8) https://doi.org/10.1103/PhysRevMaterials.2.083603
1082. Carl Boettiger, . From noise to knowledge: how randomness generates novel phenomena and reveals information. Ecology Letters 2018, 21 (8) , 1255-1267. https://doi.org/10.1111/ele.13085
1083. Basile Nguyen, Udo Seifert, Andre C. Barato. Phase transition in thermodynamically consistent biochemical oscillators. The Journal of Chemical Physics 2018, 149 (4) , 045101. https://doi.org/10.1063/1.5032104
1084. Aditya Savara, Jonathan E Sutton. SQERT-T: alleviating kinetic Monte Carlo (KMC)-stiffness in transient KMC simulations. Journal of Physics: Condensed Matter 2018, 30 (29) , 295901. https://doi.org/10.1088/1361-648X/aacb6d
1085. Ilaria Giannoccaro, Giovanni F. Massari, Giuseppe Carbone. Team Resilience in Complex and Turbulent Environments: The Effect of Size and Density of Social Interactions. Complexity 2018, 2018 , 1-11. https://doi.org/10.1155/2018/1923216
1086. Oliver K. Ernst, Thomas Bartol, Terrence Sejnowski, Eric Mjolsness. Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics. The Journal of Chemical Physics 2018, 149 (3) , 034107. https://doi.org/10.1063/1.5026403
1087. Pavol Bauer, Stefan Engblom, Sanja Mikulovic, Aleksandar Senek. Multiscale modelling via split-step methods in neural firing. Mathematical and Computer Modelling of Dynamical Systems 2018, 24 (4) , 426-445. https://doi.org/10.1080/13873954.2018.1488740
1088. Derya ALTINTAN, Vilda PURUTÇUOĞLU. Exact Stochastic Sşmulation Algorithms and Impulses in Biological Systems. International Journal of Computational and Experimental Science and Engineering 2018, 4 (2) , 41-47. https://doi.org/10.22399/ijcesen.405778
1089. Swarnavo Sarkar, Sheng Lin-Gibson. Computational Design of Photocured Polymers Using Stochastic Reaction-Diffusion Simulation. Advanced Theory and Simulations 2018, 1 (7) , 1800028. https://doi.org/10.1002/adts.201800028
1090. Mohammad Soheilypour, Mohammad R. K. Mofrad. Agent‐Based Modeling in Molecular Systems Biology. BioEssays 2018, 40 (7) , 1800020. https://doi.org/10.1002/bies.201800020
1091. Rosalyn C. Rael, Rafael D'Andrea, György Barabás, Annette Ostling. Emergent niche structuring leads to increased differences from neutrality in species abundance distributions. Ecology 2018, 99 (7) , 1633-1643. https://doi.org/10.1002/ecy.2238
1092. Shiliang Tan, Quang K. Loi, D. D. Do, D. Nicholson. A new interpretation of chemical potential in adsorption systems and the vapour–liquid interface. Adsorption 2018, 24 (5) , 425-430. https://doi.org/10.1007/s10450-018-9957-y
1093. George W. A. Constable, Alan J. McKane. Exploiting Fast-Variables to Understand Population Dynamics and Evolution. Journal of Statistical Physics 2018, 172 (1) , 3-43. https://doi.org/10.1007/s10955-017-1900-1
1094. Tuan L. Hoang, Roman Nazarov, Changwoo Kang, Jiangyuan Fan. Application of pulsed multi-ion irradiations in radiation damage research: A stochastic cluster dynamics simulation study. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2018, 427 , 9-13. https://doi.org/10.1016/j.nimb.2018.04.033
1095. Ofer Feinerman, Itai Pinkoviezky, Aviram Gelblum, Ehud Fonio, Nir S. Gov. The physics of cooperative transport in groups of ants. Nature Physics 2018, 14 (7) , 683-693. https://doi.org/10.1038/s41567-018-0107-y
1096. Alireza Sayyidmousavi, Katrin Rohlf. Reactive multi-particle collision dynamics with reactive boundary conditions. Physical Biology 2018, 15 (4) , 046007. https://doi.org/10.1088/1478-3975/aabc35
1097. Renu Maan, Garima Rani, Gautam I Menon, Pramod A Pullarkat. Modeling cell-substrate de-adhesion dynamics under fluid shear. Physical Biology 2018, 15 (4) , 046006. https://doi.org/10.1088/1478-3975/aabc66
1098. Tomislav Plesa, Konstantinos C. Zygalakis, David F. Anderson, Radek Erban. Noise control for molecular computing. Journal of The Royal Society Interface 2018, 15 (144) , 20180199. https://doi.org/10.1098/rsif.2018.0199
1099. Kunaal Joshi, Ishant Tiwari, Amitabha Nandi, P. Parmananda. Intrinsic stochastic resonance via set-point variation. Physical Review E 2018, 98 (1) https://doi.org/10.1103/PhysRevE.98.012218
1100. Chunyan Mu, Peter Dittrich, David Parker, Jonathan E. Rowe. Organisation-Oriented Coarse Graining and Refinement of Stochastic Reaction Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2018, 15 (4) , 1152-1166. https://doi.org/10.1109/TCBB.2018.2804395
1101. Seth Haney, Debajit Saha, Baranidharan Raman, Maxim Bazhenov. Differential effects of adaptation on odor discrimination. Journal of Neurophysiology 2018, 120 (1) , 171-185. https://doi.org/10.1152/jn.00389.2017
1102. Pilsung KANG. Implementing Adaptive Decisions in Stochastic Simulations via AOP. IEICE Transactions on Information and Systems 2018, E101.D (7) , 1950-1953. https://doi.org/10.1587/transinf.2018EDL8044
1103. Deena R. Schmidt, Roberto F. Galán, Peter J. Thomas, . Stochastic shielding and edge importance for Markov chains with timescale separation. PLOS Computational Biology 2018, 14 (6) , e1006206. https://doi.org/10.1371/journal.pcbi.1006206
1104. J. Kyle Medley, Kiri Choi, Matthias König, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C. Sealfon, Herbert M. Sauro, . Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology. PLOS Computational Biology 2018, 14 (6) , e1006220. https://doi.org/10.1371/journal.pcbi.1006220
1105. Sulav Duwal, Laura Dickinson, Saye Khoo, Max von Kleist, . Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes. PLOS Computational Biology 2018, 14 (6) , e1006155. https://doi.org/10.1371/journal.pcbi.1006155
1106. Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P. Banavar, Tau-Mu Yi, Otger Campàs, Linda R. Petzold, . The effect of cell geometry on polarization in budding yeast. PLOS Computational Biology 2018, 14 (6) , e1006241. https://doi.org/10.1371/journal.pcbi.1006241
1107. Shivam Gupta, Julien Varennes, Hendrik C. Korswagen, Andrew Mugler, . Temporal precision of regulated gene expression. PLOS Computational Biology 2018, 14 (6) , e1006201. https://doi.org/10.1371/journal.pcbi.1006201
1108. Adam Case, Jack H. Lutz, D. M. Stull. Reachability problems for continuous chemical reaction networks. Natural Computing 2018, 17 (2) , 223-230. https://doi.org/10.1007/s11047-017-9641-2
1109. Andrea Bernini, Linda Brodo, Pierpaolo Degano, Moreno Falaschi, Diana Hermith. Process calculi for biological processes. Natural Computing 2018, 17 (2) , 345-373. https://doi.org/10.1007/s11047-018-9673-2
1110. Antonella Lunelli, Andrea Pugliese. Final attack ratio in SIR epidemic models for multigroup populations. Ricerche di Matematica 2018, 67 (1) , 49-68. https://doi.org/10.1007/s11587-017-0349-5
1111. Arya A Das, Elizabeth Jacob. In silico prediction of ErbB signal activation from receptor expression profiles through a data analytics pipeline. Journal of Biosciences 2018, 43 (2) , 295-306. https://doi.org/10.1007/s12038-018-9747-4
1112. Linda Irons, Markus R. Owen, Reuben D. O’Dea, Bindi S. Brook. Effect of Loading History on Airway Smooth Muscle Cell-Matrix Adhesions. Biophysical Journal 2018, 114 (11) , 2679-2690. https://doi.org/10.1016/j.bpj.2018.04.026
1113. Niraj Kumar, Kourosh Zarringhalam, Rahul V. Kulkarni. Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit. Biophysical Journal 2018, 114 (11) , 2530-2539. https://doi.org/10.1016/j.bpj.2018.04.044
1114. Maike M.K. Hansen, Winnie Y. Wen, Elena Ingerman, Brandon S. Razooky, Cassandra E. Thompson, Roy D. Dar, Charles W. Chin, Michael L. Simpson, Leor S. Weinberger. A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization. Cell 2018, 173 (7) , 1609-1621.e15. https://doi.org/10.1016/j.cell.2018.04.005
1115. L. Silva-Dias, A. López-Castillo. Spontaneous symmetry breaking of population: Stochastic Lotka–Volterra model for competition among two similar preys and predators. Mathematical Biosciences 2018, 300 , 36-46. https://doi.org/10.1016/j.mbs.2018.03.017
1116. Kamil Kędzia, Wojtek Ptak, Jacek Sroka, Andrzej M. Kierzek. Simulation of multicellular populations with Petri nets and genome scale intracellular networks. Science of Computer Programming 2018, 157 , 3-16. https://doi.org/10.1016/j.scico.2017.10.002
1117. Melina R. Megaridis, Yiyang Lu, Erin N. Tevonian, Kendall M. Junger, Jennifer M. Moy, Kathrin Bohn-Wippert, Roy D. Dar. Fine-tuning of noise in gene expression with nucleosome remodeling. APL Bioengineering 2018, 2 (2) , 026106. https://doi.org/10.1063/1.5021183
1118. Tripti Bameta, Dibyendu Das, Ranjith Padinhateeri. Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer. Nucleic Acids Research 2018, 46 (10) , 4991-5000. https://doi.org/10.1093/nar/gky207
1119. Blai Vidiella, Josep Sardanyés, Ricard Solé. Exploiting delayed transitions to sustain semiarid ecosystems after catastrophic shifts. Journal of The Royal Society Interface 2018, 15 (143) , 20180083. https://doi.org/10.1098/rsif.2018.0083
1120. Ohad Vilk, Michael Assaf. Population extinction under bursty reproduction in a time-modulated environment. Physical Review E 2018, 97 (6) https://doi.org/10.1103/PhysRevE.97.062114
1121. Leo Bronstein, Heinz Koeppl. Marginal process framework: A model reduction tool for Markov jump processes. Physical Review E 2018, 97 (6) https://doi.org/10.1103/PhysRevE.97.062147
1122. Alex Bukoski, D. A. Steyn-Ross, Ashley F. Pickett, Moira L. Steyn-Ross. Anesthesia modifies subthreshold critical slowing down in a stochastic Hodgkin-Huxley-like model with inhibitory synaptic input. Physical Review E 2018, 97 (6) https://doi.org/10.1103/PhysRevE.97.062403
1123. Stella Stylianidou, Thomas J. Lampo, Andrew J. Spakowitz, Paul A. Wiggins. Strong disorder leads to scale invariance in complex biological systems. Physical Review E 2018, 97 (6) https://doi.org/10.1103/PhysRevE.97.062410
1124. Guanyu Wang, Charles S. Peskin. Entrainment of a cellular circadian oscillator by light in the presence of molecular noise. Physical Review E 2018, 97 (6) https://doi.org/10.1103/PhysRevE.97.062416
1125. Dongheon Lee, Yufang Ding, Arul Jayaraman, Joseph Sang-Il Kwon. Integrative Approach to Extract the Single-cell Dynamics of LPS-induced $\text{NF}\kappa\mathrm{B}$ Signal Pathway through Flow Cytometry Measurements and Parameter Estimation. 2018,,, 1975-1980. https://doi.org/10.23919/ACC.2018.8430917
1126. Kevin Burrage, Pamela Burrage, Ian Turner, Fanhai Zeng. On the Analysis of Mixed-Index Time Fractional Differential Equation Systems. Axioms 2018, 7 (2) , 25. https://doi.org/10.3390/axioms7020025
1127. Peter Helfer, Thomas R. Shultz, . Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking. PLOS Computational Biology 2018, 14 (5) , e1006147. https://doi.org/10.1371/journal.pcbi.1006147
1128. Fei Li, Minghan Chen, Radek Erban, Yang Cao. Reaction time for trimolecular reactions in compartment-based reaction-diffusion models. The Journal of Chemical Physics 2018, 148 (20) , 204108. https://doi.org/10.1063/1.5024927
1129. David L. Shis, Matthew R. Bennett,, Oleg A. Igoshin. Dynamics of Bacterial Gene Regulatory Networks. Annual Review of Biophysics 2018, 47 (1) , 447-467. https://doi.org/10.1146/annurev-biophys-070317-032947
1130. C. Caranica, A. Al-Omari, Z. Deng, J. Griffith, R. Nilsen, L. Mao, J. Arnold, H.-B. Schüttler, . Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa. PLOS ONE 2018, 13 (5) , e0196435. https://doi.org/10.1371/journal.pone.0196435
1131. Scott L. Nuismer, Ryan May, Andrew Basinski, Christopher H. Remien, . Controlling epidemics with transmissible vaccines. PLOS ONE 2018, 13 (5) , e0196978. https://doi.org/10.1371/journal.pone.0196978
1132. Francesca Di Patti, Laura Lavacchi, Rinat Arbel-Goren, Leora Schein-Lubomirsky, Duccio Fanelli, Joel Stavans, . Robust stochastic Turing patterns in the development of a one-dimensional cyanobacterial organism. PLOS Biology 2018, 16 (5) , e2004877. https://doi.org/10.1371/journal.pbio.2004877
1133. Andrey Koksharov, Chunkan Yu, Viatcheslav Bykov, Ulrich Maas, Mark Pfeifle, Matthias Olzmann. Quasi-Spectral Method for the Solution of the Master Equation for Unimolecular Reaction Systems. International Journal of Chemical Kinetics 2018, 50 (5) , 357-369. https://doi.org/10.1002/kin.21165
1134. Peter Schuster. Molecular evolution between chemistry and biology. European Biophysics Journal 2018, 47 (4) , 403-425. https://doi.org/10.1007/s00249-018-1281-7
1135. O. El-Atwani, E. Esquivel, M. Efe, E. Aydogan, Y.Q. Wang, E. Martinez, S.A. Maloy. Loop and void damage during heavy ion irradiation on nanocrystalline and coarse grained tungsten: Microstructure, effect of dpa rate, temperature, and grain size. Acta Materialia 2018, 149 , 206-219. https://doi.org/10.1016/j.actamat.2018.02.035
1136. Sandeep Choubey, Jane Kondev, Alvaro Sanchez. Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells. Biophysical Journal 2018, 114 (9) , 2072-2082. https://doi.org/10.1016/j.bpj.2018.03.031
1137. Carolin Loos, Katharina Moeller, Fabian Fröhlich, Tim Hucho, Jan Hasenauer. A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability. Cell Systems 2018, 6 (5) , 593-603.e13. https://doi.org/10.1016/j.cels.2018.04.008
1138. Ilario De Vincenzo, Giovanni F. Massari, Ilaria Giannoccaro, Giuseppe Carbone, Paolo Grigolini. Mimicking the collective intelligence of human groups as an optimization tool for complex problems. Chaos, Solitons & Fractals 2018, 110 , 259-266. https://doi.org/10.1016/j.chaos.2018.03.030
1139. Bijan Sarkar. Moran-evolution of cooperation: From well-mixed to heterogeneous complex networks. Physica A: Statistical Mechanics and its Applications 2018, 497 , 319-334. https://doi.org/10.1016/j.physa.2018.01.022
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1463. Matti Gralka, Diana Fusco, Stephen Martis, Oskar Hallatschek. Convection shapes the trade-off between antibiotic efficacy and the selection for resistance in spatial gradients. Physical Biology 2017, 14 (4) , 045011. https://doi.org/10.1088/1478-3975/aa7bb3
1464. Ilario De Vincenzo, Ilaria Giannoccaro, Giuseppe Carbone, Paolo Grigolini. Criticality triggers the emergence of collective intelligence in groups. Physical Review E 2017, 96 (2) https://doi.org/10.1103/PhysRevE.96.022309
1465. Deniz Kilinc, Alper Demir. Noise in Neuronal and Electronic Circuits: A General Modeling Framework and Non-Monte Carlo Simulation Techniques. IEEE Transactions on Biomedical Circuits and Systems 2017, 11 (4) , 958-974. https://doi.org/10.1109/TBCAS.2017.2679039
1466. Huy D. Vo, Roger B. Sidje. An adaptive solution to the chemical master equation using tensors. The Journal of Chemical Physics 2017, 147 (4) , 044102. https://doi.org/10.1063/1.4994917
1467. Matthias Bauer, Johannes Knebel, Matthias Lechner, Peter Pickl, Erwin Frey. Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers. eLife 2017, 6 https://doi.org/10.7554/eLife.25773
1468. Joanna Jȩdrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T Blackwell, . β-adrenergic signaling broadly contributes to LTP induction. PLOS Computational Biology 2017, 13 (7) , e1005657. https://doi.org/10.1371/journal.pcbi.1005657
1469. Giorgos Minas, David A. Rand, . Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference. PLOS Computational Biology 2017, 13 (7) , e1005676. https://doi.org/10.1371/journal.pcbi.1005676
1470. Lucas B. Newcomb, Mohammad Alaghemandi, Jason R. Green. Nonequilibrium phase coexistence and criticality near the second explosion limit of hydrogen combustion. The Journal of Chemical Physics 2017, 147 (3) , 034108. https://doi.org/10.1063/1.4994265
1471. Thomas O. McDonald, Franziska Michor. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics 2017, 33 (14) , 2221-2223. https://doi.org/10.1093/bioinformatics/btx146
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1473. Andrea Vandin. Language-based Abstractions for Dynamical Systems. Electronic Proceedings in Theoretical Computer Science 2017, 250 , 15-24. https://doi.org/10.4204/EPTCS.250.2
1474. Zhongwei Lin, Carl Tropper, Robert A. McDougal, Mohammand Nazrul Ishlam Patoary, William W. Lytton, Yiping Yao, Michael L. Hines. Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons. ACM Transactions on Modeling and Computer Simulation 2017, 27 (2) , 1-27. https://doi.org/10.1145/2987373
1475. Tobias Helms, Tom Warnke, Carsten Maus, Adelinde M. Uhrmacher. Semantics and Efficient Simulation Algorithms of an Expressive Multilevel Modeling Language. ACM Transactions on Modeling and Computer Simulation 2017, 27 (2) , 1-25. https://doi.org/10.1145/2998499
1476. Frank Delvigne, Jonathan Baert, Hosni Sassi, Patrick Fickers, Alexander Grünberger, Christian Dusny. Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses. Biotechnology Journal 2017, 12 (7) , 1600549. https://doi.org/10.1002/biot.201600549
1477. Marcus Kaiser, Robert L. Jack, Johannes Zimmer. Acceleration of Convergence to Equilibrium in Markov Chains by Breaking Detailed Balance. Journal of Statistical Physics 2017, 168 (2) , 259-287. https://doi.org/10.1007/s10955-017-1805-z
1478. Andrej Aderhold, Dirk Husmeier, Marco Grzegorczyk. Approximate Bayesian inference in semi-mechanistic models. Statistics and Computing 2017, 27 (4) , 1003-1040. https://doi.org/10.1007/s11222-016-9668-8
1479. Simon L. Freedman, Shiladitya Banerjee, Glen M. Hocky, Aaron R. Dinner. A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks. Biophysical Journal 2017, 113 (2) , 448-460. https://doi.org/10.1016/j.bpj.2017.06.003
1480. Hugo Wioland, Berengere Guichard, Yosuke Senju, Sarah Myram, Pekka Lappalainen, Antoine Jégou, Guillaume Romet-Lemonne. ADF/Cofilin Accelerates Actin Dynamics by Severing Filaments and Promoting Their Depolymerization at Both Ends. Current Biology 2017, 27 (13) , 1956-1967.e7. https://doi.org/10.1016/j.cub.2017.05.048
1481. Aarón Vázquez-Jiménez, Moisés Santillán, Jesús Rodríguez-González. How the extrinsic noise in gene expression can be controlled?. IFAC-PapersOnLine 2017, 50 (1) , 15092-15096. https://doi.org/10.1016/j.ifacol.2017.08.2236
1482. Christian Cuba Samaniego, Elisa Franco. An ultrasensitive biomolecular network for robust feedback control. IFAC-PapersOnLine 2017, 50 (1) , 10950-10956. https://doi.org/10.1016/j.ifacol.2017.08.2466
1483. Nadège Merabet, Joël Bordeneuve, Noélie Davezac. Modelling the redox imbalance in Dominant Optic Atrophy: the case of respiratory Complex I * *This project is supported by grants from the Centre National de la Recherche Scientifique, the Universite Paul Sabatier and, the Region Occitanie. N. Merabet is funded by the French Ministry for Research and Education and the Ecole Doctorale Aeronautique Astronautique for Ph.D. studies.. IFAC-PapersOnLine 2017, 50 (1) , 862-867. https://doi.org/10.1016/j.ifacol.2017.08.255
1484. Y. Boada, A. Vignoni, J. Picó. Multi-objective optimization for gene expression noise reduction in a synthetic gene circuit * *This work is partially supported by Spanish government and European Union (FEDER-CICYT DPI2014-55276-C5-1). Y.B. thanks grant FPI/2013-3242 of Universitat Politècnica de València, and also thanks the support from the Ayudas para movilidad dentro del Programa para la Formación de Personal Investigador (FPI) de la UPV para estancias 2016. A.V. thanks the Max Planck Society, the CSBD and the MPI-CBG. The authors are grateful to Prof. Dr. Ivo F. Sbalzarini for hosting Y.B in the MOSAIC Group for a research stay, also to Pietro Incadorna from the MOSAIC Group at CSBD for his help in the parallel algorithm implementation, and to Dr. Gilberto Reynoso-Meza from the PPGEPS at Pontifícia Universidade Católica do Paraná for his always helpful comments regarding the MOOD.. IFAC-PapersOnLine 2017, 50 (1) , 4472-4477. https://doi.org/10.1016/j.ifacol.2017.08.376
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1491. Ina Koch, Joachim Nöthen, Enrico Schleiff. Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets. Frontiers in Genetics 2017, 8 https://doi.org/10.3389/fgene.2017.00085
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1530. Dominik Schumacher, Silke Bergeler, Andrea Harms, Janet Vonck, Sabrina Huneke-Vogt, Erwin Frey, Lotte Søgaard-Andersen. The PomXYZ Proteins Self-Organize on the Bacterial Nucleoid to Stimulate Cell Division. Developmental Cell 2017, 41 (3) , 299-314.e13. https://doi.org/10.1016/j.devcel.2017.04.011
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1534. Claire Y. Zhao, Joseph L. Greenstein, Raimond L. Winslow. Mechanisms of the cyclic nucleotide cross-talk signaling network in cardiac L-type calcium channel regulation. Journal of Molecular and Cellular Cardiology 2017, 106 , 29-44. https://doi.org/10.1016/j.yjmcc.2017.01.013
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1674. Alexander Oleinick, Irina Svir, Christian Amatore. ‘Full fusion’ is not ineluctable during vesicular exocytosis of neurotransmitters by endocrine cells. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2017, 473 (2197) , 20160684. https://doi.org/10.1098/rspa.2016.0684
1675. Chong-Yang Wang, Zhi-Xi Wu, Michael Z. Q. Chen. Approximate-master-equation approach for the Kinouchi-Copelli neural model on networks. Physical Review E 2017, 95 (1) https://doi.org/10.1103/PhysRevE.95.012310
1676. Thomas McGrath, Nick S. Jones, Pieter Rein ten Wolde, Thomas E. Ouldridge. Biochemical Machines for the Interconversion of Mutual Information and Work. Physical Review Letters 2017, 118 (2) https://doi.org/10.1103/PhysRevLett.118.028101
1677. Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D'Agostino, Ivan Merelli. Implementing a Space-Aware Stochastic Simulator on Low-Power Architectures: A Systems Biology Case Study. 2017,,, 303-308. https://doi.org/10.1109/PDP.2017.55
1678. K. Selvakumar, K. Latha. An approach of disease-drug interaction model with Stochastic Petri Net. 2017,,, 1-4. https://doi.org/10.1109/TIMA.2017.8064813
1679. Ho-Lin Chen, David Doty. Parallelism and Time in Hierarchical Self-Assembly. SIAM Journal on Computing 2017, 46 (2) , 661-709. https://doi.org/10.1137/151004161
1680. Mihai Cucuringu, Radek Erban. ADM-CLE Approach for Detecting Slow Variables in Continuous Time Markov Chains and Dynamic Data. SIAM Journal on Scientific Computing 2017, 39 (1) , B76-B101. https://doi.org/10.1137/15M1017120
1681. Ruimeng Hu, Mike Ludkovski. Sequential Design for Ranking Response Surfaces. SIAM/ASA Journal on Uncertainty Quantification 2017, 5 (1) , 212-239. https://doi.org/10.1137/15M1045168
1682. Margaret Callahan, Daniela Calvetti, Erkki Somersalo. Beyond the Model Limit: Parameter Inference Across Scales. SIAM/ASA Journal on Uncertainty Quantification 2017, 5 (1) , 665-693. https://doi.org/10.1137/15M105505X
1683. J. L. Hart, A. Alexanderian, P. A. Gremaud. Efficient Computation of Sobol' Indices for Stochastic Models. SIAM Journal on Scientific Computing 2017, 39 (4) , A1514-A1530. https://doi.org/10.1137/16M106193X
1684. Jonatan Lindén, Pavol Bauer, Stefan Engblom, Bengt Jonsson. Exposing Inter-Process Information for Efficient Parallel Discrete Event Simulation of Spatial Stochastic Systems. 2017,,, 53-64. https://doi.org/10.1145/3064911.3064916
1685. Mohamed N. M. Bahrudeen, Sofia Startceva, Andre S. Ribeiro. Effects of Extrinsic Noise are Promoter Kinetics Dependent. 2017,,, 44-47. https://doi.org/10.1145/3093293.3093295
1686. Mansooreh Ahmadian, Shuo Wang, John Tyson, Young Cao. Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study. 2017,,, 464-473. https://doi.org/10.1145/3107411.3107437
1687. Chantal Nguyen, Kimberly J. Schlesinger, Jean M. Carlson. Data-Driven Models for Individual and Group Decision Making. 2017,,, 852-859. https://doi.org/10.1145/3110025.3116204
1688. Luca Marchetti, Rosario Lombardo, Corrado Priami. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks. Complexity 2017, 2017 , 1-12. https://doi.org/10.1155/2017/1232868
1689. Shailesh Tamrakar, Paul Richmond, Roshan M D’Souza. PI-FLAME: A parallel immune system simulator using the FLAME graphic processing unit environment. SIMULATION 2017, 93 (1) , 69-84. https://doi.org/10.1177/0037549716673724
1690. Rosario Lombardo, Corrado Priami. Graphical Modeling Meets Systems Pharmacology. Gene Regulation and Systems Biology 2017, 11 , 117762501769193. https://doi.org/10.1177/1177625017691937
1691. Sara Montagna, Andrea Omicini. Agent-Based Modelling in Multicellular Systems Biology. 2017,,, 159-178. https://doi.org/10.4018/978-1-5225-1756-6.ch007
1692. Shaojie Ding, Min Qian, Hong Qian, Xuejuan Zhang. Numerical simulations of piecewise deterministic Markov processes with an application to the stochastic Hodgkin-Huxley model. The Journal of Chemical Physics 2016, 145 (24) , 244107. https://doi.org/10.1063/1.4971429
1693. M. Navarro Jimenez, O. P. Le Maître, O. M. Knio. Global sensitivity analysis in stochastic simulators of uncertain reaction networks. The Journal of Chemical Physics 2016, 145 (24) , 244106. https://doi.org/10.1063/1.4971797
1694. Arya A. Das, T. A. Darsana, Elizabeth Jacob. Agent-based re-engineering of ErbB signaling: A modeling pipeline for integrative Systems Biology. Bioinformatics 2016, 371 , btw709. https://doi.org/10.1093/bioinformatics/btw709
1695. Yaolai Wang, Feng Liu, Wei Wang. Kinetics of transcription initiation directed by multiple cis -regulatory elements on the glnAp2 promoter. Nucleic Acids Research 2016, 44 (22) , 10530-10538. https://doi.org/10.1093/nar/gkw1150
1696. Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey, . Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli. PLOS Computational Biology 2016, 12 (12) , e1005243. https://doi.org/10.1371/journal.pcbi.1005243
1697. Irene Otero-Muras, Julio R. Banga, . Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis. PLOS ONE 2016, 11 (12) , e0166867. https://doi.org/10.1371/journal.pone.0166867
1698. Botond Cseke, David Schnoerr, Manfred Opper, Guido Sanguinetti. Expectation propagation for continuous time stochastic processes. Journal of Physics A: Mathematical and Theoretical 2016, 49 (49) , 494002. https://doi.org/10.1088/1751-8113/49/49/494002
1699. Brian Drawert, Andreas Hellander, Ben Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle, Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Chris Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold, . Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PLOS Computational Biology 2016, 12 (12) , e1005220. https://doi.org/10.1371/journal.pcbi.1005220
1700. Stefanie Winkelmann, Christof Schütte. The spatiotemporal master equation: Approximation of reaction-diffusion dynamics via Markov state modeling. The Journal of Chemical Physics 2016, 145 (21) , 214107. https://doi.org/10.1063/1.4971163
1701. Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo, . Driving Cells to the Desired State in a Bimodal Distribution through Manipulation of Internal Noise with Biologically Practicable Approaches. PLOS ONE 2016, 11 (12) , e0167563. https://doi.org/10.1371/journal.pone.0167563
1702. Brian Berkowitz, Ishai Dror, Scott K. Hansen, Harvey Scher. Measurements and models of reactive transport in geological media. Reviews of Geophysics 2016, 54 (4) , 930-986. https://doi.org/10.1002/2016RG000524
1703. Benjamin Hosemann, Marco Drache, Sabine Beuermann. Advanced Kinetic Parameter Fit Applied to Radical Copolymerizations. Macromolecular Symposia 2016, 370 (1) , 17-25. https://doi.org/10.1002/masy.201600095
1704. Enrico Bertuzzo, Flavio Finger, Lorenzo Mari, Marino Gatto, Andrea Rinaldo. On the probability of extinction of the Haiti cholera epidemic. Stochastic Environmental Research and Risk Assessment 2016, 30 (8) , 2043-2055. https://doi.org/10.1007/s00477-014-0906-3
1705. Dan Goreac, Eduard Rotenstein. Infection Time in Multistable Gene Networks. A Backward Stochastic Variational Inequality with Nonconvex Switch-Dependent Reflection Approach. Set-Valued and Variational Analysis 2016, 24 (4) , 707-734. https://doi.org/10.1007/s11228-016-0382-7
1706. Lin L. Liu, Justin Brumbaugh, Ori Bar-Nur, Zachary Smith, Matthias Stadtfeld, Alexander Meissner, Konrad Hochedlinger, Franziska Michor. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Reports 2016, 17 (12) , 3395-3406. https://doi.org/10.1016/j.celrep.2016.11.080
1707. Ankit Gupta, Benjamin Hepp, Mustafa Khammash. Noise Induces the Population-Level Entrainment of Incoherent, Uncoupled Intracellular Oscillators. Cell Systems 2016, 3 (6) , 521-531.e13. https://doi.org/10.1016/j.cels.2016.10.006
1708. Mathias Heltberg, Ryan A. Kellogg, Sandeep Krishna, Savaş Tay, Mogens H. Jensen. Noise Induces Hopping between NF-κB Entrainment Modes. Cell Systems 2016, 3 (6) , 532-539.e3. https://doi.org/10.1016/j.cels.2016.11.014
1709. Shaghayegh Hamzehlou, Yuri Reyes, Jose R. Leiza. Quantitative study on the homogeneity of networks synthesized by nitroxide-mediated radical copolymerization of styrene and divinylbenzene. European Polymer Journal 2016, 85 , 244-255. https://doi.org/10.1016/j.eurpolymj.2016.10.015
1710. Andrew Duncan, Radek Erban, Konstantinos Zygalakis. Hybrid framework for the simulation of stochastic chemical kinetics. Journal of Computational Physics 2016, 326 , 398-419. https://doi.org/10.1016/j.jcp.2016.08.034
1711. Libertad Pantoja-Hernández, Elena Álvarez-Buylla, Carlos F. Aguilar-Ibáñez, Adriana Garay-Arroyo, Alberto Soria-López, Juan Carlos Martínez-García. Retroactivity effects dependency on the transcription factors binding mechanisms. Journal of Theoretical Biology 2016, 410 , 77-106. https://doi.org/10.1016/j.jtbi.2016.08.012
1712. Choujun Zhan, Chi K. Tse, Michael Small. A general stochastic model for studying time evolution of transition networks. Physica A: Statistical Mechanics and its Applications 2016, 464 , 198-210. https://doi.org/10.1016/j.physa.2016.07.034
1713. Zhen Wang, Chris T. Bauch, Samit Bhattacharyya, Alberto d'Onofrio, Piero Manfredi, Matjaž Perc, Nicola Perra, Marcel Salathé, Dawei Zhao. Statistical physics of vaccination. Physics Reports 2016, 664 , 1-113. https://doi.org/10.1016/j.physrep.2016.10.006
1714. Hyejin Yang, Jong Ho Won, Soojin Kang, Il Joon Moon, Sung Hwa Hong, Jihwan Woo. Prediction of vowel identification for cochlear implant using a computational model. Speech Communication 2016, 85 , 19-28. https://doi.org/10.1016/j.specom.2016.10.005
1715. Atefeh Taherian Fard, Sriganesh Srihari, Jessica C Mar, Mark A Ragan. Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. npj Systems Biology and Applications 2016, 2 (1) https://doi.org/10.1038/npjsba.2016.1
1716. Huihai Wu, Axel von Kamp, Vytautas Leoncikas, Wataru Mori, Nilgun Sahin, Albert Gevorgyan, Catherine Linley, Marek Grabowski, Ahmad A Mannan, Nicholas Stoy, Graham R Stewart, Lara T Ward, David J M Lewis, Jacek Sroka, Hiroshi Matsuno, Steffen Klamt, Hans V Westerhoff, Johnjoe McFadden, Nicholas J Plant, Andrzej M Kierzek. MUFINS: multi-formalism interaction network simulator. npj Systems Biology and Applications 2016, 2 (1) https://doi.org/10.1038/npjsba.2016.32
1717. John Pickton, Keith Iain Hopcraft, Eric Jakeman. The emergence of waves in random discrete systems. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/s41598-016-0022-3
1718. Zhaojie Deng, Sam Arsenault, Cristian Caranica, James Griffith, Taotao Zhu, Ahmad Al-Omari, Heinz-Bernd Schüttler, Jonathan Arnold, Leidong Mao. Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/srep35828
1719. Kang Qiu, Li-fang Wang, Jian Shen, Alssadig A. M. Yousif, Peng He, Dan-dan Shao, Xiao-min Zhang, John B. Kirunda, Ya Jia. A van der Waals-like Transition Between Normal and Cancerous Phases in Cell Populations Dynamics of Colorectal Cancer. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/srep36620
1720. Iona K. Paterson, Andy Hoyle, Gabriela Ochoa, Craig Baker-Austin, Nick G. H. Taylor. Optimising Antibiotic Usage to Treat Bacterial Infections. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/srep37853
1721. Seth Haney, Tannishtha Reya, Maxim Bazhenov. Delayed onset of symptoms through feedback interference in chronic cancers. Convergent Science Physical Oncology 2016, 2 (4) , 045002. https://doi.org/10.1088/2057-1739/2/4/045002
1722. Manca Bizjak, Nikolaj Zimic, Miha Mraz, Miha Moškon. Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa B Oscillatory Response. Journal of Computational Biology 2016, 23 (12) , 923-933. https://doi.org/10.1089/cmb.2016.0065
1723. Orazio Palmieri, Tommaso Mazza, Stefano Castellana, Anna Panza, Tiziana Latiano, Giuseppe Corritore, Angelo Andriulli, Anna Latiano. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS: A Journal of Integrative Biology 2016, 20 (12) , 692-698. https://doi.org/10.1089/omi.2016.0147
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1725. Saurav Talukdar, Shreyas Bhaban, Donatello Materassi, Murti Salapaka. Steady state dynamics of molecular motors reveals load dependent cooperativity. 2016,,, 3356-3362. https://doi.org/10.1109/CDC.2016.7798774
1726. A. Borri, P. Palumbo, A. Singh. Noise reduction for enzymatic reactions: A case study for stochastic product clearance. 2016,,, 5851-5856. https://doi.org/10.1109/CDC.2016.7799169
1727. Jessica M. Conway, John J. Dennehy, Abhyudai Singh. Optimizing phage λ survival in a changing environment: Stochastic model predictions. 2016,,, 5881-5887. https://doi.org/10.1109/CDC.2016.7799174
1728. Huy D. Vo, Roger B. Sidje. Solving the chemical master equation by aggregation and Krylov approximations. 2016,,, 7093-7098. https://doi.org/10.1109/CDC.2016.7799362
1729. Mostafa Herajy. Semantics-based parallelization for the stochastic simulation of complex cell cycle regulations. 2016,,, 110-113. https://doi.org/10.1109/CIBEC.2016.7836132
1730. Sayed Ahmad Salehi, Keshab K. Parhi, Marc D. Riedel. Computing Polynomials by Chemical Reaction Networks. 2016,,, 1-6. https://doi.org/10.1109/GLOCOM.2016.7841678
1731. Peter J. Thomas, Andrew W. Eckford. Capacity of a Simple Intercellular Signal Transduction Channel. IEEE Transactions on Information Theory 2016, 62 (12) , 7358-7382. https://doi.org/10.1109/TIT.2016.2599178
1732. Tom Warnke, Oliver Reinhardt, Adelinde M. Uhrmacher. Population-based CTMCS and agent-based models. 2016,,, 1253-1264. https://doi.org/10.1109/WSC.2016.7822181
1733. Nicole E. Radde, Marc-Thorsten Hütt. The Physics behind Systems Biology. EPJ Nonlinear Biomedical Physics 2016, 4 (1) https://doi.org/10.1140/epjnbp/s40366-016-0034-8
1734. Kiyoshi Ezawa. General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?. BMC Bioinformatics 2016, 17 (1) https://doi.org/10.1186/s12859-016-1105-7
1735. Kiyoshi Ezawa. General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation. BMC Bioinformatics 2016, 17 (1) https://doi.org/10.1186/s12859-016-1167-6
1736. Rania Assab, Laura Temime. The role of hand hygiene in controlling norovirus spread in nursing homes. BMC Infectious Diseases 2016, 16 (1) https://doi.org/10.1186/s12879-016-1702-0
1737. Livio Bioglio, Mathieu Génois, Christian L. Vestergaard, Chiara Poletto, Alain Barrat, Vittoria Colizza. Recalibrating disease parameters for increasing realism in modeling epidemics in closed settings. BMC Infectious Diseases 2016, 16 (1) https://doi.org/10.1186/s12879-016-2003-3
1738. Alexander Lück, Verena Wolf. Generalized method of moments for estimating parameters of stochastic reaction networks. BMC Systems Biology 2016, 10 (1) https://doi.org/10.1186/s12918-016-0342-8
1739. Min K. Roh, Bernie J. Daigle. SParSE++: improved event-based stochastic parameter search. BMC Systems Biology 2016, 10 (1) https://doi.org/10.1186/s12918-016-0367-z
1740. Zbigniew Korwek, Karolina Tudelska, Paweł Nałęcz-Jawecki, Maciej Czerkies, Wiktor Prus, Joanna Markiewicz, Marek Kochańczyk, Tomasz Lipniacki. Importins promote high-frequency NF-κB oscillations increasing information channel capacity. Biology Direct 2016, 11 (1) https://doi.org/10.1186/s13062-016-0164-z
1741. Jack D. Cowan, Jeremy Neuman, Wim van Drongelen. Wilson–Cowan Equations for Neocortical Dynamics. The Journal of Mathematical Neuroscience 2016, 6 (1) https://doi.org/10.1186/s13408-015-0034-5
1742. Stefan Widgren, Stefan Engblom, Pavol Bauer, Jenny Frössling, Ulf Emanuelson, Ann Lindberg. Data-driven network modelling of disease transmission using complete population movement data: spread of VTEC O157 in Swedish cattle. Veterinary Research 2016, 47 (1) https://doi.org/10.1186/s13567-016-0366-5
1743. Nataliya G. Batina, Christopher J. Crnich, David F. Anderson, Dörte Döpfer. Identifying conditions for elimination and epidemic potential of methicillin-resistant Staphylococcus aureus in nursing homes. Antimicrobial Resistance & Infection Control 2016, 5 (1) https://doi.org/10.1186/s13756-016-0130-7
1744. Daniel Nichol, Mark Robertson-Tessi, Peter Jeavons, Alexander R.A. Anderson. Stochasticity in the Genotype-Phenotype Map: Implications for the Robustness and Persistence of Bet-Hedging. Genetics 2016, 204 (4) , 1523-1539. https://doi.org/10.1534/genetics.116.193474
1745. Laura MacCalman, Iain J. McKendrick, Matthew Denwood, Gavin Gibson, Stephen Catterall, Giles Innocent, Hola Adrakey, Joanne Crawford, Alice Davis, Brian Miller, Carla Alexander. MAPRA: Modelling Animal Pathogens: Review and Adaptation. EFSA Supporting Publications 2016, 13 (12) https://doi.org/10.2903/sp.efsa.2016.EN-1112
1746. Gian Marco Palamara, Francesco Carrara, Matthew J. Smith, Owen L. Petchey. The effects of demographic stochasticity and parameter uncertainty on predicting the establishment of introduced species. Ecology and Evolution 2016, 6 (23) , 8440-8451. https://doi.org/10.1002/ece3.2495
1747. Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi, . Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLOS Computational Biology 2016, 12 (11) , e1005222. https://doi.org/10.1371/journal.pcbi.1005222
1748. Rong Gui, Quan Liu, Yuangen Yao, Haiyou Deng, Chengzhang Ma, Ya Jia, Ming Yi. Noise Decomposition Principle in a Coherent Feed-Forward Transcriptional Regulatory Loop. Frontiers in Physiology 2016, 7 https://doi.org/10.3389/fphys.2016.00600
1749. Zhiwei He, Meng Zhan, Shuai Liu, Zebo Fang, Chenggui Yao, . An Algorithm for Finding the Singleton Attractors and Pre-Images in Strong-Inhibition Boolean Networks. PLOS ONE 2016, 11 (11) , e0166906. https://doi.org/10.1371/journal.pone.0166906
1750. Brian Drawert, Stefan Hellander, Michael Trogdon, Tau-Mu Yi, Linda Petzold. A framework for discrete stochastic simulation on 3D moving boundary domains. The Journal of Chemical Physics 2016, 145 (18) , 184113. https://doi.org/10.1063/1.4967338
1751. David Murrugarra, Jacob Miller, Alex N. Mueller. Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms. Frontiers in Neuroscience 2016, 10 https://doi.org/10.3389/fnins.2016.00513
1752. Konstantinos Tsekouras, Thomas C. Custer, Hossein Jashnsaz, Nils G. Walter, Steve Pressé, . A novel method to accurately locate and count large numbers of steps by photobleaching. Molecular Biology of the Cell 2016, 27 (22) , 3601-3615. https://doi.org/10.1091/mbc.e16-06-0404
1753. David A. Benson, Diogo Bolster. Arbitrarily complex chemical reactions on particles. Water Resources Research 2016, 52 (11) , 9190-9200. https://doi.org/10.1002/2016WR019368
1754. Benjamin Hosemann, Marco Drache, Sabine Beuermann. Experimentally Calibrated Random Walk of Branched Polymers: A Pragmatic Approach. Macromolecular Theory and Simulations 2016, 25 (6) , 508-517. https://doi.org/10.1002/mats.201600067
1755. Rachelle N. Binny, Alex James, Michael J. Plank. Collective Cell Behaviour with Neighbour-Dependent Proliferation, Death and Directional Bias. Bulletin of Mathematical Biology 2016, 78 (11) , 2277-2301. https://doi.org/10.1007/s11538-016-0222-9
1756. Iain G. Johnston, Nick S. Jones. Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations. The American Journal of Human Genetics 2016, 99 (5) , 1150-1162. https://doi.org/10.1016/j.ajhg.2016.09.016
1757. Bo Cheng, Min Lin, Yuhui Li, Guoyou Huang, Hui Yang, Guy M. Genin, Vikram S. Deshpande, Tian Jian Lu, Feng Xu. An Integrated Stochastic Model of Matrix-Stiffness-Dependent Filopodial Dynamics. Biophysical Journal 2016, 111 (9) , 2051-2061. https://doi.org/10.1016/j.bpj.2016.09.026
1758. Justin Feigelman, Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam Filipczyk, Timm Schroeder, Fabian J. Theis, Carsten Marr, Manfred Claassen. Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells. Cell Systems 2016, 3 (5) , 480-490.e13. https://doi.org/10.1016/j.cels.2016.11.001
1759. Ioannis G. Aviziotis, Nikolaos Cheimarios, Thomas Duguet, Constantin Vahlas, Andreas G. Boudouvis. Multiscale modeling and experimental analysis of chemical vapor deposited aluminum films: Linking reactor operating conditions with roughness evolution. Chemical Engineering Science 2016, 155 , 449-458. https://doi.org/10.1016/j.ces.2016.08.039
1760. Bradford P. Taylor, Jonathan Dushoff, Joshua S. Weitz. Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases. Journal of Theoretical Biology 2016, 408 , 145-154. https://doi.org/10.1016/j.jtbi.2016.08.016
1761. Valérie Voorsluijs, Yannick De Decker. Emergence of chaos in a spatially confined reactive system. Physica D: Nonlinear Phenomena 2016, 335 , 1-9. https://doi.org/10.1016/j.physd.2016.05.005
1762. Sebastian Himbert, Mindy Chapman, David W. Deamer, Maikel C. Rheinstädter. Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers. Scientific Reports 2016, 6 (1) https://doi.org/10.1038/srep31285
1763. Darka Labavić, Hildegard Meyer-Ortmanns. Rock-paper-scissors played within competing domains in predator-prey games. Journal of Statistical Mechanics: Theory and Experiment 2016, 2016 (11) , 113402. https://doi.org/10.1088/1742-5468/2016/11/113402
1764. Shay Be’er, Michael Assaf. Rare events in stochastic populations under bursty reproduction. Journal of Statistical Mechanics: Theory and Experiment 2016, 2016 (11) , 113501. https://doi.org/10.1088/1742-5468/2016/11/113501
1765. Peter G. Fennell, Sergey Melnik, James P. Gleeson. Limitations of discrete-time approaches to continuous-time contagion dynamics. Physical Review E 2016, 94 (5) https://doi.org/10.1103/PhysRevE.94.052125
1766. Haider Hasan Jafri, R. K. Brojen Singh, Ramakrishna Ramaswamy. Generalized synchrony of coupled stochastic processes with multiplicative noise. Physical Review E 2016, 94 (5) https://doi.org/10.1103/PhysRevE.94.052216
1767. Cameron Ferwerda, Ovidiu Lipan. Splitting nodes and linking channels: A method for assembling biocircuits from stochastic elementary units. Physical Review E 2016, 94 (5) https://doi.org/10.1103/PhysRevE.94.052404
1768. Spencer G. Farrell, Arnold B. Mitnitski, Kenneth Rockwood, Andrew D. Rutenberg. Network model of human aging: Frailty limits and information measures. Physical Review E 2016, 94 (5) https://doi.org/10.1103/PhysRevE.94.052409
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1770. Lance R. Williams. Programs as Polypeptides. Artificial Life 2016, 22 (4) , 451-482. https://doi.org/10.1162/ARTL_a_00213
1771. Pavol Bauer, Stefan Engblom, Stefan Widgren. Fast event-based epidemiological simulations on national scales. The International Journal of High Performance Computing Applications 2016, 30 (4) , 438-453. https://doi.org/10.1177/1094342016635723
1772. Peter Schuster. Increase in Complexity and Information through Molecular Evolution. Entropy 2016, 18 (11) , 397. https://doi.org/10.3390/e18110397
1773. Scott L. Nuismer, Benjamin M. Althouse, Ryan May, James J. Bull, Sean P. Stromberg, Rustom Antia. Eradicating infectious disease using weakly transmissible vaccines. Proceedings of the Royal Society B: Biological Sciences 2016, 283 (1841) , 20161903. https://doi.org/10.1098/rspb.2016.1903
1774. Max Schelker, Caroline Maria Mair, Fabian Jolmes, Robert-William Welke, Edda Klipp, Andreas Herrmann, Max Flöttmann, Christian Sieben, . Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency. PLOS Computational Biology 2016, 12 (10) , e1005075. https://doi.org/10.1371/journal.pcbi.1005075
1775. Luca Bortolussi, Cheng Feng. Location Aggregation of Spatial Population CTMC Models. Electronic Proceedings in Theoretical Computer Science 2016, 227 , 30-43. https://doi.org/10.4204/EPTCS.227.3
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2169. Etsuko Nonaka, Richard Svanbäck, Xavier Thibert-Plante, Göran Englund, Åke Brännström. Mechanisms by Which Phenotypic Plasticity Affects Adaptive Divergence and Ecological Speciation. The American Naturalist 2015, 186 (5) , E126-E143. https://doi.org/10.1086/683231
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2179. Simone Rizzetto, Corrado Priami, Attila Csikász-Nagy, . Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PLOS Computational Biology 2015, 11 (10) , e1004424. https://doi.org/10.1371/journal.pcbi.1004424
2180. Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni, . Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models. PLOS Computational Biology 2015, 11 (10) , e1004292. https://doi.org/10.1371/journal.pcbi.1004292
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2190. Changhong Shi, Shuqiang Wang, Tianshou Zhou, Yiguo Jiang. Post-transcriptional regulation tends to attenuate the mRNA noise and to increase the mRNA gain. Physical Biology 2015, 12 (5) , 056002. https://doi.org/10.1088/1478-3975/12/5/056002
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2196. Ramon Grima. Linear-noise approximation and the chemical master equation agree up to second-order moments for a class of chemical systems. Physical Review E 2015, 92 (4) https://doi.org/10.1103/PhysRevE.92.042124
2197. Peter Ashcroft, Arne Traulsen, Tobias Galla. When the mean is not enough: Calculating fixation time distributions in birth-death processes. Physical Review E 2015, 92 (4) https://doi.org/10.1103/PhysRevE.92.042154
2198. Ziya Kalay. Kinetics of self-assembly via facilitated diffusion: Formation of the transcription complex. Physical Review E 2015, 92 (4) https://doi.org/10.1103/PhysRevE.92.042716
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2281. Qi-ming Pei, Xuan Zhan, Li-jian Yang, Jian Shen, Li-fang Wang, Kang Qui, Ting Liu, J. B. Kirunda, A. A. M. Yousif, An-bang Li, Ya Jia. Fluctuation and noise propagation in phenotypic transition cascades of clonal populations. Physical Review E 2015, 92 (1) https://doi.org/10.1103/PhysRevE.92.012721
2282. Chenling Dong, Bin Chen. Catch-slip bonds can be dispensable for motor force regulation during skeletal muscle contraction. Physical Review E 2015, 92 (1) https://doi.org/10.1103/PhysRevE.92.012723
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2303. Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Simone Vincenzi, Luca Bolzoni. Epidemiological modelling for the assessment of bovine tuberculosis surveillance in the dairy farm network in Emilia-Romagna (Italy). Epidemics 2015, 11 , 62-70. https://doi.org/10.1016/j.epidem.2015.02.007
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2321. Ovidiu Pârvu, David Gilbert, Monika Heiner, Fei Liu, Nigel Saunders, Simon Shaw. Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes. ACM Transactions on Modeling and Computer Simulation 2015, 25 (2) , 1-25. https://doi.org/10.1145/2742546
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2334. Tommaso Biancalani, Lee DeVille, Nigel Goldenfeld. Framework for analyzing ecological trait-based models in multidimensional niche spaces. Physical Review E 2015, 91 (5) https://doi.org/10.1103/PhysRevE.91.052107
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2342. Sulav Duwal, Stefanie Winkelmann, Christof Schütte, Max von Kleist, . Optimal Treatment Strategies in the Context of ‘Treatment for Prevention’ against HIV-1 in Resource-Poor Settings. PLOS Computational Biology 2015, 11 (4) , e1004200. https://doi.org/10.1371/journal.pcbi.1004200
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2349. Pascal Kordt, Jeroen J. M. van der Holst, Mustapha Al Helwi, Wolfgang Kowalsky, Falk May, Alexander Badinski, Christian Lennartz, Denis Andrienko. Modeling of Organic Light Emitting Diodes: From Molecular to Device Properties. Advanced Functional Materials 2015, 25 (13) , 1955-1971. https://doi.org/10.1002/adfm.201403004
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2357. Alejandro Seif, Ernesto S. Loscar, Tomás S. Grigera. Aging and crystallization in a lattice glass model. Physical Review E 2015, 91 (4) https://doi.org/10.1103/PhysRevE.91.042302
2358. Blerta Shtylla, James P. Keener. Mathematical modeling of bacterial track-altering motors: Track cleaving through burnt-bridge ratchets. Physical Review E 2015, 91 (4) https://doi.org/10.1103/PhysRevE.91.042711
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2361. Francisco Chinesta, Morgan Magnin, Olivier Roux, Amine Ammar, Elias Cueto. Kinetic Theory Modeling and Efficient Numerical Simulation of Gene Regulatory Networks Based on Qualitative Descriptions. Entropy 2015, 17 (4) , 1896-1915. https://doi.org/10.3390/e17041896
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2363. Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass, Adelinde M. Uhrmacher, . Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells. PLOS Computational Biology 2015, 11 (3) , e1004106. https://doi.org/10.1371/journal.pcbi.1004106
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2366. Matthew Hartfield, Samuel Alizon, . Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants. PLOS Computational Biology 2015, 11 (3) , e1004149. https://doi.org/10.1371/journal.pcbi.1004149
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2377. Elvis Pandžić, Jérémie Rossy, Katharina Gaus. Tracking molecular dynamics without tracking: image correlation of photo-activation microscopy. Methods and Applications in Fluorescence 2015, 3 (1) , 014006. https://doi.org/10.1088/2050-6120/3/1/014006
2378. Mattia Petroni, Nikolaj Zimic, Miha Mraz, Miha Moškon. Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites. Journal of Computational Biology 2015, 22 (3) , 218-226. https://doi.org/10.1089/cmb.2014.0064
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2384. B. Ashby, K. C. King. Diversity and the maintenance of sex by parasites. Journal of Evolutionary Biology 2015, 28 (3) , 511-520. https://doi.org/10.1111/jeb.12590
2385. Cecilia Noecker, Krista Schaefer, Kelly Zaccheo, Yiding Yang, Judy Day, Vitaly Ganusov. Simple Mathematical Models Do Not Accurately Predict Early SIV Dynamics. Viruses 2015, 7 (3) , 1189-1217. https://doi.org/10.3390/v7031189
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2388. Johannes Eckstein, Nikolaus Berndt, Hermann-Georg Holzhütter, . Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion. PLOS Computational Biology 2015, 11 (2) , e1004033. https://doi.org/10.1371/journal.pcbi.1004033
2389. Manuel Barrio, Kevin Burrage, Pamela Burrage. Stochastic linear multistep methods for the simulation of chemical kinetics. The Journal of Chemical Physics 2015, 142 (6) , 064101. https://doi.org/10.1063/1.4907008
2390. Kei Sumiyoshi, Kazuki Hirata, Noriko Hiroi, Akira Funahashi. Acceleration of discrete stochastic biochemical simulation using GPGPU. Frontiers in Physiology 2015, 6 https://doi.org/10.3389/fphys.2015.00042
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2543. Kevin J. Tsai, Chuan-Hsiung Chang, . Diagnostics for Stochastic Genome-Scale Modeling via Model Slicing and Debugging. PLoS ONE 2014, 9 (11) , e110380. https://doi.org/10.1371/journal.pone.0110380
2544. Alisa Santarlasci, Gianluca Martelloni, Filippo Frizzi, Giacomo Santini, Franco Bagnoli, . Modeling Warfare in Social Animals: A "Chemical" Approach. PLoS ONE 2014, 9 (11) , e111310. https://doi.org/10.1371/journal.pone.0111310
2545. Frederic von Wegner, Nicolas Wieder, Rainer H. A. Fink. Microdomain calcium fluctuations as a colored noise process. Frontiers in Genetics 2014, 5 https://doi.org/10.3389/fgene.2014.00376
2546. Ryszard Szymanski, Stanislaw Sosnowski. On Narrowing Chain-length Distributions in Ideally Dispersed Polymerization Systems. Macromolecular Theory and Simulations 2014, 23 (9) , 550-554. https://doi.org/10.1002/mats.201400055
2547. Dirk P. Kroese, Tim Brereton, Thomas Taimre, Zdravko I. Botev. Why the Monte Carlo method is so important today. Wiley Interdisciplinary Reviews: Computational Statistics 2014, 6 (6) , 386-392. https://doi.org/10.1002/wics.1314
2548. Etsuko Nonaka, Åke Brännström, Richard Svanbäck. Assortative mating can limit the evolution of phenotypic plasticity. Evolutionary Ecology 2014, 28 (6) , 1057-1074. https://doi.org/10.1007/s10682-014-9728-5
2549. Yael Artzy-Randrup, Mercedes Pascual. Composite temporal strategies in pathogen evolution: balancing invasion and persistence. Theoretical Ecology 2014, 7 (4) , 325-334. https://doi.org/10.1007/s12080-014-0221-0
2550. Arvind R. Subramaniam, Brian M. Zid, Erin K. O’Shea. An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation. Cell 2014, 159 (5) , 1200-1211. https://doi.org/10.1016/j.cell.2014.10.043
2551. Eriko Fukuda, Satoshi Kokubo, Jun Tanimoto, Zhen Wang, Aya Hagishima, Naoki Ikegaya. Risk assessment for infectious disease and its impact on voluntary vaccination behavior in social networks. Chaos, Solitons & Fractals 2014, 68 , 1-9. https://doi.org/10.1016/j.chaos.2014.07.004
2552. Tamás Székely, Kevin Burrage. Stochastic simulation in systems biology. Computational and Structural Biotechnology Journal 2014, 12 (20-21) , 14-25. https://doi.org/10.1016/j.csbj.2014.10.003
2553. S. Sadhukhan, P. Gouze, T. Dutta. A simulation study of reactive flow in 2-D involving dissolution and precipitation in sedimentary rocks. Journal of Hydrology 2014, 519 , 2101-2110. https://doi.org/10.1016/j.jhydrol.2014.10.019
2554. Sunpeng Wang, Libin Rong. Stochastic population switch may explain the latent reservoir stability and intermittent viral blips in HIV patients on suppressive therapy. Journal of Theoretical Biology 2014, 360 , 137-148. https://doi.org/10.1016/j.jtbi.2014.06.042
2555. Paul François. Evolving phenotypic networks in silico. Seminars in Cell & Developmental Biology 2014, 35 , 90-97. https://doi.org/10.1016/j.semcdb.2014.06.012
2556. Shev MacNamara. Multiscale modeling of dorsoventral patterning in Drosophila. Seminars in Cell & Developmental Biology 2014, 35 , 82-89. https://doi.org/10.1016/j.semcdb.2014.07.001
2557. Chris Sherlock, Andrew Golightly, Colin S Gillespie. Bayesian inference for hybrid discrete-continuous stochastic kinetic models. Inverse Problems 2014, 30 (11) , 114005. https://doi.org/10.1088/0266-5611/30/11/114005
2558. Hong-Yan Shih, Nigel Goldenfeld. Path-integral calculation for the emergence of rapid evolution from demographic stochasticity. Physical Review E 2014, 90 (5) https://doi.org/10.1103/PhysRevE.90.050702
2559. Lifang Huang, Zhanjiang Yuan, Peijiang Liu, Tianshou Zhou. Feedback-induced counterintuitive correlations of gene expression noise with bursting kinetics. Physical Review E 2014, 90 (5) https://doi.org/10.1103/PhysRevE.90.052702
2560. John Zenk, Rebecca Schulman, . An Assembly Funnel Makes Biomolecular Complex Assembly Efficient. PLoS ONE 2014, 9 (10) , e111233. https://doi.org/10.1371/journal.pone.0111233
2561. Eshel Ben-Jacob, Mingyang Lu, Daniel Schultz, Jose' N. Onuchic. The physics of bacterial decision making. Frontiers in Cellular and Infection Microbiology 2014, 4 https://doi.org/10.3389/fcimb.2014.00154
2562. Juan Carlos Castro-Palacio, Tibor Nagy, Raymond J. Bemish, Markus Meuwly. Computational study of collisions between O( 3 P) and NO( 2 Π) at temperatures relevant to the hypersonic flight regime. The Journal of Chemical Physics 2014, 141 (16) , 164319. https://doi.org/10.1063/1.4897263
2563. Benjamin D. Dalziel, Kai Huang, Jemma L. Geoghegan, Nimalan Arinaminpathy, Edward J. Dubovi, Bryan T. Grenfell, Stephen P. Ellner, Edward C. Holmes, Colin R. Parrish, . Contact Heterogeneity, Rather Than Transmission Efficiency, Limits the Emergence and Spread of Canine Influenza Virus. PLoS Pathogens 2014, 10 (10) , e1004455. https://doi.org/10.1371/journal.ppat.1004455
2564. Maria L. Guerriero, Ozgur E. Akman, Gerben van Ooijen. Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure. Frontiers in Plant Science 2014, 5 https://doi.org/10.3389/fpls.2014.00564
2565. Konstantinos Biliouris, Emma Weeding, Yiannis N. Kaznessis. SynBioSS Designer Modeling Suite. 2014,,, 1-18. https://doi.org/10.1002/3527600906.mcb.20120062
2566. C. Bianca, A. Lemarchand. Determination of reaction flux from concentration fluctuations near a Hopf bifurcation. The Journal of Chemical Physics 2014, 141 (14) , 144102. https://doi.org/10.1063/1.4897325
2567. Peter F. Rowat, Priscilla E. Greenwood. The ISI distribution of the stochastic Hodgkin-Huxley neuron. Frontiers in Computational Neuroscience 2014, 8 https://doi.org/10.3389/fncom.2014.00111
2568. Vo Hong Thanh, Corrado Priami, Roberto Zunino. Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays. The Journal of Chemical Physics 2014, 141 (13) , 134116. https://doi.org/10.1063/1.4896985
2569. Umberto Picchini. Inference for SDE Models via Approximate Bayesian Computation. Journal of Computational and Graphical Statistics 2014, 23 (4) , 1080-1100. https://doi.org/10.1080/10618600.2013.866048
2570. Margit Heiske, Christine Nazaret, Jean-Pierre Mazat. Modeling the respiratory chain complexes with biothermokinetic equations — The case of complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2014, 1837 (10) , 1707-1716. https://doi.org/10.1016/j.bbabio.2014.07.013
2571. Fei Liu, Mary-Ann Blätke, Monika Heiner, Ming Yang. Modelling and simulating reaction–diffusion systems using coloured Petri nets. Computers in Biology and Medicine 2014, 53 , 297-308. https://doi.org/10.1016/j.compbiomed.2014.07.004
2572. Jin Fu, Sheng Wu, Hong Li, Linda R. Petzold. The time dependent propensity function for acceleration of spatial stochastic simulation of reaction–diffusion systems. Journal of Computational Physics 2014, 274 , 524-549. https://doi.org/10.1016/j.jcp.2014.06.025
2573. Zhilin Qu, Gang Hu, Alan Garfinkel, James N. Weiss. Nonlinear and stochastic dynamics in the heart. Physics Reports 2014, 543 (2) , 61-162. https://doi.org/10.1016/j.physrep.2014.05.002
2574. Chitra R Nayak, Aidan I Brown, Andrew D Rutenberg. Protein translocation without specific quality control in a computational model of the Tat system. Physical Biology 2014, 11 (5) , 056005. https://doi.org/10.1088/1478-3975/11/5/056005
2575. Luca Ciandrini, Izaak Neri, Jean Charles Walter, Olivier Dauloudet, Andrea Parmeggiani. Motor protein traffic regulation by supply–demand balance of resources. Physical Biology 2014, 11 (5) , 056006. https://doi.org/10.1088/1478-3975/11/5/056006
2576. Saar Rahav, Upendra Harbola. An integral fluctuation theorem for systems with unidirectional transitions. Journal of Statistical Mechanics: Theory and Experiment 2014, 2014 (10) , P10044. https://doi.org/10.1088/1742-5468/2014/10/P10044
2577. Peican Zhu, Jie Han. Asynchronous Stochastic Boolean Networks as Gene Network Models. Journal of Computational Biology 2014, 21 (10) , 771-783. https://doi.org/10.1089/cmb.2014.0057
2578. Marian Boguñá, Luis F. Lafuerza, Raúl Toral, M. Ángeles Serrano. Simulating non-Markovian stochastic processes. Physical Review E 2014, 90 (4) https://doi.org/10.1103/PhysRevE.90.042108
2579. Oleg Kogan, Michael Khasin, Baruch Meerson, David Schneider, Christopher R. Myers. Two-strain competition in quasineutral stochastic disease dynamics. Physical Review E 2014, 90 (4) https://doi.org/10.1103/PhysRevE.90.042149
2580. Michael Hinczewski, D. Thirumalai. Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise. Physical Review X 2014, 4 (4) https://doi.org/10.1103/PhysRevX.4.041017
2581. Duluxan Sritharan, Sridevi V. Sarma. Fragility in Dynamic Networks: Application to Neural Networks in the Epileptic Cortex. Neural Computation 2014, 26 (10) , 2294-2327. https://doi.org/10.1162/NECO_a_00644
2582. Melanie I. Stefan, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy, . Multi-state Modeling of Biomolecules. PLoS Computational Biology 2014, 10 (9) , e1003844. https://doi.org/10.1371/journal.pcbi.1003844
2583. E. Marshall, I. Stansfield, M. C. Romano. Ribosome recycling induces optimal translation rate at low ribosomal availability. Journal of The Royal Society Interface 2014, 11 (98) , 20140589. https://doi.org/10.1098/rsif.2014.0589
2584. Tamás Székely, Kevin Burrage, Marc Mangel, Michael B. Bonsall, . Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages. PLoS Computational Biology 2014, 10 (9) , e1003794. https://doi.org/10.1371/journal.pcbi.1003794
2585. Elife Dogan-Ciftci, Edward J. Allen. Derivation of Several SDE Systems in One- and Two-Locus Population Genetics. Stochastic Analysis and Applications 2014, 32 (5) , 761-775. https://doi.org/10.1080/07362994.2014.922030
2586. J. Hasenauer, V. Wolf, A. Kazeroonian, F. J. Theis. Method of conditional moments (MCM) for the Chemical Master Equation. Journal of Mathematical Biology 2014, 69 (3) , 687-735. https://doi.org/10.1007/s00285-013-0711-5
2587. Sebastiano de Franciscis, Giulio Caravagna, Alberto d’Onofrio. Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. Natural Computing 2014, 13 (3) , 297-307. https://doi.org/10.1007/s11047-014-9424-y
2588. Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini. A stochastic model of catalytic reaction networks in protocells. Natural Computing 2014, 13 (3) , 367-377. https://doi.org/10.1007/s11047-014-9445-6
2589. Fernando López-Caamal, Tatiana T. Marquez-Lago. Exact Probability Distributions of Selected Species in Stochastic Chemical Reaction Networks. Bulletin of Mathematical Biology 2014, 76 (9) , 2334-2361. https://doi.org/10.1007/s11538-014-9985-z
2590. Luca Ciandrini, M. Carmen Romano, Andrea Parmeggiani. Stepping and Crowding of Molecular Motors: Statistical Kinetics from an Exclusion Process Perspective. Biophysical Journal 2014, 107 (5) , 1176-1184. https://doi.org/10.1016/j.bpj.2014.07.012
2591. Jason Lloyd-Price, Huy Tran, Andre S. Ribeiro. Dynamics of small genetic circuits subject to stochastic partitioning in cell division. Journal of Theoretical Biology 2014, 356 , 11-19. https://doi.org/10.1016/j.jtbi.2014.04.018
2592. Albert J. Markvoort, Sam Sinai, Martin A. Nowak. Computer simulations of cellular group selection reveal mechanism for sustaining cooperation. Journal of Theoretical Biology 2014, 357 , 123-133. https://doi.org/10.1016/j.jtbi.2014.04.029
2593. Qianqian Ma, Caner Kazanci. How much of the storage in the ecosystem is due to cycling?. Journal of Theoretical Biology 2014, 357 , 134-142. https://doi.org/10.1016/j.jtbi.2014.05.014
2594. Adam W. Grace, Dirk P. Kroese, Werner Sandmann. Automated State-Dependent Importance Sampling for Markov Jump Processes via Sampling from the Zero-Variance Distribution. Journal of Applied Probability 2014, 51 (03) , 741-755. https://doi.org/10.1017/S0021900200011645
2595. William O. Hancock. Bidirectional cargo transport: moving beyond tug of war. Nature Reviews Molecular Cell Biology 2014, 15 (9) , 615-628. https://doi.org/10.1038/nrm3853
2596. David A. Kennedy, Vanja Dukic, Greg Dwyer. Pathogen Growth in Insect Hosts: Inferring the Importance of Different Mechanisms Using Stochastic Models and Response-Time Data. The American Naturalist 2014, 184 (3) , 407-423. https://doi.org/10.1086/677308
2597. M. Aldinucci, M. Torquati, C. Spampinato, M. Drocco, C. Misale, C. Calcagno, M. Coppo. Parallel stochastic systems biology in the cloud. Briefings in Bioinformatics 2014, 15 (5) , 798-813. https://doi.org/10.1093/bib/bbt040
2598. Peter Kreyssig, Christian Wozar, Stephan Peter, Tomás Veloz, Bashar Ibrahim, Peter Dittrich. Effects of small particle numbers on long-term behaviour in discrete biochemical systems. Bioinformatics 2014, 30 (17) , i475-i481. https://doi.org/10.1093/bioinformatics/btu453
2599. A. Lee, K.  atuszy ski. Variance bounding and geometric ergodicity of Markov chain Monte Carlo kernels for approximate Bayesian computation. Biometrika 2014, 101 (3) , 655-671. https://doi.org/10.1093/biomet/asu027
2600. Maxim S. Shkarayev, R. K. P. Zia. Exact results for a simple epidemic model on a directed network: Explorations of a system in a nonequilibrium steady state. Physical Review E 2014, 90 (3) https://doi.org/10.1103/PhysRevE.90.032107
2601. Armin P. Schoech, Nicolae Radu Zabet. Facilitated diffusion buffers noise in gene expression. Physical Review E 2014, 90 (3) https://doi.org/10.1103/PhysRevE.90.032701
2602. Jesus Miro-Bueno, Petr Sosík. Brain clock driven by neuropeptides and second messengers. Physical Review E 2014, 90 (3) https://doi.org/10.1103/PhysRevE.90.032705
2603. Joris Paijmans, Pieter Rein ten Wolde. Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression. Physical Review E 2014, 90 (3) https://doi.org/10.1103/PhysRevE.90.032708
2604. Margaret E. Johnson, Gerhard Hummer. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 2014, 4 (3) https://doi.org/10.1103/PhysRevX.4.031037
2605. Stefano Mariani. On the "Local-to-Global" Issue in Self-Organisation: Chemical Reactions with Custom Kinetic Rates. 2014,,, 61-67. https://doi.org/10.1109/SASOW.2014.14
2606. Michael Taynnan Barros, Sasitharan Balasubramaniam, Brendan Jennings. Using Information Metrics and Molecular Communication to Detect Cellular Tissue Deformation. IEEE Transactions on NanoBioscience 2014, 13 (3) , 278-288. https://doi.org/10.1109/TNB.2014.2351451
2607. FEI LIU, MONIKA HEINER, MING YANG. MODELING AND ANALYZING BIOLOGICAL SYSTEMS USING COLORED HIERARCHICAL PETRI NETS ILLUSTRATED BY C. ELEGANS VULVAL DEVELOPMENT. Journal of Biological Systems 2014, 22 (03) , 463-493. https://doi.org/10.1142/S0218339014500181
2608. Adam W. Grace, Dirk P. Kroese, Werner Sandmann. Automated State-Dependent Importance Sampling for Markov Jump Processes via Sampling from the Zero-Variance Distribution. Journal of Applied Probability 2014, 51 (3) , 741-755. https://doi.org/10.1239/jap/1409932671
2609. Sidhartha Chaudhury, Jaques Reifman, Anders Wallqvist. Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1. The Journal of Immunology 2014, 193 (5) , 2073-2086. https://doi.org/10.4049/jimmunol.1401054
2610. David Schnoerr, Guido Sanguinetti, Ramon Grima. Validity conditions for moment closure approximations in stochastic chemical kinetics. The Journal of Chemical Physics 2014, 141 (8) , 084103. https://doi.org/10.1063/1.4892838
2611. Li Xu, Kun Zhang, Jin Wang, . Exploring the Mechanisms of Differentiation, Dedifferentiation, Reprogramming and Transdifferentiation. PLoS ONE 2014, 9 (8) , e105216. https://doi.org/10.1371/journal.pone.0105216
2612. Timothy G. Vaughan, Denise Kühnert, Alex Popinga, David Welch, Alexei J. Drummond. Efficient Bayesian inference under the structured coalescent. Bioinformatics 2014, 30 (16) , 2272-2279. https://doi.org/10.1093/bioinformatics/btu201
2613. Anne-Florence Bitbol, David J. Schwab, . Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes. PLoS Computational Biology 2014, 10 (8) , e1003778. https://doi.org/10.1371/journal.pcbi.1003778
2614. Matthew L. Robb, Vahid Shahrezaei, . Stochastic Cellular Fate Decision Making by Multiple Infecting Lambda Phage. PLoS ONE 2014, 9 (8) , e103636. https://doi.org/10.1371/journal.pone.0103636
2615. Nik J. Cunniffe, Francisco F. Laranjeira, Franco M. Neri, R. Erik DeSimone, Christopher A. Gilligan, . Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus. PLoS Computational Biology 2014, 10 (8) , e1003753. https://doi.org/10.1371/journal.pcbi.1003753
2616. David Liao, Thea D. Tlsty. Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations. Interface Focus 2014, 4 (4) , 20140038. https://doi.org/10.1098/rsfs.2014.0038
2617. Bence Mélykúti, João P. Hespanha, Mustafa Khammash. Equilibrium distributions of simple biochemical reaction systems for time-scale separation in stochastic reaction networks. Journal of The Royal Society Interface 2014, 11 (97) , 20140054. https://doi.org/10.1098/rsif.2014.0054
2618. Bo Liu, Zhanjiang Yuan, Kazuyuki Aihara, Luonan Chen. Reinitiation enhances reliable transcriptional responses in eukaryotes. Journal of The Royal Society Interface 2014, 11 (97) , 20140326. https://doi.org/10.1098/rsif.2014.0326
2619. S. Bubendorfer, M. Koltai, F. Rossmann, V. Sourjik, K. M. Thormann. Secondary bacterial flagellar system improves bacterial spreading by increasing the directional persistence of swimming. Proceedings of the National Academy of Sciences 2014, 111 (31) , 11485-11490. https://doi.org/10.1073/pnas.1405820111
2620. John A. Cole, Zaida Luthey-Schulten. Whole Cell Modeling: From Single Cells to Colonies. Israel Journal of Chemistry 2014, 54 (8-9) , 1219-1229. https://doi.org/10.1002/ijch.201300147
2621. Gökçen A. Altun-Ciftçioğlu, Ayşegül Ersoy-Meriçboyu, Clifford L. Henderson. Simulation of models for multifunctional photopolymerization kinetics. Polymer Engineering & Science 2014, 54 (8) , 1737-1746. https://doi.org/10.1002/pen.23713
2622. Jae Kyoung Kim, Krešimir Josić, Matthew R. Bennett. The Validity of Quasi-Steady-State Approximations in Discrete Stochastic Simulations. Biophysical Journal 2014, 107 (3) , 783-793. https://doi.org/10.1016/j.bpj.2014.06.012
2623. Patrick Smadbeck, Yiannis N Kaznessis. Solution of chemical master equations for nonlinear stochastic reaction networks. Current Opinion in Chemical Engineering 2014, 5 , 90-95. https://doi.org/10.1016/j.coche.2014.07.001
2624. Andre Levchenko, Ilya Nemenman. Cellular noise and information transmission. Current Opinion in Biotechnology 2014, 28 , 156-164. https://doi.org/10.1016/j.copbio.2014.05.002
2625. Scott W. Robinson, Marco Fernandes, Holger Husi. Current advances in systems and integrative biology. Computational and Structural Biotechnology Journal 2014, 11 (18) , 35-46. https://doi.org/10.1016/j.csbj.2014.08.007
2626. Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri. Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Information and Computation 2014, 236 , 19-34. https://doi.org/10.1016/j.ic.2014.01.010
2627. Vashti Galpin. Hybrid semantics for Bio-PEPA. Information and Computation 2014, 236 , 122-145. https://doi.org/10.1016/j.ic.2014.01.016
2628. Mingyang Lu, José Onuchic, Eshel Ben-Jacob. Construction of an Effective Landscape for Multistate Genetic Switches. Physical Review Letters 2014, 113 (7) https://doi.org/10.1103/PhysRevLett.113.078102
2629. Daniel Ehrens, Duluxan Sritharan, Sridevi V. Sarma. Instability detector of a fragile neural network: Application to seizure detection in epilepsy. 2014,,, 6569-6572. https://doi.org/10.1109/EMBC.2014.6945133
2630. Daven Sanassy, Harold Fellermann, Natalio Krasnogor, Savas Konur, Laurentiu M. Mierla, Marian Gheorghe, Christophe Ladroue, Sara Kalvala. Modelling and Stochastic Simulation of Synthetic Biological Boolean Gates. 2014,,, 404-408. https://doi.org/10.1109/HPCC.2014.68
2631. P. Gaspard, D. Andrieux. Kinetics and thermodynamics of first-order Markov chain copolymerization. The Journal of Chemical Physics 2014, 141 (4) , 044908. https://doi.org/10.1063/1.4890821
2632. Philippe C. Faucon, Keith Pardee, Roshan M. Kumar, Hu Li, Yuin-Han Loh, Xiao Wang, . Gene Networks of Fully Connected Triads with Complete Auto-Activation Enable Multistability and Stepwise Stochastic Transitions. PLoS ONE 2014, 9 (7) , e102873. https://doi.org/10.1371/journal.pone.0102873
2633. B. Zhang, P. G. Wolynes. Stem cell differentiation as a many-body problem. Proceedings of the National Academy of Sciences 2014, 111 (28) , 10185-10190. https://doi.org/10.1073/pnas.1408561111
2634. Andreas Milias-Argeitis, John Lygeros, Mustafa Khammash. Fast variance reduction for steady-state simulation and sensitivity analysis of stochastic chemical systems using shadow function estimators. The Journal of Chemical Physics 2014, 141 (2) , 024104. https://doi.org/10.1063/1.4886935
2635. Peter Thill. Dynamic disorder and the energetic costs of information transduction. The Journal of Chemical Physics 2014, 141 (1) , 015102. https://doi.org/10.1063/1.4885725
2636. A. J. Peel, J. R. C. Pulliam, A. D. Luis, R. K. Plowright, T. J. O'Shea, D. T. S. Hayman, J. L. N. Wood, C. T. Webb, O. Restif. The effect of seasonal birth pulses on pathogen persistence in wild mammal populations. Proceedings of the Royal Society B: Biological Sciences 2014, 281 (1786) , 20132962. https://doi.org/10.1098/rspb.2013.2962
2637. Eric Neuhaus, Thomas Herrmann, Iakovos Vittorias, Dieter Lilge, Gerd Mannebach, Andrei Gonioukh, Markus Busch. Modeling the Polymeric Microstructure of LDPE in Tubular and Autoclave Reactors with a Coupled Deterministic and Stochastic Simulation Approach. Macromolecular Theory and Simulations 2014, 23 (7) , 415-428. https://doi.org/10.1002/mats.201400014
2638. Vasileios Touloupidis. Catalytic Olefin Polymerization Process Modeling: Multi-Scale Approach and Modeling Guidelines for Micro-Scale/Kinetic Modeling. Macromolecular Reaction Engineering 2014, 8 (7) , 508-527. https://doi.org/10.1002/mren.201300188
2639. Timothy J. Taylor, Istvan Z. Kiss. Interdependency and hierarchy of exact and approximate epidemic models on networks. Journal of Mathematical Biology 2014, 69 (1) , 183-211. https://doi.org/10.1007/s00285-013-0699-x
2640. Juan Carlos Cordova, Adrian O. Olivares, Yongdae Shin, Benjamin M. Stinson, Stephane Calmat, Karl R. Schmitz, Marie-Eve Aubin-Tam, Tania A. Baker, Matthew J. Lang, Robert T. Sauer. Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine. Cell 2014, 158 (3) , 647-658. https://doi.org/10.1016/j.cell.2014.05.043
2641. Adrien Senecal, Brian Munsky, Florence Proux, Nathalie Ly, Floriane E. Braye, Christophe Zimmer, Florian Mueller, Xavier Darzacq. Transcription Factors Modulate c-Fos Transcriptional Bursts. Cell Reports 2014, 8 (1) , 75-83. https://doi.org/10.1016/j.celrep.2014.05.053
2642. Jiang-Xing Chen, Jin-Xing Zhu, Ye-Hua Zhao, Wei-Gang Sun, Jiang-Rong Xu, He-ping Ying. Simulating bistable biochemical systems by means of reactive multiparticle collision dynamics. Communications in Nonlinear Science and Numerical Simulation 2014, 19 (7) , 2505-2512. https://doi.org/10.1016/j.cnsns.2013.11.013
2643. Hesam Makki, Koen N.S. Adema, Elias A.J.F. Peters, Jozua Laven, Leendert G.J. van der Ven, Rolf A.T.M. van Benthem, Gijsbertus de With. A simulation approach to study photo-degradation processes of polymeric coatings. Polymer Degradation and Stability 2014, 105 , 68-79. https://doi.org/10.1016/j.polymdegradstab.2014.03.040
2644. Srividya Iyer-Biswas, Gavin E. Crooks, Norbert F. Scherer, Aaron R. Dinner. Universality in Stochastic Exponential Growth. Physical Review Letters 2014, 113 (2) https://doi.org/10.1103/PhysRevLett.113.028101
2645. Danilo Pianini, Stefano Sebastio, Andrea Vandin. Distributed statistical analysis of complex systems modeled through a chemical metaphor. 2014,,, 416-423. https://doi.org/10.1109/HPCSim.2014.6903715
2646. Michael Taynnan Barros, Sasitharan Balasubramaniam, Brendan Jennings, Yevgeni Koucheryavy. Transmission Protocols for Calcium-Signaling-Based Molecular Communications in Deformable Cellular Tissue. IEEE Transactions on Nanotechnology 2014, 13 (4) , 779-788. https://doi.org/10.1109/TNANO.2014.2321492
2647. Ankit Gupta, Corentin Briat, Mustafa Khammash, . A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks. PLoS Computational Biology 2014, 10 (6) , e1003669. https://doi.org/10.1371/journal.pcbi.1003669
2648. R. D. Dar, N. N. Hosmane, M. R. Arkin, R. F. Siliciano, L. S. Weinberger. Screening for noise in gene expression identifies drug synergies. Science 2014, 344 (6190) , 1392-1396. https://doi.org/10.1126/science.1250220
2649. C. Bianca, A. Lemarchand. Temporal cross-correlation asymmetry and departure from equilibrium in a bistable chemical system. The Journal of Chemical Physics 2014, 140 (22) , 224105. https://doi.org/10.1063/1.4882070
2650. Tatiana T. Marquez-Lago, Mario Andrea Marchisio. Synthetic Biology: Dynamic Modeling and Construction of Cell Systems. 2014,,, 493-544. https://doi.org/10.1002/9783527631209.ch75
2651. Shankar Mukherji, Erin K O'Shea. Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance. eLife 2014, 3 https://doi.org/10.7554/eLife.02678
2652. Doraiswami Ramkrishna, Meenesh R. Singh. Population Balance Modeling: Current Status and Future Prospects. Annual Review of Chemical and Biomolecular Engineering 2014, 5 (1) , 123-146. https://doi.org/10.1146/annurev-chembioeng-060713-040241
2653. Andre Leier, Manuel Barrio, Tatiana T. Marquez-Lago. Exact model reduction with delays: closed-form distributions and extensions to fully bi-directional monomolecular reactions. Journal of The Royal Society Interface 2014, 11 (95) , 20140108. https://doi.org/10.1098/rsif.2014.0108
2654. Daniel Sánchez-Taltavull, Tomás Alarcón. Robustness of differentiation cascades with symmetric stem cell division. Journal of The Royal Society Interface 2014, 11 (95) , 20140264. https://doi.org/10.1098/rsif.2014.0264
2655. Yutian R. Zhao, Kimberley B. McAuley, Piet D. Iedema, Judit E. Puskas. Advanced Monte Carlo Model for Arborescent Polyisobutylene Production in Batch Reactor. Macromolecular Theory and Simulations 2014, 23 (6) , 383-400. https://doi.org/10.1002/mats.201400013
2656. Stefano Lazzari, Shaghayegh Hamzehlou, Yuri Reyes, Jose Ramon Leiza, Mário Rui P. F. N. Costa, Rolando C. S. Dias, Giuseppe Storti. Bulk Crosslinking Copolymerization: Comparison of Different Modeling Approaches. Macromolecular Reaction Engineering 2014, 8 (10) , 678-695. https://doi.org/10.1002/mren.201400005
2657. Matthew Graham, Thomas House. Dynamics of stochastic epidemics on heterogeneous networks. Journal of Mathematical Biology 2014, 68 (7) , 1583-1605. https://doi.org/10.1007/s00285-013-0679-1
2658. Hitoshi Mahara, Tomohiko Yamaguchi, P. Parmananda. Stochastic resonance with a mesoscopic reaction-diffusion system. Physical Review E 2014, 89 (6) https://doi.org/10.1103/PhysRevE.89.062913
2659. Francesca Parise, Jakob Ruess, John Lygeros. Grey-box techniques for the identification of a controlled gene expression model. 2014,,, 1498-1503. https://doi.org/10.1109/ECC.2014.6862244
2660. Marco Aldinucci, Maurizio Drocco, Guilherme Peretti Pezzi, Claudia Misale, Fabio Tordini, Massimo Torquati. Exercising High-Level Parallel Programming on Streams: A Systems Biology Use Case. 2014,,, 51-56. https://doi.org/10.1109/ICDCSW.2014.38
2661. Morgan Madec, Francois Pecheux, Fabienne Jezequel, Yves Gendrault, Christophe Lallement, Jacques Haiech. Opportunities and challenges for the virtual prototyping of synthetic biological functions. 2014,,, 2013-2016. https://doi.org/10.1109/ISCAS.2014.6865559
2662. Ishtiaq Maqsood, Lance D Cundy, Matt Biesecker, Jung-Han Kimn, Elise Darlington, Ethan P Hettwer, Sabina Schill, Venkat Bommisetty. Charge transport kinetics in organic bulk heterojunction morphologies: Mesoscale Monte Carlo simulation analysis. 2014,,, 1758-1761. https://doi.org/10.1109/PVSC.2014.6925261
2663. Eisa Zarepour, Mahbub Hassan, Chun Tung Chou, Adesoji A. Adesina. Frequency hopping strategies for improving terahertz sensor network performance over composition varying channels. 2014,,, 1-9. https://doi.org/10.1109/WoWMoM.2014.6918973
2664. Chinmaya Gupta, José Manuel López, Robert Azencott, Matthew R. Bennett, Krešimir Josić, William Ott. Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations. The Journal of Chemical Physics 2014, 140 (20) , 204108. https://doi.org/10.1063/1.4878662
2665. Heinrich C. R. Klein, Ulrich S. Schwarz. Studying protein assembly with reversible Brownian dynamics of patchy particles. The Journal of Chemical Physics 2014, 140 (18) , 184112. https://doi.org/10.1063/1.4873708
2666. Ronny Straube, . Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase. PLoS Computational Biology 2014, 10 (5) , e1003614. https://doi.org/10.1371/journal.pcbi.1003614
2667. Daniel John Lawson, Neeraj Oak, . Apparent Strength Conceals Instability in a Model for the Collapse of Historical States. PLoS ONE 2014, 9 (5) , e96523. https://doi.org/10.1371/journal.pone.0096523
2668. Maria Bruna, S. Jonathan Chapman, Matthew J. Smith. Model reduction for slow–fast stochastic systems with metastable behaviour. The Journal of Chemical Physics 2014, 140 (17) , 174107. https://doi.org/10.1063/1.4871694
2669. P.H.M. Van Steenberge, D.R. D’hooge, M.-F. Reyniers, G.B. Marin. Improved kinetic Monte Carlo simulation of chemical composition-chain length distributions in polymerization processes. Chemical Engineering Science 2014, 110 , 185-199. https://doi.org/10.1016/j.ces.2014.01.019
2670. Chao-Ran Cai, Zhi-Xi Wu, Jian-Yue Guan. Effect of vaccination strategies on the dynamic behavior of epidemic spreading and vaccine coverage. Chaos, Solitons & Fractals 2014, 62-63 , 36-43. https://doi.org/10.1016/j.chaos.2014.04.005
2671. David Gomez, Rahul Marathe, Veronika Bierbaum, Stefan Klumpp. Modeling stochastic gene expression in growing cells. Journal of Theoretical Biology 2014, 348 , 1-11. https://doi.org/10.1016/j.jtbi.2014.01.017
2672. Haoqian Zhang, Min Lin, Handuo Shi, Weiyue Ji, Longwen Huang, Xiaomeng Zhang, Shan Shen, Rencheng Gao, Shuke Wu, Chengzhe Tian, Zhenglin Yang, Guosheng Zhang, Siheng He, Hao Wang, Tiffany Saw, Yiwei Chen, Qi Ouyang. Programming a Pavlovian-like conditioning circuit in Escherichia coli. Nature Communications 2014, 5 (1) https://doi.org/10.1038/ncomms4102
2673. Daniel A. Charlebois, Gábor Balázsi, Mads Kærn. Coherent feedforward transcriptional regulatory motifs enhance drug resistance. Physical Review E 2014, 89 (5) https://doi.org/10.1103/PhysRevE.89.052708
2674. Joshua V. Ross, Benjamin J. Binder. Approximating spatially exclusive invasion processes. Physical Review E 2014, 89 (5) https://doi.org/10.1103/PhysRevE.89.052709
2675. Jie Li, Amin Salighehdar, Narayan Ganesan. Process Simulation of Complex Biochemical Pathways in Explicit 3D Space Enabled by Heterogeneous Computing Platform. 2014,,, 528-535. https://doi.org/10.1109/IPDPSW.2014.199
2676. Robert C. Hilborn. Modeling discrete-variable stochastic dynamics: Ecological populations, gene networks, and a nanotube ion channel. American Journal of Physics 2014, 82 (5) , 466-475. https://doi.org/10.1119/1.4870076
2677. Mario Castro, Hisse M. van Santen, María Férez, Balbino Alarcón, Grant Lythe, Carmen Molina-París. Receptor Pre-Clustering and T cell Responses: Insights into Molecular Mechanisms. Frontiers in Immunology 2014, 5 https://doi.org/10.3389/fimmu.2014.00132
2678. Milan Česka, David Šafránek, Sven Dražan, Luboš Brim, . Robustness Analysis of Stochastic Biochemical Systems. PLoS ONE 2014, 9 (4) , e94553. https://doi.org/10.1371/journal.pone.0094553
2679. Grazziela P. Figueredo, Peer-Olaf Siebers, Markus R. Owen, Jenna Reps, Uwe Aickelin, . Comparing Stochastic Differential Equations and Agent-Based Modelling and Simulation for Early-Stage Cancer. PLoS ONE 2014, 9 (4) , e95150. https://doi.org/10.1371/journal.pone.0095150
2680. Weiliang Chen, Erik De Schutter. Python-based geometry preparation and simulation visualization toolkits for STEPS. Frontiers in Neuroinformatics 2014, 8 https://doi.org/10.3389/fninf.2014.00037
2681. E. C. Dykeman, P. G. Stockley, R. Twarock. Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy. Proceedings of the National Academy of Sciences 2014, 111 (14) , 5361-5366. https://doi.org/10.1073/pnas.1319479111
2682. Peter Banda, Christof Teuscher, Darko Stefanovic. Training an asymmetric signal perceptron through reinforcement in an artificial chemistry. Journal of The Royal Society Interface 2014, 11 (93) , 20131100. https://doi.org/10.1098/rsif.2013.1100
2683. Michael F. HAGAN. Modeling Viral Capsid Assembly. 2014,,, 1-68. https://doi.org/10.1002/9781118755815.ch01
2684. Stefan Leye, Roland Ewald, Adelinde M. Uhrmacher, . Composing Problem Solvers for Simulation Experimentation: A Case Study on Steady State Estimation. PLoS ONE 2014, 9 (4) , e91948. https://doi.org/10.1371/journal.pone.0091948
2685. Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder, . Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. PLoS Computational Biology 2014, 10 (4) , e1003544. https://doi.org/10.1371/journal.pcbi.1003544
2686. Ankur Gupta, James B. Rawlings. Comparison of parameter estimation methods in stochastic chemical kinetic models: Examples in systems biology. AIChE Journal 2014, 60 (4) , 1253-1268. https://doi.org/10.1002/aic.14409
2687. C. J. Proctor, C. Macdonald, J. M. Milner, A. D. Rowan, T. E. Cawston. A Computer Simulation Approach to Assessing Therapeutic Intervention Points for the Prevention of Cytokine-Induced Cartilage Breakdown. Arthritis & Rheumatology 2014, 66 (4) , 979-989. https://doi.org/10.1002/art.38297
2688. Wim Hordijk, Mike Steel. Conditions for Evolvability of Autocatalytic Sets: A Formal Example and Analysis. Origins of Life and Evolution of Biospheres 2014, 44 (2) , 111-124. https://doi.org/10.1007/s11084-014-9374-5
2689. Alan J. McKane, Tommaso Biancalani, Tim Rogers. Stochastic Pattern Formation and Spontaneous Polarisation: The Linear Noise Approximation and Beyond. Bulletin of Mathematical Biology 2014, 76 (4) , 895-921. https://doi.org/10.1007/s11538-013-9827-4
2690. Radek Erban, Mark B. Flegg, Garegin A. Papoian. Multiscale Stochastic Reaction–Diffusion Modeling: Application to Actin Dynamics in Filopodia. Bulletin of Mathematical Biology 2014, 76 (4) , 799-818. https://doi.org/10.1007/s11538-013-9844-3
2691. Jifeng Hu, Hye-Won Kang, Hans G. Othmer. Stochastic Analysis of Reaction–Diffusion Processes. Bulletin of Mathematical Biology 2014, 76 (4) , 854-894. https://doi.org/10.1007/s11538-013-9849-y
2692. William R. Holmes, Qing Nie. Interactions and Tradeoffs Between Cell Recruitment, Proliferation, and Differentiation Affect CNS Regeneration. Biophysical Journal 2014, 106 (7) , 1528-1536. https://doi.org/10.1016/j.bpj.2014.02.010
2693. Joseph Sang-Il Kwon, Michael Nayhouse, Panagiotis D. Christofides, Gerassimos Orkoulas. Modeling and control of crystal shape in continuous protein crystallization. Chemical Engineering Science 2014, 107 , 47-57. https://doi.org/10.1016/j.ces.2013.12.005
2694. Rishi Srivastava, James B. Rawlings. Parameter estimation in stochastic chemical kinetic models using derivative free optimization and bootstrapping. Computers & Chemical Engineering 2014, 63 , 152-158. https://doi.org/10.1016/j.compchemeng.2014.01.006
2695. Pierre Magal, Shigui Ruan. Susceptible-infectious-recovered models revisited: From the individual level to the population level. Mathematical Biosciences 2014, 250 , 26-40. https://doi.org/10.1016/j.mbs.2014.02.001
2696. Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, Friedrich C. Simmel. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nature Chemistry 2014, 6 (4) , 295-302. https://doi.org/10.1038/nchem.1869
2697. Matthew Hartfield, Samuel Alizon. Epidemiological Feedbacks Affect Evolutionary Emergence of Pathogens. The American Naturalist 2014, 183 (4) , E105-E117. https://doi.org/10.1086/674795
2698. Daphne Ezer, Nicolae Radu Zabet, Boris Adryan. Physical constraints determine the logic of bacterial promoter architectures. Nucleic Acids Research 2014, 42 (7) , 4196-4207. https://doi.org/10.1093/nar/gku078
2699. K. G. Petrosyan, Chin-Kun Hu. Nonequilibrium Lyapunov function and a fluctuation relation for stochastic systems: Poisson-representation approach. Physical Review E 2014, 89 (4) https://doi.org/10.1103/PhysRevE.89.042132
2700. Matthias Reiter, Steffen Rulands, Erwin Frey. Range Expansion of Heterogeneous Populations. Physical Review Letters 2014, 112 (14) https://doi.org/10.1103/PhysRevLett.112.148103
2701. PEI-JUNG WU, CHOU-CHING K. LIN, MING-SHAUNG JU. ONE-DIMENSIONAL MODELING AND SIMULATIONS OF MIGRATION OF CULTURED FIBROBLASTS. Journal of Mechanics in Medicine and Biology 2014, 14 (02) , 1450027. https://doi.org/10.1142/S0219519414500274
2702. Can Huang, Di Liu. Strong Convergence and Speed up of Nested Stochastic Simulation Algorithm. Communications in Computational Physics 2014, 15 (4) , 1207-1236. https://doi.org/10.4208/cicp.290313.051213s
2703. Martin Robinson, Mark Flegg, Radek Erban. Adaptive two-regime method: Application to front propagation. The Journal of Chemical Physics 2014, 140 (12) , 124109. https://doi.org/10.1063/1.4868652
2704. Srijeeta Talukder, Shrabani Sen, Prantik Chakraborti, Ralf Metzler, Suman K. Banik, Pinaki Chaudhury. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA. The Journal of Chemical Physics 2014, 140 (12) , 125101. https://doi.org/10.1063/1.4869112
2705. Marco S. Nobile, Paolo Cazzaniga, Daniela Besozzi, Dario Pescini, Giancarlo Mauri, . cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS ONE 2014, 9 (3) , e91963. https://doi.org/10.1371/journal.pone.0091963
2706. M. Ali Parsa, Iurii Kozhan, Michael Wulkow, Robin A. Hutchinson. Modeling of Functional Group Distribution in Copolymerization: A Comparison of Deterministic and Stochastic Approaches. Macromolecular Theory and Simulations 2014, 23 (3) , 207-217. https://doi.org/10.1002/mats.201300156
2707. Alen Alexanderian, Francesco Rizzi, Muruhan Rathinam, Olivier P. Le Maître, Omar M. Knio. Preconditioned Bayesian Regression for Stochastic Chemical Kinetics. Journal of Scientific Computing 2014, 58 (3) , 592-626. https://doi.org/10.1007/s10915-013-9745-5
2708. Stefano Bo, Antonio Celani. Entropy Production in Stochastic Systems with Fast and Slow Time-Scales. Journal of Statistical Physics 2014, 154 (5) , 1325-1351. https://doi.org/10.1007/s10955-014-0922-1
2709. Adrian Sandu. A new look at the chemical master equation. Numerical Algorithms 2014, 65 (3) , 485-498. https://doi.org/10.1007/s11075-013-9758-z
2710. Arwen Meister, Chao Du, Ye Henry Li, Wing Hung Wong. Modeling stochastic noise in gene regulatory systems. Quantitative Biology 2014, 2 (1) , 1-29. https://doi.org/10.1007/s40484-014-0025-7
2711. Trevelyan J. McKinley, Joshua V. Ross, Rob Deardon, Alex R. Cook. Simulation-based Bayesian inference for epidemic models. Computational Statistics & Data Analysis 2014, 71 , 434-447. https://doi.org/10.1016/j.csda.2012.12.012
2712. P.K. Jithinraj, Ushasi Roy, Manoj Gopalakrishnan. Zero-order ultrasensitivity: A study of criticality and fluctuations under the total quasi-steady state approximation in the linear noise regime. Journal of Theoretical Biology 2014, 344 , 1-11. https://doi.org/10.1016/j.jtbi.2013.11.014
2713. Kevin Doherty, Martin Meere, Petri T. Piiroinen. A mathematical model of CENP-A incorporation in mammalian centromeres. Mathematical Biosciences 2014, 249 , 27-43. https://doi.org/10.1016/j.mbs.2014.01.005
2714. Maosheng Wang, Runzhi Sun. Cooperative effects of inherent stochasticity and random long-range connections on synchronization and coherence resonance in diffusively coupled calcium oscillators. Physica A: Statistical Mechanics and its Applications 2014, 398 , 243-251. https://doi.org/10.1016/j.physa.2013.12.024
2715. T. William Mather, M. Ani Hsieh. Synthesis and analysis of distributed ensemble control strategies for allocation to multiple tasks. Robotica 2014, 32 (2) , 177-192. https://doi.org/10.1017/S0263574713000994
2716. George W. A. Constable, Alan J. McKane. Fast-mode elimination in stochastic metapopulation models. Physical Review E 2014, 89 (3) https://doi.org/10.1103/PhysRevE.89.032141
2717. Alok Kumar Maity, Arnab Bandyopadhyay, Pinaki Chaudhury, Suman K. Banik. Role of functionality in two-component signal transduction: A stochastic study. Physical Review E 2014, 89 (3) https://doi.org/10.1103/PhysRevE.89.032713
2718. Qi-ming Pei, Xuan Zhan, Li-jian Yang, Chun Bao, Wei Cao, An-bang Li, Anvar Rozi, Ya Jia. Fluctuations of cell population in a colonic crypt. Physical Review E 2014, 89 (3) https://doi.org/10.1103/PhysRevE.89.032715
2719. David Gnabasik, Gita Alaghband. Discrete Time Evolution of Proteomic Biomarkers. 2014,,, 11-16. https://doi.org/10.1109/CSCI.2014.87
2720. Miha Moskon, Miha Mraz. Systematic Approach to Computational Design of Gene Regulatory Networks with Information Processing Capabilities. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2014, 11 (2) , 431-440. https://doi.org/10.1109/TCBB.2013.2295792
2721. Seon Kim, Ying Hsu, Andreas Linninger. Interpretation of Cellular Imaging and AQP4 Quantification Data in a Single Cell Simulator. Processes 2014, 2 (1) , 218-237. https://doi.org/10.3390/pr2010218
2722. Iris Hödl, Lorenzo Mari, Enrico Bertuzzo, Samir Suweis, Katharina Besemer, Andrea Rinaldo, Tom J. Battin. Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments. Environmental Microbiology 2014, 16 (3) , 802-812. https://doi.org/10.1111/1462-2920.12205
2723. Juan Carlos López Alfonso, Nick Jagiella, Luis Núñez, Miguel A. Herrero, Dirk Drasdo, . Estimating Dose Painting Effects in Radiotherapy: A Mathematical Model. PLoS ONE 2014, 9 (2) , e89380. https://doi.org/10.1371/journal.pone.0089380
2724. Cheng Lv, Xiaoguang Li, Fangting Li, Tiejun Li, . Constructing the Energy Landscape for Genetic Switching System Driven by Intrinsic Noise. PLoS ONE 2014, 9 (2) , e88167. https://doi.org/10.1371/journal.pone.0088167
2725. Davit A. Potoyan, Peter G. Wolynes. On the dephasing of genetic oscillators. Proceedings of the National Academy of Sciences 2014, 111 (6) , 2391-2396. https://doi.org/10.1073/pnas.1323433111
2726. Ana M. Avalos, Angelina M. Bilate, Martin D. Witte, Albert K. Tai, Jiang He, Maria P. Frushicheva, Peter D. Thill, Friederike Meyer-Wentrup, Christopher S. Theile, Arup K. Chakraborty, Xiaowei Zhuang, Hidde L. Ploegh. Monovalent engagement of the BCR activates ovalbumin-specific transnuclear B cells. Journal of Experimental Medicine 2014, 211 (2) , 365-379. https://doi.org/10.1084/jem.20131603
2727. Daniel T. Gillespie, Linda R. Petzold, Effrosyni Seitaridou. Validity conditions for stochastic chemical kinetics in diffusion-limited systems. The Journal of Chemical Physics 2014, 140 (5) , 054111. https://doi.org/10.1063/1.4863990
2728. Adam J. Ellery, Matthew J. Simpson, Scott W. McCue, Ruth E. Baker. Characterizing transport through a crowded environment with different obstacle sizes. The Journal of Chemical Physics 2014, 140 (5) , 054108. https://doi.org/10.1063/1.4864000
2729. Yong Zhang, Jiazhong Qian, Charalambos Papelis, Pengtao Sun, Zhongbo Yu. Improved understanding of bimolecular reactions in deceptively simple homogeneous media: From laboratory experiments to Lagrangian quantification. Water Resources Research 2014, 50 (2) , 1704-1715. https://doi.org/10.1002/2013WR014711
2730. Kinshuk Banerjee. A model of cooperativity based on restricted binding: kinetic and thermodynamic analysis. Journal of Mathematical Chemistry 2014, 52 (2) , 741-753. https://doi.org/10.1007/s10910-013-0292-y
2731. Emanuel Salazar-Cavazos, Moisés Santillán. Optimal Performance of the Tryptophan Operon of E. coli: A stochastic, Dynamical, Mathematical-Modeling Approach. Bulletin of Mathematical Biology 2014, 76 (2) , 314-334. https://doi.org/10.1007/s11538-013-9920-8
2732. Otso Ovaskainen, Dmitri Finkelshtein, Oleksandr Kutoviy, Stephen Cornell, Benjamin Bolker, Yuri Kondratiev. A general mathematical framework for the analysis of spatiotemporal point processes. Theoretical Ecology 2014, 7 (1) , 101-113. https://doi.org/10.1007/s12080-013-0202-8
2733. Kazunari Kaizu, Wiet de Ronde, Joris Paijmans, Koichi Takahashi, Filipe Tostevin, Pieter Rein ten Wolde. The Berg-Purcell Limit Revisited. Biophysical Journal 2014, 106 (4) , 976-985. https://doi.org/10.1016/j.bpj.2013.12.030
2734. Ava J. Mauro, Jon Karl Sigurdsson, Justin Shrake, Paul J. Atzberger, Samuel A. Isaacson. A First-Passage Kinetic Monte Carlo method for reaction–drift–diffusion processes. Journal of Computational Physics 2014, 259 , 536-567. https://doi.org/10.1016/j.jcp.2013.12.023
2735. Nils Christian, Alexander Skupin, Silvia Morante, Karl Jansen, Giancarlo Rossi, Oliver Ebenhöh. Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. Journal of Theoretical Biology 2014, 343 , 102-112. https://doi.org/10.1016/j.jtbi.2013.11.010
2736. Jia-Zeng Wang, Li-Po Mo, Deng-Feng Liang, Ying-Ying Fu. Intrinsic circular motions in stochastic pairwise epidemic models. Physica A: Statistical Mechanics and its Applications 2014, 395 , 209-217. https://doi.org/10.1016/j.physa.2013.10.010
2737. Matthew J. Simpson, Jesse A. Sharp, Ruth E. Baker. Distinguishing between mean-field, moment dynamics and stochastic descriptions of birth–death–movement processes. Physica A: Statistical Mechanics and its Applications 2014, 395 , 236-246. https://doi.org/10.1016/j.physa.2013.10.026
2738. Lev S Tsimring. Noise in biology. Reports on Progress in Physics 2014, 77 (2) , 026601. https://doi.org/10.1088/0034-4885/77/2/026601
2739. Kat Rock, Sam Brand, Jo Moir, Matt J Keeling. Dynamics of infectious diseases. Reports on Progress in Physics 2014, 77 (2) , 026602. https://doi.org/10.1088/0034-4885/77/2/026602
2740. Zhenhong Li, Bin Sun, Rebecca A. Clewell, Yeyejide Adeleye, Melvin E. Andersen, Qiang Zhang. Dose-Response Modeling of Etoposide-Induced DNA Damage Response. Toxicological Sciences 2014, 137 (2) , 371-384. https://doi.org/10.1093/toxsci/kft259
2741. Joanna Jaruszewicz, Marek Kimmel, Tomasz Lipniacki. Stability of bacterial toggle switches is enhanced by cell-cycle lengthening by several orders of magnitude. Physical Review E 2014, 89 (2) https://doi.org/10.1103/PhysRevE.89.022710
2742. W. Buijsman, M. Sheinman. Efficient fold-change detection based on protein-protein interactions. Physical Review E 2014, 89 (2) https://doi.org/10.1103/PhysRevE.89.022712
2743. Robert J. Concannon, Richard A. Blythe. Spatiotemporally Complete Condensation in a Non-Poissonian Exclusion Process. Physical Review Letters 2014, 112 (5) https://doi.org/10.1103/PhysRevLett.112.050603
2744. ISMAEL SANCHEZ-OSORIO, FERNANDO RAMOS, PEDRO MAYORGA, EDGAR DANTAN. FOUNDATIONS FOR MODELING THE DYNAMICS OF GENE REGULATORY NETWORKS: A MULTILEVEL-PERSPECTIVE REVIEW. Journal of Bioinformatics and Computational Biology 2014, 12 (01) , 1330003. https://doi.org/10.1142/S0219720013300037
2745. Sulian Thual, Andrew J. Majda, Samuel N. Stechmann. A Stochastic Skeleton Model for the MJO. Journal of the Atmospheric Sciences 2014, 71 (2) , 697-715. https://doi.org/10.1175/JAS-D-13-0186.1
2746. Mahdi Shirazi, Simon D. Elliott. Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory. Journal of Computational Chemistry 2014, 35 (3) , 244-259. https://doi.org/10.1002/jcc.23491
2747. Claude Gérard, Didier Gonze, Frédéric Lemaigre, Béla Novák, . A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches. PLoS Computational Biology 2014, 10 (1) , e1003455. https://doi.org/10.1371/journal.pcbi.1003455
2748. Li Xu, Feng Zhang, Kun Zhang, Erkang Wang, Jin Wang, . The Potential and Flux Landscape Theory of Ecology. PLoS ONE 2014, 9 (1) , e86746. https://doi.org/10.1371/journal.pone.0086746
2749. Marc-Oliver Gewaltig, Robert Cannon, . Current Practice in Software Development for Computational Neuroscience and How to Improve It. PLoS Computational Biology 2014, 10 (1) , e1003376. https://doi.org/10.1371/journal.pcbi.1003376
2750. Biswa Sengupta, Simon Barry Laughlin, Jeremy Edward Niven, . Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency. PLoS Computational Biology 2014, 10 (1) , e1003439. https://doi.org/10.1371/journal.pcbi.1003439
2751. Aidan I. Brown, Peter K. Kim, Andrew D. Rutenberg, . PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes. PLoS Computational Biology 2014, 10 (1) , e1003426. https://doi.org/10.1371/journal.pcbi.1003426
2752. H. J. Woo, J. Reifman. Quantitative Modeling of Virus Evolutionary Dynamics and Adaptation in Serial Passages Using Empirically Inferred Fitness Landscapes. Journal of Virology 2014, 88 (2) , 1039-1050. https://doi.org/10.1128/JVI.02958-13
2753. Hong Qian, S.C. Kou. Statistics and Related Topics in Single-Molecule Biophysics. Annual Review of Statistics and Its Application 2014, 1 (1) , 465-492. https://doi.org/10.1146/annurev-statistics-022513-115535
2754. Simon Barthelmé, Nicolas Chopin. Expectation Propagation for Likelihood-Free Inference. Journal of the American Statistical Association 2014, 109 (505) , 315-333. https://doi.org/10.1080/01621459.2013.864178
2755. Aaron B Wong, Mark A Rutherford, Mantas Gabrielaitis, Tina Pangršič, Fabian Göttfert, Thomas Frank, Susann Michanski, Stefan Hell, Fred Wolf, Carolin Wichmann, Tobias Moser. Developmental refinement of hair cell synapses tightens the coupling of Ca 2+ influx to exocytosis. The EMBO Journal 2014, 635 , n/a-n/a. https://doi.org/10.1002/embj.201387110
2756. Shinji Nakaoka. Multiscale Mathematical Modeling and Simulation of Cellular Dynamical Process. 2014,,, 269-283. https://doi.org/10.1007/7651_2014_78
2757. Domitilla Del Vecchio, Richard M. Murray. Synthetic Biology. 2014,,, 1-8. https://doi.org/10.1007/978-1-4471-5102-9_91-1
2758. Daniele Linaro, Michele Giugliano. Markov Models of Ion Channels. 2014,,, 1-14. https://doi.org/10.1007/978-1-4614-7320-6_131-1
2759. Wonryull Koh, Kim T. Blackwell. Stochastic Simulators. 2014,,, 1-10. https://doi.org/10.1007/978-1-4614-7320-6_196-2
2760. Matthias H. Hennig. Ionotropic Receptors Dynamics, Conductance Models. 2014,,, 1-5. https://doi.org/10.1007/978-1-4614-7320-6_349-1
2761. John Milton, Toru Ohira. Random Walks. 2014,,, 389-424. https://doi.org/10.1007/978-1-4614-9096-8_14
2762. Péter Érdi, Gábor Lente. Continuous Time Discrete State Stochastic Models. 2014,,, 25-70. https://doi.org/10.1007/978-1-4939-0387-0_2
2763. Christoph Schmal, Jean-Christophe Leloup, Didier Gonze. Modeling and Simulating the Arabidopsis thaliana Circadian Clock Using XPP-AUTO. 2014,,, 337-358. https://doi.org/10.1007/978-1-4939-0700-7_23
2764. Barış Atakan. Passive Molecular Communication Through Absorbers. 2014,,, 25-104. https://doi.org/10.1007/978-1-4939-0739-7_2
2765. Ignacio A. Rodriguez-Brenes, Natalia L. Komarova, Dominik Wodarz. Negative Feedback Regulation in Hierarchically Organized Tissues: Exploring the Dynamics of Tissue Regeneration and the Role of Feedback Escape in Tumor Development. 2014,,, 197-221. https://doi.org/10.1007/978-1-4939-1793-8_8
2766. Marie Beurton-Aimar, Tung Vu-Ngoc Nguyen, Sophie Colombié. Metabolic Network Reconstruction and Their Topological Analysis. 2014,,, 19-38. https://doi.org/10.1007/978-1-62703-688-7_2
2767. Tomáš Bodnár, Antonio Fasano, Adélia Sequeira. Mathematical Models for Blood Coagulation. 2014,,, 483-569. https://doi.org/10.1007/978-3-0348-0822-4_7
2768. Natalja Strelkowa. Stochastic Complexity Analysis in Synthetic Biology. 2014,,, 161-194. https://doi.org/10.1007/978-3-319-00254-5_8
2769. Matteo Cavaliere, Tommaso Mazza, Sean Sedwards. Statistical Model Checking of Membrane Systems with Peripheral Proteins: Quantifying the Role of Estrogen in Cellular Mitosis and DNA Damage. 2014,,, 43-63. https://doi.org/10.1007/978-3-319-03191-0_2
2770. Paolo Cazzaniga, Daniela Besozzi, Dario Pescini, Giancarlo Mauri. Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis. 2014,,, 65-96. https://doi.org/10.1007/978-3-319-03191-0_3
2771. John Jack, Andrei Păun, Mihaela Păun. Biochemical Networks Discrete Modeling Inspired by Membrane Systems. 2014,,, 175-221. https://doi.org/10.1007/978-3-319-03191-0_6
2772. Lasse Rosenthal, Thomas Strunskus, Franz Faupel, Jan Willem Abraham, Michael Bonitz. Kinetic Monte Carlo Simulations of Cluster Growth and Diffusion in Metal-Polymer Nanocomposites. 2014,,, 321-370. https://doi.org/10.1007/978-3-319-05437-7_10
2773. Jie Li, Amin Salighehdar, Narayan Ganesan. Simulation of Complex Biochemical Pathways in 3D Process Space via Heterogeneous Computing Platform: Preliminary Results. 2014,,, 227-232. https://doi.org/10.1007/978-3-319-05960-0_22
2774. Monika Kurpas, Katarzyna Jonak, Krzysztof Puszyński. Simulation Analysis of the ATR Module as a Detector of UV-Induced DNA Damage. 2014,,, 317-326. https://doi.org/10.1007/978-3-319-06593-9_28
2775. Moisés Santillán. Different Approaches to Analyzing a Simple Chemical Reaction. 2014,,, 15-28. https://doi.org/10.1007/978-3-319-06689-9_3
2776. Moisés Santillán. Molecule Synthesis and Degradation. 2014,,, 29-49. https://doi.org/10.1007/978-3-319-06689-9_4
2777. David J. Barnes, Dominique Chu. Evolving Parameters for a Noisy Biological System – The Impact of Alternative Approaches. 2014,,, 95-106. https://doi.org/10.1007/978-3-319-07176-3_9
2778. Tommaso Biancalani. Introduction. 2014,,, 1-17. https://doi.org/10.1007/978-3-319-07728-4_1
2779. Tommaso Biancalani. Methods. 2014,,, 19-30. https://doi.org/10.1007/978-3-319-07728-4_2
2780. Tommaso Biancalani. Noise-Induced Bistability. 2014,,, 31-61. https://doi.org/10.1007/978-3-319-07728-4_3
2781. Tommaso Biancalani. Stochastic Waves on Regular Lattices. 2014,,, 63-82. https://doi.org/10.1007/978-3-319-07728-4_4
2782. Tommaso Biancalani. Stochastic Waves on Complex Network. 2014,,, 83-98. https://doi.org/10.1007/978-3-319-07728-4_5
2783. Mostafa Herajy, Monika Heiner. A Steering Server for Collaborative Simulation of Quantitative Petri Nets. 2014,,, 374-384. https://doi.org/10.1007/978-3-319-07734-5_21
2784. Masami Hagiya, Shaoyu Wang, Ibuki Kawamata, Satoshi Murata, Teijiro Isokawa, Ferdinand Peper, Katsunobu Imai. On DNA-Based Gellular Automata. 2014,,, 177-189. https://doi.org/10.1007/978-3-319-08123-6_15
2785. Matthew R. Lakin, Darko Stefanovic. Pattern Formation by Spatially Organized Approximate Majority Reactions. 2014,,, 254-266. https://doi.org/10.1007/978-3-319-08123-6_21
2786. Mary Ann Blätke, Christian Rohr, Monika Heiner, Wolfgang Marwan. A Petri-Net-Based Framework for Biomodel Engineering. 2014,,, 317-366. https://doi.org/10.1007/978-3-319-08437-4_6
2787. Paul C. Bressloff. Probability Theory and Martingales. 2014,,, 619-643. https://doi.org/10.1007/978-3-319-08488-6_11
2788. Paul C. Bressloff. Stochastic Gene Expression and Regulatory Networks. 2014,,, 269-340. https://doi.org/10.1007/978-3-319-08488-6_6
2789. Paul C. Bressloff. Self-Organization in Cells II: Reaction-Diffusion Models. 2014,,, 497-575. https://doi.org/10.1007/978-3-319-08488-6_9
2790. Heiko Hamann, Gabriele Valentini, Yara Khaluf, Marco Dorigo. Derivation of a Micro-Macro Link for Collective Decision-Making Systems. 2014,,, 181-190. https://doi.org/10.1007/978-3-319-10762-2_18
2791. Rachel Cummings, David Doty, David Soloveichik. Probability 1 Computation with Chemical Reaction Networks. 2014,,, 37-52. https://doi.org/10.1007/978-3-319-11295-4_3
2792. Irene Otero-Muras, Julio R. Banga. Optimization Based Design of Synthetic Oscillators from Standard Biological Parts. 2014,,, 225-238. https://doi.org/10.1007/978-3-319-12982-2_16
2793. Milan Češka, Frits Dannenberg, Marta Kwiatkowska, Nicola Paoletti. Precise Parameter Synthesis for Stochastic Biochemical Systems. 2014,,, 86-98. https://doi.org/10.1007/978-3-319-12982-2_7
2794. Mario J. Pérez-Jiménez. A Bioinspired Computing Approach to Model Complex Systems. 2014,,, 20-34. https://doi.org/10.1007/978-3-319-14370-5_2
2795. Reinhard Laubenbacher, Franziska Hinkelmann, David Murrugarra, Alan Veliz-Cuba. Algebraic Models and Their Use in Systems Biology. 2014,,, 443-474. https://doi.org/10.1007/978-3-642-40193-0_21
2796. Andrey Zakharov, Dmitry Bratsun. Synchronization of Circadian Rhythms at Scale of Gene, Cell and Whole Organism. 2014,,, 345-355. https://doi.org/10.1007/978-3-642-45438-7_34
2797. Ozan Kahramanoğulları, James F. Lynch, Corrado Priami. Algorithmic Systems Ecology: Experiments on Multiple Interaction Types and Patches. 2014,,, 154-171. https://doi.org/10.1007/978-3-642-54338-8_13
2798. Roberto Barbuti, Antonio Cerone, Andrea Maggiolo-Schettini, Paolo Milazzo, Suryana Setiawan. Modelling Population Dynamics Using Grid Systems. 2014,,, 172-189. https://doi.org/10.1007/978-3-642-54338-8_14
2799. Ho-Lin Chen, Rachel Cummings, David Doty, David Soloveichik. Speed Faults in Computation by Chemical Reaction Networks. 2014,,, 16-30. https://doi.org/10.1007/978-3-662-45174-8_2
2800. Cyrille Jegourel, Axel Legay, Sean Sedwards. An Effective Heuristic for Adaptive Importance Splitting in Statistical Model Checking. 2014,,, 143-159. https://doi.org/10.1007/978-3-662-45231-8_11
2801. Alexander Andreychenko, Thilo Krüger, David Spieler. Analyzing Oscillatory Behavior with Formal Methods. 2014,,, 1-25. https://doi.org/10.1007/978-3-662-45489-3_1
2802. Anna Kolesnichenko, Valerio Senni, Alireza Pourranjabar, Anne Remke. Applying Mean-Field Approximation to Continuous Time Markov Chains. 2014,,, 242-280. https://doi.org/10.1007/978-3-662-45489-3_7
2803. Adam Runions, Richard S. Smith, Przemyslaw Prusinkiewicz. Computational Models of Auxin-Driven Development. 2014,,, 315-357. https://doi.org/10.1007/978-3-7091-1526-8_15
2804. Harvey Scher, Brian Berkowitz. Reactive Transport in Heterogeneous Media. 2014,,, 243-256. https://doi.org/10.1007/978-94-007-7534-3_21
2805. Padmini Rangamani, Granville Yuguang Xiong, Ravi Iyengar. Multiscale Modeling of Cell Shape from the Actin Cytoskeleton. 2014,,, 143-167. https://doi.org/10.1016/B978-0-12-397897-4.00002-4
2806. Marja-Leena Linne, Tuula O. Jalonen. Astrocyte–Neuron Interactions. 2014,,, 191-217. https://doi.org/10.1016/B978-0-12-397897-4.00005-X
2807. Upinder S. Bhalla. Multiscale Modeling and Synaptic Plasticity. 2014,,, 351-386. https://doi.org/10.1016/B978-0-12-397897-4.00012-7
2808. Jean-Christophe Leloup, Didier Gonze, Albert Goldbeter. Computational Models for Circadian Rhythms: Deterministic versus Stochastic Approaches. 2014,,, 183-222. https://doi.org/10.1016/B978-0-12-405926-9.00010-1
2809. Pieter Rein ten Wolde, Andrew Mugler. Importance of Crowding in Signaling, Genetic, and Metabolic Networks. 2014,,, 419-442. https://doi.org/10.1016/B978-0-12-800046-5.00012-6
2810. Dezső Boda. Monte Carlo Simulation of Electrolyte Solutions in Biology. 2014,,, 127-163. https://doi.org/10.1016/B978-0-444-63378-1.00005-7
2811. Ya Guo, Jinglu Tan. Kinetic Monte Carlo simulation of the initial phases of chlorophyll fluorescence from photosystem II. Biosystems 2014, 115 , 1-4. https://doi.org/10.1016/j.biosystems.2013.10.004
2812. Jean-Baptiste Masson, Patrice Dionne, Charlotte Salvatico, Marianne Renner, Christian G. Specht, Antoine Triller, Maxime Dahan. Mapping the Energy and Diffusion Landscapes of Membrane Proteins at the Cell Surface Using High-Density Single-Molecule Imaging and Bayesian Inference: Application to the Multiscale Dynamics of Glycine Receptors in the Neuronal Membrane. Biophysical Journal 2014, 106 (1) , 74-83. https://doi.org/10.1016/j.bpj.2013.10.027
2813. Gregory R. Smith, Lu Xie, Byoungkoo Lee, Russell Schwartz. Applying Molecular Crowding Models to Simulations of Virus Capsid Assembly In Vitro. Biophysical Journal 2014, 106 (1) , 310-320. https://doi.org/10.1016/j.bpj.2013.11.022
2814. Eder Zavala, Tatiana T. Marquez-Lago. Delays Induce Novel Stochastic Effects in Negative Feedback Gene Circuits. Biophysical Journal 2014, 106 (2) , 467-478. https://doi.org/10.1016/j.bpj.2013.12.010
2815. Jiajun Zhang, Tianshou Zhou. Promoter-mediated Transcriptional Dynamics. Biophysical Journal 2014, 106 (2) , 479-488. https://doi.org/10.1016/j.bpj.2013.12.011
2816. Ashoke De, Sudib K. Mishra. Simulation of chemical reactions induced by droplet in a phase separating media using Lattice Boltzmann–kinetic Monte-Carlo framework. Computers & Fluids 2014, 89 , 133-142. https://doi.org/10.1016/j.compfluid.2013.10.041
2817. Rui Dilão. The regulation of gene expression in eukaryotes: Bistability and oscillations in repressilator models. Journal of Theoretical Biology 2014, 340 , 199-208. https://doi.org/10.1016/j.jtbi.2013.09.010
2818. Eili Y. Klein. The impact of heterogeneous transmission on the establishment and spread of antimalarial drug resistance. Journal of Theoretical Biology 2014, 340 , 177-185. https://doi.org/10.1016/j.jtbi.2013.09.022
2819. Erida Gjini, Daniel T. Haydon, J. David Barry, Christina A. Cobbold. Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification. Journal of Theoretical Biology 2014, 341 , 111-122. https://doi.org/10.1016/j.jtbi.2013.10.001
2820. Maosheng Wang, Runzhi Sun, Wanxia Huang, Yubing Tu. Internal noise induced pattern formation and spatial coherence resonance for calcium signals of diffusively coupled cells. Physica A: Statistical Mechanics and its Applications 2014, 393 , 519-526. https://doi.org/10.1016/j.physa.2013.09.012
2821. Sten Rüdiger. Stochastic models of intracellular calcium signals. Physics Reports 2014, 534 (2) , 39-87. https://doi.org/10.1016/j.physrep.2013.09.002
2822. Romain Guy, Catherine Larédo, Elisabeta Vergu. Parametric inference for discretely observed multidimensional diffusions with small diffusion coefficient. Stochastic Processes and their Applications 2014, 124 (1) , 51-80. https://doi.org/10.1016/j.spa.2013.07.009
2823. Laith Yakob, Thomas V Riley, David L Paterson, John Marquess, Archie CA Clements. Assessing control bundles for Clostridium difficile : a review and mathematical model. Emerging Microbes & Infections 2014, 3 (1) , 1-8. https://doi.org/10.1038/emi.2014.43
2824. Lykke Pedersen, Peter H Hagedorn, Marie Wickström Lindholm, Morten Lindow. A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent. Molecular Therapy - Nucleic Acids 2014, 3 , e149. https://doi.org/10.1038/mtna.2013.72
2825. Richard S. Graham. Modelling flow-induced crystallisation in polymers. Chem. Commun. 2014, 50 (27) , 3531-3545. https://doi.org/10.1039/C3CC49668F
2826. Jason Y. W. Lai, Paolo Elvati, Angela Violi. Stochastic atomistic simulation of polycyclic aromatic hydrocarbon growth in combustion. Phys. Chem. Chem. Phys. 2014, 16 (17) , 7969-7979. https://doi.org/10.1039/C4CP00112E
2827. Ahmet Ay, Necmettin Yildirim. Dynamics matter: differences and similarities between alternatively designed mechanisms. Mol. BioSyst. 2014, 10 (7) , 1948-1957. https://doi.org/10.1039/C4MB00159A
2828. Shantanu Kadam, Kumar Vanka. The accounting of noise to solve the problem of negative populations in approximate accelerated stochastic simulations. RSC Adv. 2014, 4 (102) , 58127-58136. https://doi.org/10.1039/C4RA05865H
2829. A. K. Shchekin, I. A. Babintsev, L. Ts. Adzhemyan, N. A. Volkov. Kinetic modeling of self-aggregation in solutions with coexisting spherical and cylindrical micelles at arbitrary initial conditions. RSC Adv. 2014, 4 (93) , 51722-51733. https://doi.org/10.1039/C4RA08683J
2830. P. Rattana, J.C. Miller, I.Z. Kiss, , , . Pairwise and Edge-based Models of Epidemic Dynamics on Correlated Weighted Networks. Mathematical Modelling of Natural Phenomena 2014, 9 (2) , 58-81. https://doi.org/10.1051/mmnp/20149204
2831. Eric T. Lofgren, Rebekah W. Moehring, Deverick J. Anderson, David J. Weber, Nina H. Fefferman. A Mathematical Model to Evaluate the Routine Use of Fecal Microbiota Transplantation to Prevent Incident and Recurrent Clostridium difficile Infection. Infection Control & Hospital Epidemiology 2014, 35 (1) , 18-27. https://doi.org/10.1086/674394
2832. Jyotsana J. Parmar, John F. Marko, Ranjith Padinhateeri. Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence. Nucleic Acids Research 2014, 42 (1) , 128-136. https://doi.org/10.1093/nar/gkt854
2833. Daniel Jost. Bifurcation in epigenetics: Implications in development, proliferation, and diseases. Physical Review E 2014, 89 (1) https://doi.org/10.1103/PhysRevE.89.010701
2834. Mattias Rydenfelt, Robert Sidney Cox, Hernan Garcia, Rob Phillips. Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. Physical Review E 2014, 89 (1) https://doi.org/10.1103/PhysRevE.89.012702
2835. Qianliang Wang, Tianshou Zhou. Alternative-splicing-mediated gene expression. Physical Review E 2014, 89 (1) https://doi.org/10.1103/PhysRevE.89.012713
2836. Bhaswati Bhattacharyya, Ziya Kalay. Distribution of population-averaged observables in stochastic gene expression. Physical Review E 2014, 89 (1) https://doi.org/10.1103/PhysRevE.89.012715
2837. Tommaso Biancalani, Louise Dyson, Alan J. McKane. Noise-Induced Bistable States and Their Mean Switching Time in Foraging Colonies. Physical Review Letters 2014, 112 (3) https://doi.org/10.1103/PhysRevLett.112.038101
2838. Yutaka Okaie, Tadashi Nakano, Takahiro Hara, Shojiro Nishio. Distributing Nanomachines for Minimizing Mean Residence Time of Molecular Signals in Bionanosensor Networks. IEEE Sensors Journal 2014, 14 (1) , 218-227. https://doi.org/10.1109/JSEN.2013.2281220
2839. Evangelia Kalligiannaki, Markos A. Katsoulakis, Petr Plecháč. Spatial Two-Level Interacting Particle Simulations and Information Theory--Based Error Quantification. SIAM Journal on Scientific Computing 2014, 36 (2) , A634-A667. https://doi.org/10.1137/120887060
2840. Mark B. Flegg, S. Jonathan Chapman, Likun Zheng, Radek Erban. Analysis of the Two-Regime Method on Square Meshes. SIAM Journal on Scientific Computing 2014, 36 (3) , B561-B588. https://doi.org/10.1137/130915844
2841. David F. Anderson, Desmond J. Higham, Yu Sun. Complexity of Multilevel Monte Carlo Tau-Leaping. SIAM Journal on Numerical Analysis 2014, 52 (6) , 3106-3127. https://doi.org/10.1137/130940761
2842. Xiaoying Han, Habib N. Najm. Dynamical Structures in Stochastic Chemical Reaction Systems. SIAM Journal on Applied Dynamical Systems 2014, 13 (3) , 1328-1351. https://doi.org/10.1137/140957482
2843. Marco Aldinucci, Cristina Calcagno, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella, Massimo Torquati, Angelo Troina. On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics. BioMed Research International 2014, 2014 , 1-14. https://doi.org/10.1155/2014/207041
2844. Hernán G. Solari, Mario A. Natiello. Linear Processes in Stochastic Population Dynamics: Theory and Application to Insect Development. The Scientific World Journal 2014, 2014 , 1-15. https://doi.org/10.1155/2014/873624
2845. Filippo Castiglione, Francesco Pappalardo, Carlo Bianca, Giulia Russo, Santo Motta. Modeling Biology Spanning Different Scales: An Open Challenge. BioMed Research International 2014, 2014 , 1-9. https://doi.org/10.1155/2014/902545
2846. Qianqian Wu, Kate Smith-Miles, Tianhai Tian. Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density. BMC Bioinformatics 2014, 15 (Suppl 12) , S3. https://doi.org/10.1186/1471-2105-15-S12-S3
2847. Eleftherios Ouzounoglou, Dimitrios Kalamatianos, Evangelia Emmanouilidou, Maria Xilouri, Leonidas Stefanis, Kostas Vekrellis, Elias S Manolakos. In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Systems Biology 2014, 8 (1) , 54. https://doi.org/10.1186/1752-0509-8-54
2848. Peican Zhu, Jinghang Liang, Jie Han. Gene perturbation and intervention in context-sensitive stochastic Boolean networks. BMC Systems Biology 2014, 8 (1) , 60. https://doi.org/10.1186/1752-0509-8-60
2849. Wim Hordijk, Nilesh Vaidya, Niles Lehman. Serial transfer can aid the evolution of autocatalytic sets. Journal of Systems Chemistry 2014, 5 (1) , 4. https://doi.org/10.1186/1759-2208-5-4
2850. Deena R Schmidt, Peter J Thomas. Measuring Edge Importance: A Quantitative Analysis of the Stochastic Shielding Approximation for Random Processes on Graphs. The Journal of Mathematical Neuroscience 2014, 4 (1) , 6. https://doi.org/10.1186/2190-8567-4-6
2851. Caroline Hartley, Timothy J Taylor, Istvan Z Kiss, Simon F Farmer, Luc Berthouze. Identification of Criticality in Neuronal Avalanches: II. A Theoretical and Empirical Investigation of the Driven Case. The Journal of Mathematical Neuroscience 2014, 4 (1) , 9. https://doi.org/10.1186/2190-8567-4-9
2852. Icíar Alfaro, David González, Felipe Bordeu, Adrien Leygue, Amine Ammar, Elías Cueto, Francisco Chinesta. Real-time in silico experiments on gene regulatory networks and surgery simulation on handheld devices. Journal of Computational Surgery 2014, 1 (1) , 1. https://doi.org/10.1186/2194-3990-1-1
2853. Elías Cueto, Francisco Chinesta. Real time simulation for computational surgery: a review. Advanced Modeling and Simulation in Engineering Sciences 2014, 1 (1) , 11. https://doi.org/10.1186/2213-7467-1-11
2854. Erik Butterworth, Bartholomew E. Jardine, Gary M. Raymond, Maxwell L. Neal, James B. Bassingthwaighte. . F1000Research 2014,,, 288. https://doi.org/10.12688/f1000research.2-288.v3
2855. Andrej Aderhold, Dirk Husmeier, Marco Grzegorczyk. Statistical inference of regulatory networks for circadian regulation. Statistical Applications in Genetics and Molecular Biology 2014, 13 (3) https://doi.org/10.1515/sagmb-2013-0051
2856. Aurora Blucher, Michelle Salas, Nicholas Williams, Hannah Callender. Mathematical modeling of integrin dynamics in initial formation of focal adhesions. Involve, a Journal of Mathematics 2014, 7 (4) , 509-527. https://doi.org/10.2140/involve.2014.7.509
2857. Ankit Gupta, Mustafa Khammash. Determining the long-term behavior of cell populations: A new procedure for detecting ergodicity in large stochastic reaction networks. IFAC Proceedings Volumes 2014, 47 (3) , 1711-1716. https://doi.org/10.3182/20140824-6-ZA-1003.00291
2858. Duluxan Sritharan, Sridevi V. Sarma. Fragility in Networks: Application to the Epileptic Brain. IFAC Proceedings Volumes 2014, 47 (3) , 7505-7510. https://doi.org/10.3182/20140824-6-ZA-1003.00313
2859. IFAC Fellow, Hong Jang, Kwang-Ki K. Kim, Jay H. Lee, Richard D. Braatz. Regularized Maximum Likelihood Estimation of Sparse Stochastic Monomolecular Biochemical Reaction Networks. IFAC Proceedings Volumes 2014, 47 (3) , 9551-9556. https://doi.org/10.3182/20140824-6-ZA-1003.01125
2860. Anandh Swaminathan, Richard M. Murray. Identification of Markov Chains From Distributional Measurements and Applications to Systems Biology. IFAC Proceedings Volumes 2014, 47 (3) , 4400-4405. https://doi.org/10.3182/20140824-6-ZA-1003.02771
2861. Constantinos Siettos, . Equation-free computation of coarse-grained center manifolds of microscopic simulators. Journal of Computational Dynamics 2014, 1 (2) , 377-389. https://doi.org/10.3934/jcd.2014.1.377
2862. Thomas Meyer, Christian Tschudin. Robust Network Services with Distributed Code Rewriting. 2014,,, 506-526. https://doi.org/10.4018/978-1-4666-4301-7.ch025
2863. Nancy Lan Guo, Ying-Wooi Wan. Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways. Cancer Informatics 2014, 13s5 , CIN.S14054. https://doi.org/10.4137/CIN.S14054
2864. Laurie J. Heyer, Jeffrey L. Poet. Synthetic Biology: A New Frontier. The American Mathematical Monthly 2014, 121 (9) , 857. https://doi.org/10.4169/amer.math.monthly.121.09.857
2865. Biswajit Das, Kinshuk Banerjee, Gautam Gangopadhyay. Propensity approach to nonequilibrium thermodynamics of a chemical reaction network: Controlling single E-coli β-galactosidase enzyme catalysis through the elementary reaction steps. The Journal of Chemical Physics 2013, 139 (24) , 244104. https://doi.org/10.1063/1.4844195
2866. Arturo Marín, Héctor Tejero, Juan Carlos Nuño, Francisco Montero, . The Advantage of Arriving First: Characteristic Times in Finite Size Populations of Error-Prone Replicators. PLoS ONE 2013, 8 (12) , e83142. https://doi.org/10.1371/journal.pone.0083142
2867. Claude Gérard, Béla Novák, . microRNA as a Potential Vector for the Propagation of Robustness in Protein Expression and Oscillatory Dynamics within a ceRNA Network. PLoS ONE 2013, 8 (12) , e83372. https://doi.org/10.1371/journal.pone.0083372
2868. Diana Monteoliva, Christina B. McCarthy, Luis Diambra, . Noise Minimisation in Gene Expression Switches. PLoS ONE 2013, 8 (12) , e84020. https://doi.org/10.1371/journal.pone.0084020
2869. Erik S. Welf, Heath E. Johnson, Jason M. Haugh, . Bidirectional coupling between integrin-mediated signaling and actomyosin mechanics explains matrix-dependent intermittency of leading-edge motility. Molecular Biology of the Cell 2013, 24 (24) , 3945-3955. https://doi.org/10.1091/mbc.e13-06-0311
2870. Ciarán P. Fisher, Nicholas J. Plant, J. Bernadette Moore, Andrzej M. Kierzek. QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. Bioinformatics 2013, 29 (24) , 3181-3190. https://doi.org/10.1093/bioinformatics/btt552
2871. Ching-Cher Sanders Yan, Chao-Ping Hsu. The fluctuation-dissipation theorem for stochastic kinetics—Implications on genetic regulations. The Journal of Chemical Physics 2013, 139 (22) , 224109. https://doi.org/10.1063/1.4837235
2872. Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada, . Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells. PLoS Computational Biology 2013, 9 (12) , e1003380. https://doi.org/10.1371/journal.pcbi.1003380
2873. Naga Rajesh Tummala, Shafigh Mehraeen, Yao-Tsung Fu, Chad Risko, Jean-Luc Brédas. Materials-Scale Implications of Solvent and Temperature on [6,6]-Phenyl-C61-butyric Acid Methyl Ester (PCBM): A Theoretical Perspective. Advanced Functional Materials 2013, 23 (46) , 5800-5813. https://doi.org/10.1002/adfm.201300918
2874. Chunhe Li, Jin Wang. Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation. Journal of The Royal Society Interface 2013, 10 (89) , 20130787. https://doi.org/10.1098/rsif.2013.0787
2875. Parviez Rana Hosseini, Trevon Fuller, Ryan Harrigan, Delong Zhao, Carmen Sofia Arriola, Armandoe Gonzalez, Matthew Joshua Miller, Xiangming Xiao, Tom B. Smith, Jamie Holland Jones, Peter Daszak, . Metapopulation Dynamics Enable Persistence of Influenza A, Including A/H5N1, in Poultry. PLoS ONE 2013, 8 (12) , e80091. https://doi.org/10.1371/journal.pone.0080091
2876. Fei Liu, Monika Heiner. Modeling membrane systems using colored stochastic Petri nets. Natural Computing 2013, 12 (4) , 617-629. https://doi.org/10.1007/s11047-013-9367-8
2877. C. Finn McQuaid, Nicholas F. Britton. Network Dynamics Contribute to Structure: Nestedness in Mutualistic Networks. Bulletin of Mathematical Biology 2013, 75 (12) , 2372-2388. https://doi.org/10.1007/s11538-013-9896-4
2878. Guilherme da Costa Pereira Innocentini, Michael Forger, Alexandre Ferreira Ramos, Ovidiu Radulescu, José Eduardo Martinho Hornos. Multimodality and Flexibility of Stochastic Gene Expression. Bulletin of Mathematical Biology 2013, 75 (12) , 2600-2630. https://doi.org/10.1007/s11538-013-9909-3
2879. Benjamin L. Bangasser, David J. Odde. Master Equation-Based Analysis of a Motor-Clutch Model for Cell Traction Force. Cellular and Molecular Bioengineering 2013, 6 (4) , 449-459. https://doi.org/10.1007/s12195-013-0296-5
2880. Paola Lecca. Stochastic chemical kinetics. Biophysical Reviews 2013, 5 (4) , 323-345. https://doi.org/10.1007/s12551-013-0122-2
2881. Athel Cornish-Bowden, Gabriel Piedrafita, Federico Morán, María Luz Cárdenas, Francisco Montero. Simulating a Model of Metabolic Closure. Biological Theory 2013, 8 (4) , 383-390. https://doi.org/10.1007/s13752-013-0132-0
2882. Domitilla Del Vecchio. A control theoretic framework for modular analysis and design of biomolecular networks. Annual Reviews in Control 2013, 37 (2) , 333-345. https://doi.org/10.1016/j.arcontrol.2013.09.011
2883. A. Camacho, B. Cazelles. Does homologous reinfection drive multiple-wave influenza outbreaks? Accounting for immunodynamics in epidemiological models. Epidemics 2013, 5 (4) , 187-196. https://doi.org/10.1016/j.epidem.2013.09.003
2884. Yandong Huang, Sten Rüdiger, Jianwei Shuai. Langevin approach for stochastic Hodgkin–Huxley dynamics with discretization of channel open fraction. Physics Letters A 2013, 377 (44) , 3223-3227. https://doi.org/10.1016/j.physleta.2013.10.008
2885. James Haven, Andrew William Park. Superinfection reconciles host–parasite association and cross-species transmission. Theoretical Population Biology 2013, 90 , 129-134. https://doi.org/10.1016/j.tpb.2013.09.015
2886. Luis F. Lafuerza, Raul Toral. On the effect of heterogeneity in stochastic interacting-particle systems. Scientific Reports 2013, 3 (1) https://doi.org/10.1038/srep01189
2887. Daniel Schultz, Mingyang Lu, Trevor Stavropoulos, Jose' Onuchic, Eshel Ben-Jacob. Turning Oscillations Into Opportunities: Lessons from a Bacterial Decision Gate. Scientific Reports 2013, 3 (1) https://doi.org/10.1038/srep01668
2888. Sayak Mukherjee, Sang-Cheol Seok, Veronica J Vieland, Jayajit Das. Data-driven quantification of the robustness and sensitivity of cell signaling networks. Physical Biology 2013, 10 (6) , 066002. https://doi.org/10.1088/1478-3975/10/6/066002
2889. Dong Wang, Qian Zhuang, Ying Fan, Zeng-Ru Di. Species diversity in rock—paper—scissors game coupling with Levy flight. Chinese Physics B 2013, 22 (12) , 128702. https://doi.org/10.1088/1674-1056/22/12/128702
2890. Oksana Sorokina, Anatoly Sorokin, J. Douglas Armstrong, Vincent Danos. A simulator for spatially extended kappa models. Bioinformatics 2013, 29 (23) , 3105-3106. https://doi.org/10.1093/bioinformatics/btt523
2891. M. Scotti, F. Ciocchetta, F. Jordan. Social and landscape effects on food webs: a multi-level network simulation model. Journal of Complex Networks 2013, 1 (2) , 160-182. https://doi.org/10.1093/comnet/cnt013
2892. Niranjan Srinivas, Thomas E. Ouldridge, Petr Šulc, Joseph M. Schaeffer, Bernard Yurke, Ard A. Louis, Jonathan P. K. Doye, Erik Winfree. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Research 2013, 41 (22) , 10641-10658. https://doi.org/10.1093/nar/gkt801
2893. Kelly A. Walker, Jared H. Cole. Correlated charge transport in bilinear tunnel junction arrays. Physical Review B 2013, 88 (24) https://doi.org/10.1103/PhysRevB.88.245101
2894. Peter Ashcroft, Tobias Galla. Pattern formation in individual-based systems with time-varying parameters. Physical Review E 2013, 88 (6) https://doi.org/10.1103/PhysRevE.88.062104
2895. Chao-Ran Cai, Zhi-Xi Wu, Jian-Yue Guan. Behavior of susceptible-vaccinated–infected–recovered epidemics with diversity in the infection rate of individuals. Physical Review E 2013, 88 (6) https://doi.org/10.1103/PhysRevE.88.062805
2896. Yongguo Mei, Adria Carbo, Raquel Hontecillas, Josep Bassaganya-Riera. ENISI SDE: A novel web-based stochastic modeling tool for computational biology. 2013,,, 392-397. https://doi.org/10.1109/BIBM.2013.6732524
2897. Qianqian Wu, Kate Smith-Miles, Tianhai Tian. Approximate Bayesian computation for estimating rate constants in biochemical reaction systems. 2013,,, 416-421. https://doi.org/10.1109/BIBM.2013.6732528
2898. Fei Li, Yang Cao. Multigrid discretization method for PopZ polarization in Caulobacter cell cycle. 2013,,, 469-472. https://doi.org/10.1109/BIBM.2013.6732538
2899. Aron Hjartarson, Jakob Ruess, John Lygeros. Approximating the solution of the chemical master equation by combining finite state projection and stochastic simulation. 2013,,, 751-756. https://doi.org/10.1109/CDC.2013.6759972
2900. Xiaohua Xu, Niraj Kumar, Arjun Krishnan, Rahul V. Kulkarni. Stochastic modeling of dwell-time distributions during transcriptional pausing and initiation. 2013,,, 4068-4073. https://doi.org/10.1109/CDC.2013.6760512
2901. Reda Ammar, Therese Smith. Developing time constraints in Petri net models of biochemical processes via computation structure modeling. 2013,,, 000034-000039. https://doi.org/10.1109/ISSPIT.2013.6781850
2902. Guopeng Wei, Paul Bogdan, Radu Marculescu. Efficient Modeling and Simulation of Bacteria-Based Nanonetworks with BNSim. IEEE Journal on Selected Areas in Communications 2013, 31 (12) , 868-878. https://doi.org/10.1109/JSAC.2013.SUP2.12130019
2903. Guopeng Wei, Paul Bogdan, Radu Marculescu. Bumpy Rides: Modeling the Dynamics of Chemotactic Interacting Bacteria. IEEE Journal on Selected Areas in Communications 2013, 31 (12) , 879-890. https://doi.org/10.1109/JSAC.2013.SUP2.12130020
2904. Sebastian Nahring, Roland Ewald, Adelinde M. Uhrmacher, Carsten Maus. From standardized modeling formats to modeling languages and back — An exploration based on SBML and ML-Rules. 2013,,, 1359-1370. https://doi.org/10.1109/WSC.2013.6721522
2905. Matthieu Domenech de Cellès, Jean-Ralph Zahar, Véronique Abadie, Didier Guillemot. Limits of patient isolation measures to control extended-spectrum beta-lactamase–producing Enterobacteriaceae: model-based analysis of clinical data in a pediatric ward. BMC Infectious Diseases 2013, 13 (1) https://doi.org/10.1186/1471-2334-13-187
2906. Laith Yakob, Thomas V Riley, David L Paterson, Archie CA Clements. Clostridium difficile exposure as an insidious source of infection in healthcare settings: an epidemiological model. BMC Infectious Diseases 2013, 13 (1) https://doi.org/10.1186/1471-2334-13-376
2907. Suzy M Stiegelmeyer, Morgan C Giddings. Agent-based modeling of competence phenotype switching in Bacillus subtilis. Theoretical Biology and Medical Modelling 2013, 10 (1) https://doi.org/10.1186/1742-4682-10-23
2908. Wim Hordijk, Mike Steel. A formal model of autocatalytic sets emerging in an RNA replicator system. Journal of Systems Chemistry 2013, 4 (1) https://doi.org/10.1186/1759-2208-4-3
2909. Donatello Materassi, Subhrajit Roychowdhury, Thomas Hays, Murti Salapaka. An exact approach for studying cargo transport by an ensemble of molecular motors. BMC Biophysics 2013, 6 (1) https://doi.org/10.1186/2046-1682-6-14
2910. Thomas P. Adams, E. Penelope Holland, Richard Law, Michael J. Plank, Michael Raghib. On the growth of locally interacting plants: differential equations for the dynamics of spatial moments. Ecology 2013, 94 (12) , 2732-2743. https://doi.org/10.1890/13-0147.1
2911. Teresa Martins, Matthew Evans, Hugh Woolfenden, Richard Morris. Towards the Physics of Calcium Signalling in Plants. Plants 2013, 2 (4) , 541-588. https://doi.org/10.3390/plants2040541
2912. R. P. Joshi, A. M. Schmidt, J. Das, D. Pytel, M. J. Riese, M. Lester, J. A. Diehl, E. M. Behrens, T. Kambayashi, G. A. Koretzky. The   Isoform of Diacylglycerol Kinase Plays a Predominant Role in Regulatory T Cell Development and TCR-Mediated Ras Signaling. Science Signaling 2013, 6 (303) , ra102-ra102. https://doi.org/10.1126/scisignal.2004373
2913. Carmeline J. Dsilva, Ronen Talmon, Neta Rabin, Ronald R. Coifman, Ioannis G. Kevrekidis. Nonlinear intrinsic variables and state reconstruction in multiscale simulations. The Journal of Chemical Physics 2013, 139 (18) , 184109. https://doi.org/10.1063/1.4828457
2914. Doriano Brogioli. Violation of the mass-action law in dilute chemical systems. The Journal of Chemical Physics 2013, 139 (18) , 184102. https://doi.org/10.1063/1.4829146
2915. Kazunari Mouri, Yasushi Sako, . Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells. PLoS Computational Biology 2013, 9 (11) , e1003320. https://doi.org/10.1371/journal.pcbi.1003320
2916. Che-Chi Shu, Anushree Chatterjee, Wei-Shou Hu, Doraiswami Ramkrishna, . Role of Intracellular Stochasticity in Biofilm Growth. Insights from Population Balance Modeling. PLoS ONE 2013, 8 (11) , e79196. https://doi.org/10.1371/journal.pone.0079196
2917. Jakub Pękalski, Pawel J. Zuk, Marek Kochańczyk, Michael Junkin, Ryan Kellogg, Savaş Tay, Tomasz Lipniacki, . Spontaneous NF-κB Activation by Autocrine TNFα Signaling: A Computational Analysis. PLoS ONE 2013, 8 (11) , e78887. https://doi.org/10.1371/journal.pone.0078887
2918. Rick Quax, Andrea Apolloni, Peter M. A. Sloot. The diminishing role of hubs in dynamical processes on complex networks. Journal of The Royal Society Interface 2013, 10 (88) , 20130568. https://doi.org/10.1098/rsif.2013.0568
2919. M Ángeles Serrano, Manuel Jurado, Ramon Reigada. Negative feedback self-regulation contributes to robust and high-fidelity transmembrane signal transduction. Journal of The Royal Society Interface 2013, 10 (88) , 20130581. https://doi.org/10.1098/rsif.2013.0581
2920. Naomi J. Fox, Glenn Marion, Ross S. Davidson, Piran C. L. White, Michael R. Hutchings, . Modelling Parasite Transmission in a Grazing System: The Importance of Host Behaviour and Immunity. PLoS ONE 2013, 8 (11) , e77996. https://doi.org/10.1371/journal.pone.0077996
2921. Thomas A. Henzinger. Quantitative reactive modeling and verification. Computer Science - Research and Development 2013, 28 (4) , 331-344. https://doi.org/10.1007/s00450-013-0251-7
2922. Zhuo-li Lin, Jun Luo, Zheng-jian Chen, Jun Yi, Hong-liang Jiang, Ke-hua Tu, Li-qun Wang. A Monte Carlo simulation study of the effect of chain length on the hydrolysis of poly(lactic acid). Chinese Journal of Polymer Science 2013, 31 (11) , 1554-1562. https://doi.org/10.1007/s10118-013-1353-1
2923. Samuel A. Isaacson, Carolyn A. Larabell, Mark A. Le Gros, David M. McQueen, Charles S. Peskin. The Influence of Spatial Variation in Chromatin Density Determined by X-Ray Tomograms on the Time to Find DNA Binding Sites. Bulletin of Mathematical Biology 2013, 75 (11) , 2093-2117. https://doi.org/10.1007/s11538-013-9883-9
2924. SRIJEETA TALUKDER, SHRABANI SEN, RALF METZLER, SUMAN K BANIK, PINAKI CHAUDHURY. Stochastic optimization-based study of dimerization kinetics. Journal of Chemical Sciences 2013, 125 (6) , 1619-1627. https://doi.org/10.1007/s12039-013-0502-y
2925. Edward P. Debold, Sam Walcott, Mike Woodward, Matthew A. Turner. Direct Observation of Phosphate Inhibiting the Force-Generating Capacity of a Miniensemble of Myosin Molecules. Biophysical Journal 2013, 105 (10) , 2374-2384. https://doi.org/10.1016/j.bpj.2013.09.046
2926. Nathan Crook, Hal S. Alper. Model-based design of synthetic, biological systems. Chemical Engineering Science 2013, 103 , 2-11. https://doi.org/10.1016/j.ces.2012.12.022
2927. K.T. Blackwell. Approaches and tools for modeling signaling pathways and calcium dynamics in neurons. Journal of Neuroscience Methods 2013, 220 (2) , 131-140. https://doi.org/10.1016/j.jneumeth.2013.05.008
2928. Christian Arnold, Peter F. Stadler, Sonja J. Prohaska. Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem. Journal of Theoretical Biology 2013, 336 , 61-74. https://doi.org/10.1016/j.jtbi.2013.07.012
2929. Daisuke Takahashi, Åke Brännström, Rupert Mazzucco, Atsushi Yamauchi, Ulf Dieckmann. Abrupt community transitions and cyclic evolutionary dynamics in complex food webs. Journal of Theoretical Biology 2013, 337 , 181-189. https://doi.org/10.1016/j.jtbi.2013.08.003
2930. Hongguang Xi, Zhuoqin Yang, Marc Turcotte. Subtle interplay of stochasticity and deterministic dynamics pervades an evolutionary plausible genetic circuit for Bacillus subtilis competence. Mathematical Biosciences 2013, 246 (1) , 148-163. https://doi.org/10.1016/j.mbs.2013.08.007
2931. Erik De Schutter. The importance of stochastic signaling processes in the induction of long-term synaptic plasticity. Neural Networks 2013, 47 , 3-10. https://doi.org/10.1016/j.neunet.2012.11.015
2932. Susanna M. Messinger, Annette Ostling. Predator attack rate evolution in space: The role of ecology mediated by complex emergent spatial structure and self-shading. Theoretical Population Biology 2013, 89 , 55-63. https://doi.org/10.1016/j.tpb.2013.08.003
2933. Hideyuki Suzuki. Monte Carlo simulation of classical spin models with chaotic billiards. Physical Review E 2013, 88 (5) https://doi.org/10.1103/PhysRevE.88.052144
2934. Michael Taynnan Barros, Sasitharan Balasubramaniam, Brendan Jennings. Error control for calcium signaling based molecular communication. 2013,,, 1056-1060. https://doi.org/10.1109/ACSSC.2013.6810453
2935. Garrett Jenkinson, John Goutsias. Statistical validation of parametric approximations to the master equation. 2013,,, 1721-1725. https://doi.org/10.1109/ACSSC.2013.6810595
2936. Alper Demir, Burak Erman. Simulation of temporal stochastic phenomena in electronic and biological systems: A comparative review, examples and synergies. 2013,,, 811-818. https://doi.org/10.1109/ICCAD.2013.6691206
2937. Fernando A.F. Braz, Jader S. Cruz, Alessandra C. Faria-Campos, Sergio V.A. Campos. Probabilistic Model Checking Analysis of Palytoxin Effects on Cell Energy Reactions of the Na+/K+-ATPase. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, 10 (6) , 1530-1541. https://doi.org/10.1109/TCBB.2013.97
2938. Michael Nivala, Christopher Y. Ko, Melissa Nivala, James N. Weiss, Zhilin Qu. The emergence of subcellular pacemaker sites for calcium waves and oscillations. The Journal of Physiology 2013, 591 (21) , 5305-5320. https://doi.org/10.1113/jphysiol.2013.259960
2939. Scott J. Denholm, Rachel A. Norman, Andrew S. Hoyle, Andrew P. Shinn, Nick G. H. Taylor, . Reproductive Trade-Offs May Moderate the Impact of Gyrodactylus salaris in Warmer Climates. PLoS ONE 2013, 8 (10) , e78909. https://doi.org/10.1371/journal.pone.0078909
2940. L. A. Widmer, J. Stelling, F. J. Doyle. Note: Parameter-independent bounding of the stochastic Michaelis-Menten steady-state intrinsic noise variance. The Journal of Chemical Physics 2013, 139 (16) , 166102. https://doi.org/10.1063/1.4827496
2941. Kyung Hyuk Kim, Hong Qian, Herbert M. Sauro. Nonlinear biochemical signal processing via noise propagation. The Journal of Chemical Physics 2013, 139 (14) , 144108. https://doi.org/10.1063/1.4822103
2942. Peter Mottishaw, Bartlomiej Waclaw, Martin R Evans. An exclusion process on a tree with constant aggregate hopping rate. Journal of Physics A: Mathematical and Theoretical 2013, 46 (40) , 405003. https://doi.org/10.1088/1751-8113/46/40/405003
2943. Zhi Yang Tam, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan, . Mathematical Modeling of the Role of Mitochondrial Fusion and Fission in Mitochondrial DNA Maintenance. PLoS ONE 2013, 8 (10) , e76230. https://doi.org/10.1371/journal.pone.0076230
2944. R. Noriega, A. Salleo, A. J. Spakowitz. Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers. Proceedings of the National Academy of Sciences 2013, 110 (41) , 16315-16320. https://doi.org/10.1073/pnas.1307158110
2945. Christian Ruzanski, Julia Smirnova, Martin Rejzek, Darrell Cockburn, Henriette L. Pedersen, Marilyn Pike, William G. T. Willats, Birte Svensson, Martin Steup, Oliver Ebenhöh, Alison M. Smith, Robert A. Field. A Bacterial Glucanotransferase Can Replace the Complex Maltose Metabolism Required for Starch to Sucrose Conversion in Leaves at Night. Journal of Biological Chemistry 2013, 288 (40) , 28581-28598. https://doi.org/10.1074/jbc.M113.497867
2946. E. S. Kurkina, G. Yu. Averchuk. Monte-carlo simulation of the oscillatory dynamics of a catalytic reaction with lateral interactions. Computational Mathematics and Modeling 2013, 24 (4) , 526-542. https://doi.org/10.1007/s10598-013-9196-8
2947. James Clarke, K. A. Jane White, Katy Turner. Approximating Optimal Controls for Networks when There Are Combinations of Population-Level and Targeted Measures Available: Chlamydia Infection as a Case-Study. Bulletin of Mathematical Biology 2013, 75 (10) , 1747-1777. https://doi.org/10.1007/s11538-013-9867-9
2948. David V. Foster, Mary M. Rorick, Tanja Gesell, Laura M. Feeney, Jacob G. Foster. Dynamic landscapes: A model of context and contingency in evolution. Journal of Theoretical Biology 2013, 334 , 162-172. https://doi.org/10.1016/j.jtbi.2013.05.030
2949. Gian Marco Palamara, Gustav W. Delius, Matthew J. Smith, Owen L. Petchey. Predation effects on mean time to extinction under demographic stochasticity. Journal of Theoretical Biology 2013, 334 , 61-70. https://doi.org/10.1016/j.jtbi.2013.06.007
2950. Philipp Thomas, Arthur V. Straube, Jens Timmer, Christian Fleck, Ramon Grima. Signatures of nonlinearity in single cell noise-induced oscillations. Journal of Theoretical Biology 2013, 335 , 222-234. https://doi.org/10.1016/j.jtbi.2013.06.021
2951. Shengjun Liu, Qi Wang, Hai Feng. The correlation between intrinsic noise and extrinsic noise. Physica A: Statistical Mechanics and its Applications 2013, 392 (20) , 5138-5142. https://doi.org/10.1016/j.physa.2013.06.032
2952. Ryan J. Morris, Kym Eden, Reuben Yarwood, Line Jourdain, Rosalind J. Allen, Cait E. MacPhee. Mechanistic and environmental control of the prevalence and lifetime of amyloid oligomers. Nature Communications 2013, 4 (1) https://doi.org/10.1038/ncomms2909
2953. Changhong Shi, Tianshou Zhou, Zhanjiang Yuan. Functional tunability of biological circuits from additional toggle switches. IET Systems Biology 2013, 7 (5) , 126-134. https://doi.org/10.1049/iet-syb.2012.0056
2954. Danesh Moradigaravand, Jan Engelstädter. The Evolution of Natural Competence: Disentangling Costs and Benefits of Sex in Bacteria. The American Naturalist 2013, 182 (4) , E112-E126. https://doi.org/10.1086/671909
2955. Stacy O. Scholle, Rolf J. F. Ypma, Alun L. Lloyd, Katia Koelle. Viral Substitution Rate Variation Can Arise from the Interplay between Within-Host and Epidemiological Dynamics. The American Naturalist 2013, 182 (4) , 494-513. https://doi.org/10.1086/672000
2956. Filippos D Klironomos, Juliette de Meaux, Johannes Berg. Can we always sweep the details of RNA-processing under the carpet?. Physical Biology 2013, 10 (5) , 056007. https://doi.org/10.1088/1478-3975/10/5/056007
2957. Deepak Bhat, Manoj Gopalakrishnan. Memory, bias, and correlations in bidirectional transport of molecular-motor-driven cargoes. Physical Review E 2013, 88 (4) https://doi.org/10.1103/PhysRevE.88.042702
2958. Sayantari Ghosh, Amit Kumar Pal, Indrani Bose. Noise-induced regime shifts: A quantitative characterization. The European Physical Journal E 2013, 36 (10) https://doi.org/10.1140/epje/i2013-13123-y
2959. Zhi-Xi Wu, Hai-Feng Zhang. Peer pressure is a double-edged sword in vaccination dynamics. EPL (Europhysics Letters) 2013, 104 (1) , 10002. https://doi.org/10.1209/0295-5075/104/10002
2960. Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani. A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. Electronic Proceedings in Theoretical Computer Science 2013, 130 , 70-73. https://doi.org/10.4204/EPTCS.130.10
2961. Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco Nobile, Dario Pescini, Alessandro Re. GPU-powered Simulation Methodologies for Biological Systems. Electronic Proceedings in Theoretical Computer Science 2013, 130 , 87-91. https://doi.org/10.4204/EPTCS.130.14
2962. Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra. Recent developments in research on catalytic reaction networks. Electronic Proceedings in Theoretical Computer Science 2013, 130 , 3-13. https://doi.org/10.4204/EPTCS.130.3
2963. Martin Gruebele, D. Thirumalai. Perspective: Reaches of chemical physics in biology. The Journal of Chemical Physics 2013, 139 (12) , 121701. https://doi.org/10.1063/1.4820139
2964. S. Muy, A. Kundu, D. Lacoste. Non-invasive estimation of dissipation from non-equilibrium fluctuations in chemical reactions. The Journal of Chemical Physics 2013, 139 (12) , 124109. https://doi.org/10.1063/1.4821760
2965. L. F. Lafuerza, R. Toral. Stochastic description of delayed systems. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2013, 371 (1999) , 20120458. https://doi.org/10.1098/rsta.2012.0458
2966. Nicolae Radu Zabet, Robert Foy, Boris Adryan, . The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity. PLoS ONE 2013, 8 (9) , e73714. https://doi.org/10.1371/journal.pone.0073714
2967. Javier Garcia-Bernardo, Mary J. Dunlop, . Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops. PLoS Computational Biology 2013, 9 (9) , e1003229. https://doi.org/10.1371/journal.pcbi.1003229
2968. Rory M. Donovan, Andrew J. Sedgewick, James R. Faeder, Daniel M. Zuckerman. Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. The Journal of Chemical Physics 2013, 139 (11) , 115105. https://doi.org/10.1063/1.4821167
2969. Jun Ohkubo. Extended duality relations between birth–death processes and partial differential equations. Journal of Physics A: Mathematical and Theoretical 2013, 46 (37) , 375004. https://doi.org/10.1088/1751-8113/46/37/375004
2970. Carole J. Proctor, Delphine Boche, Douglas A. Gray, James A. R. Nicoll, . Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS ONE 2013, 8 (9) , e73631. https://doi.org/10.1371/journal.pone.0073631
2971. Gabriele Lillacci, Mustafa Khammash. The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics 2013, 29 (18) , 2311-2319. https://doi.org/10.1093/bioinformatics/btt380
2972. Marc Weber, Javier Buceta, . Stochastic Stabilization of Phenotypic States: The Genetic Bistable Switch as a Case Study. PLoS ONE 2013, 8 (9) , e73487. https://doi.org/10.1371/journal.pone.0073487
2973. Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde M. Uhrmacher, Andrea Unger. Constructing and visualizing chemical reaction networks from pi-calculus models. Formal Aspects of Computing 2013, 25 (5) , 723-742. https://doi.org/10.1007/s00165-011-0209-0
2974. Yevgeniy Frenkel, Andrew J. Majda, Boualem Khouider. Stochastic and deterministic multicloud parameterizations for tropical convection. Climate Dynamics 2013, 41 (5-6) , 1527-1551. https://doi.org/10.1007/s00382-013-1678-z
2975. Hyung Ju Hwang, Juan J. L. Velázquez. Bistable stochastic biochemical networks: large chemical networks and systems with many molecules. Journal of Mathematical Chemistry 2013, 51 (8) , 2074-2103. https://doi.org/10.1007/s10910-013-0200-5
2976. Gabriel Ciobanu. General patterns of interaction in stochastic fusion. Natural Computing 2013, 12 (3) , 429-439. https://doi.org/10.1007/s11047-012-9346-5
2977. Mieke Massink, Manuele Brambilla, Diego Latella, Marco Dorigo, Mauro Birattari. On the use of Bio-PEPA for modelling and analysing collective behaviours in swarm robotics. Swarm Intelligence 2013, 7 (2-3) , 201-228. https://doi.org/10.1007/s11721-013-0079-6
2978. Elizaveta A. Novikova, Cornelis Storm. Contractile Fibers and Catch-Bond Clusters: a Biological Force Sensor?. Biophysical Journal 2013, 105 (6) , 1336-1345. https://doi.org/10.1016/j.bpj.2013.07.039
2979. Meghan McCabe Pryor, Shalini T. Low-Nam, Ádám M. Halász, Diane S. Lidke, Bridget S. Wilson, Jeremy S. Edwards. Dynamic Transition States of ErbB1 Phosphorylation Predicted by Spatial Stochastic Modeling. Biophysical Journal 2013, 105 (6) , 1533-1543. https://doi.org/10.1016/j.bpj.2013.07.056
2980. Volker Kurz, Edward M. Nelson, Nicolas Perry, Winston Timp, Gregory Timp. Epigenetic Memory Emerging from Integrated Transcription Bursts. Biophysical Journal 2013, 105 (6) , 1526-1532. https://doi.org/10.1016/j.bpj.2013.08.010
2981. John Realpe-Gomez, Mara Baudena, Tobias Galla, Alan J. McKane, Max Rietkerk. Demographic noise and resilience in a semi-arid ecosystem model. Ecological Complexity 2013, 15 , 97-108. https://doi.org/10.1016/j.ecocom.2013.04.002
2982. Luis Mier-y-Teran-Romero, Ira B. Schwartz, Derek A.T. Cummings. Breaking the symmetry: Immune enhancement increases persistence of dengue viruses in the presence of asymmetric transmission rates. Journal of Theoretical Biology 2013, 332 , 203-210. https://doi.org/10.1016/j.jtbi.2013.04.036
2983. H. Baumann, T. Dayar, M.C. Orhan, W. Sandmann. On the numerical solution of Kronecker-based infinite level-dependent QBD processes. Performance Evaluation 2013, 70 (9) , 663-681. https://doi.org/10.1016/j.peva.2013.05.001
2984. Mariusz Żaba, Piotr Garbaczewski, Vladimir Stephanovich. Lévy flights in confining environments: Random paths and their statistics. Physica A: Statistical Mechanics and its Applications 2013, 392 (17) , 3485-3496. https://doi.org/10.1016/j.physa.2013.04.028
2985. Jason Lloyd-Price, Andre S. Ribeiro. Bistability in a stochastic RNA-mediated gene network. Physical Review E 2013, 88 (3) https://doi.org/10.1103/PhysRevE.88.032714
2986. Alok Kumar Maity, Arnab Bandyopadhyay, Sudip Chattopadhyay, Jyotipratim Ray Chaudhuri, Ralf Metzler, Pinaki Chaudhury, Suman K. Banik. Quantification of noise in bifunctionality-induced post-translational modification. Physical Review E 2013, 88 (3) https://doi.org/10.1103/PhysRevE.88.032716
2987. V. Jemseena, Manoj Gopalakrishnan. Microtubule catastrophe from protofilament dynamics. Physical Review E 2013, 88 (3) https://doi.org/10.1103/PhysRevE.88.032717
2988. J. Iranzo, A. E. Lobkovsky, Y. I. Wolf, E. V. Koonin. Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context. Journal of Bacteriology 2013, 195 (17) , 3834-3844. https://doi.org/10.1128/JB.00412-13
2989. Marifi Güler. An Investigation of the Stochastic Hodgkin-Huxley Models Under Noisy Rate Functions. Neural Computation 2013, 25 (9) , 2355-2372. https://doi.org/10.1162/NECO_a_00487
2990. Lendert Gelens, Lydia Hill, Alexandra Vandervelde, Jan Danckaert, Remy Loris, . A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli. PLoS Computational Biology 2013, 9 (8) , e1003190. https://doi.org/10.1371/journal.pcbi.1003190
2991. P. Smadbeck, Y. N. Kaznessis. A closure scheme for chemical master equations. Proceedings of the National Academy of Sciences 2013, 110 (35) , 14261-14265. https://doi.org/10.1073/pnas.1306481110
2992. Ezio Bartocci, Luca Bortolussi, Laura Nenzi, Guido Sanguinetti. On the Robustness of Temporal Properties for Stochastic Models. Electronic Proceedings in Theoretical Computer Science 2013, 125 , 3-19. https://doi.org/10.4204/EPTCS.125.1
2993. Oded Maler, Ádám M. Halász, Olivier Lebeltel, Ouri Maler. Exploring the Dynamics of Mass Action Systems. Electronic Proceedings in Theoretical Computer Science 2013, 125 , 84-91. https://doi.org/10.4204/EPTCS.125.6
2994. Jose Teles, Cristina Pina, Patrik Edén, Mattias Ohlsson, Tariq Enver, Carsten Peterson, . Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions. PLoS Computational Biology 2013, 9 (8) , e1003197. https://doi.org/10.1371/journal.pcbi.1003197
2995. Romain Bourget, Loïc Chaumont, Natalia Sapoukhina, . Timing of Pathogen Adaptation to a Multicomponent Treatment. PLoS ONE 2013, 8 (8) , e71926. https://doi.org/10.1371/journal.pone.0071926
2996. Marc Joannides, Irène Larramendy–Valverde. On Geometry and Scale of a Stochastic Chemostat. Communications in Statistics - Theory and Methods 2013, 42 (16) , 2902-2911. https://doi.org/10.1080/03610926.2012.746983
2997. H. Y. Kueh, A. Champhekar, S. L. Nutt, M. B. Elowitz, E. V. Rothenberg. Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation. Science 2013, 341 (6146) , 670-673. https://doi.org/10.1126/science.1240831
2998. Josep Díaz, Leslie Ann Goldberg, George B. Mertzios, David Richerby, Maria Serna, Paul G. Spirakis. On the fixation probability of superstars. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2013, 469 (2156) , 20130193. https://doi.org/10.1098/rspa.2013.0193
2999. Samuel A. Isaacson. A convergent reaction-diffusion master equation. The Journal of Chemical Physics 2013, 139 (5) , 054101. https://doi.org/10.1063/1.4816377
3000. I. Chattopadhyay, A. Kuchina, G. M. Suel, H. Lipson. Inverse Gillespie for inferring stochastic reaction mechanisms from intermittent samples. Proceedings of the National Academy of Sciences 2013, 110 (32) , 12990-12995. https://doi.org/10.1073/pnas.1214559110
3001. Lora Billings, Luis Mier-y-Teran-Romero, Brandon Lindley, Ira B. Schwartz, . Intervention-Based Stochastic Disease Eradication. PLoS ONE 2013, 8 (8) , e70211. https://doi.org/10.1371/journal.pone.0070211
3002. Yutian R. Zhao, Kimberley B. McAuley, Judit E. Puskas. Monte Carlo Model for Arborescent Polyisobutylene Production in the Batch Reactor. Macromolecular Theory and Simulations 2013, 22 (7) , 365-376. https://doi.org/10.1002/mats.201300114
3003. Yong Zhang, Charalambos Papelis, Pengtao Sun, Zhongbo Yu. Evaluation and linking of effective parameters in particle-based models and continuum models for mixing-limited bimolecular reactions. Water Resources Research 2013, 49 (8) , 4845-4865. https://doi.org/10.1002/wrcr.20368
3004. Dean Koch, Reinhard Illner, Junling Ma. Edge removal in random contact networks and the basic reproduction number. Journal of Mathematical Biology 2013, 67 (2) , 217-238. https://doi.org/10.1007/s00285-012-0545-6
3005. J. Carrero-Mantilla, S. Duque-Tobón. Efficient stochastic simulation of simultaneous reaction and diffusion in a gas-liquid interface. Journal of Mathematical Chemistry 2013, 51 (7) , 1864-1880. https://doi.org/10.1007/s10910-013-0188-x
3006. Suzanne M. O’Regan, John M. Drake. Theory of early warning signals of disease emergenceand leading indicators of elimination. Theoretical Ecology 2013, 6 (3) , 333-357. https://doi.org/10.1007/s12080-013-0185-5
3007. Benjamin L. Bangasser, Steven S. Rosenfeld, David J. Odde. Determinants of Maximal Force Transmission in a Motor-Clutch Model of Cell Traction in a Compliant Microenvironment. Biophysical Journal 2013, 105 (3) , 581-592. https://doi.org/10.1016/j.bpj.2013.06.027
3008. Dimitrios Milios, Stephen Gilmore. Markov Chain Simulation with Fewer Random Samples. Electronic Notes in Theoretical Computer Science 2013, 296 , 183-197. https://doi.org/10.1016/j.entcs.2013.07.012
3009. Hongguang Xi, Lixia Duan, Marc Turcotte. Point-cycle bistability and stochasticity in a regulatory circuit for Bacillus subtilis competence. Mathematical Biosciences 2013, 244 (2) , 135-147. https://doi.org/10.1016/j.mbs.2013.05.002
3010. J. Goutsias, G. Jenkinson. Markovian dynamics on complex reaction networks. Physics Reports 2013, 529 (2) , 199-264. https://doi.org/10.1016/j.physrep.2013.03.004
3011. Debashish Chowdhury. Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective. Physics Reports 2013, 529 (1) , 1-197. https://doi.org/10.1016/j.physrep.2013.03.005
3012. D Pianini, S Montagna, M Viroli. Chemical-oriented simulation of computational systems with ALCHEMIST. Journal of Simulation 2013, 7 (3) , 202-215. https://doi.org/10.1057/jos.2012.27
3013. P P González Pérez, A Omicini, M Sbaraglia. A biochemically inspired coordination-based model for simulating intracellular signalling pathways. Journal of Simulation 2013, 7 (3) , 216-226. https://doi.org/10.1057/jos.2012.28
3014. Michael Klann, Heinz Koeppl. Reaction schemes, escape times and geminate recombinations in particle-based spatial simulations of biochemical reactions. Physical Biology 2013, 10 (4) , 046005. https://doi.org/10.1088/1478-3975/10/4/046005
3015. Marcio Argollo de Menezes, Edgardo Brigatti, Veit Schwämmle. Evolving cellular automata for diversity generation and pattern recognition: deterministic versus random strategy. Journal of Statistical Mechanics: Theory and Experiment 2013, 2013 (08) , P08006. https://doi.org/10.1088/1742-5468/2013/08/P08006
3016. Huijun Jiang, Ping Wu, Zhonghuai Hou, Zhenyu Li, Jinlong Yang. Orientation-sensitive nonlinear growth of graphene: An epitaxial growth mechanism determined by geometry. Physical Review B 2013, 88 (5) https://doi.org/10.1103/PhysRevB.88.054304
3017. Fei Liu, Monika Heiner, Ming Yang. Colored Petri nets for multiscale systems biology - Current modeling and analysis capabilities in snoopy. 2013,,, 24-30. https://doi.org/10.1109/ISB.2013.6623788
3018. Pei Wang, Jinhu Lu, Li Wan, Yao Chen. A stochastic simulation algorithm for biochemical reactions with delays. 2013,,, 109-114. https://doi.org/10.1109/ISB.2013.6623803
3019. Eisa Zarepour, Mahbub Hassan, Chun Tung Chou, Adesoji A. Adesina. Nano-scale sensor networks for chemical catalysis. 2013,,, 61-66. https://doi.org/10.1109/NANO.2013.6720813
3020. MARIAN GHEORGHE, GHEORGHE PĂUN, MARIO J. PÉREZ-JIMÉNEZ, GRZEGORZ ROZENBERG. RESEARCH FRONTIERS OF MEMBRANE COMPUTING: OPEN PROBLEMS AND RESEARCH TOPICS. International Journal of Foundations of Computer Science 2013, 24 (05) , 547-623. https://doi.org/10.1142/S0129054113500202
3021. PEI-JUNG WU, CHOU-CHING K. LIN, MING-SHAUNG JU. AXIAL-SYMMETRIC MODELING AND KINEMATIC ANALYSIS OF SPREADING OF SPARSELY CULTURED FIBROBLASTS. Journal of Mechanics in Medicine and Biology 2013, 13 (04) , 1350062. https://doi.org/10.1142/S0219519413500620
3022. GIOVANNI LUCA CIAMPAGLIA. A FRAMEWORK FOR THE CALIBRATION OF SOCIAL SIMULATION MODELS. Advances in Complex Systems 2013, 16 (04n05) , 1350030. https://doi.org/10.1142/S0219525913500306
3023. D. Andrieux, P. Gaspard. Information erasure in copolymers. EPL (Europhysics Letters) 2013, 103 (3) , 30004. https://doi.org/10.1209/0295-5075/103/30004
3024. Daniel A. Charlebois, Mads Kærn. An Accelerated Method for Simulating Population Dynamics. Communications in Computational Physics 2013, 14 (2) , 461-476. https://doi.org/10.4208/cicp.130612.121012a
3025. Elisa Franco, Jongmin Kim, Friedrich C. Simmel. Transcriptional Oscillators. 2013,,, 83-112. https://doi.org/10.1002/9783527671632.ch04
3026. Patrick Hillenbrand, Georg Fritz, Ulrich Gerland, . Biological Signal Processing with a Genetic Toggle Switch. PLoS ONE 2013, 8 (7) , e68345. https://doi.org/10.1371/journal.pone.0068345
3027. Doan Tuong-Van Le, Thomas Eckert, Günther Woehlke, . Computer Simulation of Assembly and Co-operativity of Hexameric AAA ATPases. PLoS ONE 2013, 8 (7) , e67815. https://doi.org/10.1371/journal.pone.0067815
3028. Youfang Cao, Jie Liang. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method. The Journal of Chemical Physics 2013, 139 (2) , 025101. https://doi.org/10.1063/1.4811286
3029. Luca Vattuone, Marco Smerieri, Letizia Savio, Abu Md Asaduzzaman, Krishna Muralidharan, Michael J. Drake, Mario Rocca. Accretion disc origin of the Earth's water. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2013, 371 (1994) , 20110585. https://doi.org/10.1098/rsta.2011.0585
3030. Gregory C. Rutledge. Computer Modeling of Polymer Crystallization. 2013,,, 197-214. https://doi.org/10.1002/9781118541838.ch6
3031. Marek Kochańczyk, Joanna Jaruszewicz, Tomasz Lipniacki. Stochastic transitions in a bistable reaction system on the membrane. Journal of The Royal Society Interface 2013, 10 (84) , 20130151. https://doi.org/10.1098/rsif.2013.0151
3032. Joseph Sang-Il Kwon, Michael Nayhouse, Panagiotis D. Christofides, Gerassimos Orkoulas. Modeling and control of protein crystal shape and size in batch crystallization. AIChE Journal 2013, 59 (7) , 2317-2327. https://doi.org/10.1002/aic.14039
3033. Dominik Wodarz. Evolutionary dynamics of giant viruses and their virophages. Ecology and Evolution 2013, 3 (7) , 2103-2115. https://doi.org/10.1002/ece3.600
3034. Carolina Toloza Porras, Dagmar R. D'hooge, Paul H. M. Van Steenberge, Marie-Françoise Reyniers, Guy B. Marin. A Theoretical Exploration of the Potential of ICAR ATRP for One- and Two-Pot Synthesis of Well-Defined Diblock Copolymers. Macromolecular Reaction Engineering 2013, 7 (7) , 311-326. https://doi.org/10.1002/mren.201200085
3035. Rafael Callejas-Tovar, C. Alex Diaz, Julibeth M. Martinez de la Hoz, Perla B. Balbuena. Dealloying of platinum-based alloy catalysts: Kinetic Monte Carlo simulations. Electrochimica Acta 2013, 101 , 326-333. https://doi.org/10.1016/j.electacta.2013.01.053
3036. Petros Koumoutsakos, Justin Feigelman. Multiscale stochastic simulations of chemical reactions with regulated scale separation. Journal of Computational Physics 2013, 244 , 290-297. https://doi.org/10.1016/j.jcp.2012.11.030
3037. Sumit Verma, Tafizur Rehman, Abhijit Chatterjee. A cluster expansion model for rate constants of surface diffusion processes on Ag, Al, Cu, Ni, Pd and Pt(100) surfaces. Surface Science 2013, 613 , 114-125. https://doi.org/10.1016/j.susc.2013.03.022
3038. S. Semsey, L. Jauffred, Z. Csiszovszki, J. Erdossy, V. Steger, S. Hansen, S. Krishna. The effect of LacI autoregulation on the performance of the lactose utilization system in Escherichia coli. Nucleic Acids Research 2013, 41 (13) , 6381-6390. https://doi.org/10.1093/nar/gkt351
3039. Ingo Homrighausen, Anton A. Winkler, Erwin Frey. Fluctuation effects in the pair-annihilation process with Lévy dynamics. Physical Review E 2013, 88 (1) https://doi.org/10.1103/PhysRevE.88.012111
3040. Steve Pressé, Kingshuk Ghosh, Julian Lee, Ken A. Dill. Principles of maximum entropy and maximum caliber in statistical physics. Reviews of Modern Physics 2013, 85 (3) , 1115-1141. https://doi.org/10.1103/RevModPhys.85.1115
3041. Marco S. Nobile, Giancarlo Mauri. Evolutionary inference of biochemical reaction networks accelerated on graphics processing units. 2013,,, 668-670. https://doi.org/10.1109/HPCSim.2013.6641490
3042. Andre S. Ribeiro. Kinetics of gene expression in bacteria — From models to measurements, and back again. Canadian Journal of Chemistry 2013, 91 (7) , 487-494. https://doi.org/10.1139/cjc-2012-0409
3043. Jeremy Neuman, Bert Kiewiet, Jack D Cowan, Wim van Drongelen. Observations of dynamical behavior in a stochastic Wilson-Cowan population with plasticity. BMC Neuroscience 2013, 14 (S1) https://doi.org/10.1186/1471-2202-14-S1-P400
3044. G. Yu. Averchuk, E. S. Kurkina. Comparative analysis of Monte Carlo methods via the example of calculating the complex dynamics of a lattice model for a chemical reaction. Moscow University Computational Mathematics and Cybernetics 2013, 37 (3) , 89-96. https://doi.org/10.3103/S0278641913030023
3045. Vijesh J. Bhute, Abhijit Chatterjee. Building a kinetic Monte Carlo model with a chosen accuracy. The Journal of Chemical Physics 2013, 138 (24) , 244112. https://doi.org/10.1063/1.4812319
3046. Koichi Fujimoto, Satoshi Sawai, . A Design Principle of Group-level Decision Making in Cell Populations. PLoS Computational Biology 2013, 9 (6) , e1003110. https://doi.org/10.1371/journal.pcbi.1003110
3047. Diane M. Longo, Jangir Selimkhanov, Jeffrey D. Kearns, Jeff Hasty, Alexander Hoffmann, Lev S. Tsimring, . Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module. PLoS Computational Biology 2013, 9 (6) , e1003112. https://doi.org/10.1371/journal.pcbi.1003112
3048. Ivana Bozic, Johannes G Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Sup Moon, Amin Yaqubie, Nicole Kelly, Dung T Le, Evan J Lipson, Paul B Chapman, Luis A Diaz, Bert Vogelstein, Martin A Nowak. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife 2013, 2 https://doi.org/10.7554/eLife.00747
3049. Angel Goñi-Moreno, Martyn Amos, Fernando de la Cruz, . Multicellular Computing Using Conjugation for Wiring. PLoS ONE 2013, 8 (6) , e65986. https://doi.org/10.1371/journal.pone.0065986
3050. J. E. Jun, M. Yang, H. Chen, A. K. Chakraborty, J. P. Roose. Activation of Extracellular Signal-Regulated Kinase but Not of p38 Mitogen-Activated Protein Kinase Pathways in Lymphocytes Requires Allosteric Activation of SOS. Molecular and Cellular Biology 2013, 33 (12) , 2470-2484. https://doi.org/10.1128/MCB.01593-12
3051. J. A. Vazquez Diosdado, P. Ashwin, K. I. Kohary, C. D. Wright. Response to “Comment on ‘Threshold switching via electric field induced crystallization in phase change memory devices’” [Appl. Phys. Lett. 102, 236101 (2012)]. Applied Physics Letters 2013, 102 (23) , 236102. https://doi.org/10.1063/1.4809722
3052. Daniela Besozzi. Computational Methods in Systems Biology: Case Studies and Biological Insights. Electronic Proceedings in Theoretical Computer Science 2013, 116 , 3-10. https://doi.org/10.4204/EPTCS.116.1
3053. Matthew Hartfield, Samuel Alizon, . Introducing the Outbreak Threshold in Epidemiology. PLoS Pathogens 2013, 9 (6) , e1003277. https://doi.org/10.1371/journal.ppat.1003277
3054. Jae Kyoung Kim, Trachette L. Jackson, . Mechanisms That Enhance Sustainability of p53 Pulses. PLoS ONE 2013, 8 (6) , e65242. https://doi.org/10.1371/journal.pone.0065242
3055. Samuel J. Pinches, Gabriel da Silva. On the Separation of Timescales in Chemically Activated Reactions. International Journal of Chemical Kinetics 2013, 45 (6) , 387-396. https://doi.org/10.1002/kin.20774
3056. Giovanni De Matteis, Alex Graudenzi, Marco Antoniotti. A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. Journal of Mathematical Biology 2013, 66 (7) , 1409-1462. https://doi.org/10.1007/s00285-012-0539-4
3057. Sara Montagna, Mirko Viroli, Jose Luis Fernandez-Marquez, Giovanna Di Marzo Serugendo, Franco Zambonelli. Injecting Self-Organisation into Pervasive Service Ecosystems. Mobile Networks and Applications 2013, 18 (3) , 398-412. https://doi.org/10.1007/s11036-012-0411-1
3058. Purushottam D. Dixit. Quantifying Extrinsic Noise in Gene Expression Using the Maximum Entropy Framework. Biophysical Journal 2013, 104 (12) , 2743-2750. https://doi.org/10.1016/j.bpj.2013.05.010
3059. Premal Shah, Yang Ding, Malwina Niemczyk, Grzegorz Kudla, Joshua B. Plotkin. Rate-Limiting Steps in Yeast Protein Translation. Cell 2013, 153 (7) , 1589-1601. https://doi.org/10.1016/j.cell.2013.05.049
3060. Rebecca Mancy, Patrick Prosser, Simon Rogers. Discrete and continuous time simulations of spatial ecological processes predict different final population sizes and interspecific competition outcomes. Ecological Modelling 2013, 259 , 50-61. https://doi.org/10.1016/j.ecolmodel.2013.03.013
3061. Yushu Yang, Muruhan Rathinam. Tau leaping of stiff stochastic chemical systems via local central limit approximation. Journal of Computational Physics 2013, 242 , 581-606. https://doi.org/10.1016/j.jcp.2013.02.011
3062. Rob J. De Boer, Alan S. Perelson. Quantifying T lymphocyte turnover. Journal of Theoretical Biology 2013, 327 , 45-87. https://doi.org/10.1016/j.jtbi.2012.12.025
3063. Alexandros Sopasakis. Traffic Updating Mechanisms for Stochastic Lattice-Free Dynamics. Procedia - Social and Behavioral Sciences 2013, 80 , 837-845. https://doi.org/10.1016/j.sbspro.2013.05.045
3064. Joanna Jaruszewicz, Tomasz Lipniacki. Toggle switch: noise determines the winning gene. Physical Biology 2013, 10 (3) , 035007. https://doi.org/10.1088/1478-3975/10/3/035007
3065. Darka Labavić, Hannes Nagel, Wolfhard Janke, Hildegard Meyer-Ortmanns. Caveats in modeling a common motif in genetic circuits. Physical Review E 2013, 87 (6) https://doi.org/10.1103/PhysRevE.87.062706
3066. Michael Nayhouse, Joseph Sang-Il Kwon, Gerassimos Orkoulas, Panagiotis D. Christofides. Modeling and control of protein crystal shape distribution. 2013,,, 1896-1901. https://doi.org/10.1109/ACC.2013.6580112
3067. Hyungman Park, Andreas Gerstlauer. Toward a fast stochastic simulation processor for biochemical reaction networks. 2013,,, 50-58. https://doi.org/10.1109/ASAP.2013.6567550
3068. F. Débarre, O. Ronce, S. Gandon. Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments. Journal of Evolutionary Biology 2013, 26 (6) , 1185-1202. https://doi.org/10.1111/jeb.12132
3069. Anna Kolbus, Bogdan Nowakowski, Andrzej L. Kawczyński. Distributions of first passage times in a bistable thermochemical system with a low temperature stationary state. The European Physical Journal B 2013, 86 (6) https://doi.org/10.1140/epjb/e2013-31146-9
3070. Jerzy Gorecki, Adam Gorecki, Annie Lemarchand, Bogdan Nowakowski. Information resonance in a model excitable system. The European Physical Journal B 2013, 86 (6) https://doi.org/10.1140/epjb/e2013-40054-y
3071. И.Р. Акбердин, I.R. Akberdin. In Silico Cell: Challenges and Perspectives. Математическая биология и биоинформатика 2013, 8 (1) , 295-315. https://doi.org/10.17537/2013.8.295
3072. Garrett Jenkinson, John Goutsias. Statistically testing the validity of analytical and computational approximations to the chemical master equation. The Journal of Chemical Physics 2013, 138 (20) , 204108. https://doi.org/10.1063/1.4807390
3073. David Bruce Borenstein, Yigal Meir, Joshua W. Shaevitz, Ned S. Wingreen, . Non-Local Interaction via Diffusible Resource Prevents Coexistence of Cooperators and Cheaters in a Lattice Model. PLoS ONE 2013, 8 (5) , e63304. https://doi.org/10.1371/journal.pone.0063304
3074. Ivan Chang, Pierre Baldi. A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions. Bioinformatics 2013, 29 (10) , 1299-1307. https://doi.org/10.1093/bioinformatics/btt140
3075. Jeremy D. Schmit. Kinetic theory of amyloid fibril templating. The Journal of Chemical Physics 2013, 138 (18) , 185102. https://doi.org/10.1063/1.4803658
3076. Anatoly Malevanets, Styliani Consta. Variation of droplet acidity during evaporation. The Journal of Chemical Physics 2013, 138 (18) , 184312. https://doi.org/10.1063/1.4804303
3077. S.-W. Teng, S. Mukherji, J. R. Moffitt, S. de Buyl, E. K. O'Shea. Robust Circadian Oscillations in Growing Cyanobacteria Require Transcriptional Feedback. Science 2013, 340 (6133) , 737-740. https://doi.org/10.1126/science.1230996
3078. Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre, Carine Brouat, . Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus. PLoS Computational Biology 2013, 9 (5) , e1003039. https://doi.org/10.1371/journal.pcbi.1003039
3079. Filipe Grácio, Joaquim Cabral, Bruce Tidor, . Modeling Stem Cell Induction Processes. PLoS ONE 2013, 8 (5) , e60240. https://doi.org/10.1371/journal.pone.0060240
3080. Daniel T. Gillespie, Andreas Hellander, Linda R. Petzold. Perspective: Stochastic algorithms for chemical kinetics. The Journal of Chemical Physics 2013, 138 (17) , 170901. https://doi.org/10.1063/1.4801941
3081. Simone Pigolotti, Ludvig Lizana, Daniel Otzen, Kim Sneppen. Quality control system response to stochastic growth of amyloid fibrils. FEBS Letters 2013, 587 (9) , 1405-1410. https://doi.org/10.1016/j.febslet.2013.03.018
3082. Hyung Ju Hwang, Juan J. L. Velázquez. Bistable stochastic biochemical networks: highly specific systems with few chemicals. Journal of Mathematical Chemistry 2013, 51 (5) , 1343-1375. https://doi.org/10.1007/s10910-013-0150-y
3083. Matthew J. Simpson, Benjamin J. Binder, Parvathi Haridas, Benjamin K. Wood, Katrina K. Treloar, D. L. Sean McElwain, Ruth E. Baker. Experimental and Modelling Investigation of Monolayer Development with Clustering. Bulletin of Mathematical Biology 2013, 75 (5) , 871-889. https://doi.org/10.1007/s11538-013-9839-0
3084. Andrew R. Kanarek, Colleen T. Webb, Michael Barfield, Robert D. Holt. Allee effects, aggregation, and invasion success. Theoretical Ecology 2013, 6 (2) , 153-164. https://doi.org/10.1007/s12080-012-0167-z
3085. Paolo Dini, Chrystopher L. Nehaniv, Attila Egri-Nagy, Maria J. Schilstra. Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction. Biosystems 2013, 112 (2) , 145-162. https://doi.org/10.1016/j.biosystems.2013.03.003
3086. Didier Gonze. Modeling the effect of cell division on genetic oscillators. Journal of Theoretical Biology 2013, 325 , 22-33. https://doi.org/10.1016/j.jtbi.2013.02.001
3087. Mirko Viroli. On competitive self-composition in pervasive services. Science of Computer Programming 2013, 78 (5) , 556-568. https://doi.org/10.1016/j.scico.2012.10.002
3088. Edward J. Allen. A Stochastic Analysis of Power Doubling Time for a Subcritical System. Stochastic Analysis and Applications 2013, 31 (3) , 528-537. https://doi.org/10.1080/07362994.2013.777287
3089. Rinat Arbel-Goren, Asaf Tal, Tamar Friedlander, Shiri Meshner, Nina Costantino, Donald L. Court, Joel Stavans. Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli. Nucleic Acids Research 2013, 41 (9) , 4825-4834. https://doi.org/10.1093/nar/gkt184
3090. Tetsuo Katsuragi, Naoaki Ono, Keiichi Yasumoto, Md. Altaf-Ul-Amin, Masami Y. Hirai, Kansuporn Sriyudthsak, Yuji Sawada, Yui Yamashita, Yukako Chiba, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito, Fumihide Shiraishi, Shigehiko Kanaya. SS-mPMG and SS-GA: Tools for Finding Pathways and Dynamic Simulation of Metabolic Networks. Plant and Cell Physiology 2013, 54 (5) , 728-739. https://doi.org/10.1093/pcp/pct052
3091. Shafigh Mehraeen, Veaceslav Coropceanu, Jean-Luc Brédas. Role of band states and trap states in the electrical properties of organic semiconductors: Hopping versus mobility edge model. Physical Review B 2013, 87 (19) https://doi.org/10.1103/PhysRevB.87.195209
3092. Congping Lin, Peter Ashwin, Gero Steinberg. Motor-mediated bidirectional transport along an antipolar microtubule bundle: A mathematical model. Physical Review E 2013, 87 (5) https://doi.org/10.1103/PhysRevE.87.052709
3093. Jorge Luis Hita, José María Ortiz de Zárate. Spatial correlations in nonequilibrium reaction-diffusion problems by the Gillespie algorithm. Physical Review E 2013, 87 (5) https://doi.org/10.1103/PhysRevE.87.052802
3094. Hong-Li Zeng, Mikko Alava, Erik Aurell, John Hertz, Yasser Roudi. Maximum Likelihood Reconstruction for Ising Models with Asynchronous Updates. Physical Review Letters 2013, 110 (21) https://doi.org/10.1103/PhysRevLett.110.210601
3095. Jean-Benoît Lalanne, Paul François. Principles of Adaptive Sorting Revealed by In Silico Evolution. Physical Review Letters 2013, 110 (21) https://doi.org/10.1103/PhysRevLett.110.218102
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3097. Ruoyu Luo, Lin Ye, Chenyang Tao, Kankan Wang, . Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise. PLoS ONE 2013, 8 (4) , e62380. https://doi.org/10.1371/journal.pone.0062380
3098. Ryota Nishino, Takahiro Sakaue, Hiizu Nakanishi, . Transcription Fluctuation Effects on Biochemical Oscillations. PLoS ONE 2013, 8 (4) , e60938. https://doi.org/10.1371/journal.pone.0060938
3099. Katri Hituri, Marja-Leena Linne, . Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations. PLoS ONE 2013, 8 (4) , e59618. https://doi.org/10.1371/journal.pone.0059618
3100. Wenliang Zhang, Yuan Lin, Jin Qian, Weiqiu Chen, Huajian Gao. Tuning Molecular Adhesion via Material Anisotropy. Advanced Functional Materials 2013, 94 , n/a-n/a. https://doi.org/10.1002/adfm.201300069
3101. David A. Benson, Diogo Bolster, Amir Paster. Communication: A full solution of the annihilation reaction A + B → ∅ based on time-subordination. The Journal of Chemical Physics 2013, 138 (13) , 131101. https://doi.org/10.1063/1.4800799
3102. Ilker Tunc, Maxim S. Shkarayev, Leah B. Shaw. Epidemics in Adaptive Social Networks with Temporary Link Deactivation. Journal of Statistical Physics 2013, 151 (1-2) , 355-366. https://doi.org/10.1007/s10955-012-0667-7
3103. José E.R. Cury, Fabio L. Baldissera. Systems Biology, Synthetic Biology and Control Theory: A promising golden braid. Annual Reviews in Control 2013, 37 (1) , 57-67. https://doi.org/10.1016/j.arcontrol.2013.03.006
3104. Bahram Houchmandzadeh, Marcel Vallade. Exact results for fixation probability of bithermal evolutionary graphs. Biosystems 2013, 112 (1) , 49-54. https://doi.org/10.1016/j.biosystems.2013.03.020
3105. Daniel Jost, Andrzej Nowojewski, Erel Levine. Regulating the Many to Benefit the Few: Role of Weak Small RNA Targets. Biophysical Journal 2013, 104 (8) , 1773-1782. https://doi.org/10.1016/j.bpj.2013.02.020
3106. Michał Komorowski, Jacek Miękisz, Michael P.H. Stumpf. Decomposing Noise in Biochemical Signaling Systems Highlights the Role of Protein Degradation. Biophysical Journal 2013, 104 (8) , 1783-1793. https://doi.org/10.1016/j.bpj.2013.02.027
3107. Siu-Kei Chow, Cameron Smith, Thomas MacCarthy, Mary Ann Pohl, Aviv Bergman, Arturo Casadevall. Disease-Enhancing Antibodies Improve the Efficacy of Bacterial Toxin-Neutralizing Antibodies. Cell Host & Microbe 2013, 13 (4) , 417-428. https://doi.org/10.1016/j.chom.2013.03.001
3108. Qiang Zhang, Douglas E. Kline, Sudin Bhattacharya, Robert B. Crawford, Rory B. Conolly, Russell S. Thomas, Melvin E. Andersen, Norbert E. Kaminski. All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicology and Applied Pharmacology 2013, 268 (1) , 17-26. https://doi.org/10.1016/j.taap.2013.01.015
3109. NICOLAS OURY, GORDON PLOTKIN. Multi-level modelling via stochastic multi-level multiset rewriting. Mathematical Structures in Computer Science 2013, 23 (02) , 471-503. https://doi.org/10.1017/S0960129512000199
3110. Pu Han, Liang Ren Niestemski, Jeffrey E Barrick, Michael W Deem. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. Physical Biology 2013, 10 (2) , 025004. https://doi.org/10.1088/1478-3975/10/2/025004
3111. Tyler M Earnest, Elijah Roberts, Michael Assaf, Karin Dahmen, Zaida Luthey-Schulten. DNA looping increases the range of bistability in a stochastic model of the lac genetic switch. Physical Biology 2013, 10 (2) , 026002. https://doi.org/10.1088/1478-3975/10/2/026002
3112. Claudio Borile, Amos Maritan, Miguel A Muñoz. The effect of quenched disorder in neutral theories. Journal of Statistical Mechanics: Theory and Experiment 2013, 2013 (04) , P04032. https://doi.org/10.1088/1742-5468/2013/04/P04032
3113. Peter Banda, Christof Teuscher, Matthew R. Lakin. Online Learning in a Chemical Perceptron. Artificial Life 2013, 19 (2) , 195-219. https://doi.org/10.1162/ARTL_a_00105
3114. Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo, Raffaele Calogero. Multi-level model for the investigation of oncoantigen-driven vaccination effect. BMC Bioinformatics 2013, 14 (S6) https://doi.org/10.1186/1471-2105-14-S6-S11
3115. Andrey Pavlovich Zakharov, Dmitry Anatolievich Bratsun. Synchronization of circadian rhythms in the scale of a gene, a cell and a whole organism. Computer Research and Modeling 2013, 5 (2) , 255-270. https://doi.org/10.20537/2076-7633-2013-5-2-255-270
3116. Evgeniy Khain, Baruch Meerson. Velocity fluctuations of noisy reaction fronts propagating into a metastable state. Journal of Physics A: Mathematical and Theoretical 2013, 46 (12) , 125002. https://doi.org/10.1088/1751-8113/46/12/125002
3117. Tina Toni, Bruce Tidor, . Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology. PLoS Computational Biology 2013, 9 (3) , e1002960. https://doi.org/10.1371/journal.pcbi.1002960
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3120. Scott M. Duke-Sylvester, Roman Biek, Leslie A. Real. Molecular evolutionary signatures reveal the role of host ecological dynamics in viral disease emergence and spread. Philosophical Transactions of the Royal Society B: Biological Sciences 2013, 368 (1614) , 20120194. https://doi.org/10.1098/rstb.2012.0194
3121. Keigo Ikezaki, Tomotaka Komori, Toshio Yanagida, . Spontaneous Detachment of the Leading Head Contributes to Myosin VI Backward Steps. PLoS ONE 2013, 8 (3) , e58912. https://doi.org/10.1371/journal.pone.0058912
3122. A. Cournac, J. Plumbridge. DNA Looping in Prokaryotes: Experimental and Theoretical Approaches. Journal of Bacteriology 2013, 195 (6) , 1109-1119. https://doi.org/10.1128/JB.02038-12
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3126. Meggan E. Craft, Hawthorne L. Beyer, Daniel T. Haydon, . Estimating the Probability of a Major Outbreak from the Timing of Early Cases: An Indeterminate Problem?. PLoS ONE 2013, 8 (3) , e57878. https://doi.org/10.1371/journal.pone.0057878
3127. P. Francois, G. Voisinne, E. D. Siggia, G. Altan-Bonnet, M. Vergassola. Phenotypic model for early T-cell activation displaying sensitivity, specificity, and antagonism. Proceedings of the National Academy of Sciences 2013, 110 (10) , E888-E897. https://doi.org/10.1073/pnas.1300752110
3128. Shinji Nakaoka, Kazuyuki Aihara. Stochastic simulation of structured skin cell population dynamics. Journal of Mathematical Biology 2013, 66 (4-5) , 807-835. https://doi.org/10.1007/s00285-012-0618-6
3129. Kenny Jolley, Richard S. Graham. Flow-induced nucleation in polymer melts: a study of the GO model for pure and bimodal blends, under shear and extensional flow. Rheologica Acta 2013, 52 (3) , 271-286. https://doi.org/10.1007/s00397-012-0663-5
3130. Vilda Purutçuoğlu. Inference of the stochastic MAPK pathway by modified diffusion bridge method. Central European Journal of Operations Research 2013, 21 (2) , 415-429. https://doi.org/10.1007/s10100-012-0237-8
3131. Susanna M. Messinger, Annette Ostling. The influence of host demography, pathogen virulence, and relationships with pathogen virulence on the evolution of pathogen transmission in a spatial context. Evolutionary Ecology 2013, 27 (2) , 353-380. https://doi.org/10.1007/s10682-012-9594-y
3132. Peter Milner, Colin S. Gillespie, Darren J. Wilkinson. Moment closure based parameter inference of stochastic kinetic models. Statistics and Computing 2013, 23 (2) , 287-295. https://doi.org/10.1007/s11222-011-9310-8
3133. Prapanporn Rattana, Konstantin B. Blyuss, Ken T. D. Eames, Istvan Z. Kiss. A Class of Pairwise Models for Epidemic Dynamics on Weighted Networks. Bulletin of Mathematical Biology 2013, 75 (3) , 466-490. https://doi.org/10.1007/s11538-013-9816-7
3134. Dong Ding, David A. Benson, Amir Paster, Diogo Bolster. Modeling bimolecular reactions and transport in porous media via particle tracking. Advances in Water Resources 2013, 53 , 56-65. https://doi.org/10.1016/j.advwatres.2012.11.001
3135. Anastasis Georgoulas, Maria Luisa Guerriero. A Software Interface Between the Narrative Language and Bio-PEPA. Electronic Notes in Theoretical Computer Science 2013, 293 , 51-65. https://doi.org/10.1016/j.entcs.2013.02.018
3136. Eva Sciacca, Salvatore Spinella, Cristina Calcagno, Ferruccio Damiani, Mario Coppo. Parameter Identification and Assessment of Nutrient Transporters in AM Symbiosis through Stochastic Simulations. Electronic Notes in Theoretical Computer Science 2013, 293 , 83-96. https://doi.org/10.1016/j.entcs.2013.02.020
3137. Xu-Sheng Zhang, Daniela De Angelis, Peter J. White, Andre Charlett, Richard G. Pebody, John McCauley. Co-circulation of influenza A virus strains and emergence of pandemic via reassortment: The role of cross-immunity. Epidemics 2013, 5 (1) , 20-33. https://doi.org/10.1016/j.epidem.2012.10.003
3138. Adriano Santana, Alberto Zobelli, Jani Kotakoski, Andrey Chuvilin, Elena Bichoutskaia. Inclusion of radiation damage dynamics in high-resolution transmission electron microscopy image simulations: The example of graphene. Physical Review B 2013, 87 (9) https://doi.org/10.1103/PhysRevB.87.094110
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3141. Koichiro Uriu, Saúl Ares, Andrew C. Oates, Luis G. Morelli. Dynamics of mobile coupled phase oscillators. Physical Review E 2013, 87 (3) https://doi.org/10.1103/PhysRevE.87.032911
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3147. Pedro Rafael Costa, Marcio Luis Acencio, Ney Lemke, . Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation. PLoS ONE 2013, 8 (2) , e57328. https://doi.org/10.1371/journal.pone.0057328
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3152. David Dolan, Glyn Nelson, Anze Zupanic, Graham Smith, Daryl Shanley, . Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci. PLoS ONE 2013, 8 (2) , e55190. https://doi.org/10.1371/journal.pone.0055190
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3166. Lusha W. Liang, Razika Hussein, Dena H. S. Block, Han N. Lim. Minimal Effect of Gene Clustering on Expression in Escherichia coli. Genetics 2013, 193 (2) , 453-465. https://doi.org/10.1534/genetics.112.147199
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3168. Andrea Rocco, Andrzej M. Kierzek, Johnjoe McFadden, . Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations. PLoS ONE 2013, 8 (1) , e54272. https://doi.org/10.1371/journal.pone.0054272
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3310. Tim Rogers, Alan J McKane, Axel G Rossberg. Spontaneous genetic clustering in populations of competing organisms. Physical Biology 2012, 9 (6) , 066002. https://doi.org/10.1088/1478-3975/9/6/066002
3311. E. Alipour, J. F. Marko. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Research 2012, 40 (22) , 11202-11212. https://doi.org/10.1093/nar/gks925
3312. Enrique Martínez, Alfredo Caro. Atomistic modeling of long-term evolution of twist boundaries under vacancy supersaturation. Physical Review B 2012, 86 (21) https://doi.org/10.1103/PhysRevB.86.214109
3313. Basil S. Bayati, Philip A. Eckhoff. Influence of high-order nonlinear fluctuations in the multivariate susceptible-infectious-recovered master equation. Physical Review E 2012, 86 (6) https://doi.org/10.1103/PhysRevE.86.062103
3314. Kyung Hyuk Kim, Herbert M. Sauro. Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations. 2012,,, 5330-5335. https://doi.org/10.1109/CDC.2012.6425827
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3318. Fernando J. Barros. A compositional approach for modeling and simulation of bio-molecular systems. 2012,,, 1-12. https://doi.org/10.1109/WSC.2012.6465260
3319. Robin Aguilée, David Claessen, Amaury Lambert. ADAPTIVE RADIATION DRIVEN BY THE INTERPLAY OF ECO-EVOLUTIONARY AND LANDSCAPE DYNAMICS. Evolution 2012, 7 , no-no. https://doi.org/10.1111/evo.12008
3320. Michael D. F. Thom, Calvin Dytham. FEMALE CHOOSINESS LEADS TO THE EVOLUTION OF INDIVIDUALLY DISTINCTIVE MALES. Evolution 2012, 66 (12) , 3736-3742. https://doi.org/10.1111/j.1558-5646.2012.01732.x
3321. Bernie J Daigle, Min K Roh, Linda R Petzold, Jarad Niemi. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinformatics 2012, 13 (1) https://doi.org/10.1186/1471-2105-13-68
3322. Thomas Hladish, Eugene Melamud, Luis Alberto Barrera, Alison Galvani, Lauren Ancel Meyers. EpiFire: An open source C++ library and application for contact network epidemiology. BMC Bioinformatics 2012, 13 (1) https://doi.org/10.1186/1471-2105-13-76
3323. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Sonia Colombo, Enzo Martegani. The role of feedback control mechanisms on the establishment of oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae. EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012 (1) https://doi.org/10.1186/1687-4153-2012-10
3324. David Murrugarra, Alan Veliz-Cuba, Boris Aguilar, Seda Arat, Reinhard Laubenbacher. Modeling stochasticity and variability in gene regulatory networks. EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012 (1) https://doi.org/10.1186/1687-4153-2012-5
3325. Onder Suvak, Alper Demir. Phase computations and phase models for discrete molecular oscillators. EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012 (1) https://doi.org/10.1186/1687-4153-2012-6
3326. Aleksandr Andreychenko, Linar Mikeev, David Spieler, Verena Wolf. Approximate maximum likelihood estimation for stochastic chemical kinetics. EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012 (1) https://doi.org/10.1186/1687-4153-2012-9
3327. Zoran Konkoli. Mathematical explanation of the predictive power of the X-level approach reaction noise estimator method. Theoretical Biology and Medical Modelling 2012, 9 (1) https://doi.org/10.1186/1742-4682-9-12
3328. Tamás Székely, Kevin Burrage, Radek Erban, Konstantinos C Zygalakis. A higher-order numerical framework for stochastic simulation of chemical reaction systems. BMC Systems Biology 2012, 6 (1) https://doi.org/10.1186/1752-0509-6-85
3329. Wim Hordijk, Mike Steel. Autocatalytic sets extended: Dynamics, inhibition, and a generalization. Journal of Systems Chemistry 2012, 3 (1) https://doi.org/10.1186/1759-2208-3-5
3330. TuǦrul Dayar, M. Can Orhan. Kronecker-Based Infinite Level-Dependent QBD Processes. Journal of Applied Probability 2012, 49 (4) , 1166-1187. https://doi.org/10.1239/jap/1354716665
3331. M. Scotti, N. Gjata, C. Livi, F. Jordán. Dynamical effects of weak trophic interactions in a stochastic food web simulation. Community Ecology 2012, 13 (2) , 230-237. https://doi.org/10.1556/ComEc.13.2012.2.13
3332. Benjamin M. Althouse, Justin Lessler, Amadou A. Sall, Mawlouth Diallo, Kathryn A. Hanley, Douglas M. Watts, Scott C. Weaver, Derek A. T. Cummings, . Synchrony of Sylvatic Dengue Isolations: A Multi-Host, Multi-Vector SIR Model of Dengue Virus Transmission in Senegal. PLoS Neglected Tropical Diseases 2012, 6 (11) , e1928. https://doi.org/10.1371/journal.pntd.0001928
3333. Yuting Xu, Yueheng Lan. The N-leap method for stochastic simulation of coupled chemical reactions. The Journal of Chemical Physics 2012, 137 (20) , 204103. https://doi.org/10.1063/1.4767343
3334. Juan Atalaya. Mass loading induced dephasing in nanomechanical resonators. Journal of Physics: Condensed Matter 2012, 24 (47) , 475301. https://doi.org/10.1088/0953-8984/24/47/475301
3335. E. L. Read, A. A. Tovo-Dwyer, A. K. Chakraborty. Stochastic effects are important in intrahost HIV evolution even when viral loads are high. Proceedings of the National Academy of Sciences 2012, 109 (48) , 19727-19732. https://doi.org/10.1073/pnas.1206940109
3336. Jason Lloyd-Price, Abhishekh Gupta, Andre S. Ribeiro. SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations. Bioinformatics 2012, 28 (22) , 3004-3005. https://doi.org/10.1093/bioinformatics/bts556
3337. Adriana Compagnoni, Mariangiola Dezani-Ciancaglini, Paola Giannini, Karin Sauer, Vishakha Sharma, Angelo Troina. Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions. Electronic Proceedings in Theoretical Computer Science 2012, 100 , 101-106. https://doi.org/10.4204/EPTCS.100.7
3338. TaiJung Choi, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam. Stochastic operator-splitting method for reaction-diffusion systems. The Journal of Chemical Physics 2012, 137 (18) , 184102. https://doi.org/10.1063/1.4764108
3339. Ivan Komarov, Roshan M. D'Souza, . Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units. PLoS ONE 2012, 7 (11) , e46693. https://doi.org/10.1371/journal.pone.0046693
3340. James Currie, Mario Castro, Grant Lythe, Ed Palmer, Carmen Molina-París. A stochastic T cell response criterion. Journal of The Royal Society Interface 2012, 9 (76) , 2856-2870. https://doi.org/10.1098/rsif.2012.0205
3341. Jaroslav Albert, Marianne Rooman, . Design Principles of a Genetic Alarm Clock. PLoS ONE 2012, 7 (11) , e47256. https://doi.org/10.1371/journal.pone.0047256
3342. David Thorsley, Eric Klavins, . Estimation and Discrimination of Stochastic Biochemical Circuits from Time-Lapse Microscopy Data. PLoS ONE 2012, 7 (11) , e47151. https://doi.org/10.1371/journal.pone.0047151
3343. Krishnan Radhakrishnan, Ádám Halász, Meghan M. McCabe, Jeremy S. Edwards, Bridget S. Wilson. Mathematical Simulation of Membrane Protein Clustering for Efficient Signal Transduction. Annals of Biomedical Engineering 2012, 40 (11) , 2307-2318. https://doi.org/10.1007/s10439-012-0599-z
3344. Md. Jahoor Alam, Nishat Fatima, Gurumayum Reenaroy Devi, Ravins, R.K. Brojen Singh. The enhancement of stability of p53 in MTBP induced p53–MDM2 regulatory network. Biosystems 2012, 110 (2) , 74-83. https://doi.org/10.1016/j.biosystems.2012.09.005
3345. F. Campillo, C. Lobry. Effect of population size in a predator–prey model. Ecological Modelling 2012, 246 , 1-10. https://doi.org/10.1016/j.ecolmodel.2012.07.015
3346. Mostafa Herajy, Monika Heiner. Hybrid representation and simulation of stiff biochemical networks. Nonlinear Analysis: Hybrid Systems 2012, 6 (4) , 942-959. https://doi.org/10.1016/j.nahs.2012.05.004
3347. Chunbo Lou, Brynne Stanton, Ying-Ja Chen, Brian Munsky, Christopher A Voigt. Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nature Biotechnology 2012, 30 (11) , 1137-1142. https://doi.org/10.1038/nbt.2401
3348. Virginie Poullain, Scott L. Nuismer. Infection Genetics and the Likelihood of Host Shifts in Coevolving Host-Parasite Interactions. The American Naturalist 2012, 180 (5) , 618-628. https://doi.org/10.1086/667889
3349. E. Gjini, D. T. Haydon, J. D. Barry, C. A. Cobbold. The Impact of Mutation and Gene Conversion on the Local Diversification of Antigen Genes in African Trypanosomes. Molecular Biology and Evolution 2012, 29 (11) , 3321-3331. https://doi.org/10.1093/molbev/mss166
3350. Dominique Chu, Tobias von der Haar. The architecture of eukaryotic translation. Nucleic Acids Research 2012, 40 (20) , 10098-10106. https://doi.org/10.1093/nar/gks825
3351. Khachik Sargsyan, Cosmin Safta, Bert Debusschere, Habib Najm. Multiparameter Spectral Representation of Noise-Induced Competence in Bacillus Subtilis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9 (6) , 1709-1723. https://doi.org/10.1109/TCBB.2012.107
3352. R. Zug, A. Koehncke, P. Hammerstein. Epidemiology in evolutionary time: the case of Wolbachia horizontal transmission between arthropod host species. Journal of Evolutionary Biology 2012, 25 (11) , 2149-2160. https://doi.org/10.1111/j.1420-9101.2012.02601.x
3353. Christopher C. Drovandi, Anthony N. Pettitt. Likelihood-Free Inference for Transmission Rates of Nosocomial Pathogens. 2012,,, 374-387. https://doi.org/10.1002/9781118394472.ch22
3354. Gábor Lente. Stochastic mapping of first order reaction networks: A systematic comparison of the stochastic and deterministic kinetic approaches. The Journal of Chemical Physics 2012, 137 (16) , 164101. https://doi.org/10.1063/1.4758458
3355. Danesh Moradigaravand, Jan Engelstädter, . The Effect of Bacterial Recombination on Adaptation on Fitness Landscapes with Limited Peak Accessibility. PLoS Computational Biology 2012, 8 (10) , e1002735. https://doi.org/10.1371/journal.pcbi.1002735
3356. Valerii M. Sukhorukov, Daniel Dikov, Andreas S. Reichert, Michael Meyer-Hermann, . Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics. PLoS Computational Biology 2012, 8 (10) , e1002745. https://doi.org/10.1371/journal.pcbi.1002745
3357. Wonryull Koh, Kim T. Blackwell. Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations. The Journal of Chemical Physics 2012, 137 (15) , 154111. https://doi.org/10.1063/1.4758459
3358. Donald McEachron. Chronobioengineering: Introduction to Biological Rhythms with Applications, Volume 1. Synthesis Lectures on Biomedical Engineering 2012, 7 (2) , 1-286. https://doi.org/10.2200/S00446ED1V01Y201208BME043
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3360. Stéphane Ransac, Margit Heiske, Jean-Pierre Mazat. From in silico to in spectro kinetics of respiratory complex I. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2012, 1817 (10) , 1958-1969. https://doi.org/10.1016/j.bbabio.2012.03.037
3361. Lu Xie, Gregory R. Smith, Xian Feng, Russell Schwartz. Surveying Capsid Assembly Pathways through Simulation-Based Data Fitting. Biophysical Journal 2012, 103 (7) , 1545-1554. https://doi.org/10.1016/j.bpj.2012.08.057
3362. Angela H. Chau, Jessica M. Walter, Jaline Gerardin, Chao Tang, Wendell A. Lim. Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization. Cell 2012, 151 (2) , 320-332. https://doi.org/10.1016/j.cell.2012.08.040
3363. Craig C. Jolley, Koji L. Ode, Hiroki R. Ueda. A Design Principle for a Posttranslational Biochemical Oscillator. Cell Reports 2012, 2 (4) , 938-950. https://doi.org/10.1016/j.celrep.2012.09.006
3364. Criseida Zamora-Chimal, Moisés Santillán, Jesús Rodríguez-González. Influence of the feedback loops in the trp operon of B. subtilis on the system dynamic response and noise amplitude. Journal of Theoretical Biology 2012, 310 , 119-131. https://doi.org/10.1016/j.jtbi.2012.06.014
3365. C. Turner, M. Kohandel. Quantitative approaches to cancer stem cells and epithelial–mesenchymal transition. Seminars in Cancer Biology 2012, 22 (5-6) , 374-378. https://doi.org/10.1016/j.semcancer.2012.04.005
3366. J. BARTLETT, M. J. PLANK. EPIDEMIC DYNAMICS ON RANDOM AND SCALE-FREE NETWORKS. The ANZIAM Journal 2012, 54 (1-2) , 3-22. https://doi.org/10.1017/S1446181112000302
3367. Henk Jan Ham, Rob J Boer. Cell division curtails helper phenotype plasticity and expedites helper T‐cell differentiation. Immunology & Cell Biology 2012, 90 (9) , 860-868. https://doi.org/10.1038/icb.2012.23
3368. Chunyan Fan, D. D. Do, D. Nicholson. The concept of mean free path in the kinetic Monte Carlo description of bulk fluid behaviour, vapour–liquid equilibria and surface adsorption of argon. Molecular Simulation 2012, 38 (12) , 1001-1009. https://doi.org/10.1080/08927022.2012.682280
3369. Qianqian Wu, Kate Smith-Miles, Tianhai Tian. A two-variable model for stochastic modelling of chemical events with multi-step reactions. 2012,,, 1-6. https://doi.org/10.1109/BIBM.2012.6392681
3370. Zhen Liu, Yang Cao. Approximation of a multi-scale model based on multiple site phosphorylation. 2012,,, 9-16. https://doi.org/10.1109/BIBMW.2012.6470304
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3372. Daniel A. Charlebois, Mads Kærn. What all the noise is about: the physical basis of cellular individuality. Canadian Journal of Physics 2012, 90 (10) , 919-923. https://doi.org/10.1139/p2012-091
3373. Shahriar Karim, Gregery T Buzzard, David M Umulis. Efficient calculation of steady state probability distribution for stochastic biochemical reaction network. BMC Genomics 2012, 13 (S6) https://doi.org/10.1186/1471-2164-13-S6-S10
3374. Samuel Alizon, Carsten Magnus. Modelling the Course of an HIV Infection: Insights from Ecology and Evolution. Viruses 2012, 4 (10) , 1984-2013. https://doi.org/10.3390/v4101984
3375. Yucheng Hu, Assyr Abdulle, Tiejun Li. Boosted Hybrid Method for Solving Chemical Reaction Systems with Multiple Scales in Time and Population Size. Communications in Computational Physics 2012, 12 (4) , 981-1005. https://doi.org/10.4208/cicp.190411.301111a
3376. Jun Ohkubo. Counting statistics for genetic switches based on effective interaction approximation. The Journal of Chemical Physics 2012, 137 (12) , 125102. https://doi.org/10.1063/1.4754537
3377. Benjamin J. Z. Quigley, Diana García López, Angus Buckling, Alan J. McKane, Sam P. Brown. The mode of host–parasite interaction shapes coevolutionary dynamics and the fate of host cooperation. Proceedings of the Royal Society B: Biological Sciences 2012, 279 (1743) , 3742-3748. https://doi.org/10.1098/rspb.2012.0769
3378. Nathan Eidelson, Baron Peters. Transition path sampling for discrete master equations with absorbing states. The Journal of Chemical Physics 2012, 137 (9) , 094106. https://doi.org/10.1063/1.4747338
3379. Amine Ammar, Elías Cueto, Francisco Chinesta. Reduction of the chemical master equation for gene regulatory networks using proper generalized decompositions. International Journal for Numerical Methods in Biomedical Engineering 2012, 28 (9) , 960-973. https://doi.org/10.1002/cnm.2476
3380. Ryszard Szymanski, Stanislaw Sosnowski. Modeling of Low Concentrations of Reactive Species in Kinetic Monte Carlo Simulations. Macromolecular Theory and Simulations 2012, 21 (8) , 510-515. https://doi.org/10.1002/mats.201200012
3381. Pilsung Kang. Modular implementation of dynamic algorithm switching in parallel simulations. Cluster Computing 2012, 15 (3) , 321-332. https://doi.org/10.1007/s10586-012-0205-z
3382. Luca Bortolussi, Alberto Policriti. Studying cancer-cell populations by programmable models of networks. Network Modeling Analysis in Health Informatics and Bioinformatics 2012, 1 (3) , 117-133. https://doi.org/10.1007/s13721-012-0010-x
3383. M. Gherardi, T. Jourdan, S. Le Bourdiec, G. Bencteux. Hybrid deterministic/stochastic algorithm for large sets of rate equations. Computer Physics Communications 2012, 183 (9) , 1966-1973. https://doi.org/10.1016/j.cpc.2012.04.020
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3385. C. Kazanci, Q. Ma. Extending ecological network analysis measures to dynamic ecosystem models. Ecological Modelling 2012, 242 , 180-188. https://doi.org/10.1016/j.ecolmodel.2012.05.021
3386. Uwe Franz, Volkmar Liebscher, Stefan Zeiser. Piecewise-Deterministic Markov Processes as Limits of Markov Jump Processes. Advances in Applied Probability 2012, 44 (03) , 729-748. https://doi.org/10.1017/S0001867800005851
3387. Van T. Nguyen, D.D. Do, D. Nicholson, E.A. Ustinov. Application of the kinetic Monte Carlo method in the microscopic description of argon adsorption on graphite. Molecular Physics 2012, 110 (18) , 2281-2294. https://doi.org/10.1080/00268976.2012.675450
3388. Tina Koestler, Arndt von Haeseler, Ingo Ebersberger. REvolver: Modeling Sequence Evolution under Domain Constraints. Molecular Biology and Evolution 2012, 29 (9) , 2133-2145. https://doi.org/10.1093/molbev/mss078
3389. Baruch Barzel, Ofer Biham. Stochastic analysis of complex reaction networks using binomial moment equations. Physical Review E 2012, 86 (3) https://doi.org/10.1103/PhysRevE.86.031126
3390. Adam J. Ellery, Matthew J. Simpson, Scott W. McCue, Ruth E. Baker. Moments of action provide insight into critical times for advection-diffusion-reaction processes. Physical Review E 2012, 86 (3) https://doi.org/10.1103/PhysRevE.86.031136
3391. Louise Dyson, Philip K. Maini, Ruth E. Baker. Macroscopic limits of individual-based models for motile cell populations with volume exclusion. Physical Review E 2012, 86 (3) https://doi.org/10.1103/PhysRevE.86.031903
3392. Lorenzo Fagiano, Mustafa Khammash. Simulation of stochastic systems via polynomial chaos expansions and convex optimization. Physical Review E 2012, 86 (3) https://doi.org/10.1103/PhysRevE.86.036702
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3394. K. V. Wendelsdorf, M. Alam, J. Bassaganya-Riera, K. Bisset, S. Eubank, R. Hontecillas, S. Hoops, M. Marathe. ENteric Immunity SImulator: A Tool for In Silico Study of Gastroenteric Infections. IEEE Transactions on NanoBioscience 2012, 11 (3) , 273-288. https://doi.org/10.1109/TNB.2012.2211891
3395. Claude Gérard, Didier Gonze, Albert Goldbeter. Effect of positive feedback loops on the robustness of oscillations in the network of cyclin-dependent kinases driving the mammalian cell cycle. FEBS Journal 2012, 279 (18) , 3411-3431. https://doi.org/10.1111/j.1742-4658.2012.08585.x
3396. Carsten Marr, Michael Strasser, Michael Schwarzfischer, Timm Schroeder, Fabian J. Theis. Multi-scale modeling of GMP differentiation based on single-cell genealogies. FEBS Journal 2012, 279 (18) , 3488-3500. https://doi.org/10.1111/j.1742-4658.2012.08664.x
3397. C. Cianci, F. Di Patti, D. Fanelli, L. Barletti. Analytical study of non Gaussian fluctuations in a stochastic scheme of autocatalytic reactions. The European Physical Journal Special Topics 2012, 212 (1) , 5-22. https://doi.org/10.1140/epjst/e2012-01651-x
3398. Paola Lecca, Daniele Morpurgo. Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth. BMC Bioinformatics 2012, 13 (S14) https://doi.org/10.1186/1471-2105-13-S14-S14
3399. Uwe Franz, Volkmar Liebscher, Stefan Zeiser. Piecewise-Deterministic Markov Processes as Limits of Markov Jump Processes. Advances in Applied Probability 2012, 44 (3) , 729-748. https://doi.org/10.1239/aap/1346955262
3400. Marco Drache, Georg Drache. Simulating Controlled Radical Polymerizations with mcPolymer—A Monte Carlo Approach. Polymers 2012, 4 (3) , 1416-1442. https://doi.org/10.3390/polym4031416
3401. Miha Moskon, Miha Mraz. MODELLING AND ANALYSING THE INFORMATION PROCESSING CAPABILITIES OF SIMPLE BIOLOGICAL SYSTEMS. Mathematical Modelling and Analysis 2012, 17 (4) , 467-484. https://doi.org/10.3846/13926292.2012.706651
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3403. Julian Lee, Steve Pressé. A derivation of the master equation from path entropy maximization. The Journal of Chemical Physics 2012, 137 (7) , 074103. https://doi.org/10.1063/1.4743955
3404. R. W. Friddle, A. Noy, J. J. De Yoreo. Interpreting the widespread nonlinear force spectra of intermolecular bonds. Proceedings of the National Academy of Sciences 2012, 109 (34) , 13573-13578. https://doi.org/10.1073/pnas.1202946109
3405. Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio. Effects of delayed immune-response in tumor immune-system interplay. Electronic Proceedings in Theoretical Computer Science 2012, 92 , 106-121. https://doi.org/10.4204/EPTCS.92.8
3406. Alexandre David, Dehui Du, Kim G. Larsen, Axel Legay, Marius Mikučionis, Danny Bøgsted Poulsen, Sean Sedwards. Statistical Model Checking for Stochastic Hybrid Systems. Electronic Proceedings in Theoretical Computer Science 2012, 92 , 122-136. https://doi.org/10.4204/EPTCS.92.9
3407. Zoltán Ható, Dezső Boda, Tamás Kristóf. Simulation of steady-state diffusion: Driving force ensured by dual control volumes or local equilibrium Monte Carlo. The Journal of Chemical Physics 2012, 137 (5) , 054109. https://doi.org/10.1063/1.4739255
3408. H.-J. Woo, J. Reifman. A quantitative quasispecies theory-based model of virus escape mutation under immune selection. Proceedings of the National Academy of Sciences 2012, 109 (32) , 12980-12985. https://doi.org/10.1073/pnas.1117201109
3409. Maximilian E. R. Weiss, Florian Paulus, Dirk Steinhilber, Anatoly N. Nikitin, Rainer Haag, Christof Schütte. Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. Macromolecular Theory and Simulations 2012, 21 (7) , 470-481. https://doi.org/10.1002/mats.201200003
3410. Shaghayegh Hamzehlou, Yuri Reyes, Jose R. Leiza. Detailed Microstructure Investigation of Acrylate/Methacrylate Functional Copolymers by Kinetic Monte Carlo Simulation. Macromolecular Reaction Engineering 2012, 6 (8) , 319-329. https://doi.org/10.1002/mren.201200016
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3412. Jacob A. McGill, Babatunde A. Ogunnaike, Dionisios G. Vlachos. Efficient gradient estimation using finite differencing and likelihood ratios for kinetic Monte Carlo simulations. Journal of Computational Physics 2012, 231 (21) , 7170-7186. https://doi.org/10.1016/j.jcp.2012.06.037
3413. Weihan Li, Sandeep Krishna, Simone Pigolotti, Namiko Mitarai, Mogens H. Jensen. Switching between oscillations and homeostasis in competing negative and positive feedback motifs. Journal of Theoretical Biology 2012, 307 , 205-210. https://doi.org/10.1016/j.jtbi.2012.04.011
3414. M. Scott. Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation. IET Systems Biology 2012, 6 (4) , 116-124. https://doi.org/10.1049/iet-syb.2011.0031
3415. M.R. Roussel, T. Tang. Simulation of mRNA diffusion in the nuclear environment. IET Systems Biology 2012, 6 (4) , 125-133. https://doi.org/10.1049/iet-syb.2011.0032
3416. E.W.J. Wallace, L.R. Petzold, D.T. Gillespie, K.R. Sanft. Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. IET Systems Biology 2012, 6 (4) , 102-115. https://doi.org/10.1049/iet-syb.2011.0038
3417. R Zunino. On computation and synchronization costs in spatial distributed simulation. Journal of Simulation 2012, 6 (3) , 193-204. https://doi.org/10.1057/jos.2012.9
3418. Tim Rogers, William Clifford-Brown, Catherine Mills, Tobias Galla. Stochastic oscillations of adaptive networks: application to epidemic modelling. Journal of Statistical Mechanics: Theory and Experiment 2012, 2012 (08) , P08018. https://doi.org/10.1088/1742-5468/2012/08/P08018
3419. Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, Namiko Mitarai. Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Research 2012, 40 (14) , 6424-6434. https://doi.org/10.1093/nar/gks297
3420. Jiri Vohradsky. Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Research 2012, 40 (15) , 7096-7103. https://doi.org/10.1093/nar/gks440
3421. Martin Körner, Mario Einax, Philipp Maass. Capture numbers and island size distributions in models of submonolayer surface growth. Physical Review B 2012, 86 (8) https://doi.org/10.1103/PhysRevB.86.085403
3422. Christian A. Yates, Ruth E. Baker, Radek Erban, Philip K. Maini. Going from microscopic to macroscopic on nonuniform growing domains. Physical Review E 2012, 86 (2) https://doi.org/10.1103/PhysRevE.86.021921
3423. Hsu Kiang Ooi, Lan Ma. Modeling cell-to-cell stochastic variability in intrinsic apoptosis pathway. 2012,,, 5498-5501. https://doi.org/10.1109/EMBC.2012.6347239
3424. Changhong Shi, Tianshou Zhou. Functional tunability of biological circuits from tinkers. 2012,,, 63-72. https://doi.org/10.1109/ISB.2012.6314114
3425. BING LIU, P. S. THIAGARAJAN. MODELING AND ANALYSIS OF BIOPATHWAYS DYNAMICS. Journal of Bioinformatics and Computational Biology 2012, 10 (04) , 1231001. https://doi.org/10.1142/S0219720012310014
3426. Michael Nivala, Zhilin Qu. Calcium alternans in a couplon network model of ventricular myocytes: role of sarcoplasmic reticulum load. American Journal of Physiology-Heart and Circulatory Physiology 2012, 303 (3) , H341-H352. https://doi.org/10.1152/ajpheart.00302.2012
3427. Animesh Agarwal, Rhys Adams, Gastone C. Castellani, Harel Z. Shouval. On the precision of quasi steady state assumptions in stochastic dynamics. The Journal of Chemical Physics 2012, 137 (4) , 044105. https://doi.org/10.1063/1.4731754
3428. Sheng Wu, Jin Fu, Hong Li, Linda Petzold. Automatic identification of model reductions for discrete stochastic simulation. The Journal of Chemical Physics 2012, 137 (3) , 034106. https://doi.org/10.1063/1.4733563
3429. Rajamanickam Murugan, . Theory on the Dynamics of Feedforward Loops in the Transcription Factor Networks. PLoS ONE 2012, 7 (7) , e41027. https://doi.org/10.1371/journal.pone.0041027
3430. R. Vinu, Linda J. Broadbelt. Unraveling Reaction Pathways and Specifying Reaction Kinetics for Complex Systems. Annual Review of Chemical and Biomolecular Engineering 2012, 3 (1) , 29-54. https://doi.org/10.1146/annurev-chembioeng-062011-081108
3431. Hiroyuki Kuwahara, Russell Schwartz. Stochastic steady state gain in a gene expression process with mRNA degradation control. Journal of The Royal Society Interface 2012, 9 (72) , 1589-1598. https://doi.org/10.1098/rsif.2011.0757
3432. Ferenc Jordán, Nerta Gjata, Shu Mei, Catherine M. Yule, . Simulating Food Web Dynamics along a Gradient: Quantifying Human Influence. PLoS ONE 2012, 7 (7) , e40280. https://doi.org/10.1371/journal.pone.0040280
3433. Sebastian Grauwin, Guillaume Beslon, Éric Fleury, Sara Franceschelli, Celine Robardet, Jean‐Baptiste Rouquier, Pablo Jensen. Complex systems science: Dreams of universality, interdisciplinarity reality. Journal of the American Society for Information Science and Technology 2012, 63 (7) , 1327-1338. https://doi.org/10.1002/asi.22644
3434. Ambhighainath Ganesan, Jin Zhang. How cells process information: Quantification of spatiotemporal signaling dynamics. Protein Science 2012, 21 (7) , 918-928. https://doi.org/10.1002/pro.2089
3435. Imad Hoteit, Nawwaf Kharma, Luc Varin. Computational simulation of a gene regulatory network implementing an extendable synchronous single-input delay flip-flop. Biosystems 2012, 109 (1) , 57-71. https://doi.org/10.1016/j.biosystems.2012.01.004
3436. Haokai Lu, Peng Li. Stochastic projective methods for simulating stiff chemical reacting systems. Computer Physics Communications 2012, 183 (7) , 1427-1442. https://doi.org/10.1016/j.cpc.2012.02.018
3437. Zoran Konkoli. Modeling reaction noise with a desired accuracy by using the X level approach reaction noise estimator (XARNES) method. Journal of Theoretical Biology 2012, 305 , 1-14. https://doi.org/10.1016/j.jtbi.2012.04.005
3438. Tommaso Biancalani, Tim Rogers, Alan J. McKane. Noise-induced metastability in biochemical networks. Physical Review E 2012, 86 (1) https://doi.org/10.1103/PhysRevE.86.010106
3439. John Realpe-Gomez, Tobias Galla, Alan J. McKane. Demographic noise and piecewise deterministic Markov processes. Physical Review E 2012, 86 (1) https://doi.org/10.1103/PhysRevE.86.011137
3440. Elena F. Koslover, Andrew J. Spakowitz. Force fluctuations impact kinetics of biomolecular systems. Physical Review E 2012, 86 (1) https://doi.org/10.1103/PhysRevE.86.011906
3441. C. Borile, M. A. Muñoz, S. Azaele, Jayanth R. Banavar, A. Maritan. Spontaneously Broken Neutral Symmetry in an Ecological System. Physical Review Letters 2012, 109 (3) https://doi.org/10.1103/PhysRevLett.109.038102
3442. Joseph L. Simonis. Demographic stochasticity reduces the synchronizing effect of dispersal in predator–prey metapopulations. Ecology 2012, 93 (7) , 1517-1524. https://doi.org/10.1890/11-0460.1
3443. G. Jack Peterson, Steve Pressé, Kristin S. Peterson, Ken A. Dill, . Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology. PLoS ONE 2012, 7 (6) , e39052. https://doi.org/10.1371/journal.pone.0039052
3444. Debby Lipschutz-Powell, John A. Woolliams, Piter Bijma, Andrea B. Doeschl-Wilson, . Indirect Genetic Effects and the Spread of Infectious Disease: Are We Capturing the Full Heritable Variation Underlying Disease Prevalence?. PLoS ONE 2012, 7 (6) , e39551. https://doi.org/10.1371/journal.pone.0039551
3445. Rebecca B. Hoyle, Daniele Avitabile, Andrzej M. Kierzek, . Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity. PLoS Computational Biology 2012, 8 (6) , e1002396. https://doi.org/10.1371/journal.pcbi.1002396
3446. Erik M. Volz, James S. Koopman, Melissa J. Ward, Andrew Leigh Brown, Simon D. W. Frost, . Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection. PLoS Computational Biology 2012, 8 (6) , e1002552. https://doi.org/10.1371/journal.pcbi.1002552
3447. R. Zachariah Aandahl, Josephine F. Reyes, Scott A. Sisson, Mark M. Tanaka, . A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis. PLoS Computational Biology 2012, 8 (6) , e1002573. https://doi.org/10.1371/journal.pcbi.1002573
3448. Jorge A. Vázquez Diosdado, Peter Ashwin, Krisztian I. Kohary, C. David Wright. Threshold switching via electric field induced crystallization in phase-change memory devices. Applied Physics Letters 2012, 100 (25) , 253105. https://doi.org/10.1063/1.4729551
3449. Philip Gerlee, Sven Nelander, . The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion. PLoS Computational Biology 2012, 8 (6) , e1002556. https://doi.org/10.1371/journal.pcbi.1002556
3450. Philipp Thomas, Hannes Matuschek, Ramon Grima, . Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion. PLoS ONE 2012, 7 (6) , e38518. https://doi.org/10.1371/journal.pone.0038518
3451. E. Jakeman, K. I. Hopcraft. Laguerre population processes. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2012, 468 (2142) , 1741-1757. https://doi.org/10.1098/rspa.2011.0557
3452. Ivan Komarov, Roshan M. D’Souza, Jose-Juan Tapia, . Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units. PLoS ONE 2012, 7 (6) , e37370. https://doi.org/10.1371/journal.pone.0037370
3453. Srabanti Chaudhury, Alan S. Perelson, Nikolai A. Sinitstyn, . Spontaneous Clearance of Viral Infections by Mesoscopic Fluctuations. PLoS ONE 2012, 7 (6) , e38549. https://doi.org/10.1371/journal.pone.0038549
3454. Nicolas Glade. On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization. Acta Biotheoretica 2012, 60 (1-2) , 55-82. https://doi.org/10.1007/s10441-012-9149-1
3455. WenLiang Zhang, Jin Qian, HaiMin Yao, WeiQiu Chen, HuaJian Gao. Effects of functionally graded materials on dynamics of molecular bond clusters. Science China Physics, Mechanics and Astronomy 2012, 55 (6) , 980-988. https://doi.org/10.1007/s11433-012-4726-5
3456. Alessandro Filisetti, Alex Graudenzi, Roberto Serra, Marco Villani, Rudolf M. Füchslin, Norman Packard, Stuart A. Kauffman, Irene Poli. A stochastic model of autocatalytic reaction networks. Theory in Biosciences 2012, 131 (2) , 85-93. https://doi.org/10.1007/s12064-011-0136-x
3457. Ch. Nagaiah, S. Rüdiger, G. Warnecke, M. Falcke. Adaptive space and time numerical simulation of reaction–diffusion models for intracellular calcium dynamics. Applied Mathematics and Computation 2012, 218 (20) , 10194-10210. https://doi.org/10.1016/j.amc.2012.03.100
3458. Hongying Li, Jianhong Bi. The influence of interplay of external and internal noise on the detection of weak stimulus in a cell system. Applied Mathematical Modelling 2012, 36 (6) , 2323-2328. https://doi.org/10.1016/j.apm.2011.08.028
3459. Tatjana Petrov, Arnab Ganguly, Heinz Koeppl. Model Decomposition and Stochastic Fragments. Electronic Notes in Theoretical Computer Science 2012, 284 , 105-124. https://doi.org/10.1016/j.entcs.2012.05.018
3460. Josephine F. Reyes, Carmen H.S. Chan, Mark M. Tanaka. Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. Infection, Genetics and Evolution 2012, 12 (4) , 811-818. https://doi.org/10.1016/j.meegid.2011.05.018
3461. Koichiro Uriu, Saúl Ares, Andrew C Oates, Luis G Morelli. Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions. Physical Biology 2012, 9 (3) , 036006. https://doi.org/10.1088/1478-3975/9/3/036006
3462. Nicolae Radu Zabet, Boris Adryan. A comprehensive computational model of facilitated diffusion in prokaryotes. Bioinformatics 2012, 28 (11) , 1517-1524. https://doi.org/10.1093/bioinformatics/bts178
3463. Anna Melbinger, Louis Reese, Erwin Frey. Microtubule Length Regulation by Molecular Motors. Physical Review Letters 2012, 108 (25) https://doi.org/10.1103/PhysRevLett.108.258104
3464. A. S. R. Ferreira, M. Arcak, E. D. Sontag. A decomposition-based approach to stability analysis of large-scale stochastic systems. 2012,,, 6382-6387. https://doi.org/10.1109/ACC.2012.6315416
3465. R. Ghaemi, D. Del Vecchio. Stochastic analysis of retroactivity in transcriptional networks through singular perturbation. 2012,,, 2731-2736. https://doi.org/10.1109/ACC.2012.6315645
3466. Massimo Monti, Thomas Meyer, Christian Tschudin, Marco Luise. Signal processing applied to chemically inspired communication protocols. 2012,,, 1144-1148. https://doi.org/10.1109/ICC.2012.6363733
3467. Paul Fearnhead, Dennis Prangle. Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 2012, 74 (3) , 419-474. https://doi.org/10.1111/j.1467-9868.2011.01010.x
3468. Yossi Ben-Zion, Nadav M. Shnerb. Coherence, conservation and patch-occupancy analysis. Oikos 2012, 121 (6) , 985-997. https://doi.org/10.1111/j.1600-0706.2011.19991.x
3469. Dmitry Anatolievich Bratsun, Alexey V. Zyuzgin. Effect of subcritical excitation of oscillations in stochastic systems with time delay. Part II. Control of fluid equilibrium. Computer Research and Modeling 2012, 4 (2) , 369-389. https://doi.org/10.20537/2076-7633-2012-4-2-369-389
3470. Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman, . Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution. PLoS Computational Biology 2012, 8 (5) , e1002534. https://doi.org/10.1371/journal.pcbi.1002534
3471. Patricio Orio, Daniel Soudry, . Simple, Fast and Accurate Implementation of the Diffusion Approximation Algorithm for Stochastic Ion Channels with Multiple States. PLoS ONE 2012, 7 (5) , e36670. https://doi.org/10.1371/journal.pone.0036670
3472. Chunhe Li, Erkang Wang, Jin Wang. Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations. The Journal of Chemical Physics 2012, 136 (19) , 194108. https://doi.org/10.1063/1.4716466
3473. C. G. Bowsher, P. S. Swain. Identifying sources of variation and the flow of information in biochemical networks. Proceedings of the National Academy of Sciences 2012, 109 (20) , E1320-E1328. https://doi.org/10.1073/pnas.1119407109
3474. Silvana Ilie, Alexandra Teslya. An adaptive stepsize method for the chemical Langevin equation. The Journal of Chemical Physics 2012, 136 (18) , 184101. https://doi.org/10.1063/1.4711143
3475. Richard Lakerveld, George Stephanopoulos, Paul I. Barton. A master-equation approach to simulate kinetic traps during directed self-assembly. The Journal of Chemical Physics 2012, 136 (18) , 184109. https://doi.org/10.1063/1.4716190
3476. Ganhui Lan, Sean X. Sun. Mechanochemical models of processive molecular motors. Molecular Physics 2012, 110 (9-10) , 1017-1034. https://doi.org/10.1080/00268976.2012.677863
3477. Mark B. Flegg, S. Jonathan Chapman, Radek Erban. The two-regime method for optimizing stochastic reaction–diffusion simulations. Journal of The Royal Society Interface 2012, 9 (70) , 859-868. https://doi.org/10.1098/rsif.2011.0574
3478. Vladimir P. Zhdanov. Periodic perturbation of genetic oscillations. Chaos, Solitons & Fractals 2012, 45 (5) , 577-587. https://doi.org/10.1016/j.chaos.2011.12.008
3479. Samuel Bottani, Basil Grammaticos. Stochastic and deterministic simulations of a delayed genetic oscillation model: Investigating the validity of reductions. Chaos, Solitons & Fractals 2012, 45 (5) , 588-602. https://doi.org/10.1016/j.chaos.2011.12.012
3480. Gabriel Piedrafita, Athel Cornish-Bowden, Federico Morán, Francisco Montero. Size matters: Influence of stochasticity on the self-maintenance of a simple model of metabolic closure. Journal of Theoretical Biology 2012, 300 , 143-151. https://doi.org/10.1016/j.jtbi.2012.01.013
3481. Leonardo Martins, Jarno Mäkelä, Antti Häkkinen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, José M. Fonseca, Andre S. Ribeiro. Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time. Journal of Theoretical Biology 2012, 301 , 83-94. https://doi.org/10.1016/j.jtbi.2012.02.015
3482. Matthew R. Lakin, Loïc Paulevé, Andrew Phillips. Stochastic simulation of multiple process calculi for biology. Theoretical Computer Science 2012, 431 , 181-206. https://doi.org/10.1016/j.tcs.2011.12.057
3483. Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Simone Tini. Foundational aspects of multiscale modeling of biological systems with process algebras. Theoretical Computer Science 2012, 431 , 96-116. https://doi.org/10.1016/j.tcs.2011.12.058
3484. Livio Bioglio, Mariangiola Dezani-Ciancaglini, Paola Giannini, Angelo Troina. Typed stochastic semantics for the calculus of looping sequences. Theoretical Computer Science 2012, 431 , 165-180. https://doi.org/10.1016/j.tcs.2011.12.062
3485. Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Eva Sciacca, Salvatore Spinella, Angelo Troina. Simulation techniques for the calculus of wrapped compartments. Theoretical Computer Science 2012, 431 , 75-95. https://doi.org/10.1016/j.tcs.2011.12.063
3486. Jia-Zeng Wang, Min Qian, Hong Qian. Circular stochastic fluctuations in SIS epidemics with heterogeneous contacts among sub-populations. Theoretical Population Biology 2012, 81 (3) , 223-231. https://doi.org/10.1016/j.tpb.2012.01.002
3487. William H. Mather, Jeff Hasty, Lev S. Tsimring. Fast stochastic algorithm for simulating evolutionary population dynamics. Bioinformatics 2012, 28 (9) , 1230-1238. https://doi.org/10.1093/bioinformatics/bts130
3488. Nicolae Radu Zabet, Boris Adryan. GRiP: a computational tool to simulate transcription factor binding in prokaryotes. Bioinformatics 2012, 28 (9) , 1287-1289. https://doi.org/10.1093/bioinformatics/bts132
3489. Julien Derr, Michael L. Manapat, Sudha Rajamani, Kevin Leu, Ramon Xulvi-Brunet, Isaac Joseph, Martin A. Nowak, Irene A. Chen. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences. Nucleic Acids Research 2012, 40 (10) , 4711-4722. https://doi.org/10.1093/nar/gks065
3490. Alexander Dobrinevski, Erwin Frey. Extinction in neutrally stable stochastic Lotka-Volterra models. Physical Review E 2012, 85 (5) https://doi.org/10.1103/PhysRevE.85.051903
3491. Ciara E. Dangerfield, David Kay, Kevin Burrage. Modeling ion channel dynamics through reflected stochastic differential equations. Physical Review E 2012, 85 (5) https://doi.org/10.1103/PhysRevE.85.051907
3492. Thomas E. Woolley, Ruth E. Baker, Eamonn A. Gaffney, Philip K. Maini, Sungrim Seirin-Lee. Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems. Physical Review E 2012, 85 (5) https://doi.org/10.1103/PhysRevE.85.051914
3493. C. Madsen, C. J. Myers, N. Roehner, C. Winstead, Zhen Zhang. Utilizing stochastic model checking to analyze genetic circuits. 2012,,, 379-386. https://doi.org/10.1109/CIBCB.2012.6217255
3494. T. William Mather, M. Ani Hsieh. Ensemble synthesis of distributed control and communication strategies. 2012,,, 4248-4253. https://doi.org/10.1109/ICRA.2012.6225048
3495. L. Dematte. Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9 (3) , 655-667. https://doi.org/10.1109/TCBB.2011.106
3496. T. Mazza, P. Ballarini, R. Guido, D. Prandi. The Relevance of Topology in Parallel Simulation of Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9 (3) , 911-923. https://doi.org/10.1109/TCBB.2012.27
3497. Liufang Xu, Hualin Shi, Haidong Feng, Jin Wang. The energy pump and the origin of the non-equilibrium flux of the dynamical systems and the networks. The Journal of Chemical Physics 2012, 136 (16) , 165102. https://doi.org/10.1063/1.3703514
3498. Kinshuk Banerjee, Biswajit Das, Gautam Gangopadhyay. Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: An index of cooperativity. The Journal of Chemical Physics 2012, 136 (15) , 154502. https://doi.org/10.1063/1.3703505
3499. Samanthe M. Lyons, Ashok Prasad, . Cross-Talk and Information Transfer in Mammalian and Bacterial Signaling. PLoS ONE 2012, 7 (4) , e34488. https://doi.org/10.1371/journal.pone.0034488
3500. Na Yi, Gang Zhuang, Liang Da, Yifei Wang. Improved delay-leaping simulation algorithm for biochemical reaction systems with delays. The Journal of Chemical Physics 2012, 136 (14) , 144108. https://doi.org/10.1063/1.3702433
3501. B. Munsky, G. Neuert, A. van Oudenaarden. Using Gene Expression Noise to Understand Gene Regulation. Science 2012, 336 (6078) , 183-187. https://doi.org/10.1126/science.1216379
3502. Robert C. Hilborn, Benjamin Brookshire, Jenna Mattingly, Anusha Purushotham, Anuraag Sharma, . The Transition between Stochastic and Deterministic Behavior in an Excitable Gene Circuit. PLoS ONE 2012, 7 (4) , e34536. https://doi.org/10.1371/journal.pone.0034536
3503. F. Carrara, F. Altermatt, I. Rodriguez-Iturbe, A. Rinaldo. Dendritic connectivity controls biodiversity patterns in experimental metacommunities. Proceedings of the National Academy of Sciences 2012, 109 (15) , 5761-5766. https://doi.org/10.1073/pnas.1119651109
3504. Matthias Vigelius, Bernd Meyer, . Multi-Dimensional, Mesoscopic Monte Carlo Simulations of Inhomogeneous Reaction-Drift-Diffusion Systems on Graphics-Processing Units. PLoS ONE 2012, 7 (4) , e33384. https://doi.org/10.1371/journal.pone.0033384
3505. E. A. Ustinov, D. D. Do. Two-dimensional order-disorder transition of argon monolayer adsorbed on graphitized carbon black: Kinetic Monte Carlo method. The Journal of Chemical Physics 2012, 136 (13) , 134702. https://doi.org/10.1063/1.3698194
3506. Maria Luisa Guerriero, Alexandra Pokhilko, Aurora Piñas Fernández, Karen J. Halliday, Andrew J. Millar, Jane Hillston. Stochastic properties of the plant circadian clock. Journal of The Royal Society Interface 2012, 9 (69) , 744-756. https://doi.org/10.1098/rsif.2011.0378
3507. Gilles Wainrib, Michèle Thieullen, Khashayar Pakdaman. Reduction of stochastic conductance-based neuron models with time-scales separation. Journal of Computational Neuroscience 2012, 32 (2) , 327-346. https://doi.org/10.1007/s10827-011-0355-7
3508. Adiel Loinger, Yael Shemla, Itamar Simon, Hanah Margalit, Ofer Biham. Competition between Small RNAs: A Quantitative View. Biophysical Journal 2012, 102 (8) , 1712-1721. https://doi.org/10.1016/j.bpj.2012.01.058
3509. Jay M Newby. Isolating intrinsic noise sources in a stochastic genetic switch. Physical Biology 2012, 9 (2) , 026002. https://doi.org/10.1088/1478-3975/9/2/026002
3510. Daniel A. Dalquen, Maria Anisimova, Gaston H. Gonnet, Christophe Dessimoz. ALF—A Simulation Framework for Genome Evolution. Molecular Biology and Evolution 2012, 29 (4) , 1115-1123. https://doi.org/10.1093/molbev/msr268
3511. Adam J. Ellery, Matthew J. Simpson, Scott W. McCue, Ruth E. Baker. Critical time scales for advection-diffusion-reaction processes. Physical Review E 2012, 85 (4) https://doi.org/10.1103/PhysRevE.85.041135
3512. Fan Bai, Tohru Minamino, Zhanghan Wu, Keiichi Namba, Jianhua Xing. Coupling between Switching Regulation and Torque Generation in Bacterial Flagellar Motor. Physical Review Letters 2012, 108 (17) https://doi.org/10.1103/PhysRevLett.108.178105
3513. Rodrigo Hamede, Jim Bashford, Menna Jones, Hamish McCallum. Simulating devil facial tumour disease outbreaks across empirically derived contact networks. Journal of Applied Ecology 2012, 49 (2) , 447-456. https://doi.org/10.1111/j.1365-2664.2011.02103.x
3514. Tanya L. Leise, Connie W. Wang, Paula J. Gitis, David K. Welsh, . Persistent Cell-Autonomous Circadian Oscillations in Fibroblasts Revealed by Six-Week Single-Cell Imaging of PER2::LUC Bioluminescence. PLoS ONE 2012, 7 (3) , e33334. https://doi.org/10.1371/journal.pone.0033334
3515. Yu-Rim Lim, Seong-Jun Park, Sang-Youb Lee, Jae-Young Sung. Nonclassical Chemical Kinetics for Description of Chemical Fluctuation in a Dynamically Heterogeneous Biological System. Bulletin of the Korean Chemical Society 2012, 33 (3) , 963-970. https://doi.org/10.5012/bkcs.2012.33.3.963
3516. Patrick B. Warren, Rosalind J. Allen. Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting. The Journal of Chemical Physics 2012, 136 (10) , 104106. https://doi.org/10.1063/1.3690092
3517. Matteo Ceccarelli, Attilio V Vargiu, Paolo Ruggerone. A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins. Journal of Physics: Condensed Matter 2012, 24 (10) , 104012. https://doi.org/10.1088/0953-8984/24/10/104012
3518. Hsih-Te Yang, Minoru S. H. Ko, . Stochastic Modeling for the Expression of a Gene Regulated by Competing Transcription Factors. PLoS ONE 2012, 7 (3) , e32376. https://doi.org/10.1371/journal.pone.0032376
3519. Kevin D. Fowler, Vijay K. Kuchroo, Arup K. Chakraborty, . A Model for How Signal Duration Can Determine Distinct Outcomes of Gene Transcription Programs. PLoS ONE 2012, 7 (3) , e33018. https://doi.org/10.1371/journal.pone.0033018
3520. Gabriel E. Leventhal, Roger Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer, . Inferring Epidemic Contact Structure from Phylogenetic Trees. PLoS Computational Biology 2012, 8 (3) , e1002413. https://doi.org/10.1371/journal.pcbi.1002413
3521. Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones, . Mitochondrial Variability as a Source of Extrinsic Cellular Noise. PLoS Computational Biology 2012, 8 (3) , e1002416. https://doi.org/10.1371/journal.pcbi.1002416
3522. Nicolas Mirouze, Yaanik Desai, Arjun Raj, David Dubnau, . Spo0A∼P Imposes a Temporal Gate for the Bimodal Expression of Competence in Bacillus subtilis. PLoS Genetics 2012, 8 (3) , e1002586. https://doi.org/10.1371/journal.pgen.1002586
3523. M. Massink, D. Latella, A. Bracciali, M. D. Harrison, J. Hillston. Scalable context-dependent analysis of emergency egress models. Formal Aspects of Computing 2012, 24 (2) , 267-302. https://doi.org/10.1007/s00165-011-0188-1
3524. Brian J. Ross. The evolution of higher-level biochemical reaction models. Genetic Programming and Evolvable Machines 2012, 13 (1) , 3-31. https://doi.org/10.1007/s10710-011-9144-3
3525. Zvi Tamari, Naama Barkai. Improved readout precision of the Bicoid morphogen gradient by early decoding. Journal of Biological Physics 2012, 38 (2) , 317-329. https://doi.org/10.1007/s10867-011-9250-8
3526. P. Li, L. R. Nie, C. Z. Shu, S. Hu, Q. Shao. Effect of Correlated Dichotomous Noises on Stochastic Resonance in a Linear System. Journal of Statistical Physics 2012, 146 (6) , 1184-1202. https://doi.org/10.1007/s10955-012-0427-8
3527. M. P. D. Dobay, A. Piera Alberola, E. R. Mendoza, J. O. Rädler. Modeling nanoparticle uptake and intracellular distribution using stochastic process algebras. Journal of Nanoparticle Research 2012, 14 (4) https://doi.org/10.1007/s11051-012-0821-9
3528. Michael Amrein, Hans R. Künsch. Rate estimation in partially observed Markov jump processes with measurement errors. Statistics and Computing 2012, 22 (2) , 513-526. https://doi.org/10.1007/s11222-011-9244-1
3529. Ranjith Padinhateeri, Anatoly B. Kolomeisky, David Lacoste. Random Hydrolysis Controls the Dynamic Instability of Microtubules. Biophysical Journal 2012, 102 (6) , 1274-1283. https://doi.org/10.1016/j.bpj.2011.12.059
3530. Sebastian Getfert, Peter Reimann. Hidden Multiple Bond Effects in Dynamic Force Spectroscopy. Biophysical Journal 2012, 102 (5) , 1184-1193. https://doi.org/10.1016/j.bpj.2012.01.037
3531. Jiajun Zhang, Luonan Chen, Tianshou Zhou. Analytical Distribution and Tunability of Noise in a Model of Promoter Progress. Biophysical Journal 2012, 102 (6) , 1247-1257. https://doi.org/10.1016/j.bpj.2012.02.001
3532. Haidong Feng, Bo Han, Jin Wang. Landscape and Global Stability of Nonadiabatic and Adiabatic Oscillations in a Gene Network. Biophysical Journal 2012, 102 (5) , 1001-1010. https://doi.org/10.1016/j.bpj.2012.02.002
3533. N. Kim, M.O. Ripple, R. Springett. Measurement of the Mitochondrial Membrane Potential and pH Gradient from the Redox Poise of the Hemes of the bc1 Complex. Biophysical Journal 2012, 102 (5) , 1194-1203. https://doi.org/10.1016/j.bpj.2012.02.003
3534. Erin L. O’Brien, Elizabeth Van Itallie, Matthew R. Bennett. Modeling synthetic gene oscillators. Mathematical Biosciences 2012, 236 (1) , 1-15. https://doi.org/10.1016/j.mbs.2012.01.001
3535. L. Felicetti, M. Femminella, G. Reali. A simulation tool for nanoscale biological networks. Nano Communication Networks 2012, 3 (1) , 2-18. https://doi.org/10.1016/j.nancom.2011.09.002
3536. Michaela Knapp-Mohammady, Norman H. March. Can liquid supercooling and glassy-like structure be invoked to interpret collective cell behaviour in the human body?. Physics and Chemistry of Liquids 2012, 50 (2) , 137-151. https://doi.org/10.1080/00319104.2011.609959
3537. Tobias Galla. Fluctuations in meta-population exclusion processes. Journal of Statistical Mechanics: Theory and Experiment 2012, 2012 (03) , P03008. https://doi.org/10.1088/1742-5468/2012/03/P03008
3538. Suresh Kumar Poovathingal, Jan Gruber, Li Fang Ng, Barry Halliwell, Rudiyanto Gunawan. Maximizing signal-to-noise ratio in the random mutation capture assay. Nucleic Acids Research 2012, 40 (5) , e35-e35. https://doi.org/10.1093/nar/gkr1221
3539. Pierre-André Noël, Antoine Allard, Laurent Hébert-Dufresne, Vincent Marceau, Louis J. Dubé. Propagation on networks: An exact alternative perspective. Physical Review E 2012, 85 (3) https://doi.org/10.1103/PhysRevE.85.031118
3540. C. Bunch, N. Chohan, C. Krintz. Supporting placement and data consistency strategies using hybrid clouds. 2012,,, 1-8. https://doi.org/10.1109/AERO.2012.6187353
3541. JUAN G. DIAZ OCHOA, MICHAEL WULKOW. DNA DAMAGES AS A DEPOLYMERIZATION PROCESS. International Journal of Modern Physics C 2012, 23 (03) , 1250018. https://doi.org/10.1142/S0129183112500180
3542. HUAHAI QIU, TIANSHOU ZHOU. FEEDBACK-INDUCED COMPLEX DYNAMICS IN A TWO-COMPONENT REGULATORY CIRCUIT. International Journal of Bifurcation and Chaos 2012, 22 (03) , 1250059. https://doi.org/10.1142/S0218127412500599
3543. Yevgeniy Frenkel, Andrew J. Majda, Boualem Khouider. Using the Stochastic Multicloud Model to Improve Tropical Convective Parameterization: A Paradigm Example. Journal of the Atmospheric Sciences 2012, 69 (3) , 1080-1105. https://doi.org/10.1175/JAS-D-11-0148.1
3544. Ambarish Nag, Michael Monine, Alan S. Perelson, Byron Goldstein, . Modeling and Simulation of Aggregation of Membrane Protein LAT with Molecular Variability in the Number of Binding Sites for Cytosolic Grb2-SOS1-Grb2. PLoS ONE 2012, 7 (3) , e28758. https://doi.org/10.1371/journal.pone.0028758
3545. Matteo Semplice, Andrea Veglio, Giovanni Naldi, Guido Serini, Andrea Gamba, . A Bistable Model of Cell Polarity. PLoS ONE 2012, 7 (2) , e30977. https://doi.org/10.1371/journal.pone.0030977
3546. David Frigola, Laura Casanellas, José M. Sancho, Marta Ibañes, . Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise. PLoS ONE 2012, 7 (2) , e31407. https://doi.org/10.1371/journal.pone.0031407
3547. Éva Dóka, Gábor Lente. Stochastic mapping of the Michaelis-Menten mechanism. The Journal of Chemical Physics 2012, 136 (5) , 054111. https://doi.org/10.1063/1.3681942
3548. Efrat Seri, Nadav M. Shnerb. Sustainability without coexistence state in Durrett–Levin hawk–dove model. Theoretical Ecology 2012, 5 (1) , 51-60. https://doi.org/10.1007/s12080-010-0099-4
3549. Giulio Alessandro De Leo, Luca Bolzoni. Getting a free ride on poultry farms: how highly pathogenic avian influenza may persist in spite of its virulence. Theoretical Ecology 2012, 5 (1) , 23-35. https://doi.org/10.1007/s12080-011-0136-y
3550. R. Vinu, Seth E. Levine, Lin Wang, Linda J. Broadbelt. Detailed mechanistic modeling of poly(styrene peroxide) pyrolysis using kinetic Monte Carlo simulation. Chemical Engineering Science 2012, 69 (1) , 456-471. https://doi.org/10.1016/j.ces.2011.10.071
3551. Nuris Figueroa-Morales, Kalet León, Roberto Mulet. Stochastic approximation to the T cell mediated specific response of the immune system. Journal of Theoretical Biology 2012, 295 , 37-46. https://doi.org/10.1016/j.jtbi.2011.11.003
3552. T.G. Vaughan, P.D. Drummond, A.J. Drummond. Within-host demographic fluctuations and correlations in early retroviral infection. Journal of Theoretical Biology 2012, 295 , 86-99. https://doi.org/10.1016/j.jtbi.2011.11.016
3553. Pei Wang, Jinhu Lü, Maciej J. Ogorzalek. Global relative parameter sensitivities of the feed-forward loops in genetic networks. Neurocomputing 2012, 78 (1) , 155-165. https://doi.org/10.1016/j.neucom.2011.05.034
3554. Giulio Caravagna, Jane Hillston. Bio-PEPAd: A non-Markovian extension of Bio-PEPA. Theoretical Computer Science 2012, 419 , 26-49. https://doi.org/10.1016/j.tcs.2011.11.028
3555. Elisabeth Fischer-Friedrich, Benjamin M Friedrich, Nir S Gov. FtsZ rings and helices: physical mechanisms for the dynamic alignment of biopolymers in rod-shaped bacteria. Physical Biology 2012, 9 (1) , 016009. https://doi.org/10.1088/1478-3975/9/1/016009
3556. Rui-ting Zhang, Han-shuang Chen, Zhong-huai Hou. Stability and Flipping Dynamics of Delayed Genetic Toggle Switch. Chinese Journal of Chemical Physics 2012, 25 (1) , 53-59. https://doi.org/10.1088/1674-0068/25/01/53-59
3557. Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini. Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions. IEEE Transactions on Parallel and Distributed Systems 2012, 23 (2) , 280-287. https://doi.org/10.1109/TPDS.2011.157
3558. T. Rogers, A. J. McKane, A. G. Rossberg. Demographic noise can lead to the spontaneous formation of species. EPL (Europhysics Letters) 2012, 97 (4) , 40008. https://doi.org/10.1209/0295-5075/97/40008
3559. Shantanu Kadam, Kumar Vanka. A new approximate method for the stochastic simulation of chemical systems: The representative reaction approach. Journal of Computational Chemistry 2012, 33 (3) , 276-285. https://doi.org/10.1002/jcc.21971
3560. Zhen Liu, Yang Pu, Fei Li, Clifford A. Shaffer, Stefan Hoops, John J. Tyson, Yang Cao. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. The Journal of Chemical Physics 2012, 136 (3) , 034105. https://doi.org/10.1063/1.3677190
3561. Patrick W. Sheppard, Muruhan Rathinam, Mustafa Khammash. A pathwise derivative approach to the computation of parameter sensitivities in discrete stochastic chemical systems. The Journal of Chemical Physics 2012, 136 (3) , 034115. https://doi.org/10.1063/1.3677230
3562. D. Chu, N. Zabet, T. von der Haar. A novel and versatile computational tool to model translation. Bioinformatics 2012, 28 (2) , 292-293. https://doi.org/10.1093/bioinformatics/btr650
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3565. Colin S. Gillespie. Stochastic simulation of chemically reacting systems using multi-core processors. The Journal of Chemical Physics 2012, 136 (1) , 014101. https://doi.org/10.1063/1.3670416
3566. Alessandro Romanel, Lars Juhl Jensen, Luca Cardelli, Attila Csikász-Nagy, . Transcriptional Regulation Is a Major Controller of Cell Cycle Transition Dynamics. PLoS ONE 2012, 7 (1) , e29716. https://doi.org/10.1371/journal.pone.0029716
3567. Farida Chamchod, Shigui Ruan, . Modeling the Spread of Methicillin-Resistant Staphylococcus aureus in Nursing Homes for Elderly. PLoS ONE 2012, 7 (1) , e29757. https://doi.org/10.1371/journal.pone.0029757
3568. Hans-Heinrich Carstensen, Anthony M. Dean. A quantitative kinetic analysis of CO elimination from phenoxy radicals. International Journal of Chemical Kinetics 2012, 44 (1) , 75-89. https://doi.org/10.1002/kin.20622
3569. Allan Clark, Vashti Galpin, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston. Formal Methods for Checking the Consistency of Biological Models. 2012,,, 461-475. https://doi.org/10.1007/978-1-4419-7210-1_27
3570. Alan J. McKane. Stochastic Processes. 2012,,, 3097-3113. https://doi.org/10.1007/978-1-4614-1800-9_193
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3572. Tuğrul Dayar. Introduction. 2012,,, 1-7. https://doi.org/10.1007/978-1-4614-4190-8_1
3573. Tuğrul Dayar. Preliminaries. 2012,,, 9-19. https://doi.org/10.1007/978-1-4614-4190-8_2
3574. Tuğrul Dayar. Iterative Methods. 2012,,, 21-35. https://doi.org/10.1007/978-1-4614-4190-8_3
3575. Tuğrul Dayar. Decompositional Methods. 2012,,, 37-56. https://doi.org/10.1007/978-1-4614-4190-8_4
3576. Tuğrul Dayar. Matrix-Analytic Methods. 2012,,, 57-73. https://doi.org/10.1007/978-1-4614-4190-8_5
3577. Tuğrul Dayar. Conclusion. 2012,,, 75-75. https://doi.org/10.1007/978-1-4614-4190-8_6
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3579. Wolfgang Marwan, Christian Rohr, Monika Heiner. Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks. 2012,,, 409-437. https://doi.org/10.1007/978-1-61779-361-5_21
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3585. A. P. J. Jansen. Kinetic Monte Carlo Algorithms. 2012,,, 37-71. https://doi.org/10.1007/978-3-642-29488-4_3
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3587. Marco Aldinucci, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella, Massimo Torquati, Angelo Troina. On Parallelizing On-Line Statistics for Stochastic Biological Simulations. 2012,,, 3-12. https://doi.org/10.1007/978-3-642-29740-3_2
3588. Mieke Massink, Diego Latella. Fluid Analysis of Foraging Ants. 2012,,, 152-165. https://doi.org/10.1007/978-3-642-30829-1_11
3589. Monika Heiner, Mostafa Herajy, Fei Liu, Christian Rohr, Martin Schwarick. Snoopy – A Unifying Petri Net Tool. 2012,,, 398-407. https://doi.org/10.1007/978-3-642-31131-4_22
3590. Cyrille Jegourel, Axel Legay, Sean Sedwards. Cross-Entropy Optimisation of Importance Sampling Parameters for Statistical Model Checking. 2012,,, 327-342. https://doi.org/10.1007/978-3-642-31424-7_26
3591. Fernando A. F. Braz, Jader S. Cruz, Alessandra C. Faria-Campos, Sérgio V. A. Campos. A Probabilistic Model Checking Approach to Investigate the Palytoxin Effects on the Na + /K + -ATPase. 2012,,, 84-96. https://doi.org/10.1007/978-3-642-31927-3_8
3592. Ho-Lin Chen, David Doty, David Soloveichik. Deterministic Function Computation with Chemical Reaction Networks. 2012,,, 25-42. https://doi.org/10.1007/978-3-642-32208-2_3
3593. Mieke Massink, Manuele Brambilla, Diego Latella, Marco Dorigo, Mauro Birattari. Analysing Robot Swarm Decision-Making with Bio-PEPA. 2012,,, 25-36. https://doi.org/10.1007/978-3-642-32650-9_3
3594. Fernando A. F. Braz, Jader S. Cruz, Alessandra C. Faria-Campos, Sérgio V. A. Campos. Palytoxin Inhibits the Sodium-Potassium Pump – An Investigation of an Electrophysiological Model Using Probabilistic Model Checking. 2012,,, 35-50. https://doi.org/10.1007/978-3-642-33296-8_5
3595. Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja, Andre Ribeiro. Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks. 2012,,, 307-321. https://doi.org/10.1007/978-3-642-33636-2_18
3596. Ilya Potapov, Evgenii Volkov. Effects of Molecular Noise on the Multistability in a Synthetic Genetic Oscillator. 2012,,, 386-389. https://doi.org/10.1007/978-3-642-33636-2_27
3597. Paolo Ballarini, Jarno Mäkelä, Andre S. Ribeiro. Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics. 2012,,, 29-48. https://doi.org/10.1007/978-3-642-33636-2_4
3598. Đurica Nikolić, Corrado Priami, Roberto Zunino. A Rule-Based and Imperative Language for Biochemical Modeling and Simulation. 2012,,, 16-32. https://doi.org/10.1007/978-3-642-33826-7_2
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3600. Alexandre David, Kim Guldstrand Larsen, Axel Legay, Marius Mikučionis, Danny Bøgsted Poulsen, Sean Sedwards. Runtime Verification of Biological Systems. 2012,,, 388-404. https://doi.org/10.1007/978-3-642-34026-0_29
3601. Oana Andrei, Muffy Calder. Trend-Based Analysis of a Population Model of the AKAP Scaffold Protein. 2012,,, 1-25. https://doi.org/10.1007/978-3-642-35524-0_1
3602. Alessio Angius, András Horváth, Verena Wolf. Quasi Product Form Approximation for Markov Models of Reaction Networks. 2012,,, 26-52. https://doi.org/10.1007/978-3-642-35524-0_2
3603. Ezio Bartocci, Pietro Liò, Emanuela Merelli, Nicola Paoletti. Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study. 2012,,, 53-76. https://doi.org/10.1007/978-3-642-35524-0_3
3604. Cristian Versari, Gianluigi Zavattaro. Complex Functional Rates in Rule-Based Languages for Biochemistry. 2012,,, 123-150. https://doi.org/10.1007/978-3-642-35524-0_6
3605. Qixia Yuan, Panuwat Trairatphisan, Jun Pang, Sjouke Mauw, Monique Wiesinger, Thomas Sauter. Probabilistic Model Checking of the PDGF Signaling Pathway. 2012,,, 151-180. https://doi.org/10.1007/978-3-642-35524-0_7
3606. Andrzej Mizera, Eugen Czeizler, Ion Petre. Self-assembly Models of Variable Resolution. 2012,,, 181-203. https://doi.org/10.1007/978-3-642-35524-0_8
3607. Paolo Milazzo, Antonella Del Corso, Andrea Maggiolo-Schettini, Umberto Mura, Roberto Barbuti. Modelling Biochemical Pathways with the Calculus of Looping Sequences. 2012,,, 105-125. https://doi.org/10.1007/978-88-470-2571-4_6
3608. Frederic von Wegner, Nicolas Wieder, Rainer H. A. Fink. Simulation Strategies for Calcium Microdomains and Calcium-Regulated Calcium Channels. 2012,,, 553-567. https://doi.org/10.1007/978-94-007-2888-2_25
3609. Upinder S. Bhalla. Multi-compartmental Models of Neurons. 2012,,, 193-225. https://doi.org/10.1007/978-94-007-3858-4_7
3610. Paola Lecca. A Process-Algebra Model of the Cell Mechanics of Autoreactive Lymphocytes Recruitment. 2012,,, 311-333. https://doi.org/10.1007/978-94-007-4068-6_15
3611. Yike Guo, Xian Yang. System Biology Approach to Study Cancer Related Pathways. 2012,,, 39-67. https://doi.org/10.1007/978-94-007-4819-4_2
3612. Thomas Schendel, Rüdiger Thul, James Sneyd, Martin Falcke. How does the ryanodine receptor in the ventricular myocyte wake up: by a single or by multiple open L-type Ca2+ channels?. European Biophysics Journal 2012, 41 (1) , 27-39. https://doi.org/10.1007/s00249-011-0755-7
3613. A. C. Tsoumanis, C. I. Siettos. Detection of coarse-grained unstable states of microscopic/stochastic systems: a timestepper-based iterative protocol. Nonlinear Dynamics 2012, 67 (1) , 103-117. https://doi.org/10.1007/s11071-011-9962-0
3614. Jacob Stewart-Ornstein, Hana El-Samad. Stochastic Modeling of Cellular Networks. 2012,,, 111-137. https://doi.org/10.1016/B978-0-12-388403-9.00005-9
3615. Ann E. Cowan, Ion I. Moraru, James C. Schaff, Boris M. Slepchenko, Leslie M. Loew. Spatial Modeling of Cell Signaling Networks. 2012,,, 195-221. https://doi.org/10.1016/B978-0-12-388403-9.00008-4
3616. Erik S. Welf, Jason M. Haugh. Stochastic Models of Cell Protrusion Arising From Spatiotemporal Signaling and Adhesion Dynamics. 2012,,, 223-241. https://doi.org/10.1016/B978-0-12-388403-9.00009-6
3617. Qianqian Ma, Caner Kazanci. An Individual-Based Approach for Studying System-Wide Properties of Ecological Networks. 2012,,, 201-215. https://doi.org/10.1016/B978-0-444-59396-2.00013-4
3618. Federica Ciocchetta, Davide Prandi, Michele Forlin, Ferenc Jordán. A Network Model of the Hierarchical Organization of Supra-Individual Biosystems. 2012,,, 517-532. https://doi.org/10.1016/B978-0-444-59396-2.00030-4
3619. Michael Strasser, Fabian J. Theis, Carsten Marr. Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression. Biophysical Journal 2012, 102 (1) , 19-29. https://doi.org/10.1016/j.bpj.2011.11.4000
3620. Biswajit Das, Gautam Gangopadhyay. Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study. Chemical Physics 2012, 393 (1) , 58-64. https://doi.org/10.1016/j.chemphys.2011.11.024
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3625. Lei Zhang, Kelly Radtke, Likun Zheng, Anna Q Cai, Thomas F Schilling, Qing Nie. Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Molecular Systems Biology 2012, 8 (1) , 613. https://doi.org/10.1038/msb.2012.45
3626. Mahmoud K. F. Abouelnasr, Berend Smit. Diffusion in confinement: kinetic simulations of self- and collective diffusion behavior of adsorbed gases. Physical Chemistry Chemical Physics 2012, 14 (33) , 11600. https://doi.org/10.1039/c2cp41147d
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3628. Nigel F. Reuel, Bin Mu, Jingqing Zhang, Allison Hinckley, Michael S. Strano. Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. Chemical Society Reviews 2012, 41 (17) , 5744. https://doi.org/10.1039/c2cs35142k
3629. Raúl Guantes, Bastien Cayrol, Florent Busi, Véronique Arluison. Positive regulatory dynamics by a small noncoding RNA: speeding up responses under temperature stress. Molecular BioSystems 2012, 8 (6) , 1707. https://doi.org/10.1039/c2mb05479e
3630. Matthew J. Hamer, Jonathan A. D. Wattis, Richard S. Graham. A method to project the rate kinetics of high dimensional barrier crossing problems onto a tractable 1D system. Soft Matter 2012, 8 (44) , 11396. https://doi.org/10.1039/c2sm25635e
3631. Ashok Garai, Bartlomiej Waclaw, Hannes Nagel, Hildegard Meyer-Ortmanns. Stochastic description of a bistable frustrated unit. Journal of Statistical Mechanics: Theory and Experiment 2012, 2012 (01) , P01009. https://doi.org/10.1088/1742-5468/2012/01/P01009
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3633. Mirco Tribastone, Stephen Gilmore, Jane Hillston. Scalable Differential Analysis of Process Algebra Models. IEEE Transactions on Software Engineering 2012, 38 (1) , 205-219. https://doi.org/10.1109/TSE.2010.82
3634. Harish Chandran, Nikhil Gopalkrishnan, John Reif. Tile Complexity of Linear Assemblies. SIAM Journal on Computing 2012, 41 (4) , 1051-1073. https://doi.org/10.1137/110822487
3635. Stephan Menz, Juan C. Latorre, Christof Schütte, Wilhelm Huisinga. Hybrid Stochastic--Deterministic Solution of the Chemical Master Equation. Multiscale Modeling & Simulation 2012, 10 (4) , 1232-1262. https://doi.org/10.1137/110825716
3636. David F. Anderson, Masanori Koyama. Weak Error Analysis of Numerical Methods for Stochastic Models of Population Processes. Multiscale Modeling & Simulation 2012, 10 (4) , 1493-1524. https://doi.org/10.1137/110849699
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3639. Vilda Purutçuoğlu, Ernst Wit. Estimating Network Kinetics of the MAPK/ERK Pathway Using Biochemical Data. Mathematical Problems in Engineering 2012, 2012 , 1-34. https://doi.org/10.1155/2012/752631
3640. Carole J. Proctor, Douglas A. Gray. A Unifying Hypothesis for Familial and Sporadic Alzheimer's Disease. International Journal of Alzheimer's Disease 2012, 2012 , 1-9. https://doi.org/10.1155/2012/978742
3641. Frank Emmert-Streib, Antti Häkkinen, Andre S Ribeiro. Detecting sequence dependent transcriptional pauses from RNA and protein number time series. BMC Bioinformatics 2012, 13 (1) , 152. https://doi.org/10.1186/1471-2105-13-152
3642. Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio. Fine-tuning anti-tumor immunotherapies via stochastic simulations. BMC Bioinformatics 2012, 13 (Suppl 4) , S8. https://doi.org/10.1186/1471-2105-13-S4-S8
3643. Bahram Houchmandzadeh, Marcel Vallade. Selection for altruism through random drift in variable size populations. BMC Evolutionary Biology 2012, 12 (1) , 61. https://doi.org/10.1186/1471-2148-12-61
3644. Yonatan Savir, Nir Waysbort, Yaron E Antebi, Tsvi Tlusty, Nir Friedman. Balancing speed and accuracy of polyclonal T cell activation: a role for extracellular feedback. BMC Systems Biology 2012, 6 (1) , 111. https://doi.org/10.1186/1752-0509-6-111
3645. Jinghang Liang, Jie Han. Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks. BMC Systems Biology 2012, 6 (1) , 113. https://doi.org/10.1186/1752-0509-6-113
3646. Iain Hepburn, Weiliang Chen, Stefan Wils, Erik De Schutter. STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies. BMC Systems Biology 2012, 6 (1) , 36. https://doi.org/10.1186/1752-0509-6-36
3647. Rachel S Koh, Mary J Dunlop. Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network. BMC Systems Biology 2012, 6 (1) , 47. https://doi.org/10.1186/1752-0509-6-47
3648. Steffen Waldherr, Bernard Haasdonk. Efficient parametric analysis of the chemical master equation through model order reduction. BMC Systems Biology 2012, 6 (1) , 81. https://doi.org/10.1186/1752-0509-6-81
3649. Vijay Chickarmane, Victor Olariu, Carsten Peterson. Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency. BMC Systems Biology 2012, 6 (1) , 98. https://doi.org/10.1186/1752-0509-6-98
3650. Andrea Asztalos, Marcus Daniels, Anurag Sethi, Tongye Shen, Paul Langan, Antonio Redondo, Sandrasegaram Gnanakaran. A coarse-grained model for synergistic action of multiple enzymes on cellulose. Biotechnology for Biofuels 2012, 5 (1) , 55. https://doi.org/10.1186/1754-6834-5-55
3651. Ryota Aisu, Takehiko Horita. Stochastic extinction of tumor cells due to synchronization effect through time periodic treatment in a tumor-immune interaction model. Nonlinear Theory and Its Applications, IEICE 2012, 3 (2) , 191-199. https://doi.org/10.1587/nolta.3.191
3652. Thomas Meyer, Christian Tschudin. Robust Network Services with Distributed Code Rewriting. 2012,,, 36-57. https://doi.org/10.4018/978-1-61350-092-7.ch003
3653. Marc Hafner, Heinz Koeppl. Stochastic Simulations in Systems Biology. 2012,,, 267-286. https://doi.org/10.4018/978-1-61350-116-0.ch012
3654. Miha Moškon, Miha Mraz. Modeling as the Essential Step in the Construction of Biological Computer Structures. International Journal of Computer Theory and Engineering 2012, , 556-560. https://doi.org/10.7763/IJCTE.2012.V4.531
3655. Rajesh Ramaswamy, Ivo F. Sbalzarini. Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. The Journal of Chemical Physics 2011, 135 (24) , 244103. https://doi.org/10.1063/1.3666988
3656. Anton Camacho, Sébastien Ballesteros, Andrea L. Graham, Fabrice Carrat, Oliver Ratmann, Bernard Cazelles. Explaining rapid reinfections in multiple-wave influenza outbreaks: Tristan da Cunha 1971 epidemic as a case study. Proceedings of the Royal Society B: Biological Sciences 2011, 278 (1725) , 3635-3643. https://doi.org/10.1098/rspb.2011.0300
3657. Min K. Roh, Bernie J. Daigle, Dan T. Gillespie, Linda R. Petzold. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events. The Journal of Chemical Physics 2011, 135 (23) , 234108. https://doi.org/10.1063/1.3668100
3658. Yishai Shimoni, German Nudelman, Fernand Hayot, Stuart C. Sealfon, . Multi-Scale Stochastic Simulation of Diffusion-Coupled Agents and Its Application to Cell Culture Simulation. PLoS ONE 2011, 6 (12) , e29298. https://doi.org/10.1371/journal.pone.0029298
3659. R Murugan. Theory on thermodynamic coupling of site-specific DNA–protein interactions with fluctuations in DNA-binding domains. Journal of Physics A: Mathematical and Theoretical 2011, 44 (50) , 505002. https://doi.org/10.1088/1751-8113/44/50/505002
3660. Karsten Reuter. First-Principles Kinetic Monte Carlo Simulations for Heterogeneous Catalysis: Concepts, Status, and Frontiers. 2011,,, 71-111. https://doi.org/10.1002/9783527639878.ch3
3661. V. Garcia-Morales, K. Krischer. Superstatistics in nanoscale electrochemical systems. Proceedings of the National Academy of Sciences 2011, 108 (49) , 19535-19539. https://doi.org/10.1073/pnas.1109844108
3662. Andrew Golightly, Darren J. Wilkinson. Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo. Interface Focus 2011, 1 (6) , 807-820. https://doi.org/10.1098/rsfs.2011.0047
3663. Mohammad Najafi, Hossein Roghani-Mamaqani, Vahid Haddadi-Asl, Mehdi Salami-Kalajahi. A simulation of kinetics and chain length distribution of styrene FRP and ATRP: Chain-length-dependent termination. Advances in Polymer Technology 2011, 30 (4) , 257-268. https://doi.org/10.1002/adv.20221
3664. W. H. Mather, J. Hasty, L. S. Tsimring, R. J. Williams. Factorized time-dependent distributions for certain multiclass queueing networks and an application to enzymatic processing networks. Queueing Systems 2011, 69 (3-4) , 313-328. https://doi.org/10.1007/s11134-011-9216-3
3665. Marco J. Morelli, Rosalind J. Allen, Pieter Rein ten Wolde. Effects of Macromolecular Crowding on Genetic Networks. Biophysical Journal 2011, 101 (12) , 2882-2891. https://doi.org/10.1016/j.bpj.2011.10.053
3666. Michail Stamatakis, Dionisios G. Vlachos. Equivalence of on-lattice stochastic chemical kinetics with the well-mixed chemical master equation in the limit of fast diffusion. Computers & Chemical Engineering 2011, 35 (12) , 2602-2610. https://doi.org/10.1016/j.compchemeng.2011.05.008
3667. David D. Jenkins, Gregory D. Peterson. AESS: Accelerated Exact Stochastic Simulation. Computer Physics Communications 2011, 182 (12) , 2580-2586. https://doi.org/10.1016/j.cpc.2011.07.013
3668. Ferenc Jordán, Marco Scotti, Corrado Priami. Process algebra-based computational tools in ecological modelling. Ecological Complexity 2011, 8 (4) , 357-363. https://doi.org/10.1016/j.ecocom.2011.07.006
3669. Jo A. Helmuth, Sylvain Reboux, Ivo F. Sbalzarini. Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. Journal of Computational Science 2011, 2 (4) , 324-334. https://doi.org/10.1016/j.jocs.2011.08.006
3670. C.M. Field, D.K. Summers. Multicopy plasmid stability: Revisiting the dimer catastrophe. Journal of Theoretical Biology 2011, 291 , 119-127. https://doi.org/10.1016/j.jtbi.2011.09.006
3671. Mary Sehl, Hua Zhou, Janet S. Sinsheimer, Kenneth L. Lange. Extinction models for cancer stem cell therapy. Mathematical Biosciences 2011, 234 (2) , 132-146. https://doi.org/10.1016/j.mbs.2011.09.005
3672. Daniele Miorandi. A stochastic model for molecular communications. Nano Communication Networks 2011, 2 (4) , 205-212. https://doi.org/10.1016/j.nancom.2011.04.005
3673. Rajesh Ramaswamy, Ivo F. Sbalzarini. Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Scientific Reports 2011, 1 (1) https://doi.org/10.1038/srep00154
3674. Michail Stamatakis, Rhys M. Adams, Gábor Balázsi. A common repressor pool results in indeterminacy of extrinsic noise. Chaos: An Interdisciplinary Journal of Nonlinear Science 2011, 21 (4) , 047523. https://doi.org/10.1063/1.3658618
3675. Sebastián Bouzat, Fernando Falo. Tug of war of molecular motors: the effects of uneven load sharing. Physical Biology 2011, 8 (6) , 066010. https://doi.org/10.1088/1478-3975/8/6/066010
3676. Sheng-Jun Liu, Qi Wang, Bo Liu, Shi-Wei Yan, Fumihiko Sakata. Noise transmission and delay-induced stochastic oscillations in biochemical network motifs. Chinese Physics B 2011, 20 (12) , 128703. https://doi.org/10.1088/1674-1056/20/12/128703
3677. Shunsuke Teraguchi, Yutaro Kumagai, Alexis Vandenbon, Shizuo Akira, Daron M Standley. Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations. Physical Review E 2011, 84 (6) https://doi.org/10.1103/PhysRevE.84.062903
3678. Md. Shahriar Karim, David M. Umulis, Gregery T. Buzzard. Steady state probability approximation applied to stochastic model of biological network. 2011,,, 56-59. https://doi.org/10.1109/GENSiPS.2011.6169442
3679. Tianhai Tian. Stochastic dynamics of a Hepatitis B virus transmission model. 2011,,, 496-500. https://doi.org/10.1109/ITiME.2011.6130884
3680. R. AGUILÉE, A. LAMBERT, D. CLAESSEN. Ecological speciation in dynamic landscapes. Journal of Evolutionary Biology 2011, 24 (12) , 2663-2677. https://doi.org/10.1111/j.1420-9101.2011.02392.x
3681. SHIVENDRA G. TEWARI. STOCHASTIC SIMULATION OF A DIMER SODIUM PUMP. Journal of Biological Systems 2011, 19 (04) , 551-560. https://doi.org/10.1142/S0218339011003920
3682. DOMINIK HEINZMANN, A. D. BARBOUR, PAUL R. TORGERSON. A MECHANISTIC INDIVIDUAL-BASED TWO-HOST INTERACTION MODEL FOR THE TRANSMISSION OF A PARASITIC DISEASE. International Journal of Biomathematics 2011, 04 (04) , 443-460. https://doi.org/10.1142/S1793524511001313
3683. Peter F. Rowat, Priscilla E. Greenwood. Identification and Continuity of the Distributions of Burst-Length and Interspike Intervals in the Stochastic Morris-Lecar Neuron. Neural Computation 2011, 23 (12) , 3094-3124. https://doi.org/10.1162/NECO_a_00209
3684. Johann C Detilleux. Effectiveness analysis of resistance and tolerance to infection. Genetics Selection Evolution 2011, 43 (1) https://doi.org/10.1186/1297-9686-43-9
3685. Botond Sipos, Tim Massingham, Gregory E Jordan, Nick Goldman. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics 2011, 12 (1) https://doi.org/10.1186/1471-2105-12-104
3686. Jukka Intosalmi, Tiina Manninen, Keijo Ruohonen, Marja-Leena Linne. Computational study of noise in a large signal transduction network. BMC Bioinformatics 2011, 12 (1) https://doi.org/10.1186/1471-2105-12-252
3687. Michail Stamatakis, Kyriacos Zygourakis. Deterministic and stochastic population-level simulations of an artificial lac operon genetic network. BMC Bioinformatics 2011, 12 (1) https://doi.org/10.1186/1471-2105-12-301
3688. Benjamin Roche, John M Drake, Pejman Rohani. An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses. BMC Bioinformatics 2011, 12 (1) https://doi.org/10.1186/1471-2105-12-87
3689. Olli-Pekka Smolander, Meenakshisundaram Kandhavelu, Henrik Mannerström, Eero Lihavainen, Shanmugapriya Kalaichelvan, Shannon Healy, Olli Yli-Harja, Matti Karp, Andre S Ribeiro. Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. BMC Molecular Biology 2011, 12 (1) https://doi.org/10.1186/1471-2199-12-21
3690. Zhouyi Xu, Xiaodong Cai. Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems. EURASIP Journal on Bioinformatics and Systems Biology 2011, 2011 (1) https://doi.org/10.1186/1687-4153-2011-797251
3691. Marc Weber, Javier Buceta. Noise regulation by quorum sensing in low mRNA copy number systems. BMC Systems Biology 2011, 5 (1) https://doi.org/10.1186/1752-0509-5-11
3692. Christos Josephides, Alan M Moses. Modeling the evolution of a classic genetic switch. BMC Systems Biology 2011, 5 (1) https://doi.org/10.1186/1752-0509-5-24
3693. Dmitry Anatolievich Bratsun. Effect of subcritical excitation of oscillations in stochastic systems with time delay. Part I. Regulation of gene expression. Computer Research and Modeling 2011, 3 (4) , 421-438. https://doi.org/10.20537/2076-7633-2011-3-4-421-438
3694. Hiroaki Takagi, Masatoshi Nishikawa. Mechanochemical Coupling Revealed by the Fluctuation Analysis of Different Biomolecular Motors. 2011,,, 419-435. https://doi.org/10.1002/9781118131374.ch15
3695. Joshua H. Goldwyn, Eric Shea-Brown, . The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations. PLoS Computational Biology 2011, 7 (11) , e1002247. https://doi.org/10.1371/journal.pcbi.1002247
3696. Zhuo Song, Yang Cao, David C. Samuels, . Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study. PLoS Computational Biology 2011, 7 (11) , e1002287. https://doi.org/10.1371/journal.pcbi.1002287
3697. M. R. Lakin, S. Youssef, F. Polo, S. Emmott, A. Phillips. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics 2011, 27 (22) , 3211-3213. https://doi.org/10.1093/bioinformatics/btr543
3698. Philipp Thomas, Arthur V. Straube, Ramon Grima. Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks. The Journal of Chemical Physics 2011, 135 (18) , 181103. https://doi.org/10.1063/1.3661156
3699. Krešimir Josić, José Manuel López, William Ott, LieJune Shiau, Matthew R. Bennett, . Stochastic Delay Accelerates Signaling in Gene Networks. PLoS Computational Biology 2011, 7 (11) , e1002264. https://doi.org/10.1371/journal.pcbi.1002264
3700. Sudin Bhattacharya, Qiang Zhang, Melvin E. Andersen. Role of Core Biological Motifs in Dose-Response Modeling: An Example with Switchlike Circuits. 2011,,, 147-173. https://doi.org/10.1002/9781118016435.ch7
3701. Pietro de Anna, Tanguy Le Borgne, Marco Dentz, Diogo Bolster, Philippe Davy. Anomalous kinetics in diffusion limited reactions linked to non-Gaussian concentration probability distribution function. The Journal of Chemical Physics 2011, 135 (17) , 174104. https://doi.org/10.1063/1.3655895
3702. Bruno M.C. Martins, Peter S. Swain, . Trade-Offs and Constraints in Allosteric Sensing. PLoS Computational Biology 2011, 7 (11) , e1002261. https://doi.org/10.1371/journal.pcbi.1002261
3703. Richard S. Graham. Molecular modelling of flow-induced crystallisation in polymers. Journal of Engineering Mathematics 2011, 71 (3) , 237-251. https://doi.org/10.1007/s10665-010-9425-5
3704. Jonathan D. Touboul, G. Bard Ermentrout. Finite-size and correlation-induced effects in mean-field dynamics. Journal of Computational Neuroscience 2011, 31 (3) , 453-484. https://doi.org/10.1007/s10827-011-0320-5
3705. David Arthur Stanley, Berj L. Bardakjian, Mark L. Spano, William L. Ditto. Stochastic amplification of calcium-activated potassium currents in Ca2+ microdomains. Journal of Computational Neuroscience 2011, 31 (3) , 647-666. https://doi.org/10.1007/s10827-011-0328-x
3706. Mohammad Najafi, Hossein Roghani-Mamaqani, Mehdi Salami-Kalajahi, Vahid Haddadi-Asl. An exhaustive study of chain-length-dependent and diffusion-controlled free radical and atom-transfer radical polymerization of styrene. Journal of Polymer Research 2011, 18 (6) , 1539-1555. https://doi.org/10.1007/s10965-010-9559-1
3707. Chitra R. Nayak, Andrew D. Rutenberg. Quantification of Fluorophore Copy Number from Intrinsic Fluctuations during Fluorescence Photobleaching. Biophysical Journal 2011, 101 (9) , 2284-2293. https://doi.org/10.1016/j.bpj.2011.09.032
3708. Melissa Nivala, Paavo Korge, Michael Nivala, James N. Weiss, Zhilin Qu. Linking Flickering to Waves and Whole-Cell Oscillations in a Mitochondrial Network Model. Biophysical Journal 2011, 101 (9) , 2102-2111. https://doi.org/10.1016/j.bpj.2011.09.038
3709. Kathryn T. Applegate, Sebastien Besson, Alexandre Matov, Maria H. Bagonis, Khuloud Jaqaman, Gaudenz Danuser. plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics. Journal of Structural Biology 2011, 176 (2) , 168-184. https://doi.org/10.1016/j.jsb.2011.07.009
3710. Or Givan, Nehemia Schwartz, Assaf Cygelberg, Lewi Stone. Predicting epidemic thresholds on complex networks: Limitations of mean-field approaches. Journal of Theoretical Biology 2011, 288 , 21-28. https://doi.org/10.1016/j.jtbi.2011.07.015
3711. Carles Bretó, Edward L. Ionides. Compound Markov counting processes and their applications to modeling infinitesimally over-dispersed systems. Stochastic Processes and their Applications 2011, 121 (11) , 2571-2591. https://doi.org/10.1016/j.spa.2011.07.005
3712. Bo Liu, Sheng-Jun Liu, Qi Wang, Shi-Wei Yan, Yi-Zhao Geng, Fumihiko Sakata, Xing-Fa Gao. Stochastic Nature in Cellular Processes. Communications in Theoretical Physics 2011, 56 (5) , 913-921. https://doi.org/10.1088/0253-6102/56/5/19
3713. L. F. Lafuerza, R. Toral. Exact solution of a stochastic protein dynamics model with delayed degradation. Physical Review E 2011, 84 (5) https://doi.org/10.1103/PhysRevE.84.051121
3714. Douglas Swanson, Ned S. Wingreen. Active Biopolymers Confer Fast Reorganization Kinetics. Physical Review Letters 2011, 107 (21) https://doi.org/10.1103/PhysRevLett.107.218103
3715. Soma Saha, Somdeb Ghose, R. Adhikari, Arti Dua. Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations. Physical Review Letters 2011, 107 (21) https://doi.org/10.1103/PhysRevLett.107.218301
3716. Andrew E. Noble, Alan Hastings, William F. Fagan. Multivariate Moran Process with Lotka-Volterra Phenomenology. Physical Review Letters 2011, 107 (22) https://doi.org/10.1103/PhysRevLett.107.228101
3717. Anna Dari, Adi. R. Bulsara, William L. Ditto, Xiao Wang. Reprogrammable biological logic gate that exploits noise. 2011,,, 337-340. https://doi.org/10.1109/BioCAS.2011.6107796
3718. Chiara Damiani, Paola Lecca. Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation. 2011,,, 129-134. https://doi.org/10.1109/EMS.2011.58
3719. Loic Pauleve, Morgan Magnin, Olivier Roux. Tuning Temporal Features within the Stochastic π-Calculus. IEEE Transactions on Software Engineering 2011, 37 (6) , 858-871. https://doi.org/10.1109/TSE.2010.95
3720. Calum Brown, Richard Law, Janine B. Illian, David F. R. P. Burslem. Linking ecological processes with spatial and non-spatial patterns in plant communities. Journal of Ecology 2011, 99 (6) , 1402-1414. https://doi.org/10.1111/j.1365-2745.2011.01877.x
3721. B. Nowakowski, A. L. Kawczyński, A. Kolbus, A. Lemarchand. Coherence resonances in excitable thermochemical systems induced by scaled reaction heat. The European Physical Journal B 2011, 84 (1) , 137-145. https://doi.org/10.1140/epjb/e2011-20288-5
3722. Michael T Tolley, Hod Lipson. On-line assembly planning for stochastically reconfigurable systems. The International Journal of Robotics Research 2011, 30 (13) , 1566-1584. https://doi.org/10.1177/0278364911398160
3723. Srijeeta Talukder, Pinaki Chaudhury, Ralf Metzler, Suman K. Banik. Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization. The Journal of Chemical Physics 2011, 135 (16) , 165103. https://doi.org/10.1063/1.3654958
3724. . Stochastic effects in biological control systems. 2011,,, 255-278. https://doi.org/10.1201/b11153-9
3725. Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, Lingchong You, . Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks. PLoS Computational Biology 2011, 7 (10) , e1002209. https://doi.org/10.1371/journal.pcbi.1002209
3726. Andre Leier, Tatiana T. Marquez-Lago. Correction factors for boundary diffusion in reaction-diffusion master equations. The Journal of Chemical Physics 2011, 135 (13) , 134109. https://doi.org/10.1063/1.3634003
3727. Gerardo Odriozola. Ion-specific colloidal aggregation: Population balance equations and potential of mean force. The Journal of Chemical Physics 2011, 135 (13) , 134704. https://doi.org/10.1063/1.3644769
3728. Marc Bailly-Bechet, Arndt Benecke, Wolf Dietrich Hardt, Valentina Lanza, Alexander Sturm, Riccardo Zecchina. An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology 2011, 63 (4) , 637-662. https://doi.org/10.1007/s00285-010-0385-1
3729. Janine Imada, Brian J. Ross. Evolutionary Synthesis of Stochastic Gene Network Models Using Feature-based Search Spaces. New Generation Computing 2011, 29 (4) , 365-390. https://doi.org/10.1007/s00354-009-0115-7
3730. D. Kulasiri, Y. He, S. Samarasinghe. Robustness of circadian rhythms in the presence of molecular fluctuations: An investigation based on a mechanistic, statistical theory and a simulation algorithm. Biosystems 2011, 106 (1) , 57-66. https://doi.org/10.1016/j.biosystems.2011.06.008
3731. S. Guerrero, E.E. Wolf. Kinetic Monte Carlo simulation of the preferential oxidation of CO using normally distributed rate probabilities. Chemical Engineering Science 2011, 66 (20) , 4477-4487. https://doi.org/10.1016/j.ces.2011.05.008
3732. Alessio Angius, András Horváth. Product Form Approximation of Transient Probabilities in Stochastic Reaction Networks. Electronic Notes in Theoretical Computer Science 2011, 277 , 3-14. https://doi.org/10.1016/j.entcs.2011.09.031
3733. Eva Sciacca, Salvatore Spinella, Andrea Genre, Cristina Calcagno. Analysis of Calcium Spiking in Plant Root Epidermis through CWC Modeling. Electronic Notes in Theoretical Computer Science 2011, 277 , 65-76. https://doi.org/10.1016/j.entcs.2011.09.036
3734. Ammar Tighezza, Daifallah Aldhayan, Abdullah Almthar. Implementation of Net-Event Monte Carlo algorithm in chemical kinetics simulation software of complex isothermal reacting systems. Journal of Saudi Chemical Society 2011, 15 (4) , 351-355. https://doi.org/10.1016/j.jscs.2011.04.008
3735. Zhilin Qu, Alan Garfinkel, James N. Weiss, Melissa Nivala. Multi-scale modeling in biology: How to bridge the gaps between scales?. Progress in Biophysics and Molecular Biology 2011, 107 (1) , 21-31. https://doi.org/10.1016/j.pbiomolbio.2011.06.004
3736. Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini. Spatial Calculus of Looping Sequences. Theoretical Computer Science 2011, 412 (43) , 5976-6001. https://doi.org/10.1016/j.tcs.2011.01.020
3737. Tetsuya J Kobayashi, Atsushi Kamimura. Dynamics of intracellular information decoding. Physical Biology 2011, 8 (5) , 055007. https://doi.org/10.1088/1478-3975/8/5/055007
3738. Jin Yang, William S Hlavacek. The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Physical Biology 2011, 8 (5) , 055009. https://doi.org/10.1088/1478-3975/8/5/055009
3739. Peter Hinow, Vahid Rezania, Manu Lopus, Mary Ann Jordan, Jack A Tuszyński. Modeling the effects of drug binding on the dynamic instability of microtubules. Physical Biology 2011, 8 (5) , 056004. https://doi.org/10.1088/1478-3975/8/5/056004
3740. Peng Li, Lin-Ru Nie, Xiu-Min Lü, Qi-Bo Zhang. Effect of inertial mass on a linear system driven by dichotomous noise and a periodic signal. Chinese Physics B 2011, 20 (10) , 100502. https://doi.org/10.1088/1674-1056/20/10/100502
3741. Jarno Mäkelä, Heikki Huttunen, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro. Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli. Bioinformatics 2011, 27 (19) , 2714-2720. https://doi.org/10.1093/bioinformatics/btr471
3742. Gregory Bulnes Cuetara, Massimiliano Esposito, Pierre Gaspard. Fluctuation theorems for capacitively coupled electronic currents. Physical Review B 2011, 84 (16) https://doi.org/10.1103/PhysRevB.84.165114
3743. T. Guérin, J. Prost, J.-F. Joanny. Bidirectional motion of motor assemblies and the weak-noise escape problem. Physical Review E 2011, 84 (4) https://doi.org/10.1103/PhysRevE.84.041901
3744. Christoph M. Meier, Jostein Starrfelt, Hanna Kokko. Mate limitation causes sexes to coevolve towards more similar dispersal kernels. Oikos 2011, 120 (10) , 1459-1468. https://doi.org/10.1111/j.1600-0706.2011.19487.x
3745. Y. D. Huang, S. Rüdiger, J. W. Shuai. Modified Langevin approach for a stochastic calcium puff model. The European Physical Journal B 2011, 83 (3) , 401-407. https://doi.org/10.1140/epjb/e2011-20517-y
3746. Jasmin Fisher, David Harel, Thomas A. Henzinger. Biology as reactivity. Communications of the ACM 2011, 54 (10) , 72-82. https://doi.org/10.1145/2001269.2001289
3747. Jivika Govil, Jivesh Govil, Aishvarya Gupta, Vidhi Gupta. Nano Technology/Networks in Molecular Communication: An Advance Step of Electrical Communications. Applied Mechanics and Materials 2011, 110-116 , 3770-3776. https://doi.org/10.4028/www.scientific.net/AMM.110-116.3770
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3863. Tianhai Tian. Stochastic Modeling of Gene Regulatory Networks. 2011,,, 13-37. https://doi.org/10.1002/9783527638079.ch2
3864. Wonryull Koh, Kim T. Blackwell. An accelerated algorithm for discrete stochastic simulation of reaction–diffusion systems using gradient-based diffusion and tau-leaping. The Journal of Chemical Physics 2011, 134 (15) , 154103. https://doi.org/10.1063/1.3572335
3865. Rishi Srivastava, Eric L. Haseltine, Ethan Mastny, James B. Rawlings. The stochastic quasi-steady-state assumption: Reducing the model but not the noise. The Journal of Chemical Physics 2011, 134 (15) , 154109. https://doi.org/10.1063/1.3580292
3866. Gašper Tkačik, Aleksandra M Walczak. Information transmission in genetic regulatory networks: a review. Journal of Physics: Condensed Matter 2011, 23 (15) , 153102. https://doi.org/10.1088/0953-8984/23/15/153102
3867. G. Klingbeil, R. Erban, M. Giles, P. K. Maini. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB. Bioinformatics 2011, 27 (8) , 1170-1171. https://doi.org/10.1093/bioinformatics/btr068
3868. Sheng Wu, Jin Fu, Yang Cao, Linda Petzold. Michaelis–Menten speeds up tau-leaping under a wide range of conditions. The Journal of Chemical Physics 2011, 134 (13) , 134112. https://doi.org/10.1063/1.3576123
3869. Attila Csikász-Nagy, Luca Cardelli, Orkun S. Soyer. Response dynamics of phosphorelays suggest their potential utility in cell signalling. Journal of The Royal Society Interface 2011, 8 (57) , 480-488. https://doi.org/10.1098/rsif.2010.0336
3870. Mamdouh Al-Harthi. Stochastic model for living radical polymerisation of styrene initiated by epoxide radical ring opening. The Canadian Journal of Chemical Engineering 2011, 89 (2) , 384-391. https://doi.org/10.1002/cjce.20416
3871. David M. Golden, John R. Barker. Pressure- and temperature-dependent combustion reactions. Combustion and Flame 2011, 158 (4) , 602-617. https://doi.org/10.1016/j.combustflame.2010.08.011
3872. Thomas Adams, Graeme Ackland, Glenn Marion, Colin Edwards. Effects of local interaction and dispersal on the dynamics of size-structured populations. Ecological Modelling 2011, 222 (8) , 1414-1422. https://doi.org/10.1016/j.ecolmodel.2011.02.006
3873. J.R. Schramski, C. Kazanci, E.W. Tollner. Network environ theory, simulation, and EcoNet® 2.0. Environmental Modelling & Software 2011, 26 (4) , 419-428. https://doi.org/10.1016/j.envsoft.2010.10.003
3874. Matthias Jeschke, Roland Ewald, Adelinde M. Uhrmacher. Exploring the performance of spatial stochastic simulation algorithms. Journal of Computational Physics 2011, 230 (7) , 2562-2574. https://doi.org/10.1016/j.jcp.2010.12.030
3875. Marek Bodnar, Urszula Foryś, Jan Poleszczuk. Analysis of biochemical reactions models with delays. Journal of Mathematical Analysis and Applications 2011, 376 (1) , 74-83. https://doi.org/10.1016/j.jmaa.2010.10.038
3876. Michael C. Mackey, Marta Tyran-Kamińska, Romain Yvinec. Molecular distributions in gene regulatory dynamics. Journal of Theoretical Biology 2011, 274 (1) , 84-96. https://doi.org/10.1016/j.jtbi.2011.01.020
3877. Michael Assaf, Mauro Mobilia. Fixation of a deleterious allele under mutation pressure and finite selection intensity. Journal of Theoretical Biology 2011, 275 (1) , 93-103. https://doi.org/10.1016/j.jtbi.2011.01.025
3878. Elisabeth Fischer-Friedrich, Nir Gov. Modeling FtsZ ring formation in the bacterial cell—anisotropic aggregation via mutual interactions of polymer rods. Physical Biology 2011, 8 (2) , 026007. https://doi.org/10.1088/1478-3975/8/2/026007
3879. Hongxia Fu, Hu Chen, Xinghua Zhang, Yuanyuan Qu, John F. Marko, Jie Yan. Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Research 2011, 39 (8) , 3473-3481. https://doi.org/10.1093/nar/gkq1278
3880. Joshua H. Goldwyn, Nikita S. Imennov, Michael Famulare, Eric Shea-Brown. Stochastic differential equation models for ion channel noise in Hodgkin-Huxley neurons. Physical Review E 2011, 83 (4) https://doi.org/10.1103/PhysRevE.83.041908
3881. Jun Ohkubo. Approximation scheme based on effective interactions for stochastic gene regulation. Physical Review E 2011, 83 (4) https://doi.org/10.1103/PhysRevE.83.041915
3882. Baruch Barzel, Ofer Biham. Binomial Moment Equations for Stochastic Reaction Systems. Physical Review Letters 2011, 106 (15) https://doi.org/10.1103/PhysRevLett.106.150602
3883. Nick G.H. Taylor, Rachel A. Norman, Keith Way, Edmund J. Peeler. Modelling the koi herpesvirus (KHV) epidemic highlights the importance of active surveillance within a national control policy. Journal of Applied Ecology 2011, 48 (2) , 348-355. https://doi.org/10.1111/j.1365-2664.2010.01926.x
3884. JUAN G. DIAZ OCHOA. STOCHASTIC TIME DELAYS IN REGULATORY NETWORKS AND MODEL REDUCTION. International Journal of Modern Physics C 2011, 22 (04) , 385-399. https://doi.org/10.1142/S0129183111016312
3885. PETROS KOUMOUTSAKOS, BASIL BAYATI, FLORIAN MILDE, GERARDO TAURIELLO. PARTICLE SIMULATIONS OF MORPHOGENESIS. Mathematical Models and Methods in Applied Sciences 2011, 21 (supp01) , 955-1006. https://doi.org/10.1142/S021820251100543X
3886. Nikolaus Correll, Alcherio Martinoli. Modeling and designing self-organized aggregation in a swarm of miniature robots. The International Journal of Robotics Research 2011, 30 (5) , 615-626. https://doi.org/10.1177/0278364911403017
3887. Paulien Hogeweg, . The Roots of Bioinformatics in Theoretical Biology. PLoS Computational Biology 2011, 7 (3) , e1002021. https://doi.org/10.1371/journal.pcbi.1002021
3888. Eeva Toivari, Tiina Manninen, Amit K. Nahata, Tuula O. Jalonen, Marja-Leena Linne, . Effects of Transmitters and Amyloid-Beta Peptide on Calcium Signals in Rat Cortical Astrocytes: Fura-2AM Measurements and Stochastic Model Simulations. PLoS ONE 2011, 6 (3) , e17914. https://doi.org/10.1371/journal.pone.0017914
3889. T. Zhu, Y. Hu, Z.-M. Ma, D.-X. Zhang, T. Li, Z. Yang. Efficient simulation under a population genetics model of carcinogenesis. Bioinformatics 2011, 27 (6) , 837-843. https://doi.org/10.1093/bioinformatics/btr025
3890. Richard I. Joh, Joshua S. Weitz, . To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages. PLoS Computational Biology 2011, 7 (3) , e1002006. https://doi.org/10.1371/journal.pcbi.1002006
3891. Matthew Scott, Francis J. Poulin, Herbert Tang. Approximating intrinsic noise in continuous multispecies models. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2011, 467 (2127) , 718-737. https://doi.org/10.1098/rspa.2010.0275
3892. Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, Rob Phillips, Jané Kondev, . Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression. PLoS Computational Biology 2011, 7 (3) , e1001100. https://doi.org/10.1371/journal.pcbi.1001100
3893. Desmond J. Higham, Somkid Intep, Xuerong Mao, Lukasz Szpruch. Hybrid simulation of autoregulation within transcription and translation. BIT Numerical Mathematics 2011, 51 (1) , 177-196. https://doi.org/10.1007/s10543-011-0322-8
3894. John Jack, Andrei Păun, Alfonso Rodríguez-Patón. A review of the nondeterministic waiting time algorithm. Natural Computing 2011, 10 (1) , 139-149. https://doi.org/10.1007/s11047-010-9195-z
3895. M. Wilhelm, M. Chhetri, J. Rychtář, O. Rueppell. A Game Theoretical Analysis of the Mating Sign Behavior in the Honey Bee. Bulletin of Mathematical Biology 2011, 73 (3) , 626-638. https://doi.org/10.1007/s11538-010-9544-1
3896. Chris McCaig, Mike Begon, Rachel Norman, Carron Shankland. A rigorous approach to investigating common assumptions about disease transmission. Theory in Biosciences 2011, 130 (1) , 19-29. https://doi.org/10.1007/s12064-010-0106-8
3897. Peter Schuster. Mathematical modeling of evolution. Solved and open problems. Theory in Biosciences 2011, 130 (1) , 71-89. https://doi.org/10.1007/s12064-010-0110-z
3898. Kyung Hyuk Kim, Herbert M. Sauro. Measuring Retroactivity from Noise in Gene Regulatory Networks. Biophysical Journal 2011, 100 (5) , 1167-1177. https://doi.org/10.1016/j.bpj.2010.12.3737
3899. Gábor Balázsi, Alexander van Oudenaarden, James J. Collins. Cellular Decision Making and Biological Noise: From Microbes to Mammals. Cell 2011, 144 (6) , 910-925. https://doi.org/10.1016/j.cell.2011.01.030
3900. Sabrina L. Spencer, Peter K. Sorger. Measuring and Modeling Apoptosis in Single Cells. Cell 2011, 144 (6) , 926-939. https://doi.org/10.1016/j.cell.2011.03.002
3901. Chunhe Li, Erkang Wang, Jin Wang. Landscape and flux decomposition for exploring global natures of non-equilibrium dynamical systems under intrinsic statistical fluctuations. Chemical Physics Letters 2011, 505 (1-3) , 75-80. https://doi.org/10.1016/j.cplett.2011.02.020
3902. D. Fernàndez-Garcia, X. Sanchez-Vila. Optimal reconstruction of concentrations, gradients and reaction rates from particle distributions. Journal of Contaminant Hydrology 2011, 120-121 , 99-114. https://doi.org/10.1016/j.jconhyd.2010.05.001
3903. Marco Dentz, Tanguy Le Borgne, Andreas Englert, Branko Bijeljic. Mixing, spreading and reaction in heterogeneous media: A brief review. Journal of Contaminant Hydrology 2011, 120-121 , 1-17. https://doi.org/10.1016/j.jconhyd.2010.05.002
3904. Martin Beck, Maya Topf, Zachary Frazier, Harianto Tjong, Min Xu, Shihua Zhang, Frank Alber. Exploring the spatial and temporal organization of a cell’s proteome. Journal of Structural Biology 2011, 173 (3) , 483-496. https://doi.org/10.1016/j.jsb.2010.11.011
3905. Subhasis Banerjee, Indrani Bose. Transient pulse formation in jasmonate signaling pathway. Journal of Theoretical Biology 2011, 273 (1) , 188-196. https://doi.org/10.1016/j.jtbi.2010.12.037
3906. A.N. Gorban. Kinetic path summation, multi-sheeted extension of master equation, and evaluation of ergodicity coefficient. Physica A: Statistical Mechanics and its Applications 2011, 390 (6) , 1009-1025. https://doi.org/10.1016/j.physa.2010.11.030
3907. S. A. Isaacson, D. M. McQueen, Charles S. Peskin. The influence of volume exclusion by chromatin on the time required to find specific DNA binding sites by diffusion. Proceedings of the National Academy of Sciences 2011, 108 (9) , 3815-3820. https://doi.org/10.1073/pnas.1018821108
3908. Anna Melbinger, Tobias Reichenbach, Thomas Franosch, Erwin Frey. Driven transport on parallel lanes with particle exclusion and obstruction. Physical Review E 2011, 83 (3) https://doi.org/10.1103/PhysRevE.83.031923
3909. Fernando Peruani, Tobias Klauss, Andreas Deutsch, Anja Voss-Boehme. Traffic Jams, Gliders, and Bands in the Quest for Collective Motion of Self-Propelled Particles. Physical Review Letters 2011, 106 (12) https://doi.org/10.1103/PhysRevLett.106.128101
3910. Zhang Kuan, Qin Rui-bin, Zheng Hao-ran, Niu Jun-qing. An Agent-based Modeling Approach for Stochastic Molecular Events of Biochemical Networks. 2011,,, 759-763. https://doi.org/10.1109/ICICTA.2011.197
3911. A Sabnis, R W Harrison. A Continuous-Time, Discrete-State Method for Simulating the Dynamics of Biochemical Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, 8 (2) , 335-341. https://doi.org/10.1109/TCBB.2010.97
3912. P. Lecca, O. Kahramanogullari, D. Morpurgo, C. Priami, Ross A. Soo. Modelling and Estimating Dynamics of Tumor Shrinkage with BlenX and Kinfer. 2011,,, 75-80. https://doi.org/10.1109/UKSIM.2011.24
3913. C. C. Drovandi, A. N. Pettitt. Estimation of Parameters for Macroparasite Population Evolution Using Approximate Bayesian Computation. Biometrics 2011, 67 (1) , 225-233. https://doi.org/10.1111/j.1541-0420.2010.01410.x
3914. V. P. Zhdanov. Are the complex distributed genetic networks inherently oscillatory and chaotic?. JETP Letters 2011, 93 (1) , 41-45. https://doi.org/10.1134/S0021364011010097
3915. O. V. Belov. Modeling base excision repair in Escherichia coli bacterial cells. Physics of Particles and Nuclei Letters 2011, 8 (2) , 141-148. https://doi.org/10.1134/S1547477111020038
3916. JUAN G. DIAZ OCHOA. INFECTION SPREAD AND VIRUS RELEASE IN VITRO IN CELL POPULATIONS AS A SYSTEM WITH PERCOLATION. International Journal of Modern Physics C 2011, 22 (03) , 249-262. https://doi.org/10.1142/S0129183111016191
3917. Christian A. Yates, Kevin Burrage. Look before you leap: A confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping. The Journal of Chemical Physics 2011, 134 (8) , 084109. https://doi.org/10.1063/1.3554385
3918. Matthew J. Riese, Jashanpreet Grewal, Jayajit Das, Tao Zou, Vineet Patil, Arup K. Chakraborty, Gary A. Koretzky. Decreased Diacylglycerol Metabolism Enhances ERK Activation and Augments CD8 + T Cell Functional Responses. Journal of Biological Chemistry 2011, 286 (7) , 5254-5265. https://doi.org/10.1074/jbc.M110.171884
3919. Gerardo Odriozola, Ludovic Berthier. Equilibrium equation of state of a hard sphere binary mixture at very large densities using replica exchange Monte Carlo simulations. The Journal of Chemical Physics 2011, 134 (5) , 054504. https://doi.org/10.1063/1.3541248
3920. Yang Pu, Layne T. Watson, Yang Cao. Stiffness detection and reduction in discrete stochastic simulation of biochemical systems. The Journal of Chemical Physics 2011, 134 (5) , 054105. https://doi.org/10.1063/1.3548838
3921. Guillermo Rodrigo, Javier Carrera, Alfonso Jaramillo, Santiago F. Elena. Optimal viral strategies for bypassing RNA silencing. Journal of The Royal Society Interface 2011, 8 (55) , 257-268. https://doi.org/10.1098/rsif.2010.0264
3922. Clive G. Bowsher. Information processing by biochemical networks: a dynamic approach. Journal of The Royal Society Interface 2011, 8 (55) , 186-200. https://doi.org/10.1098/rsif.2010.0287
3923. John E. Pearson, Paul Krapivsky, Alan S. Perelson, . Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions. PLoS Computational Biology 2011, 7 (2) , e1001058. https://doi.org/10.1371/journal.pcbi.1001058
3924. Jennifer Lindquist, Junling Ma, P. van den Driessche, Frederick H. Willeboordse. Effective degree network disease models. Journal of Mathematical Biology 2011, 62 (2) , 143-164. https://doi.org/10.1007/s00285-010-0331-2
3925. Vassilios Sotiropoulos, Yiannis N. Kaznessis. Analytical derivation of moment equations in stochastic chemical kinetics. Chemical Engineering Science 2011, 66 (3) , 268-277. https://doi.org/10.1016/j.ces.2010.10.024
3926. Carme Àlvarez, Ioannis Chatzigiannakis, Amalia Duch, Joaquim Gabarró, Othon Michail, Maria Serna, Paul G. Spirakis. Computational models for networks of tiny artifacts: A survey. Computer Science Review 2011, 5 (1) , 7-25. https://doi.org/10.1016/j.cosrev.2010.09.001
3927. Thomas Adams, Graeme Ackland, Glenn Marion, Colin Edwards. Understanding plantation transformation using a size-structured spatial population model. Forest Ecology and Management 2011, 261 (3) , 799-809. https://doi.org/10.1016/j.foreco.2010.10.036
3928. Yue Hao, Liufang Xu, Hualin Shi. Theoretical Analysis of Catalytic-sRNA-Mediated Gene Silencing. Journal of Molecular Biology 2011, 406 (1) , 195-204. https://doi.org/10.1016/j.jmb.2010.12.008
3929. Carel Pretorius, Peter Dodd, Robin Wood. An investigation into the statistical properties of TB episodes in a South African community with high HIV prevalence. Journal of Theoretical Biology 2011, 270 (1) , 154-163. https://doi.org/10.1016/j.jtbi.2010.10.012
3930. Bo Liu, Shiwei Yan, Qi Wang, Shengjun Liu. Oscillatory expression and variability in p53 regulatory network. Physica D: Nonlinear Phenomena 2011, 240 (3) , 259-264. https://doi.org/10.1016/j.physd.2010.09.004
3931. Berend Snijder, Lucas Pelkmans. Origins of regulated cell-to-cell variability. Nature Reviews Molecular Cell Biology 2011, 12 (2) , 119-125. https://doi.org/10.1038/nrm3044
3932. Ben Harland, Sam Walcott, Sean X Sun. Adhesion dynamics and durotaxis in migrating cells. Physical Biology 2011, 8 (1) , 015011. https://doi.org/10.1088/1478-3975/8/1/015011
3933. Alberto Corradin, Barbara Di Camillo, Vincenzo Ciminale, Gianna Toffolo, Claudio Cobelli. Sensitivity Analysis of Retrovirus HTLV-1 Transactivation. Journal of Computational Biology 2011, 18 (2) , 183-193. https://doi.org/10.1089/cmb.2010.0219
3934. Matthew J. Simpson, Ruth E. Baker, Scott W. McCue. Models of collective cell spreading with variable cell aspect ratio: A motivation for degenerate diffusion models. Physical Review E 2011, 83 (2) https://doi.org/10.1103/PhysRevE.83.021901
3935. Gerardo Aquino, Diana Clausznitzer, Sylvain Tollis, Robert G. Endres. Optimal receptor-cluster size determined by intrinsic and extrinsic noise. Physical Review E 2011, 83 (2) https://doi.org/10.1103/PhysRevE.83.021914
3936. Hauke Hinsch, Louis Reese, Erwin Frey. Hinsch, Reese, and Frey Reply:. Physical Review Letters 2011, 106 (7) https://doi.org/10.1103/PhysRevLett.106.079602
3937. Marco Aldinucci, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Massimo Torquati, Angelo Troina. On Designing Multicore-Aware Simulators for Biological Systems. 2011,,, 318-325. https://doi.org/10.1109/PDP.2011.81
3938. Abhyudai Singh, João P. Hespanha. Approximate Moment Dynamics for Chemically Reacting Systems. IEEE Transactions on Automatic Control 2011, 56 (2) , 414-418. https://doi.org/10.1109/TAC.2010.2088631
3939. Supravat Dey, Dibyendu Das, R. Rajesh. Lattice models for ballistic aggregation in one dimension. EPL (Europhysics Letters) 2011, 93 (4) , 44001. https://doi.org/10.1209/0295-5075/93/44001
3940. Di Liu. Stochastic Simulation of the Cell Cycle Model for Budding Yeast. Communications in Computational Physics 2011, 9 (2) , 390-405. https://doi.org/10.4208/cicp.311009.100310a
3941. Bernie J. Daigle, Min K. Roh, Dan T. Gillespie, Linda R. Petzold. Automated estimation of rare event probabilities in biochemical systems. The Journal of Chemical Physics 2011, 134 (4) , 044110. https://doi.org/10.1063/1.3522769
3942. Yushu Yang, Muruhan Rathinam, Jinglai Shen. Integral tau methods for stiff stochastic chemical systems. The Journal of Chemical Physics 2011, 134 (4) , 044129. https://doi.org/10.1063/1.3532768
3943. A Proeme, R A Blythe, M R Evans. Dynamical transition in the open-boundary totally asymmetric exclusion process. Journal of Physics A: Mathematical and Theoretical 2011, 44 (3) , 035003. https://doi.org/10.1088/1751-8113/44/3/035003
3944. Ryszard Szymanski. On the Incorrectness of the Factor 2 in the Radical Termination Equation. Macromolecular Theory and Simulations 2011, 20 (1) , 8-12. https://doi.org/10.1002/mats.201000048
3945. Matthias Vigelius, Aidan Lane, Bernd Meyer. Accelerating reaction–diffusion simulations with general-purpose graphics processing units. Bioinformatics 2011, 27 (2) , 288-290. https://doi.org/10.1093/bioinformatics/btq622
3946. A. Mugler, B. Grinshpun, R. Franks, C. H. Wiggins. Statistical method for revealing form-function relations in biological networks. Proceedings of the National Academy of Sciences 2011, 108 (2) , 446-451. https://doi.org/10.1073/pnas.1008898108
3947. Uwe Jandt, An-Ping Zeng. Modeling of Intracellular Transport and Compartmentation. 2011,,, 221-249. https://doi.org/10.1007/10_2011_104
3948. David F. Anderson, Thomas G. Kurtz. Continuous Time Markov Chain Models for Chemical Reaction Networks. 2011,,, 3-42. https://doi.org/10.1007/978-1-4419-6766-4_1
3949. Kevin Burrage, Pamela M. Burrage, André Leier, Tatiana Marquez-Lago, Dan V. Nicolau. Stochastic Simulation for Spatial Modelling of Dynamic Processes in a Living Cell. 2011,,, 43-62. https://doi.org/10.1007/978-1-4419-6766-4_2
3950. Kyung Hyuk Kim, Deepak Chandran, Herbert M. Sauro. Toward Modularity in Synthetic Biology: Design Patterns and Fan-out. 2011,,, 117-138. https://doi.org/10.1007/978-1-4419-6766-4_6
3951. Ettore Mosca, Luciano Milanesi. Modeling Biochemical Pathways. 2011,,, 111-126. https://doi.org/10.1007/978-1-4419-6800-5_6
3952. Kepa Ruiz-Mirazo, Gabriel Piedrafita, Fulvio Ciriaco, Fabio Mavelli. Stochastic Simulations of Mixed-Lipid Compartments: From Self-Assembling Vesicles to Self-Producing Protocells. 2011,,, 689-696. https://doi.org/10.1007/978-1-4419-7046-6_70
3953. Shev MacNamara, Kevin Burrage. Stochastic Modelling of T Cell Homeostasis for Two Competing Clonotypes Via the Master Equation. 2011,,, 207-225. https://doi.org/10.1007/978-1-4419-7725-0_10
3954. Carmen Molina-París, Grant Lythe, Emily Stirk. Multivariate Competition Processes: A Model for Two Competing T Cell Clonotypes. 2011,,, 187-205. https://doi.org/10.1007/978-1-4419-7725-0_9
3955. Antoine Spicher, Olivier Michel, Jean-Louis Giavitto. Interaction-Based Simulations for Integrative Spatial Systems Biology. 2011,,, 195-231. https://doi.org/10.1007/978-1-4419-7964-3_10
3956. Thomas Millat, Olaf Wolkenhauer, Ralf-Jörg Fischer, Hubert Bahl. Modeling of Cellular Processes: Methods, Data, and Requirements. 2011,,, 429-447. https://doi.org/10.1007/978-1-60761-987-1_27
3957. Xiu-Deng Zheng, Yi Tao. Stochastic Analysis of Gene Expression. 2011,,, 123-151. https://doi.org/10.1007/978-1-61779-086-7_7
3958. Edda Klipp. Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade. 2011,,, 323-343. https://doi.org/10.1007/978-1-61779-173-4_19
3959. Axel Kowald, Christoph Wierling. Standards, Tools, and Databases for the Analysis of Yeast ‘Omics Data. 2011,,, 345-365. https://doi.org/10.1007/978-1-61779-173-4_20
3960. Ivan Mura. Stochastic Modeling. 2011,,, 121-151. https://doi.org/10.1007/978-1-84996-474-6_7
3961. Jean-Louis Giavitto, Antoine Spicher. Computer Morphogenesis. 2011,,, 315-339. https://doi.org/10.1007/978-3-642-13174-5_18
3962. Paul G. Spirakis. Population Protocols and Related Models. 2011,,, 109-159. https://doi.org/10.1007/978-3-642-14849-1_5
3963. Matteo Casadei, Marco Mamei, Cynthia Villalba, Mirko Viroli, Franco Zambonelli. Middleware Infrastructures for Self-organising Pervasive Computing Systems. 2011,,, 313-344. https://doi.org/10.1007/978-3-642-17348-6_13
3964. Peter Schuster. Physical Principles of Evolution. 2011,,, 45-79. https://doi.org/10.1007/978-3-642-18137-5_2
3965. Michael T. Tolley, Jonathan D. Hiller, Hod Lipson. Evolutionary Design and Assembly Planning for Stochastic Modular Robots. 2011,,, 211-225. https://doi.org/10.1007/978-3-642-18272-3_14
3966. Daniel A. Charlebois, Theodore J. Perkins, Mads Kaern. Stochastic Gene Expression and the Processing and Propagation of Noisy Signals in Genetic Networks. 2011,,, 89-112. https://doi.org/10.1007/978-3-642-19621-8_5
3967. Andre S. Ribeiro, Jason Lloyd-Price. Information Propagation in the Long-Term Behavior of Gene Regulatory Networks. 2011,,, 195-217. https://doi.org/10.1007/978-3-642-19621-8_9
3968. Antti Häkkinen, Fred G. Biddle, Olli-Pekka Smolander, Olli Yli-Harja, Andre S. Ribeiro. Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. 2011,,, 1-12. https://doi.org/10.1007/978-3-642-19748-2_1
3969. Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo. Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach. 2011,,, 61-84. https://doi.org/10.1007/978-3-642-19748-2_4
3970. Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Elena Grassi, Mike Guether, Angelo Troina. Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis. 2011,,, 85-109. https://doi.org/10.1007/978-3-642-19748-2_5
3971. Loïc Paulevé, Morgan Magnin, Olivier Roux. Refining Dynamics of Gene Regulatory Networks in a Stochastic π-Calculus Framework. 2011,,, 171-191. https://doi.org/10.1007/978-3-642-19748-2_8
3972. Mieke Massink, Diego Latella, Andrea Bracciali, Jane Hillston. Modelling Non-linear Crowd Dynamics in Bio-PEPA. 2011,,, 96-110. https://doi.org/10.1007/978-3-642-19811-3_8
3973. Allan Clark, Stephen Gilmore. Evaluating Service Level Agreements Using Observational Probes. 2011,,, 467-485. https://doi.org/10.1007/978-3-642-20401-2_22
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4202. Marko Marhl, Marko Gosak, Matjaž Perc, Etienne Roux. Importance of cell variability for calcium signaling in rat airway myocytes. Biophysical Chemistry 2010, 148 (1-3) , 42-50. https://doi.org/10.1016/j.bpc.2010.02.006
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4212. Natsuki Tanaka, Garegin A. Papoian. Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations. Journal of Theoretical Biology 2010, 264 (2) , 490-500. https://doi.org/10.1016/j.jtbi.2010.02.022
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4220. Quan-Xing Liu, Rong-Hua Wang, Zhen Jin, Johan van de Koppel, David Alonso. Spatial self-organization in a multi-strain host–pathogen system. Journal of Statistical Mechanics: Theory and Experiment 2010, 2010 (05) , P05017. https://doi.org/10.1088/1742-5468/2010/05/P05017
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4228. William C Eva, Grégory Mermoud, Alcherio Martinoli. Comparing and modeling distributed control strategies for miniature self-assembling robots. 2010,,, 1438-1445. https://doi.org/10.1109/ROBOT.2010.5509666
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4230. Hong Li, Linda Petzold. Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit. The International Journal of High Performance Computing Applications 2010, 24 (2) , 107-116. https://doi.org/10.1177/1094342009106066
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4232. John Wambaugh, Imran Shah, . Simulating Microdosimetry in a Virtual Hepatic Lobule. PLoS Computational Biology 2010, 6 (4) , e1000756. https://doi.org/10.1371/journal.pcbi.1000756
4233. Ming-Chang Huang, Jinn-Wen Wu, Yu-Pin Luo, Karen G. Petrosyan. Fluctuations in gene regulatory networks as Gaussian colored noise. The Journal of Chemical Physics 2010, 132 (15) , 155101. https://doi.org/10.1063/1.3385468
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4237. Ruth E. Baker, Christian A. Yates, Radek Erban. From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains. Bulletin of Mathematical Biology 2010, 72 (3) , 719-762. https://doi.org/10.1007/s11538-009-9467-x
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4239. Longhua Hu, Garegin A. Papoian. Mechano-Chemical Feedbacks Regulate Actin Mesh Growth in Lamellipodial Protrusions. Biophysical Journal 2010, 98 (8) , 1375-1384. https://doi.org/10.1016/j.bpj.2009.11.054
4240. Pavel I. Zhuravlev, Bryan S. Der, Garegin A. Papoian. Design of Active Transport Must Be Highly Intricate: A Possible Role of Myosin and Ena/VASP for G-Actin Transport in Filopodia. Biophysical Journal 2010, 98 (8) , 1439-1448. https://doi.org/10.1016/j.bpj.2009.12.4325
4241. Areli Hernández-Valdez, Moisés Santillán, Eduardo S. Zeron. Cycling expression and cooperative operator interaction in the trp operon of Escherichia coli. Journal of Theoretical Biology 2010, 263 (3) , 340-352. https://doi.org/10.1016/j.jtbi.2009.12.005
4242. Darren M. Green. A strategic model for epidemic control in aquaculture. Preventive Veterinary Medicine 2010, 94 (1-2) , 119-127. https://doi.org/10.1016/j.prevetmed.2009.12.004
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4244. Paolo Ballarini, Maria Luisa Guerriero. Query-based verification of qualitative trends and oscillations in biochemical systems. Theoretical Computer Science 2010, 411 (20) , 2019-2036. https://doi.org/10.1016/j.tcs.2010.02.010
4245. Ramiz Daniel, Ronen Almog, Yosi Shacham-Diamand. Stochastic signaling in biochemical cascades and genetic systems in genetically engineered living cells. Physical Review E 2010, 81 (4) https://doi.org/10.1103/PhysRevE.81.041903
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4247. Andre S. Ribeiro, Jason Lloyd-Price, Brenda A. Eales, Fred G. Biddle. Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse. Adaptive Behavior 2010, 18 (2) , 116-131. https://doi.org/10.1177/1059712309339859
4248. Luis Mier-y-Terán-Romero, Mary Silber, Vassily Hatzimanikatis, . The Origins of Time-Delay in Template Biopolymerization Processes. PLoS Computational Biology 2010, 6 (4) , e1000726. https://doi.org/10.1371/journal.pcbi.1000726
4249. Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov, . Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction. PLoS Computational Biology 2010, 6 (3) , e1000723. https://doi.org/10.1371/journal.pcbi.1000723
4250. D. Soloveichik, G. Seelig, E. Winfree. DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences 2010, 107 (12) , 5393-5398. https://doi.org/10.1073/pnas.0909380107
4251. Tiina Rajala, Antti Häkkinen, Shannon Healy, Olli Yli-Harja, Andre S. Ribeiro, . Effects of Transcriptional Pausing on Gene Expression Dynamics. PLoS Computational Biology 2010, 6 (3) , e1000704. https://doi.org/10.1371/journal.pcbi.1000704
4252. Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin, . Detailed Simulations of Cell Biology with Smoldyn 2.1. PLoS Computational Biology 2010, 6 (3) , e1000705. https://doi.org/10.1371/journal.pcbi.1000705
4253. V. Garcia-Morales, K. Krischer. Fluctuation enhanced electrochemical reaction rates at the nanoscale. Proceedings of the National Academy of Sciences 2010, 107 (10) , 4528-4532. https://doi.org/10.1073/pnas.0909240107
4254. Krishna A. Iyengar, Leonard A. Harris, Paulette Clancy. Accurate implementation of leaping in space: The spatial partitioned-leaping algorithm. The Journal of Chemical Physics 2010, 132 (9) , 094101. https://doi.org/10.1063/1.3310808
4255. Zheng-Hong Luo, De-Pan Shi, Yong Zhu. Multiple active site Monte Carlo model for heterogeneous Ziegler-Natta propylene polymerization. Journal of Applied Polymer Science 2010, 115 (5) , 2962-2970. https://doi.org/10.1002/app.31388
4256. Jacob J. Hughey, Timothy K. Lee, Markus W. Covert. Computational modeling of mammalian signaling networks. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2010, 2 (2) , 194-209. https://doi.org/10.1002/wsbm.52
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4258. Satya Nanda Vel Arjunan, Masaru Tomita. A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Systems and Synthetic Biology 2010, 4 (1) , 35-53. https://doi.org/10.1007/s11693-009-9047-2
4259. Ben Adams, Michael Boots. How important is vertical transmission in mosquitoes for the persistence of dengue? Insights from a mathematical model. Epidemics 2010, 2 (1) , 1-10. https://doi.org/10.1016/j.epidem.2010.01.001
4260. Baris Atakan, Ozgur B. Akan. Deterministic capacity of information flow in molecular nanonetworks. Nano Communication Networks 2010, 1 (1) , 31-42. https://doi.org/10.1016/j.nancom.2010.03.003
4261. M. Pineda, R. Imbihl, L. Schimansky-Geier. Effects of surface size on minimalistic stochastic models for the catalytic CO oxidation. Physica A: Statistical Mechanics and its Applications 2010, 389 (6) , 1178-1188. https://doi.org/10.1016/j.physa.2009.11.024
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4263. Laura Muñoz-Salazar, Gerardo Odriozola. Phase behaviour and separation kinetics of symmetric non-additive hard discs. Molecular Simulation 2010, 36 (3) , 175-185. https://doi.org/10.1080/08927020903141027
4264. Li-ping Xiong, Yu-qiang Ma, Lei-han Tang. Attenuation of transcriptional bursting in mRNA transport. Physical Biology 2010, 7 (1) , 016005. https://doi.org/10.1088/1478-3975/7/1/016005
4265. Fabio Mavelli, Pasquale Stano. Kinetic models for autopoietic chemical systems: the role of fluctuations in a homeostatic regime. Physical Biology 2010, 7 (1) , 016010. https://doi.org/10.1088/1478-3975/7/1/016010
4266. María Rodríguez Martínez, Jordi Soriano, Tsvi Tlusty, Yitzhak Pilpel, Itay Furman. Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop. Physical Review E 2010, 81 (3) https://doi.org/10.1103/PhysRevE.81.031924
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4269. D. A. Henderson, R. J. Boys, D. J. Wilkinson. Bayesian Calibration of a Stochastic Kinetic Computer Model Using Multiple Data Sources. Biometrics 2010, 66 (1) , 249-256. https://doi.org/10.1111/j.1541-0420.2009.01245.x
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4271. Arup K. Chakraborty, Andrej Košmrlj. Statistical Mechanical Concepts in Immunology. Annual Review of Physical Chemistry 2010, 61 (1) , 283-303. https://doi.org/10.1146/annurev.physchem.59.032607.093537
4272. Murat Cirit, Matej Krajcovic, Colin K. Choi, Erik S. Welf, Alan F. Horwitz, Jason M. Haugh, . Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells. PLoS Computational Biology 2010, 6 (2) , e1000688. https://doi.org/10.1371/journal.pcbi.1000688
4273. Ozgur E. Akman, Maria Luisa Guerriero, Laurence Loewe, Carl Troein. Complementary approaches to understanding the plant circadian clock. Electronic Proceedings in Theoretical Computer Science 2010, 19 , 1-19. https://doi.org/10.4204/EPTCS.19.1
4274. Brian Drawert, Michael J. Lawson, Linda Petzold, Mustafa Khammash. The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. The Journal of Chemical Physics 2010, 132 (7) , 074101. https://doi.org/10.1063/1.3310809
4275. Sashi Marella, Bard Ermentrout, . Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks. PLoS Computational Biology 2010, 6 (2) , e1000679. https://doi.org/10.1371/journal.pcbi.1000679
4276. Daniel Andor-Ardó, A. J. Hudspeth, Marcelo O. Magnasco, Oreste Piro. Modeling the resonant release of synaptic transmitter by hair cells as an example of biological oscillators with cooperative steps. Proceedings of the National Academy of Sciences 2010, 107 (5) , 2019-2024. https://doi.org/10.1073/pnas.0914372107
4277. Chang Hyeong Lee, Roger Lui. A reduction method for multiple time scale stochastic reaction networks with non-unique equilibrium probability. Journal of Mathematical Chemistry 2010, 47 (2) , 750-770. https://doi.org/10.1007/s10910-009-9598-1
4278. TieJun Xiao, ZhongHuai Hou. Fluctuation theorem for entropy production in a chemical reaction channel. Science China Chemistry 2010, 53 (2) , 396-401. https://doi.org/10.1007/s11426-010-0070-7
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4280. Joris Slegers. A Langevin Interpretation of PEPA Models. Electronic Notes in Theoretical Computer Science 2010, 261 , 71-89. https://doi.org/10.1016/j.entcs.2010.01.006
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4283. Nick D.L. Owens, Jon Timmis, Andrew Greensted, Andy Tyrrell. Elucidation of T cell signalling models. Journal of Theoretical Biology 2010, 262 (3) , 452-470. https://doi.org/10.1016/j.jtbi.2009.10.017
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4422. Sebastian J. Schreiber, James O. Lloyd‐Smith. Invasion Dynamics in Spatially Heterogeneous Environments. The American Naturalist 2009, 174 (4) , 490-505. https://doi.org/10.1086/605405
4423. Luo-Luo Jiang, Tao Zhou, Matjaž Perc, Xin Huang, Bing-Hong Wang. Emergence of target waves in paced populations of cyclically competing species. New Journal of Physics 2009, 11 (10) , 103001. https://doi.org/10.1088/1367-2630/11/10/103001
4424. Xin-jun Peng, Yi-fei Wang. Efficient Stochastic Simulation Algorithm for Chemically Reacting Systems Based on Support Vector Regression. Chinese Journal of Chemical Physics 2009, 22 (5) , 502-510. https://doi.org/10.1088/1674-0068/22/05/502-510
4425. Andrew Mugler, Aleksandra M. Walczak, Chris H. Wiggins. Spectral solutions to stochastic models of gene expression with bursts and regulation. Physical Review E 2009, 80 (4) https://doi.org/10.1103/PhysRevE.80.041921
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4427. P.M. Burrage, K. Burrage, K. Kurowski, M. Lorenc, D.V. Nicolau Jr, M. Swain, M.A. Ragan. A Parallel Plasma Membrane Simulation. 2009,,, 105-112. https://doi.org/10.1109/HiBi.2009.18
4428. Ettore Mosca, Paolo Cazzaniga, Ivan Merelli, Dario Pescini, Giancarlo Mauri, Luciano Milanesi. Stochastic Simulations on a Grid Framework for Parameter Sweep Applications in Biological Models. 2009,,, 33-42. https://doi.org/10.1109/HiBi.2009.19
4429. Bing Wang, Yiping Yao, Yuliang Zhao, Bonan Hou, Shaoliang Peng. Experimental Analysis of Optimistic Synchronization Algorithms for Parallel Simulation of Reaction-Diffusion Systems. 2009,,, 91-100. https://doi.org/10.1109/HiBi.2009.22
4430. Jose Juan Tapia, Roshan D'Souza. Data-parallel algorithms for large-scale real-time simulation of the cellular potts model on graphics processing units. 2009,,, 1411-1418. https://doi.org/10.1109/ICSMC.2009.5346282
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4432. Santhosh Palani, Casim A. Sarkar, . Integrating Extrinsic and Intrinsic Cues into a Minimal Model of Lineage Commitment for Hematopoietic Progenitors. PLoS Computational Biology 2009, 5 (9) , e1000518. https://doi.org/10.1371/journal.pcbi.1000518
4433. A. Singer, R. Erban, I. G. Kevrekidis, R. R. Coifman. Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proceedings of the National Academy of Sciences 2009, 106 (38) , 16090-16095. https://doi.org/10.1073/pnas.0905547106
4434. Richard C. van der Wath, Anne Wilson, Elisa Laurenti, Andreas Trumpp, Pietro Liò, . Estimating Dormant and Active Hematopoietic Stem Cell Kinetics through Extensive Modeling of Bromodeoxyuridine Label-Retaining Cell Dynamics. PLoS ONE 2009, 4 (9) , e6972. https://doi.org/10.1371/journal.pone.0006972
4435. Xiaofeng Dai, Olli Yli-Harja, Andre S. Ribeiro. Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources. Bioinformatics 2009, 25 (18) , 2362-2368. https://doi.org/10.1093/bioinformatics/btp411
4436. Hugo F. Hernández, Klaus Tauer. Modeling of Molecular Transfer in Heterophase Polymerization. Macromolecular Reaction Engineering 2009, 3 (7) , 375-397. https://doi.org/10.1002/mren.200900016
4437. C. E. Dangerfield, J. V. Ross, M. J. Keeling. Integrating stochasticity and network structure into an epidemic model. Journal of The Royal Society Interface 2009, 6 (38) , 761-774. https://doi.org/10.1098/rsif.2008.0410
4438. Jianhong Ou, Chikara Furusawa, Tetsuya Yomo, Hiroshi Shimizu. Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system. Biosystems 2009, 97 (3) , 160-164. https://doi.org/10.1016/j.biosystems.2009.06.002
4439. Basil Bayati, Philippe Chatelain, Petros Koumoutsakos. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics 2009, 228 (16) , 5908-5916. https://doi.org/10.1016/j.jcp.2009.05.004
4440. Andre S. Ribeiro, Xiaofeng Dai, Olli Yli-Harja. Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch. Journal of Theoretical Biology 2009, 260 (1) , 66-76. https://doi.org/10.1016/j.jtbi.2009.05.025
4441. Werner Sandmann. Sequential estimation for prescribed statistical accuracy in stochastic simulation of biological systems. Mathematical Biosciences 2009, 221 (1) , 43-53. https://doi.org/10.1016/j.mbs.2009.06.006
4442. Julia Rausenberger, Christian Fleck, Jens Timmer, Markus Kollmann. Signatures of gene expression noise in cellular systems. Progress in Biophysics and Molecular Biology 2009, 100 (1-3) , 57-66. https://doi.org/10.1016/j.pbiomolbio.2009.06.003
4443. Matthew R. Bennett, Jeff Hasty. Microfluidic devices for measuring gene network dynamics in single cells. Nature Reviews Genetics 2009, 10 (9) , 628-638. https://doi.org/10.1038/nrg2625
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4445. Yan Hao, Peter Kemper, Gregory D. Smith. Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation. Chaos: An Interdisciplinary Journal of Nonlinear Science 2009, 19 (3) , 037107. https://doi.org/10.1063/1.3223663
4446. Alexandre Wagemakers, Javier M. Buldú, Miguel A. F. Sanjuán, Oscar de Luis, Adriana Izquierdo, Antonio Coloma. Entraining synthetic genetic oscillators. Chaos: An Interdisciplinary Journal of Nonlinear Science 2009, 19 (3) , 033139. https://doi.org/10.1063/1.3231089
4447. Daniel Hexner, Yariv Kafri. Tug of war in motility assay experiments. Physical Biology 2009, 6 (3) , 036016. https://doi.org/10.1088/1478-3975/6/3/036016
4448. Mary Sehl, Alexander V. Alekseyenko, Kenneth L. Lange. Accurate Stochastic Simulation via the Step Anticipation τ -Leaping (SAL) Algorithm. Journal of Computational Biology 2009, 16 (9) , 1195-1208. https://doi.org/10.1089/cmb.2008.0249
4449. Mieszko Lis, Maxim N. Artyomov, Srinivas Devadas, Arup K. Chakraborty. Efficient stochastic simulation of reaction–diffusion processes via direct compilation. Bioinformatics 2009, 25 (17) , 2289-2291. https://doi.org/10.1093/bioinformatics/btp387
4450. Patrick B. Warren. Cells, cancer, and rare events: Homeostatic metastability in stochastic nonlinear dynamical models of skin cell proliferation. Physical Review E 2009, 80 (3) https://doi.org/10.1103/PhysRevE.80.030903
4451. Baruch Barzel, Ofer Biham. Stochastic analysis of dimerization systems. Physical Review E 2009, 80 (3) https://doi.org/10.1103/PhysRevE.80.031117
4452. Matthew Scott. Long delay times in reaction rates increase intrinsic fluctuations. Physical Review E 2009, 80 (3) https://doi.org/10.1103/PhysRevE.80.031129
4453. A. Veglio, A. Gamba, M. Nicodemi, F. Bussolino, G. Serini. Symmetry breaking mechanism for epithelial cell polarization. Physical Review E 2009, 80 (3) https://doi.org/10.1103/PhysRevE.80.031919
4454. Richard S. Graham, Peter D. Olmsted. Coarse-Grained Simulations of Flow-Induced Nucleation in Semicrystalline Polymers. Physical Review Letters 2009, 103 (11) https://doi.org/10.1103/PhysRevLett.103.115702
4455. Y.N. Kaznessis. Multiscale models for synthetic biology. 2009,,, 6408-6411. https://doi.org/10.1109/IEMBS.2009.5333516
4456. Zhen Liu, Yang Cao. Stochastic simulation methods for biochemical models with multi-state species. 2009,,, 363-368. https://doi.org/10.1109/TIC-STH.2009.5444473
4457. P.A. Varadarajan, D. Del Vecchio. Design and Characterization of a Three-terminal Transcriptional Device Through Polymerase Per Second. IEEE Transactions on NanoBioscience 2009, 8 (3) , 281-289. https://doi.org/10.1109/TNB.2009.2028687
4458. AIMIN CHEN, JIAJUN ZHANG, ZHANJIANG YUAN, TIANSHOU ZHOU. NON-PROPAGATION OF NOISE IN INTRACELLULAR METABOLIC POOLS. Journal of Biological Systems 2009, 17 (03) , 511-527. https://doi.org/10.1142/S0218339009002909
4459. ROBERTO BARBUTI, ANDREA MAGGIOLO-SCHETTINI, PAOLO MILAZZO, ANGELO TROINA. A METHODOLOGY FOR THE STOCHASTIC MODELING AND SIMULATION OF SYMPATRIC SPECIATION BY SEXUAL SELECTION. Journal of Biological Systems 2009, 17 (03) , 349-376. https://doi.org/10.1142/S0218339009002922
4460. Fayette W. Shaw, Eric Klavins. Distributed Estimation and State Assignment for Stochastically Interacting Robots*. IFAC Proceedings Volumes 2009, 42 (20) , 276-281. https://doi.org/10.3182/20090924-3-IT-4005.00047
4461. Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho, Masaki Sasai, . Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo. PLoS Computational Biology 2009, 5 (8) , e1000486. https://doi.org/10.1371/journal.pcbi.1000486
4462. Ben Adams, Durrell D. Kapan, . Man Bites Mosquito: Understanding the Contribution of Human Movement to Vector-Borne Disease Dynamics. PLoS ONE 2009, 4 (8) , e6763. https://doi.org/10.1371/journal.pone.0006763
4463. Mamdouh A. Al-Harthi, Jabarullah K. Masihullah, Sarfraz H. Abbasi, João B. P. Soares. Dynamic Monte Carlo Simulation of ATRP in a Batch Reactor. Macromolecular Theory and Simulations 2009, 18 (6) , 307-316. https://doi.org/10.1002/mats.200900001
4464. Pinaki Chaudhury, Ralf Metzler, Suman K Banik. Finding the optimum activation energy in DNA breathing dynamics: a simulated annealing approach. Journal of Physics A: Mathematical and Theoretical 2009, 42 (33) , 335101. https://doi.org/10.1088/1751-8113/42/33/335101
4465. Thomas Fournier, Jean-Pierre Gabriel, Christian Mazza, Jerôme Pasquier, José Galbete, Nicolas Mermod. Stochastic Models and Numerical Algorithms for a Class of Regulatory Gene Networks. Bulletin of Mathematical Biology 2009, 71 (6) , 1394-1431. https://doi.org/10.1007/s11538-009-9407-9
4466. E.W. Tollner, J.R. Schramski, C. Kazanci, B.C. Patten. Implications of network particle tracking (NPT) for ecological model interpretation. Ecological Modelling 2009, 220 (16) , 1904-1912. https://doi.org/10.1016/j.ecolmodel.2009.04.018
4467. Vincent Danos. Agile Modelling of Cellular Signalling (Invited Paper). Electronic Notes in Theoretical Computer Science 2009, 229 (4) , 3-10. https://doi.org/10.1016/j.entcs.2009.07.070
4468. Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo. An intermediate language for the stochastic simulation of biological systems. Theoretical Computer Science 2009, 410 (33-34) , 3085-3109. https://doi.org/10.1016/j.tcs.2008.09.032
4469. J. Barnat, L. Brim, I. Černá, S. Dražan, J. Fabriková, D. Šafránek. On algorithmic analysis of transcriptional regulation by LTL model checking. Theoretical Computer Science 2009, 410 (33-34) , 3128-3148. https://doi.org/10.1016/j.tcs.2009.02.017
4470. Federica Ciocchetta, Jane Hillston. Bio-PEPA: A framework for the modelling and analysis of biological systems. Theoretical Computer Science 2009, 410 (33-34) , 3065-3084. https://doi.org/10.1016/j.tcs.2009.02.037
4471. Cristian Versari, Nadia Busi. Stochastic biological modelling in the presence of multiple compartments. Theoretical Computer Science 2009, 410 (33-34) , 3039-3064. https://doi.org/10.1016/j.tcs.2009.03.038
4472. Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips. A process model of Rho GTP-binding proteins. Theoretical Computer Science 2009, 410 (33-34) , 3166-3185. https://doi.org/10.1016/j.tcs.2009.04.029
4473. Richard Svanbäck, Mario Pineda‐Krch, Michael Doebeli. Fluctuating Population Dynamics Promotes the Evolution of Phenotypic Plasticity. The American Naturalist 2009, 174 (2) , 176-189. https://doi.org/10.1086/600112
4474. Pierre Gaspard, Thomas Gilbert. Heat transport in stochastic energy exchange models of locally confined hard spheres. Journal of Statistical Mechanics: Theory and Experiment 2009, 2009 (08) , P08020. https://doi.org/10.1088/1742-5468/2009/08/P08020
4475. W. Fletcher, Z. Yang. INDELible: A Flexible Simulator of Biological Sequence Evolution. Molecular Biology and Evolution 2009, 26 (8) , 1879-1888. https://doi.org/10.1093/molbev/msp098
4476. Matthew Parker, Alex Kamenev. Extinction in the Lotka-Volterra model. Physical Review E 2009, 80 (2) https://doi.org/10.1103/PhysRevE.80.021129
4477. Tobias Galla. Intrinsic fluctuations in stochastic delay systems: Theoretical description and application to a simple model of gene regulation. Physical Review E 2009, 80 (2) https://doi.org/10.1103/PhysRevE.80.021909
4478. C. Metzner, M. Sajitz-Hermstein, M. Schmidberger, B. Fabry. Noise and critical phenomena in biochemical signaling cycles at small molecule numbers. Physical Review E 2009, 80 (2) https://doi.org/10.1103/PhysRevE.80.021915
4479. Adiel Loinger, Ofer Biham. Analysis of Genetic Toggle Switch Systems Encoded on Plasmids. Physical Review Letters 2009, 103 (6) https://doi.org/10.1103/PhysRevLett.103.068104
4480. C. Turner, A. R. Stinchcombe, M. Kohandel, S. Singh, S. Sivaloganathan. Characterization of brain cancer stem cells: a mathematical approach. Cell Proliferation 2009, 42 (4) , 529-540. https://doi.org/10.1111/j.1365-2184.2009.00619.x
4481. Alexandre Roger Raymond Péry, Frederic Yves Bois. Stochasticity in Physiologically Based Kinetics Models: Implications for Cancer Risk Assessment. Risk Analysis 2009, 29 (8) , 1182-1191. https://doi.org/10.1111/j.1539-6924.2009.01242.x
4482. Markus Basan, Thomas Risler, Jean‐François Joanny, Xavier Sastre‐Garau, Jacques Prost. Homeostatic competition drives tumor growth and metastasis nucleation. HFSP Journal 2009, 3 (4) , 265-272. https://doi.org/10.2976/1.3086732
4483. John Jack, Andrei Păun. The Nondeterministic Waiting Time Algorithm: A Review. Electronic Proceedings in Theoretical Computer Science 2009, 3 , 29-46. https://doi.org/10.4204/EPTCS.3.3
4484. Sheng Li, Joseph N. S. Eisenberg, Ian H. Spicknall, James S. Koopman. Dynamics and Control of Infections Transmitted From Person to Person Through the Environment. American Journal of Epidemiology 2009, 170 (2) , 257-265. https://doi.org/10.1093/aje/kwp116
4485. Pavel I. Zhuravlev, Garegin A. Papoian. Molecular noise of capping protein binding induces macroscopic instability in filopodial dynamics. Proceedings of the National Academy of Sciences 2009, 106 (28) , 11570-11575. https://doi.org/10.1073/pnas.0812746106
4486. Tibor Kalmar, Chea Lim, Penelope Hayward, Silvia Muñoz-Descalzo, Jennifer Nichols, Jordi Garcia-Ojalvo, Alfonso Martinez Arias, . Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells. PLoS Biology 2009, 7 (7) , e1000149. https://doi.org/10.1371/journal.pbio.1000149
4487. Shev MacNamara, Kevin Burrage. Krylov and steady-state techniques for the solution of the chemical master equation for the mitogen-activated protein kinase cascade. Numerical Algorithms 2009, 51 (3) , 281-307. https://doi.org/10.1007/s11075-008-9239-y
4488. YanHang Xie, YuBing Gong, Bo Xu, FuWen Sun. Colored noise-enhanced intrinsic stochastic oscillations in CO oxidation on nanometer-sized Pd particles. Science in China Series B: Chemistry 2009, 52 (7) , 887-892. https://doi.org/10.1007/s11426-009-0057-4
4489. Alessandro Abate, Ashish Tiwari, Shankar Sastry. Box invariance in biologically-inspired dynamical systems. Automatica 2009, 45 (7) , 1601-1610. https://doi.org/10.1016/j.automatica.2009.02.028
4490. Ya Jia, Wangheng Liu, Anbang Li, Lijian Yang, Xuan Zhan. Intrinsic noise in post-transcriptional gene regulation by small non-coding RNA. Biophysical Chemistry 2009, 143 (1-2) , 60-69. https://doi.org/10.1016/j.bpc.2009.04.001
4491. Antonella Lunelli, Andrea Pugliese, Caterina Rizzo. Epidemic patch models applied to pandemic influenza: Contact matrix, stochasticity, robustness of predictions. Mathematical Biosciences 2009, 220 (1) , 24-33. https://doi.org/10.1016/j.mbs.2009.03.008
4492. Quan-Xing Liu, Rong-Hua Wang, Zhen Jin. Persistence, extinction and spatio-temporal synchronization of SIRS spatial models. Journal of Statistical Mechanics: Theory and Experiment 2009, 2009 (07) , P07007. https://doi.org/10.1088/1742-5468/2009/07/P07007
4493. Xiaodong Cai, Zhi-Min Yuan. Stochastic Modeling and Simulation of the p53-MDM2/MDMX Loop. Journal of Computational Biology 2009, 16 (7) , 917-933. https://doi.org/10.1089/cmb.2008.0231
4494. Jun Tang, Xianqing Yang, Jun Ma, Ya Jia. Noise effect on persistence of memory in a positive-feedback gene regulatory circuit. Physical Review E 2009, 80 (1) https://doi.org/10.1103/PhysRevE.80.011907
4495. Jun Ohkubo. Variational principle of counting statistics in master equations. Physical Review E 2009, 80 (1) https://doi.org/10.1103/PhysRevE.80.012101
4496. Xiaohua Cui, Robert J. Rovetti, Ling Yang, Alan Garfinkel, James N. Weiss, Zhilin Qu. Period-Doubling Bifurcation in an Array of Coupled Stochastically Excitable Elements Subjected to Global Periodic Forcing. Physical Review Letters 2009, 103 (4) https://doi.org/10.1103/PhysRevLett.103.044102
4497. Xin Li, Jan Kierfeld, Reinhard Lipowsky. Actin Polymerization and Depolymerization Coupled to Cooperative Hydrolysis. Physical Review Letters 2009, 103 (4) https://doi.org/10.1103/PhysRevLett.103.048102
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4499. V. Sotiropoulos, M.-N. Contou-Carrere, P. Daoutidis, Y.N. Kaznessis. Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009, 6 (3) , 470-482. https://doi.org/10.1109/TCBB.2009.23
4500. N. A. Sinitsyn, N. Hengartner, I. Nemenman. Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proceedings of the National Academy of Sciences 2009, 106 (26) , 10546-10551. https://doi.org/10.1073/pnas.0809340106
4501. Rajesh Ramaswamy, Nélido González-Segredo, Ivo F. Sbalzarini. A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of Chemical Physics 2009, 130 (24) , 244104. https://doi.org/10.1063/1.3154624
4502. P. Rohani, R. Breban, D. E. Stallknecht, J. M. Drake. Environmental transmission of low pathogenicity avian influenza viruses and its implications for pathogen invasion. Proceedings of the National Academy of Sciences 2009, 106 (25) , 10365-10369. https://doi.org/10.1073/pnas.0809026106
4503. A. Garg, K. Mohanram, A. Di Cara, G. De Micheli, I. Xenarios. Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics 2009, 25 (12) , i101-i109. https://doi.org/10.1093/bioinformatics/btp214
4504. Nicholas Geard, Kai Willadsen. Dynamical approaches to modeling developmental gene regulatory networks. Birth Defects Research Part C: Embryo Today: Reviews 2009, 87 (2) , 131-142. https://doi.org/10.1002/bdrc.20150
4505. Indra Schroeder, Ulf-Peter Hansen. Interference of Shot Noise of Open-Channel Current with Analysis of Fast Gating: Patchers do not (Yet) Have to Care. Journal of Membrane Biology 2009, 229 (3) , 153-163. https://doi.org/10.1007/s00232-009-9183-3
4506. Rui Zhu, Aurélien de la Lande, Rui Zhang, Dennis R. Salahub. Exploring the molecular origin of the high selectivity of multisubunit RNA polymerases by stochastic kinetic models. Interdisciplinary Sciences: Computational Life Sciences 2009, 1 (2) , 91-98. https://doi.org/10.1007/s12539-009-0031-3
4507. Ying Wang, Qianshu Li, Ji Luo. Explicit calcium bursting stochastic resonance. Biophysical Chemistry 2009, 142 (1-3) , 40-45. https://doi.org/10.1016/j.bpc.2009.03.002
4508. Laleh Mollazadeh-Beidokhti, Farshid Mohammad-Rafiee, Helmut Schiessel. Active Nucleosome Displacement: A Theoretical Approach. Biophysical Journal 2009, 96 (11) , 4387-4398. https://doi.org/10.1016/j.bpj.2009.02.071
4509. Aleksandra M. Walczak, Peter G. Wolynes. Gene-Gene Cooperativity in Small Networks. Biophysical Journal 2009, 96 (11) , 4525-4541. https://doi.org/10.1016/j.bpj.2009.03.005
4510. Stefan Braunewell, Stefan Bornholdt. Reliability of regulatory networks and its evolution. Journal of Theoretical Biology 2009, 258 (4) , 502-512. https://doi.org/10.1016/j.jtbi.2009.02.013
4511. Margaritis Voliotis, Netta Cohen, Carmen Molina-París, Tanniemola B. Liverpool. Backtracking and Proofreading in DNA Transcription. Physical Review Letters 2009, 102 (25) https://doi.org/10.1103/PhysRevLett.102.258101
4512. Jun-Qing Niu, Kuan Zhang, Haoran Zheng. An Agent-Based Modeling Approach at Molecular Scale for Biochemical Networks: Simulating from Stochastic Molecular Events. 2009,,, 1-4. https://doi.org/10.1109/ICBBE.2009.5162306
4513. Roland Ewald, Stefan Leye, Adelinde M. Uhrmacher. An Efficient and Adaptive Mechanism for Parallel Simulation Replication. 2009,,, 104-113. https://doi.org/10.1109/PADS.2009.11
4514. P. P. Dennis, M. Ehrenberg, D. Fange, H. Bremer. Varying Rate of RNA Chain Elongation during rrn Transcription in Escherichia coli. Journal of Bacteriology 2009, 191 (11) , 3740-3746. https://doi.org/10.1128/JB.00128-09
4515. XIANPING GUO, QIULI LIU, TIANSHOU ZHOU. OPTIMAL CONTROL OF STOCHASTIC FLUCTUATIONS IN BIOCHEMICAL REACTIONS. Journal of Biological Systems 2009, 17 (02) , 283-301. https://doi.org/10.1142/S0218339009002806
4516. FERHAT AY, TAMER KAHVECI, VALÉRIE DE CRÉCY-LAGARD. A FAST AND ACCURATE ALGORITHM FOR COMPARATIVE ANALYSIS OF METABOLIC PATHWAYS. Journal of Bioinformatics and Computational Biology 2009, 07 (03) , 389-428. https://doi.org/10.1142/S0219720009004163
4517. David J. Wales. Calculating rate constants and committor probabilities for transition networks by graph transformation. The Journal of Chemical Physics 2009, 130 (20) , 204111. https://doi.org/10.1063/1.3133782
4518. Smita Agrawal, Colin Archer, David V. Schaffer, . Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling. PLoS Computational Biology 2009, 5 (5) , e1000390. https://doi.org/10.1371/journal.pcbi.1000390
4519. Mamdouh Al-Harthi, Masihullah J. Khan, Sarfraz H. Abbasi, João B. P. Soares. Gradient Copolymers by ATRP in Semibatch Reactors: Dynamic Monte Carlo Simulation. Macromolecular Reaction Engineering 2009, 3 (4) , 148-159. https://doi.org/10.1002/mren.200800055
4520. Shreepriya Das, Haris Vikalo, Arjang Hassibi. On scaling laws of biosensors: A stochastic approach. Journal of Applied Physics 2009, 105 (10) , 102021. https://doi.org/10.1063/1.3116125
4521. N. Fernandez, Q. Chang, D. W. Buster, D. J. Sharp, A. Ma. A model for the regulatory network controlling the dynamics of kinetochore microtubule plus-ends and poleward flux in metaphase. Proceedings of the National Academy of Sciences 2009, 106 (19) , 7846-7851. https://doi.org/10.1073/pnas.0813228106
4522. Yishai Shimoni, Shoshy Altuvia, Hanah Margalit, Ofer Biham, . Stochastic Analysis of the SOS Response in Escherichia coli. PLoS ONE 2009, 4 (5) , e5363. https://doi.org/10.1371/journal.pone.0005363
4523. Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal Das. Parametric modeling of protein–DNA binding kinetics: A discrete event based simulation approach. Discrete Applied Mathematics 2009, 157 (10) , 2395-2415. https://doi.org/10.1016/j.dam.2008.06.046
4524. Peter Schuster. Genotypes and Phenotypes in the Evolution of Molecules. European Review 2009, 17 (2) , 281-319. https://doi.org/10.1017/S1062798709000787
4525. Wang Hong-Li, Fu Zheng-Ping, Xu Xin-Hang, Ouyang Qi. Stochasticity in the yeast mating pathway. Chinese Physics B 2009, 18 (5) , 2082-2095. https://doi.org/10.1088/1674-1056/18/5/060
4526. Richard P. Boland, Tobias Galla, Alan J. McKane. Limit cycles, complex Floquet multipliers, and intrinsic noise. Physical Review E 2009, 79 (5) https://doi.org/10.1103/PhysRevE.79.051131
4527. Leonard A. Harris, Aaron M. Piccirilli, Emily R. Majusiak, Paulette Clancy. Quantifying stochastic effects in biochemical reaction networks using partitioned leaping. Physical Review E 2009, 79 (5) https://doi.org/10.1103/PhysRevE.79.051906
4528. Kenta Odagiri, Kazuo Takatsuka. Traveling excitable waves successively generated in a nonlinear proliferation system. Physical Review E 2009, 79 (5) https://doi.org/10.1103/PhysRevE.79.056219
4529. R. Grima. Noise-Induced Breakdown of the Michaelis-Menten Equation in Steady-State Conditions. Physical Review Letters 2009, 102 (21) https://doi.org/10.1103/PhysRevLett.102.218103
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4533. Shreepriya Das, Haris Vikalo, Arjang Hassibi. Stochastic modeling of reaction kinetics in biosensors using the Fokker Planck equation. 2009,,, 1-4. https://doi.org/10.1109/GENSIPS.2009.5174363
4534. Zhouyi Xu, Xiaodong Cai. Modified K-leap method for stochastic simulation of genetic networks with small number of molecules. 2009,,, 1-4. https://doi.org/10.1109/GENSIPS.2009.5174373
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4536. K. Fujibayashi, S. Murata. Precise Simulation Model for DNA Tile Self-Assembly. IEEE Transactions on Nanotechnology 2009, 8 (3) , 361-368. https://doi.org/10.1109/TNANO.2008.2011776
4537. Corrado Priami. Algorithmic systems biology. Communications of the ACM 2009, 52 (5) , 80-88. https://doi.org/10.1145/1506409.1506427
4538. Calvin Dytham. Evolved dispersal strategies at range margins. Proceedings of the Royal Society B: Biological Sciences 2009, 276 (1661) , 1407-1413. https://doi.org/10.1098/rspb.2008.1535
4539. A. M. Walczak, A. Mugler, C. H. Wiggins. A stochastic spectral analysis of transcriptional regulatory cascades. Proceedings of the National Academy of Sciences 2009, 106 (16) , 6529-6534. https://doi.org/10.1073/pnas.0811999106
4540. Eric Mjolsness, David Orendorff, Philippe Chatelain, Petros Koumoutsakos. An exact accelerated stochastic simulation algorithm. The Journal of Chemical Physics 2009, 130 (14) , 144110. https://doi.org/10.1063/1.3078490
4541. Kazunari Mouri, Jose C. Nacher, Tatsuya Akutsu, . A Mathematical Model for the Detection Mechanism of DNA Double-Strand Breaks Depending on Autophosphorylation of ATM. PLoS ONE 2009, 4 (4) , e5131. https://doi.org/10.1371/journal.pone.0005131
4542. Martin Tchernookov, Aryeh Warmflash, Aaron R. Dinner. Critical behavior of a model for catalyzed autoamplification. The Journal of Chemical Physics 2009, 130 (13) , 134906. https://doi.org/10.1063/1.3101649
4543. Chang Hyeong Lee, Kyeong-Hun Kim, Pilwon Kim. A moment closure method for stochastic reaction networks. The Journal of Chemical Physics 2009, 130 (13) , 134107. https://doi.org/10.1063/1.3103264
4544. Yujiro Richard Yamada, Charles S. Peskin. A Look-Ahead Model for the Elongation Dynamics of Transcription. Biophysical Journal 2009, 96 (8) , 3015-3031. https://doi.org/10.1016/j.bpj.2008.12.3955
4545. Ambarish Nag, Michael I. Monine, James R. Faeder, Byron Goldstein. Aggregation of Membrane Proteins by Cytosolic Cross-Linkers: Theory and Simulation of the LAT-Grb2-SOS1 System. Biophysical Journal 2009, 96 (7) , 2604-2623. https://doi.org/10.1016/j.bpj.2009.01.019
4546. Dominique Chu, Nicolae Radu Zabet, Boris Mitavskiy. Models of transcription factor binding: Sensitivity of activation functions to model assumptions. Journal of Theoretical Biology 2009, 257 (3) , 419-429. https://doi.org/10.1016/j.jtbi.2008.11.026
4547. Elan Gin, Martin Falcke, Larry E. Wagner, David I. Yule, James Sneyd. Markov chain Monte Carlo fitting of single-channel data from inositol trisphosphate receptors. Journal of Theoretical Biology 2009, 257 (3) , 460-474. https://doi.org/10.1016/j.jtbi.2008.12.020
4548. Richard A. Lawson, Clifford L. Henderson. Mesoscale simulation of molecular resists: The effect of PAG distribution homogeneity on LER. Microelectronic Engineering 2009, 86 (4-6) , 741-744. https://doi.org/10.1016/j.mee.2008.12.042
4549. S. Grundman, L. Komárková, J. Rychtář. A Hawk-Dove game in finite kleptoparasitic populations. Journal of Interdisciplinary Mathematics 2009, 12 (2) , 181-201. https://doi.org/10.1080/09720502.2009.10700621
4550. Andre S. Ribeiro, Olli-Pekka Smolander, Tiina Rajala, Antti Häkkinen, Olli Yli-Harja. Delayed Stochastic Model of Transcription at the Single Nucleotide Level. Journal of Computational Biology 2009, 16 (4) , 539-553. https://doi.org/10.1089/cmb.2008.0153
4551. Andrea Unger, Heidrun Schumann. Visual support for the understanding of simulation processes. 2009,,, 57-64. https://doi.org/10.1109/PACIFICVIS.2009.4906838
4552. Sven Van Segbroeck, Ann Nowé, Tom Lenaerts. Stochastic Simulation of the Chemoton. Artificial Life 2009, 15 (2) , 213-226. https://doi.org/10.1162/artl.2009.15.2.15203
4553. Ardo van den Hout, Fiona E Matthews. A piecewise-constant Markov model and the effects of study design on the estimation of life expectancies in health and ill health. Statistical Methods in Medical Research 2009, 18 (2) , 145-162. https://doi.org/10.1177/0962280208089090
4554. Yucheng Hu, Tiejun Li. Highly accurate tau-leaping methods with random corrections. The Journal of Chemical Physics 2009, 130 (12) , 124109. https://doi.org/10.1063/1.3091269
4555. Mirco Tribastone, Adam Duguid, Stephen Gilmore. The PEPA eclipse plugin. ACM SIGMETRICS Performance Evaluation Review 2009, 36 (4) , 28-33. https://doi.org/10.1145/1530873.1530880
4556. Sotiria Lampoudi, Dan T. Gillespie, Linda R. Petzold. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. The Journal of Chemical Physics 2009, 130 (9) , 094104. https://doi.org/10.1063/1.3074302
4557. Matthew H. Flamm, Scott L. Diamond, Talid Sinno. Lattice kinetic Monte Carlo simulations of convective-diffusive systems. The Journal of Chemical Physics 2009, 130 (9) , 094904. https://doi.org/10.1063/1.3078518
4558. Michael L. Simpson, Chris D. Cox, Michael S. Allen, James M. McCollum, Roy D. Dar, David K. Karig, John F. Cooke. Noise in biological circuits. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 2009, 1 (2) , 214-225. https://doi.org/10.1002/wnan.22
4559. Aliaksandr A. Halavatyi, Petr V. Nazarov, Sandrine Medves, Marleen van Troys, Christophe Ampe, Mikalai Yatskou, Evelyne Friederich. An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments. Biophysical Chemistry 2009, 140 (1-3) , 24-34. https://doi.org/10.1016/j.bpc.2008.11.006
4560. Paul C. Bressloff, Berton A. Earnshaw. A Dynamic Corral Model of Receptor Trafficking at a Synapse. Biophysical Journal 2009, 96 (5) , 1786-1802. https://doi.org/10.1016/j.bpj.2008.12.3889
4561. Padinhateeri Ranjith, David Lacoste, Kirone Mallick, Jean-François Joanny. Nonequilibrium Self-Assembly of a Filament Coupled to ATP/GTP Hydrolysis. Biophysical Journal 2009, 96 (6) , 2146-2159. https://doi.org/10.1016/j.bpj.2008.12.3920
4562. Gayatri Muthukrishnan, Yangrong Zhang, Shankar Shastry, William O. Hancock. The Processivity of Kinesin-2 Motors Suggests Diminished Front-Head Gating. Current Biology 2009, 19 (5) , 442-447. https://doi.org/10.1016/j.cub.2009.01.058
4563. Federica Ciocchetta, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston. Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems. Electronic Notes in Theoretical Computer Science 2009, 232 , 17-38. https://doi.org/10.1016/j.entcs.2009.02.048
4564. Craig R. Powell, Richard P. Boland. The effects of stochastic population dynamics on food web structure. Journal of Theoretical Biology 2009, 257 (1) , 170-180. https://doi.org/10.1016/j.jtbi.2008.11.006
4565. Marko Gosak, Marko Marhl, Matjaž Perc. Pacemaker-guided noise-induced spatial periodicity in excitable media. Physica D: Nonlinear Phenomena 2009, 238 (5) , 506-515. https://doi.org/10.1016/j.physd.2008.11.007
4566. Vincent Danos, Linus J. Schumacher. How liquid is biological signalling?. Theoretical Computer Science 2009, 410 (11) , 1003-1012. https://doi.org/10.1016/j.tcs.2008.10.037
4567. Dominik Heinzmann. Extinction Times in Multitype Markov Branching Processes. Journal of Applied Probability 2009, 46 (01) , 296-307. https://doi.org/10.1017/S0021900200005374
4568. David Soloveichik. Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping. Journal of Computational Biology 2009, 16 (3) , 501-522. https://doi.org/10.1089/cmb.2008.0063
4569. Paul Smolen, Douglas A. Baxter, John H. Byrne. Interlinked dual-time feedback loops can enhance robustness to stochasticity and persistence of memory. Physical Review E 2009, 79 (3) https://doi.org/10.1103/PhysRevE.79.031902
4570. Christophe Deroulers, Marine Aubert, Mathilde Badoual, Basil Grammaticos. Modeling tumor cell migration: From microscopic to macroscopic models. Physical Review E 2009, 79 (3) https://doi.org/10.1103/PhysRevE.79.031917
4571. L. Mollazadeh-Beidokhti, J. Deseigne, D. Lacoste, F. Mohammad-Rafiee, H. Schiessel. Stochastic model for nucleosome sliding under an external force. Physical Review E 2009, 79 (3) https://doi.org/10.1103/PhysRevE.79.031922
4572. Thierry Dauxois, Francesca Di Patti, Duccio Fanelli, Alan J. McKane. Enhanced stochastic oscillations in autocatalytic reactions. Physical Review E 2009, 79 (3) https://doi.org/10.1103/PhysRevE.79.036112
4573. Daniel A. Henderson, Richard J. Boys, Kim J. Krishnan, Conor Lawless, Darren J. Wilkinson. Bayesian Emulation and Calibration of a Stochastic Computer Model of Mitochondrial DNA Deletions in Substantia Nigra Neurons. Journal of the American Statistical Association 2009, 104 (485) , 76-87. https://doi.org/10.1198/jasa.2009.0005
4574. H.-P. Breuer, J. Piilo. Stochastic jump processes for non-Markovian quantum dynamics. EPL (Europhysics Letters) 2009, 85 (5) , 50004. https://doi.org/10.1209/0295-5075/85/50004
4575. Dominik Heinzmann. Extinction Times in Multitype Markov Branching Processes. Journal of Applied Probability 2009, 46 (1) , 296-307. https://doi.org/10.1239/jap/1238592131
4576. S.S.I. Abd El Gawad. The Mollusk Gastropod Lanistes carinatus (Olivier, 1804) as Abiomonitor for Some Trace Metals in the Nile River. International Journal of Zoological Research 2009, 5 (3) , 115-125. https://doi.org/10.3923/ijzr.2009.115.125
4577. Alessandro Barbato, Carlo Seghi, Carlo Cavallotti. An ab initio Rice-Ramsperger-Kassel-Marcus/master equation investigation of SiH4 decomposition kinetics using a kinetic Monte Carlo approach. The Journal of Chemical Physics 2009, 130 (7) , 074108. https://doi.org/10.1063/1.3077561
4578. Vladimir P Zhdanov. Interplay of bistable kinetics of gene expression during cellular growth. Journal of Physics A: Mathematical and Theoretical 2009, 42 (6) , 065102. https://doi.org/10.1088/1751-8113/42/6/065102
4579. Tina Toni, David Welch, Natalja Strelkowa, Andreas Ipsen, Michael P.H Stumpf. Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. Journal of The Royal Society Interface 2009, 6 (31) , 187-202. https://doi.org/10.1098/rsif.2008.0172
4580. Colby J. Tanner. Individual experience-based foraging can generate community territorial structure for competing ant species. Behavioral Ecology and Sociobiology 2009, 63 (4) , 591-603. https://doi.org/10.1007/s00265-008-0694-1
4581. Jegathambal Palanichamy, Torsten Becker, Martin Spiller, Jürgen Köngeter, Sankaralingam Mohan. Multicomponent reaction modelling using a stochastic algorithm. Computing and Visualization in Science 2009, 12 (2) , 51-61. https://doi.org/10.1007/s00791-007-0080-y
4582. Michail Stamatakis, Nikos V. Mantzaris. Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network. Biophysical Journal 2009, 96 (3) , 887-906. https://doi.org/10.1016/j.bpj.2008.10.028
4583. Madeleine Leisner, Jan-Timm Kuhr, Joachim O. Rädler, Erwin Frey, Berenike Maier. Kinetics of Genetic Switching into the State of Bacterial Competence. Biophysical Journal 2009, 96 (3) , 1178-1188. https://doi.org/10.1016/j.bpj.2008.10.034
4584. Boanerges Aleman-Meza, Yihai Yu, Heinz-Bernd Schüttler, Jonathan Arnold, Thiab R. Taha. KINSOLVER: A simulator for computing large ensembles of biochemical and gene regulatory networks. Computers & Mathematics with Applications 2009, 57 (3) , 420-435. https://doi.org/10.1016/j.camwa.2008.10.086
4585. J. Kielbassa, R. Bortfeldt, S. Schuster, I. Koch. Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets. Computational Biology and Chemistry 2009, 33 (1) , 46-61. https://doi.org/10.1016/j.compbiolchem.2008.07.022
4586. Ann Zahle Andersen, Ana Lúcia Carvalho, Ana Rute Neves, Helena Santos, Ursula Kummer, Lars Folke Olsen. The metabolic pH response in Lactococcus lactis: An integrative experimental and modelling approach. Computational Biology and Chemistry 2009, 33 (1) , 71-83. https://doi.org/10.1016/j.compbiolchem.2008.08.001
4587. Paolo Ballarini, Radu Mardare, Ivan Mura. Analysing Biochemical Oscillation through Probabilistic Model Checking. Electronic Notes in Theoretical Computer Science 2009, 229 (1) , 3-19. https://doi.org/10.1016/j.entcs.2009.02.002
4588. Soufiene Benkirane, Jane Hillston, Chris McCaig, Rachel Norman, Carron Shankland. Improved Continuous Approximation of PEPA Models through Epidemiological Examples. Electronic Notes in Theoretical Computer Science 2009, 229 (1) , 59-74. https://doi.org/10.1016/j.entcs.2009.02.005
4589. Luca Bortolussi, Alberto Policriti. The Importance of Being (A Little Bit) Discrete. Electronic Notes in Theoretical Computer Science 2009, 229 (1) , 75-92. https://doi.org/10.1016/j.entcs.2009.02.006
4590. Federica Ciocchetta, Andrea Degasperi, Jane Hillston, Muffy Calder. Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA. Electronic Notes in Theoretical Computer Science 2009, 229 (1) , 145-163. https://doi.org/10.1016/j.entcs.2009.02.010
4591. Michael Beil, Sebastian Lück, Frank Fleischer, Stéphanie Portet, Wolfgang Arendt, Volker Schmidt. Simulating the formation of keratin filament networks by a piecewise-deterministic Markov process. Journal of Theoretical Biology 2009, 256 (4) , 518-532. https://doi.org/10.1016/j.jtbi.2008.09.044
4592. Michael Manapat, Hisashi Ohtsuki, Reinhard Bürger, Martin A. Nowak. Originator dynamics. Journal of Theoretical Biology 2009, 256 (4) , 586-595. https://doi.org/10.1016/j.jtbi.2008.10.006
4593. Jinzhi Lei. Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters. Journal of Theoretical Biology 2009, 256 (4) , 485-492. https://doi.org/10.1016/j.jtbi.2008.10.028
4594. Darren J. Wilkinson. Stochastic modelling for quantitative description of heterogeneous biological systems. Nature Reviews Genetics 2009, 10 (2) , 122-133. https://doi.org/10.1038/nrg2509
4595. Zheng Zhi-Zhen, Wang Ai-Ling. Phase transitions in cellular automata models of spatial susceptible–infected–resistant–susceptible epidemics. Chinese Physics B 2009, 18 (2) , 489-500. https://doi.org/10.1088/1674-1056/18/2/019
4596. Andrew D. Jackson, Simone Pigolotti. Statistics of trajectories in two-state master equations. Physical Review E 2009, 79 (2) https://doi.org/10.1103/PhysRevE.79.021121
4597. Marta L. Guerra, M. A. Novotny, Hiroshi Watanabe, Nobuyasu Ito. Efficiency of rejection-free methods for dynamic Monte Carlo studies of off-lattice interacting particles. Physical Review E 2009, 79 (2) https://doi.org/10.1103/PhysRevE.79.026706
4598. Pierre-Emmanuel Morant, Quentin Thommen, François Lemaire, Constant Vandermoëre, Benjamin Parent, Marc Lefranc. Oscillations in the Expression of a Self-Repressed Gene Induced by a Slow Transcriptional Dynamics. Physical Review Letters 2009, 102 (6) https://doi.org/10.1103/PhysRevLett.102.068104
4599. William Mather, Matthew R. Bennett, Jeff Hasty, Lev S. Tsimring. Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits. Physical Review Letters 2009, 102 (6) https://doi.org/10.1103/PhysRevLett.102.068105
4600. JIALIANG WU, EBERHARD VOIT. HYBRID MODELING IN BIOCHEMICAL SYSTEMS THEORY BY MEANS OF FUNCTIONAL PETRI NETS. Journal of Bioinformatics and Computational Biology 2009, 07 (01) , 107-134. https://doi.org/10.1142/S0219720009004047
4601. Dirk Müller, Jörg Stelling, . Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures. PLoS Computational Biology 2009, 5 (1) , e1000279. https://doi.org/10.1371/journal.pcbi.1000279
4602. Thorsten Lenser, Günter Theißen, Peter Dittrich, . Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins. PLoS Computational Biology 2009, 5 (1) , e1000264. https://doi.org/10.1371/journal.pcbi.1000264
4603. A. Prasad, J. Zikherman, J. Das, J. P. Roose, A. Weiss, A. K. Chakraborty. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. Proceedings of the National Academy of Sciences 2009, 106 (2) , 528-533. https://doi.org/10.1073/pnas.0805981105
4604. Katherine V. Wendelsdorf, Zhuo Song, Yang Cao, David C. Samuels, . An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors. PLoS Computational Biology 2009, 5 (1) , e1000261. https://doi.org/10.1371/journal.pcbi.1000261
4605. N. Hori, G. Chikenji, R. S. Berry, S. Takada. Folding energy landscape and network dynamics of small globular proteins. Proceedings of the National Academy of Sciences 2009, 106 (1) , 73-78. https://doi.org/10.1073/pnas.0811560106
4606. Alan Gilbert, Friedrich Srienc. Optimized evolution in the cytostat: A Monte Carlo simulation. Biotechnology and Bioengineering 2009, 102 (1) , 221-231. https://doi.org/10.1002/bit.22045
4607. Marco Drache. Modeling the Product Composition During Controlled Radical Polymerizations with Mono- and Bifunctional Alkoxyamines. Macromolecular Symposia 2009, 275-276 (1) , 52-58. https://doi.org/10.1002/masy.200950106
4608. Herbert M. Sauro. Network Dynamics. 2009,,, 269-309. https://doi.org/10.1007/978-1-59745-243-4_13
4609. Haluk Resat, Linda Petzold, Michel F. Pettigrew. Kinetic Modeling of Biological Systems. 2009,,, 311-335. https://doi.org/10.1007/978-1-59745-243-4_14
4610. Subhadip Raychaudhuri, Philippos Raychaudhuri. Computational Modeling of Receptor-Ligand Binding and Cellular Signaling Processes. 2009,,, 1-21. https://doi.org/10.1007/978-1-59745-397-4_3
4611. Pedro Mendes, Stefan Hoops, Sven Sahle, Ralph Gauges, Joseph Dada, Ursula Kummer. Computational Modeling of Biochemical Networks Using COPASI. 2009,,, 17-59. https://doi.org/10.1007/978-1-59745-525-1_2
4612. James R. Faeder, Michael L. Blinov, William S. Hlavacek. Rule-Based Modeling of Biochemical Systems with BioNetGen. 2009,,, 113-167. https://doi.org/10.1007/978-1-59745-525-1_5
4613. Henry Mirsky, Jörg Stelling, Rudiyanto Gunawan, Neda Bagheri, Stephanie R. Taylor, Eric Kwei, Jason E. Shoemaker, Francis J. Doyle III. Automatic Control in Systems Biology. 2009,,, 1335-1360. https://doi.org/10.1007/978-3-540-78831-7_75
4614. Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano. Formal Models of the Calyx of Held. 2009,,, 331-366. https://doi.org/10.1007/978-3-540-88869-7_18
4615. Marta Kwiatkowska, Gethin Norman, David Parker. Quantitative Verification Techniques for Biological Processes. 2009,,, 391-409. https://doi.org/10.1007/978-3-540-88869-7_20
4616. Luca Cardelli. Artificial Biochemistry. 2009,,, 429-462. https://doi.org/10.1007/978-3-540-88869-7_22
4617. Maria Luisa Guerriero, Davide Prandi, Corrado Priami, Paola Quaglia. Process Calculi Abstractions for Biology. 2009,,, 463-486. https://doi.org/10.1007/978-3-540-88869-7_23
4618. Jane Hillston, Adam Duguid. Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style. 2009,,, 487-504. https://doi.org/10.1007/978-3-540-88869-7_24
4619. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri. A Multi-volume Approach to Stochastic Modeling with Membrane Systems. 2009,,, 519-542. https://doi.org/10.1007/978-3-540-88869-7_26
4620. Matthew Cook, David Soloveichik, Erik Winfree, Jehoshua Bruck. Programmability of Chemical Reaction Networks. 2009,,, 543-584. https://doi.org/10.1007/978-3-540-88869-7_27
4621. Vincenzo Manca. Log-gain Principles for Metabolic P Systems. 2009,,, 585-605. https://doi.org/10.1007/978-3-540-88869-7_28
4622. Kazufumi Mizunuma, Masami Hagiya. Hybrid Method for Simulating Small-Number Molecular Systems. 2009,,, 607-620. https://doi.org/10.1007/978-3-540-88869-7_29
4623. John Jack, Andrei Păun, Alfonso Rodríguez-Patón. Effects of HIV-1 Proteins on the Fas-Mediated Apoptotic Signaling Cascade: A Computational Study of Latent CD4+ T Cell Activation. 2009,,, 246-259. https://doi.org/10.1007/978-3-540-95885-7_18
4624. Dario Pescini, Paolo Cazzaniga, Claudio Ferretti, Giancarlo Mauri. First Steps Towards a Wet Implementation for τ-DPP. 2009,,, 355-373. https://doi.org/10.1007/978-3-540-95885-7_25
4625. Mylène Maurin, Morgan Magnin, Olivier Roux. Modeling of Genetic Regulatory Network in Stochastic π-Calculus. 2009,,, 282-294. https://doi.org/10.1007/978-3-642-00727-9_27
4626. Stephen Tyree, Rayus Kuplicki, Trevor Sarratt, Scott Fujan, John Hale. GridSPiM: A Framework for Simple Locality and Containment in the Stochastic π-Calculus. 2009,,, 409-423. https://doi.org/10.1007/978-3-642-00727-9_38
4627. Daniela Besozzi, Paolo Cazzaniga, Giancarlo Mauri, Dario Pescini, Leonardo Vanneschi. A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems. 2009,,, 116-127. https://doi.org/10.1007/978-3-642-01184-9_11
4628. Allan Clark, Stephen Gilmore, Mirco Tribastone. Quantitative Analysis of Web Services Using SRMC. 2009,,, 296-339. https://doi.org/10.1007/978-3-642-01918-0_8
4629. Emma Norling, Craig R. Powell, Bruce Edmonds. Cross-Disciplinary Views on Modelling Complex Systems. 2009,,, 183-194. https://doi.org/10.1007/978-3-642-01991-3_14
4630. Mirko Viroli, Matteo Casadei. Biochemical Tuple Spaces for Self-organising Coordination. 2009,,, 143-162. https://doi.org/10.1007/978-3-642-02053-7_8
4631. Luo-Luo Jiang, Wen-Xu Wang, Xin Huang, Bing-Hong Wang. Spiral Waves Emergence in a Cyclic Predator-Prey Model. 2009,,, 894-899. https://doi.org/10.1007/978-3-642-02466-5_89
4632. Jesús M. Miró Bueno, Alfonso Rodríguez-Patón. A New Model of Synthetic Genetic Oscillator Based on Trans-Acting Repressor Ribozyme. 2009,,, 1170-1177. https://doi.org/10.1007/978-3-642-02481-8_177
4633. Joseph O. Dada, Pedro Mendes. Design and Architecture of Web Services for Simulation of Biochemical Systems. 2009,,, 182-195. https://doi.org/10.1007/978-3-642-02879-3_15
4634. Harish Chandran, Nikhil Gopalkrishnan, John Reif. The Tile Complexity of Linear Assemblies. 2009,,, 235-253. https://doi.org/10.1007/978-3-642-02927-1_21
4635. Frédéric Didier, Thomas A. Henzinger, Maria Mateescu, Verena Wolf. Approximation of Event Probabilities in Noisy Cellular Processes. 2009,,, 173-188. https://doi.org/10.1007/978-3-642-03845-7_12
4636. Sumit K. Jha, Edmund M. Clarke, Christopher J. Langmead, Axel Legay, André Platzer, Paolo Zuliani. A Bayesian Approach to Model Checking Biological Systems. 2009,,, 218-234. https://doi.org/10.1007/978-3-642-03845-7_15
4637. Mathias John, Cédric Lhoussaine, Joachim Niehren. Dynamic Compartments in the Imperative π-Calculus. 2009,,, 235-250. https://doi.org/10.1007/978-3-642-03845-7_16
4638. Ozgur E. Akman, Federica Ciocchetta, Andrea Degasperi, Maria Luisa Guerriero. Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network. 2009,,, 52-67. https://doi.org/10.1007/978-3-642-03845-7_4
4639. Giampaolo Bella, Pietro Liò. Formal Analysis of the Genetic Toggle. 2009,,, 96-110. https://doi.org/10.1007/978-3-642-03845-7_7
4640. John Jack, Andrei Păun. Discrete Modeling of Biochemical Signaling with Memory Enhancement. 2009,,, 200-215. https://doi.org/10.1007/978-3-642-04186-0_10
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4759. Nil Geisweiller, Jane Hillston, Marco Stenico. Relating continuous and discrete PEPA models of signalling pathways. Theoretical Computer Science 2008, 404 (1-2) , 97-111. https://doi.org/10.1016/j.tcs.2008.04.012
4760. Pierre-Louis Curien, Vincent Danos, Jean Krivine, Min Zhang. Computational self-assembly. Theoretical Computer Science 2008, 404 (1-2) , 61-75. https://doi.org/10.1016/j.tcs.2008.04.014
4761. Vincenzo Manca. The metabolic algorithm for P systems: Principles and applications. Theoretical Computer Science 2008, 404 (1-2) , 142-155. https://doi.org/10.1016/j.tcs.2008.04.015
4762. B. Wilson, J.S. Edwards, D.G. Vlachos, W. Shu, M.A. Raymond-Stinz, S. Steinberg, M.-Y. Hsieh, S. Yang. Stochastic simulations of ErbB homo and heterodimerisation: potential impacts of receptor conformational state and spatial segregation. IET Systems Biology 2008, 2 (5) , 256-272. https://doi.org/10.1049/iet-syb:20070073
4763. Y. Cao, Z. Liu. Detailed comparison between StochSim and SSA. IET Systems Biology 2008, 2 (5) , 334-341. https://doi.org/10.1049/iet-syb:20070074
4764. M. Khammash, B. Munsky. Transient analysis of stochastic switches and trajectories with applications to gene regulatory networks. IET Systems Biology 2008, 2 (5) , 323-333. https://doi.org/10.1049/iet-syb:20070082
4765. R.V. Kulkarni, X. Xu. Modelling of processes governing subcellular localisation of MinD in Escherichia coli. IET Systems Biology 2008, 2 (5) , 285-292. https://doi.org/10.1049/iet-syb:20070083
4766. I. Nemenman, C.H. Wiggins, A. Mugler, E. Ziv. Serially regulated biological networks fully realise a constrained set of functions. IET Systems Biology 2008, 2 (5) , 313-322. https://doi.org/10.1049/iet-syb:20080097
4767. Tianshou Zhou, Jiajun Zhang, Zhanjiang Yuan, Luonan Chen. Synchronization of genetic oscillators. Chaos: An Interdisciplinary Journal of Nonlinear Science 2008, 18 (3) , 037126. https://doi.org/10.1063/1.2978183
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4769. Richard P Boland, Tobias Galla, Alan J McKane. How limit cycles and quasi-cycles are related in systems with intrinsic noise. Journal of Statistical Mechanics: Theory and Experiment 2008, 2008 (09) , P09001. https://doi.org/10.1088/1742-5468/2008/09/P09001
4770. R. Blossey, C. V. Giuraniuc. Mean-field versus stochastic models for transcriptional regulation. Physical Review E 2008, 78 (3) https://doi.org/10.1103/PhysRevE.78.031909
4771. Jin Yang, Michael I. Monine, James R. Faeder, William S. Hlavacek. Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Physical Review E 2008, 78 (3) https://doi.org/10.1103/PhysRevE.78.031910
4772. Masatoshi Nishikawa, Hiroaki Takagi, Tatsuo Shibata, Atsuko H. Iwane, Toshio Yanagida. Fluctuation Analysis of Mechanochemical Coupling Depending on the Type of Biomolecular Motors. Physical Review Letters 2008, 101 (12) https://doi.org/10.1103/PhysRevLett.101.128103
4773. Jongrae Kim, D.G. Bates, I. Postlethwaite. Evaluation of Stochastic Effects on Biomolecular Networks Using the Generalized Nyquist Stability Criterion. IEEE Transactions on Automatic Control 2008, 53 (8) , 1937-1941. https://doi.org/10.1109/TAC.2008.929463
4774. T. Reichenbach, T. Franosch, E. Frey. Domain wall delocalization, dynamics and fluctuations in an exclusion process with two internal states. The European Physical Journal E 2008, 27 (1) https://doi.org/10.1140/epje/i2008-10350-3
4775. Clark A. Miller, Daniel A. Beard. The Effects of Reversibility and Noise on Stochastic Phosphorylation Cycles and Cascades. Biophysical Journal 2008, 95 (5) , 2183-2192. https://doi.org/10.1529/biophysj.107.126185
4776. Michael I. Monine, Jason M. Haugh. Signal Transduction at Point-Blank Range: Analysis of a Spatial Coupling Mechanism for Pathway Crosstalk. Biophysical Journal 2008, 95 (5) , 2172-2182. https://doi.org/10.1529/biophysj.108.128892
4777. J. Wang, L. Xu, E. Wang. Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations. Proceedings of the National Academy of Sciences 2008, 105 (34) , 12271-12276. https://doi.org/10.1073/pnas.0800579105
4778. Michael Klein, R. D. Levine, F. Remacle. Principles of design of a set-reset finite state logic nanomachine. Journal of Applied Physics 2008, 104 (4) , 044509. https://doi.org/10.1063/1.2970060
4779. R. Maithreye, Ram Rup Sarkar, Veena K. Parnaik, Somdatta Sinha, . Delay-Induced Transient Increase and Heterogeneity in Gene Expression in Negatively Auto-Regulated Gene Circuits. PLoS ONE 2008, 3 (8) , e2972. https://doi.org/10.1371/journal.pone.0002972
4780. Marco J. Morelli, Pieter Rein ten Wolde. Reaction Brownian dynamics and the effect of spatial fluctuations on the gain of a push-pull network. The Journal of Chemical Physics 2008, 129 (5) , 054112. https://doi.org/10.1063/1.2958287
4781. Neda Bagheri, Stephanie R Taylor, Kirsten Meeker, Linda R Petzold, Francis J Doyle. Synchrony and entrainment properties of robust circadian oscillators. Journal of The Royal Society Interface 2008, 5 (suppl_1) https://doi.org/10.1098/rsif.2008.0045.focus
4782. Didier Gonze, Michel Jacquet, Albert Goldbeter. Stochastic modelling of nucleocytoplasmic oscillations of the transcription factor Msn2 in yeast. Journal of The Royal Society Interface 2008, 5 (suppl_1) https://doi.org/10.1098/rsif.2008.0141.focus
4783. C. D. Cox, J. M. McCollum, M. S. Allen, R. D. Dar, M. L. Simpson. Using noise to probe and characterize gene circuits. Proceedings of the National Academy of Sciences 2008, 105 (31) , 10809-10814. https://doi.org/10.1073/pnas.0804829105
4784. Rajesh Krishnan, Carla C. Purdy. Circuit development using biological components: Principles, models and experimental feasibility. Analog Integrated Circuits and Signal Processing 2008, 56 (1-2) , 153-161. https://doi.org/10.1007/s10470-007-9094-0
4785. Yang Cao, Linda Petzold. Slow-scale tau-leaping method. Computer Methods in Applied Mechanics and Engineering 2008, 197 (43-44) , 3472-3479. https://doi.org/10.1016/j.cma.2008.02.024
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4787. Werner Sandmann. Discrete-time stochastic modeling and simulation of biochemical networks. Computational Biology and Chemistry 2008, 32 (4) , 292-297. https://doi.org/10.1016/j.compbiolchem.2008.03.018
4788. Vahid Shahrezaei, Peter S Swain. The stochastic nature of biochemical networks. Current Opinion in Biotechnology 2008, 19 (4) , 369-374. https://doi.org/10.1016/j.copbio.2008.06.011
4789. Ross S. Davidson, Glenn Marion, Michael R. Hutchings. Effects of host social hierarchy on disease persistence. Journal of Theoretical Biology 2008, 253 (3) , 424-433. https://doi.org/10.1016/j.jtbi.2008.03.021
4790. François Fages, Sylvain Soliman. Abstract interpretation and types for systems biology. Theoretical Computer Science 2008, 403 (1) , 52-70. https://doi.org/10.1016/j.tcs.2008.04.024
4791. Youfang Cao, Hsiao-Mei Lu, Jie Liang. Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage λ. 2008,,, 611-614. https://doi.org/10.1109/IEMBS.2008.4649227
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4793. Ruiqi Wang, Chunguang Li, Luonan Chen, K. Aihara. Modeling and Analyzing Biological Oscillations in Molecular Networks. Proceedings of the IEEE 2008, 96 (8) , 1361-1385. https://doi.org/10.1109/JPROC.2008.925448
4794. Judith A. Megerle, Georg Fritz, Ulrich Gerland, Kirsten Jung, Joachim O. Rädler. Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System. Biophysical Journal 2008, 95 (4) , 2103-2115. https://doi.org/10.1529/biophysj.107.127191
4795. Haijun Gong, Debrup Sengupta, Adam D. Linstedt, Russell Schwartz. Simulated De Novo Assembly of Golgi Compartments by Selective Cargo Capture during Vesicle Budding and Targeted Vesicle Fusion. Biophysical Journal 2008, 95 (4) , 1674-1688. https://doi.org/10.1529/biophysj.107.127498
4796. Kohei Eguchi, Mitsumasa Yoda, Tomoki P. Terada, Masaki Sasai. Mechanism of Robust Circadian Oscillation of KaiC Phosphorylation In Vitro. Biophysical Journal 2008, 95 (4) , 1773-1784. https://doi.org/10.1529/biophysj.107.127555
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4798. Christian L. Althaus, Rob J. De Boer, . Dynamics of Immune Escape during HIV/SIV Infection. PLoS Computational Biology 2008, 4 (7) , e1000103. https://doi.org/10.1371/journal.pcbi.1000103
4799. Raymond Kapral. Multiparticle Collision Dynamics: Simulation of Complex Systems on Mesoscales. 2008,,, 89-146. https://doi.org/10.1002/9780470371572.ch2
4800. Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen, . The Generation of Promoter-Mediated Transcriptional Noise in Bacteria. PLoS Computational Biology 2008, 4 (7) , e1000109. https://doi.org/10.1371/journal.pcbi.1000109
4801. Dana Angluin, James Aspnes, David Eisenstat. A simple population protocol for fast robust approximate majority. Distributed Computing 2008, 21 (2) , 87-102. https://doi.org/10.1007/s00446-008-0059-z
4802. Stéphane Ransac, Nicolas Parisey, Jean-Pierre Mazat. The loneliness of the electrons in the bc1 complex. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2008, 1777 (7-8) , 1053-1059. https://doi.org/10.1016/j.bbabio.2008.05.003
4803. Shigehiro Miura, Tetsuya Shimokawa, Taishin Nomura. Stochastic simulations on a model of circadian rhythm generation. Biosystems 2008, 93 (1-2) , 133-140. https://doi.org/10.1016/j.biosystems.2008.05.002
4804. Ying Wang, Qianshu Li. System-size resonance for intracellular and intercellular calcium signaling. Biophysical Chemistry 2008, 136 (1) , 32-37. https://doi.org/10.1016/j.bpc.2008.04.003
4805. Corbett C. Battaile. The Kinetic Monte Carlo method: Foundation, implementation, and application. Computer Methods in Applied Mechanics and Engineering 2008, 197 (41-42) , 3386-3398. https://doi.org/10.1016/j.cma.2008.03.010
4806. Katrin Rohlf, Simon Fraser, Raymond Kapral. Reactive multiparticle collision dynamics. Computer Physics Communications 2008, 179 (1-3) , 132-139. https://doi.org/10.1016/j.cpc.2008.01.027
4807. Robert C. Hilborn, Jessie D. Erwin. Stochastic coherence in an oscillatory gene circuit model. Journal of Theoretical Biology 2008, 253 (2) , 349-354. https://doi.org/10.1016/j.jtbi.2008.03.012
4808. Moxun Tang. The mean and noise of stochastic gene transcription. Journal of Theoretical Biology 2008, 253 (2) , 271-280. https://doi.org/10.1016/j.jtbi.2008.03.023
4809. Ni Ming, Wang Si-Yuan, Ouyang Qi. Modelling the SOS Response by Semi-Stochastic Simulation. Chinese Physics Letters 2008, 25 (7) , 2702-2705. https://doi.org/10.1088/0256-307X/25/7/102
4810. Cécile Monthus, Thomas Garel. Non-equilibrium dynamics of disordered systems: renormalization flow towards an ‘infinite disorder’ fixed point at large times. Journal of Statistical Mechanics: Theory and Experiment 2008, 2008 (07) , P07002. https://doi.org/10.1088/1742-5468/2008/07/P07002
4811. Marc Benayoun, Edward Wallace, Tanya Baker, Jack Cowan, Wim van Drongelen. Biologically plausible statistics from a Markov model of spiking cortical networks. BMC Neuroscience 2008, 9 (S1) https://doi.org/10.1186/1471-2202-9-S1-P38
4812. Lorin S. Milescu, Tadashi Yamanishi, Krzysztof Ptak, Murtaza Z. Mogri, Jeffrey C. Smith. Real-Time Kinetic Modeling of Voltage-Gated Ion Channels Using Dynamic Clamp. Biophysical Journal 2008, 95 (1) , 66-87. https://doi.org/10.1529/biophysj.107.118190
4813. Pankaj Mehta, Ranjan Mukhopadhyay, Ned S Wingreen. Exponential sensitivity of noise-driven switching in genetic networks. Physical Biology 2008, 5 (2) , 026005. https://doi.org/10.1088/1478-3975/5/2/026005
4814. Richard P. Sear. Nucleation in the presence of slow microscopic dynamics. The Journal of Chemical Physics 2008, 128 (21) , 214513. https://doi.org/10.1063/1.2928844
4815. Luca Bortolussi, Alberto Policriti. Modeling Biological Systems in Stochastic Concurrent Constraint Programming. Constraints 2008, 13 (1-2) , 66-90. https://doi.org/10.1007/s10601-007-9034-8
4816. R. J. Boys, D. J. Wilkinson, T. B. L. Kirkwood. Bayesian inference for a discretely observed stochastic kinetic model. Statistics and Computing 2008, 18 (2) , 125-135. https://doi.org/10.1007/s11222-007-9043-x
4817. Amitabha Nandi, Ram Ramaswamy. Synchronization of coupled stochastic oscillators: The effect of topology. Pramana 2008, 70 (6) , 1165-1174. https://doi.org/10.1007/s12043-008-0121-1
4818. Vladimir P. Zhdanov. Kinetic oscillations in the expression of messenger RNA, regulatory protein, and nonprotein coding RNA. Chemical Physics Letters 2008, 458 (4-6) , 359-362. https://doi.org/10.1016/j.cplett.2008.04.111
4819. Yubing Gong, Bo Xu, Xiaoguang Ma. Enhancement of stochastic reaction rate oscillations by external noise in CO oxidation on nanometer-sized Pd particles. Chemical Physics Letters 2008, 458 (4-6) , 351-354. https://doi.org/10.1016/j.cplett.2008.05.014
4820. A.G. Rossberg. Part–whole relations between food webs and the validity of local food-web descriptions. Ecological Complexity 2008, 5 (2) , 121-131. https://doi.org/10.1016/j.ecocom.2008.02.003
4821. Joel Z. Bandstra, Susan L. Brantley. Surface evolution of dissolving minerals investigated with a kinetic Ising model. Geochimica et Cosmochimica Acta 2008, 72 (11) , 2587-2600. https://doi.org/10.1016/j.gca.2008.02.023
4822. David Thorsley, Eric Klavins. Model reduction of stochastic processes using Wasserstein pseudometrics. 2008,,, 1374-1381. https://doi.org/10.1109/ACC.2008.4586684
4823. Brian Munsky, Mustafa Khammash. Computation of switch time distributions in stochastic gene regulatory networks. 2008,,, 2761-2766. https://doi.org/10.1109/ACC.2008.4586911
4824. Sivakumar Pitchaiah, Antonios Armaou. Online system-identification using subspace algorithms for the control of microscopic processes. 2008,,, 4413-4418. https://doi.org/10.1109/ACC.2008.4587189
4825. Matthias Jeschke, Alfred Park, Roland Ewald, Richard Fujimoto, Adelinde M. Uhrmacher. Parallel and Distributed Spatial Simulation of Chemical Reactions. 2008,,, 51-59. https://doi.org/10.1109/PADS.2008.20
4826. Erik De Schutter, . Why Are Computational Neuroscience and Systems Biology So Separate?. PLoS Computational Biology 2008, 4 (5) , e1000078. https://doi.org/10.1371/journal.pcbi.1000078
4827. André Leier, Tatiana T. Marquez-Lago, Kevin Burrage. Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise. The Journal of Chemical Physics 2008, 128 (20) , 205107. https://doi.org/10.1063/1.2919124
4828. Alexander Slepoy, Aidan P. Thompson, Steven J. Plimpton. A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks. The Journal of Chemical Physics 2008, 128 (20) , 205101. https://doi.org/10.1063/1.2919546
4829. Gerhard Stock, Kingshuk Ghosh, Ken A. Dill. Maximum Caliber: A variational approach applied to two-state dynamics. The Journal of Chemical Physics 2008, 128 (19) , 194102. https://doi.org/10.1063/1.2918345
4830. Jason M. Haugh. Mathematical Modelling of Biological Signaling Networks. 2008,,https://doi.org/10.1002/9780470048672.wecb646
4831. Sean M. Cory, Theodore J. Perkins, . Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation. PLoS Computational Biology 2008, 4 (5) , e1000064. https://doi.org/10.1371/journal.pcbi.1000064
4832. Vladimir P. Zhdanov. Interplay of master regulatory proteins and mRNA in gene expression: 3D Monte Carlo simulations. Chemical Physics Letters 2008, 456 (4-6) , 247-252. https://doi.org/10.1016/j.cplett.2008.03.047
4833. Zheming Zheng, Ryan M. Stephens, Richard D. Braatz, Richard C. Alkire, Linda R. Petzold. A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition. Journal of Computational Physics 2008, 227 (10) , 5184-5199. https://doi.org/10.1016/j.jcp.2008.01.056
4834. Joseph Fass, Chi Pak, James Bamburg, Alex Mogilner. Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation. Journal of Theoretical Biology 2008, 252 (1) , 173-183. https://doi.org/10.1016/j.jtbi.2008.01.001
4835. Andr Horv, Daniele Manini. Parameter Estimation of Kinetic Rates in Stochastic Reaction Networks by the EM Method. 2008,,, 713-717. https://doi.org/10.1109/BMEI.2008.237
4836. Petar M. Djuric, Monica F. Bugallo, Vibha Mane. On new stochastic approaches for solving forward and backward problems of biochemical networks. 2008,,, 99-103. https://doi.org/10.1109/ITW.2008.4578630
4837. Marco J. Morelli, Sorin Tănase-Nicola, Rosalind J. Allen, Pieter Rein ten Wolde. Reaction Coordinates for the Flipping of Genetic Switches. Biophysical Journal 2008, 94 (9) , 3413-3423. https://doi.org/10.1529/biophysj.107.116699
4838. Yueheng Lan, Garegin A. Papoian. The Stochastic Dynamics of Filopodial Growth. Biophysical Journal 2008, 94 (10) , 3839-3852. https://doi.org/10.1529/biophysj.107.123778
4839. Xiudeng Zheng, Yi Tao. Additivity of noise propagation in a protein cascade. The Journal of Chemical Physics 2008, 128 (16) , 165104. https://doi.org/10.1063/1.2897919
4840. David Andrieux, Pierre Gaspard. Fluctuation theorem and mesoscopic chemical clocks. The Journal of Chemical Physics 2008, 128 (15) , 154506. https://doi.org/10.1063/1.2894475
4841. Zhouyi Xu, Xiaodong Cai. Unbiased τ-leap methods for stochastic simulation of chemically reacting systems. The Journal of Chemical Physics 2008, 128 (15) , 154112. https://doi.org/10.1063/1.2894479
4842. Simone Pigolotti, Angelo Vulpiani. Coarse graining of master equations with fast and slow states. The Journal of Chemical Physics 2008, 128 (15) , 154114. https://doi.org/10.1063/1.2907242
4843. Jun Ohkubo, Nadav Shnerb, David A. Kessler. Transition Phenomena Induced by Internal Noise and Quasi-Absorbing State. Journal of the Physical Society of Japan 2008, 77 (4) , 044002. https://doi.org/10.1143/JPSJ.77.044002
4844. João B. P. Soares, A. E. Hamielec. Chain Length Distributions of Polyolefins Made in Stopped-Flow Reactors for Non-Instantaneous Site Activation. Macromolecular Reaction Engineering 2008, 2 (2) , 115-125. https://doi.org/10.1002/mren.200700043
4845. Hanh T.H Nguyen, Pejman Rohani. Noise, nonlinearity and seasonality: the epidemics of whooping cough revisited. Journal of The Royal Society Interface 2008, 5 (21) , 403-413. https://doi.org/10.1098/rsif.2007.1168
4846. Jordi Ferrer, Clara Prats, Daniel López. Individual-based Modelling: An Essential Tool for Microbiology. Journal of Biological Physics 2008, 34 (1-2) , 19-37. https://doi.org/10.1007/s10867-008-9082-3
4847. Fu Zheng-Ping, Xu Xin-Hang, Wang Hong-Li, Ouyang Qi. Stochastic Simulation of Turing Patterns. Chinese Physics Letters 2008, 25 (4) , 1220-1223. https://doi.org/10.1088/0256-307X/25/4/016
4848. Amodsen Chotia, Matthieu Viteau, Thibault Vogt, Daniel Comparat, Pierre Pillet. Kinetic Monte Carlo modeling of dipole blockade in Rydberg excitation experiment. New Journal of Physics 2008, 10 (4) , 045031. https://doi.org/10.1088/1367-2630/10/4/045031
4849. David Lepzelter, Jin Wang. Exact probabilistic solution of spatial-dependent stochastics and associated spatial potential landscape for the bicoid protein. Physical Review E 2008, 77 (4) https://doi.org/10.1103/PhysRevE.77.041917
4850. Bastien Fernandez, Lev S. Tsimring. Athermal Dynamics of Strongly Coupled Stochastic Three-State Oscillators. Physical Review Letters 2008, 100 (16) https://doi.org/10.1103/PhysRevLett.100.165705
4851. Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano. Stochastic models for the in silico simulation of synaptic processes. BMC Bioinformatics 2008, 9 (S4) https://doi.org/10.1186/1471-2105-9-S4-S7
4852. Ralf Jungmann, Stephan Renner, Friedrich C. Simmel. From DNA nanotechnology to synthetic biology. HFSP Journal 2008, 2 (2) , 99-109. https://doi.org/10.2976/1.2896331
4853. Thomas C. Castonguay, Feng Wang. Kinetic Monte Carlo modeling of chemical reactions coupled with heat transfer. The Journal of Chemical Physics 2008, 128 (12) , 124706. https://doi.org/10.1063/1.2877443
4854. J. F. Cahoon, K. R. Sawyer, J. P. Schlegel, C. B. Harris. Determining Transition-State Geometries in Liquids Using 2D-IR. Science 2008, 319 (5871) , 1820-1823. https://doi.org/10.1126/science.1154041
4855. Kamakshi Sureka, Bhaswar Ghosh, Arunava Dasgupta, Joyoti Basu, Manikuntala Kundu, Indrani Bose, . Positive Feedback and Noise Activate the Stringent Response Regulator Rel in Mycobacteria. PLoS ONE 2008, 3 (3) , e1771. https://doi.org/10.1371/journal.pone.0001771
4856. Edward J. Allen, Linda J. S. Allen, Armando Arciniega, Priscilla E. Greenwood. Construction of Equivalent Stochastic Differential Equation Models. Stochastic Analysis and Applications 2008, 26 (2) , 274-297. https://doi.org/10.1080/07362990701857129
4857. Wen Zhou, Xin-jun Peng, Xiang Liu, Zheng-lou Yan, Yi-fei Wang. “Final all possible steps” approach for accelerating stochastic simulation of coupled chemical reactions. Applied Mathematics and Mechanics 2008, 29 (3) , 379-387. https://doi.org/10.1007/s10483-008-0309-x
4858. J. Timmis, P. Andrews, N. Owens, E. Clark. An interdisciplinary perspective on artificial immune systems. Evolutionary Intelligence 2008, 1 (1) , 5-26. https://doi.org/10.1007/s12065-007-0004-2
4859. Antoine Spicher, Olivier Michel, Mikolaj Cieslak, Jean-Louis Giavitto, Przemyslaw Prusinkiewicz. Stochastic P systems and the simulation of biochemical processes with dynamic compartments. Biosystems 2008, 91 (3) , 458-472. https://doi.org/10.1016/j.biosystems.2006.12.009
4860. F. Fontana, V. Manca. Predator–prey dynamics in P systems ruled by metabolic algorithm. Biosystems 2008, 91 (3) , 545-557. https://doi.org/10.1016/j.biosystems.2006.12.010
4861. Daniela Besozzi, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri. Modelling metapopulations with stochastic membrane systems. Biosystems 2008, 91 (3) , 499-514. https://doi.org/10.1016/j.biosystems.2006.12.011
4862. David W. Corne, Pierluigi Frisco. Dynamics of HIV infection studied with cellular automata and conformon-P systems. Biosystems 2008, 91 (3) , 531-544. https://doi.org/10.1016/j.biosystems.2007.01.007
4863. Francisco José Romero-Campero, Mario J. Pérez-Jiménez. Modelling gene expression control using P systems: The Lac Operon, a case study. Biosystems 2008, 91 (3) , 438-457. https://doi.org/10.1016/j.biosystems.2007.02.011
4864. Dan V. Nicolau, Kevin Burrage. Stochastic simulation of chemical reactions in spatially complex media. Computers & Mathematics with Applications 2008, 55 (5) , 1007-1018. https://doi.org/10.1016/j.camwa.2006.12.085
4865. A.M. Bersani, E. Bersani, L. Mastroeni. Deterministic and stochastic models of enzymatic networks—applications to pharmaceutical research. Computers & Mathematics with Applications 2008, 55 (5) , 879-888. https://doi.org/10.1016/j.camwa.2006.12.092
4866. Attila Felinger. Molecular dynamic theories in chromatography. Journal of Chromatography A 2008, 1184 (1-2) , 20-41. https://doi.org/10.1016/j.chroma.2007.12.066
4867. David Andrieux, Pierre Gaspard. Temporal disorder and fluctuation theorem in chemical reactions. Physical Review E 2008, 77 (3) https://doi.org/10.1103/PhysRevE.77.031137
4868. Monica F. Bugallo, Petar M. Djuric. A stochastic approach to solving inverse problems of biochemical networks. 2008,,, 649-652. https://doi.org/10.1109/ICASSP.2008.4517693
4869. Zhouyi Xu, Xiaodong Cai. Unbiased τ-leap methods for stochastic simulation of biochemical systems. 2008,,, 657-660. https://doi.org/10.1109/ICASSP.2008.4517695
4870. MARKO GOSAK, MARKO MARHL, MATJAŽ PERC. CHAOS BETWEEN STOCHASTICITY AND PERIODICITY IN THE PRISONER'S DILEMMA GAME. International Journal of Bifurcation and Chaos 2008, 18 (03) , 869-875. https://doi.org/10.1142/S0218127408020720
4871. Stephen Gilmore, Jane Hillston. Performance evaluation comes to life. ACM SIGMETRICS Performance Evaluation Review 2008, 35 (4) , 3-13. https://doi.org/10.1145/1364644.1364650
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4873. Matthias Jeschke, Roland Ewald, Alfred Park, Richard Fujimoto, Adelinde M. Uhrmacher. A parallel and distributed discrete event approach for spatial cell-biological simulations. ACM SIGMETRICS Performance Evaluation Review 2008, 35 (4) , 22-31. https://doi.org/10.1145/1364644.1364652
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4886. Sangram Bagh, Mostafizur Mazumder, Tharsan Velauthapillai, Vandit Sardana, Guang Qiang Dong, Ashok B. Movva, Len H. Lim, David R. McMillen. Plasmid-borne prokaryotic gene expression: Sources of variability and quantitative system characterization. Physical Review E 2008, 77 (2) https://doi.org/10.1103/PhysRevE.77.021919
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4951. Francisco J. Romero-Campero, Mario J. Pérez-Jiménez. A Model of the Quorum Sensing System in Vibrio fischeri Using P Systems. Artificial Life 2008, 14 (1) , 95-109. https://doi.org/10.1162/artl.2008.14.1.95
4952. Margaritis Voliotis, Netta Cohen, Carmen Molina-París, Tanniemola B. Liverpool. Fluctuations, Pauses, and Backtracking in DNA Transcription. Biophysical Journal 2008, 94 (2) , 334-348. https://doi.org/10.1529/biophysj.107.105767
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4959. Gowri Srinivasan, Daniel M. Tartakovsky, Bruce A. Robinson, Alejandro B. Aceves. Quantification of uncertainty in geochemical reactions. Water Resources Research 2007, 43 (12) https://doi.org/10.1029/2007WR006003
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4966. Carole J Proctor, Maria Tsirigotis, Douglas A Gray. An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline. BMC Systems Biology 2007, 1 (1) https://doi.org/10.1186/1752-0509-1-17
4967. YuFeng Wu, Ekaterina Myasnikova, John Reinitz. Master equation simulation analysis of immunostained Bicoid morphogen gradient. BMC Systems Biology 2007, 1 (1) https://doi.org/10.1186/1752-0509-1-52
4968. Vassilios Sotiropoulos, Yiannis N Kaznessis. Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. BMC Systems Biology 2007, 1 (1) https://doi.org/10.1186/1752-0509-1-7
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4987. Ernest W. Tollner, Caner Kazanci. Defining an ecological thermodynamics using discrete simulation approaches. Ecological Modelling 2007, 208 (1) , 68-79. https://doi.org/10.1016/j.ecolmodel.2007.04.030
4988. Caner Kazancı. EcoNet: A new software for ecological modeling, simulation and network analysis. Ecological Modelling 2007, 208 (1) , 3-8. https://doi.org/10.1016/j.ecolmodel.2007.04.031
4989. H. Kimura, H. Okano, R.J. Tanaka. Stochastic approach to molecular interactions and computational theory of metabolic and genetic regulations. Journal of Theoretical Biology 2007, 248 (4) , 590-607. https://doi.org/10.1016/j.jtbi.2007.06.017
4990. Amitabha Nandi, Santhosh G., R. K. Brojen Singh, Ram Ramaswamy. Effective mechanisms for the synchronization of stochastic oscillators. Physical Review E 2007, 76 (4) https://doi.org/10.1103/PhysRevE.76.041136
4991. K. M. Puskar, A. Parisi-Amon, S. Ta’asan, R. Schwartz, P. R. LeDuc. Modeling molecular interactions to understand spatial crowding effects on heterodimer formations. Physical Review E 2007, 76 (4) https://doi.org/10.1103/PhysRevE.76.041904
4992. Scott B. Baden, Terrence J. Sejnowski, Thomas M. Bartol, Joel Stiles. Toward Petascale Simulation of Cellular Microphysiology. 2007,,, 628-634. https://doi.org/10.1109/BIBE.2007.4375626
4993. Alessandro Abate, Yu Bai, Nathalie Sznajder, Carolyn Talcott, Ashish Tiwari. Quantitative and Probabilistic Modeling in Pathway Logic. 2007,,, 922-929. https://doi.org/10.1109/BIBE.2007.4375669
4994. Jingwei Zhang, Layne T. Watson. A Modified Uniformization Method for the Chemical Master Equation. 2007,,, 1429-1433. https://doi.org/10.1109/BIBE.2007.4375761
4995. V. S. Gayathri, M. Rao. Fluctuation-induced chiral symmetry breaking in autocatalytic reaction-diffusion systems. Europhysics Letters (EPL) 2007, 80 (2) , 28001. https://doi.org/10.1209/0295-5075/80/28001
4996. Guang Qiang Dong, Luke Jakobowski, Marco A. J. Iafolla, David R. McMillen. Simplification of Stochastic Chemical Reaction Models with Fast and Slow Dynamics. Journal of Biological Physics 2007, 33 (1) , 67-95. https://doi.org/10.1007/s10867-007-9043-2
4997. Chantal Valeriani, Rosalind J. Allen, Marco J. Morelli, Daan Frenkel, Pieter Rein ten Wolde. Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling. The Journal of Chemical Physics 2007, 127 (11) , 114109. https://doi.org/10.1063/1.2767625
4998. Yurie Okabe, Yuu Yagi, Masaki Sasai. Effects of the DNA state fluctuation on single-cell dynamics of self-regulating gene. The Journal of Chemical Physics 2007, 127 (10) , 105107. https://doi.org/10.1063/1.2768353
4999. Tatiana T. Marquez-Lago, Kevin Burrage. Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics. The Journal of Chemical Physics 2007, 127 (10) , 104101. https://doi.org/10.1063/1.2771548
5000. Ben Harland, Sean X. Sun. Path ensembles and path sampling in nonequilibrium stochastic systems. The Journal of Chemical Physics 2007, 127 (10) , 104103. https://doi.org/10.1063/1.2775439
5001. Georg Fritz, Nicolas E. Buchler, Terence Hwa, Ulrich Gerland. Designing sequential transcription logic: a simple genetic circuit for conditional memory. Systems and Synthetic Biology 2007, 1 (2) , 89-98. https://doi.org/10.1007/s11693-007-9006-8
5002. Ethan A. Mastny, Eric L. Haseltine, James B. Rawlings. Two classes of quasi-steady-state model reductions for stochastic kinetics. The Journal of Chemical Physics 2007, 127 (9) , 094106. https://doi.org/10.1063/1.2764480
5003. Luca Bortolussi, Alberto Policriti. Stochastic Concurrent Constraint Programming and Differential Equations. Electronic Notes in Theoretical Computer Science 2007, 190 (3) , 27-42. https://doi.org/10.1016/j.entcs.2007.07.003
5004. Brian Munsky, Mustafa Khammash. A multiple time interval finite state projection algorithm for the solution to the chemical master equation. Journal of Computational Physics 2007, 226 (1) , 818-835. https://doi.org/10.1016/j.jcp.2007.05.016
5005. Adam Bobrowski, Tomasz Lipniacki, Katarzyna Pichór, Ryszard Rudnicki. Asymptotic behavior of distributions of mRNA and protein levels in a model of stochastic gene expression. Journal of Mathematical Analysis and Applications 2007, 333 (2) , 753-769. https://doi.org/10.1016/j.jmaa.2006.11.043
5006. Chen Xiao, Ao Ling. Accelerated Stochastic Simulation of Large Chemical Systems. Chinese Physics Letters 2007, 24 (9) , 2509-2512. https://doi.org/10.1088/0256-307X/24/9/013
5007. Jun Ohkubo. A field theoretic approach to master equations and a variational method beyond the Poisson ansatz. Journal of Statistical Mechanics: Theory and Experiment 2007, 2007 (09) , P09017-P09017. https://doi.org/10.1088/1742-5468/2007/09/P09017
5008. M. Andrecut, S.A. Kauffman. A Physical Analogy of the Genetic Toggle Switch. Journal of Computational Biology 2007, 14 (7) , 973-983. https://doi.org/10.1089/cmb.2007.0038
5009. Dominique Chu. Evolving genetic regulatory networks for systems biology. 2007,,, 875-882. https://doi.org/10.1109/CEC.2007.4424562
5010. Luca Bianco, Vincenzo Manca, Luca Marchetti, Michele Petterlini. Psim: a simulator for biomolecular dynamics based on P systems. 2007,,, 883-887. https://doi.org/10.1109/CEC.2007.4424563
5011. Luca Cardelli. Invited Talk: A Process Algebra Master Equation. 2007,,, 219-226. https://doi.org/10.1109/QEST.2007.26
5012. Tiequan Zhang, Woo Tae Kim, Russell Schwartz. Investigating Scaling Effects on Virus Capsid-Like Self-Assembly Using Discrete Event Simulations. IEEE Transactions on NanoBioscience 2007, 6 (3) , 235-241. https://doi.org/10.1109/TNB.2007.903484
5013. Jonathan M. Read, Matt J. Keeling. Stochasticity generates an evolutionary instability for infectious disease. Ecology Letters 2007, 10 (9) , 818-827. https://doi.org/10.1111/j.1461-0248.2007.01078.x
5014. S. Rüdiger, J.W. Shuai, W. Huisinga, C. Nagaiah, G. Warnecke, I. Parker, M. Falcke. Hybrid Stochastic and Deterministic Simulations of Calcium Blips. Biophysical Journal 2007, 93 (6) , 1847-1857. https://doi.org/10.1529/biophysj.106.099879
5015. Hugh Chaffey-Millar, Don Stewart, Manuel M. T. Chakravarty, Gabriele Keller, Christopher Barner-Kowollik. A Parallelised High Performance Monte Carlo Simulation Approach for Complex Polymerisation Kinetics. Macromolecular Theory and Simulations 2007, 16 (6) , 575-592. https://doi.org/10.1002/mats.200700028
5016. P. Ranjith, J. Yan, J. F. Marko. Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts. Proceedings of the National Academy of Sciences 2007, 104 (34) , 13649-13654. https://doi.org/10.1073/pnas.0701459104
5017. Erel Levine, Zhongge Zhang, Thomas Kuhlman, Terence Hwa, . Quantitative Characteristics of Gene Regulation by Small RNA. PLoS Biology 2007, 5 (9) , e229. https://doi.org/10.1371/journal.pbio.0050229
5018. G. C. P. Innocentini, J. E. M. Hornos. Modeling stochastic gene expression under repression. Journal of Mathematical Biology 2007, 55 (3) , 413-431. https://doi.org/10.1007/s00285-007-0090-x
5019. Helen J. Edwards, Calvin Dytham, Jonathan W. Pitchford, David Righton. Prey Selection, Vertical Migrations and the Impacts of Harvesting Upon the Population Dynamics of a Predator-Prey System. Bulletin of Mathematical Biology 2007, 69 (6) , 1827-1846. https://doi.org/10.1007/s11538-007-9194-0
5020. Mark F. Schumaker. Single-Occupancy Binding in Simple Bounded and Unbounded Systems. Bulletin of Mathematical Biology 2007, 69 (6) , 1979-2003. https://doi.org/10.1007/s11538-007-9201-5
5021. Nicola Bruti-Liberati, Eckhard Platen. Strong approximations of stochastic differential equations with jumps. Journal of Computational and Applied Mathematics 2007, 205 (2) , 982-1001. https://doi.org/10.1016/j.cam.2006.03.040
5022. Chaitanya S. Deo, Maria A. Okuniewski, Srinivasan G. Srivilliputhur, Stuart A. Maloy, Mike I. Baskes, Michael R. James, James F. Stubbins. The effects of helium on irradiation damage in single crystal iron. Journal of Nuclear Materials 2007, 367-370 , 451-456. https://doi.org/10.1016/j.jnucmat.2007.03.117
5023. Yi Tao, Xiudeng Zheng, Yuehua Sun. Effect of feedback regulation on stochastic gene expression. Journal of Theoretical Biology 2007, 247 (4) , 827-836. https://doi.org/10.1016/j.jtbi.2007.03.024
5024. P. Gaspard, E. Gerritsma. The stochastic chemomechanics of the -ATPase molecular motor. Journal of Theoretical Biology 2007, 247 (4) , 672-686. https://doi.org/10.1016/j.jtbi.2007.03.034
5025. Andre S. Ribeiro, Stuart A. Kauffman. Noisy attractors and ergodic sets in models of gene regulatory networks. Journal of Theoretical Biology 2007, 247 (4) , 743-755. https://doi.org/10.1016/j.jtbi.2007.04.020
5026. C. P. Calderon. Local diffusion models for stochastic reacting systems: estimation issues in equation-free numerics. Molecular Simulation 2007, 33 (9-10) , 713-731. https://doi.org/10.1080/08927020701344740
5027. Maciej Dobrzyński, Jordi Vidal Rodríguez, Jaap A. Kaandorp, Joke G. Blom. Computational methods for diffusion-influenced biochemical reactions. Bioinformatics 2007, 23 (15) , 1969-1977. https://doi.org/10.1093/bioinformatics/btm278
5028. Jianzhong Hu, Stuart C. Sealfon, Fernand Hayot, Ciriyam Jayaprakash, Madhu Kumar, Audrey C. Pendleton, Arnaud Ganee, Ana Fernandez-Sesma, Thomas M. Moran, James G. Wetmur. Chromosome-specific and noisy IFNB1 transcription in individual virus-infected human primary dendritic cells. Nucleic Acids Research 2007, 35 (15) , 5232-5241. https://doi.org/10.1093/nar/gkm557
5029. Manoj Gopalakrishnan, Peter Borowski, Frank Jülicher, Martin Zapotocky. Response and fluctuations of a two-state signaling module with feedback. Physical Review E 2007, 76 (2) https://doi.org/10.1103/PhysRevE.76.021904
5030. Baruch Barzel, Ofer Biham, Raz Kupferman. Evaluation of the multiplane method for efficient simulations of reaction networks. Physical Review E 2007, 76 (2) https://doi.org/10.1103/PhysRevE.76.026703
5031. Youfang Cao, Jie Liang. An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules. 2007,,, 4599-4602. https://doi.org/10.1109/IEMBS.2007.4353364
5032. K. F. Murphy, G. Balazsi, J. J. Collins. Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences 2007, 104 (31) , 12726-12731. https://doi.org/10.1073/pnas.0608451104
5033. R. R. Vallabhajosyula, H. M. Sauro. Stochastic simulation GUI for biochemical networks. Bioinformatics 2007, 23 (14) , 1859-1861. https://doi.org/10.1093/bioinformatics/btm231
5034. Paola Lecca, Corrado Priami. Cell Cycle Control in Eukaryotes: A BioSpi model. Electronic Notes in Theoretical Computer Science 2007, 180 (3) , 51-63. https://doi.org/10.1016/j.entcs.2004.08.072
5035. Matteo Cavaliere, Sean Sedwards. Membrane Systems with Peripheral Proteins: Transport and Evolution. Electronic Notes in Theoretical Computer Science 2007, 171 (2) , 37-53. https://doi.org/10.1016/j.entcs.2007.05.006
5036. Federica Ciocchetta, Corrado Priami. Biological Transactions for Quantitative Models. Electronic Notes in Theoretical Computer Science 2007, 171 (2) , 55-67. https://doi.org/10.1016/j.entcs.2007.05.007
5037. Verena Wolf. Modelling of Biochemical Reactions by Stochastic Automata Networks. Electronic Notes in Theoretical Computer Science 2007, 171 (2) , 197-208. https://doi.org/10.1016/j.entcs.2007.05.017
5038. M.E. Kavousanakis, R. Erban, A.G. Boudouvis, C.W. Gear, I.G. Kevrekidis. Projective and coarse projective integration for problems with continuous symmetries. Journal of Computational Physics 2007, 225 (1) , 382-407. https://doi.org/10.1016/j.jcp.2006.12.003
5039. Robert J. Conrado, Thomas J. Mansell, Jeffrey D. Varner, Matthew P. DeLisa. Stochastic reaction–diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway. Metabolic Engineering 2007, 9 (4) , 355-363. https://doi.org/10.1016/j.ymben.2007.05.002
5040. M. Ullah, O. Wolkenhauer. Family tree of Markov models in systems biology. IET Systems Biology 2007, 1 (4) , 247-254. https://doi.org/10.1049/iet-syb:20070017
5041. Yi Ming, Jia Ya, Liu Quan, Zhu Chun-Lian, Yang Li-Jian. A Coarse Estimation of Cell Size Region from a Mesoscopic Stochastic Cell Cycle Model. Chinese Physics Letters 2007, 24 (7) , 1829-1832. https://doi.org/10.1088/0256-307X/24/7/012
5042. Shannon F. Stewman, Aaron R. Dinner. Lattice model for self-assembly with application to the formation of cytoskeletal-like structures. Physical Review E 2007, 76 (1) https://doi.org/10.1103/PhysRevE.76.016103
5043. Johan Ugander, Mary J. Dunlop, Richard M. Murray. Analysis of a Digital Clock for Molecular Computing. 2007,,, 1595-1599. https://doi.org/10.1109/ACC.2007.4282583
5044. Shrikant V. Savant. Stochastic Simulation Techniques in Systems Biology. 2007,,, 1311-1316. https://doi.org/10.1109/ACC.2007.4283011
5045. Brian Munsky, Slaven Peles, Mustafa Khammash. Stochastic analysis of gene regulatory networks using finite state projections and singular perturbation. 2007,,, 1323-1328. https://doi.org/10.1109/ACC.2007.4283077
5046. Ming Ni, Si-Yuan Wang, Ji-Kun Li, Qi Ouyang. Simulating the Temporal Modulation of Inducible DNA Damage Response in Escherichia coli. Biophysical Journal 2007, 93 (1) , 62-73. https://doi.org/10.1529/biophysj.106.090712
5047. Masahiro Ueda, Tatsuo Shibata. Stochastic Signal Processing and Transduction in Chemotactic Response of Eukaryotic Cells. Biophysical Journal 2007, 93 (1) , 11-20. https://doi.org/10.1529/biophysj.106.100263
5048. Daniel Schultz, José N. Onuchic, Peter G. Wolynes. Understanding stochastic simulations of the smallest genetic networks. The Journal of Chemical Physics 2007, 126 (24) , 245102. https://doi.org/10.1063/1.2741544
5049. Bruno Delord, Hugues Berry, Emmanuel Guigon, Stéphane Genet, . A New Principle for Information Storage in an Enzymatic Pathway Model. PLoS Computational Biology 2007, 3 (6) , e124. https://doi.org/10.1371/journal.pcbi.0030124
5050. Pawel Paszek. Modeling Stochasticity in Gene Regulation: Characterization in the Terms of the Underlying Distribution Function. Bulletin of Mathematical Biology 2007, 69 (5) , 1567-1601. https://doi.org/10.1007/s11538-006-9176-7
5051. Melissa Vellela, Hong Qian. A Quasistationary Analysis of a Stochastic Chemical Reaction: Keizer’s Paradox. Bulletin of Mathematical Biology 2007, 69 (5) , 1727-1746. https://doi.org/10.1007/s11538-006-9188-3
5052. Xinjun Peng, Wen Zhou, Yifei Wang. Efficient binomial leap method for simulating chemical kinetics. The Journal of Chemical Physics 2007, 126 (22) , 224109. https://doi.org/10.1063/1.2741252
5053. Yang Cao, Daniel T. Gillespie, Linda R. Petzold. Adaptive explicit-implicit tau-leaping method with automatic tau selection. The Journal of Chemical Physics 2007, 126 (22) , 224101. https://doi.org/10.1063/1.2745299
5054. Jaewook Joo, Eric Harvill, Réka Albert. Effects of Noise on Ecological Invasion Processes: Bacteriophage-Mediated Competition in Bacteria. Journal of Statistical Physics 2007, 128 (1-2) , 229-256. https://doi.org/10.1007/s10955-006-9182-z
5055. Claudia Lerma, Trine Krogh-Madsen, Michael Guevara, Leon Glass. Stochastic Aspects of Cardiac Arrhythmias. Journal of Statistical Physics 2007, 128 (1-2) , 347-374. https://doi.org/10.1007/s10955-006-9191-y
5056. Beata Hat, Pawel Paszek, Marek Kimmel, Kazimierz Piechor, Tomasz Lipniacki. How the Number of Alleles Influences Gene Expression. Journal of Statistical Physics 2007, 128 (1-2) , 511-533. https://doi.org/10.1007/s10955-006-9218-4
5057. Mamdouh Al-Harthi, Long Shun Cheng, João B. P. Soares, Leonardo C. Simon. Atom-transfer radical polymerization of styrene with bifunctional and monofunctional initiators: Experimental and mathematical modeling results. Journal of Polymer Science Part A: Polymer Chemistry 2007, 45 (11) , 2212-2224. https://doi.org/10.1002/pola.21988
5058. Matteo Casadei, Luca Gardelli, Mirko Viroli. Simulating Emergent Properties of Coordination in Maude: the Collective Sort Case. Electronic Notes in Theoretical Computer Science 2007, 175 (2) , 59-80. https://doi.org/10.1016/j.entcs.2007.05.022
5059. Muruhan Rathinam, Hana El Samad. Reversible-equivalent-monomolecular tau: A leaping method for “small number and stiff” stochastic chemical systems. Journal of Computational Physics 2007, 224 (2) , 897-923. https://doi.org/10.1016/j.jcp.2006.10.034
5060. Rui Zhu, Andre S. Ribeiro, Dennis Salahub, Stuart A. Kauffman. Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models. Journal of Theoretical Biology 2007, 246 (4) , 725-745. https://doi.org/10.1016/j.jtbi.2007.01.021
5061. Edoardo Milotti, Alessio Del Fabbro, Chiara Dalla Pellegrina, Roberto Chignola. Dynamics of allosteric action in multisite protein modification. Physica A: Statistical Mechanics and its Applications 2007, 379 (1) , 133-150. https://doi.org/10.1016/j.physa.2006.12.034
5062. M. Pineda, L. Schimansky-Geier, R Imbihl. Fluctuation-induced phase transition in a spatially extended model for catalytic CO oxidation. Physical Review E 2007, 75 (6) https://doi.org/10.1103/PhysRevE.75.061107
5063. Andre S. Ribeiro. Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions. Physical Review E 2007, 75 (6) https://doi.org/10.1103/PhysRevE.75.061903
5064. Tiina Manninen, Andre Ribeiro, Jason Lloyd-Price, Marja-Leena Linne, Keijo Ruohonen, Olli Yli-Harja, Stuart A. Kauffman. Parameter Estimation and Tuning of Firefly Luciferase Pathway Model. 2007,,, 1-4. https://doi.org/10.1109/GENSIPS.2007.4365829
5065. Y. Chushak, B. Foy, J. Frazier. Stochastic Simulations of Cellular Biological Processes. 2007,,, 425-429. https://doi.org/10.1109/HPCMP-UGC.2007.70
5066. Daniel Forger, Didier Gonze, David Virshup, David K. Welsh. Beyond Intuitive Modeling: Combining Biophysical Models with Innovative Experiments to Move the Circadian Clock Field Forward. Journal of Biological Rhythms 2007, 22 (3) , 200-210. https://doi.org/10.1177/0748730407301823
5067. Tao You, Alistair JP Brown, George M Coghill. A quantitative model for the GCN4 translational control in Saccharomyces cerevisiae. BMC Systems Biology 2007, 1 (S1) https://doi.org/10.1186/1752-0509-1-S1-P1
5068. Joseph Levine, Hao Yuan Kueh, Leonid Mirny. Intrinsic Fluctuations, Robustness, and Tunability in Signaling Cycles. Biophysical Journal 2007, 92 (12) , 4473-4481. https://doi.org/10.1529/biophysj.106.088856
5069. Nikos V. Mantzaris. From Single-Cell Genetic Architecture to Cell Population Dynamics: Quantitatively Decomposing the Effects of Different Population Heterogeneity Sources for a Genetic Network with Positive Feedback Architecture. Biophysical Journal 2007, 92 (12) , 4271-4288. https://doi.org/10.1529/biophysj.106.100271
5070. E. Levine, T. Hwa. Stochastic fluctuations in metabolic pathways. Proceedings of the National Academy of Sciences 2007, 104 (22) , 9224-9229. https://doi.org/10.1073/pnas.0610987104
5071. Yi Tao, Ross Cressman. Stochastic Fluctuations Through Intrinsic Noise in Evolutionary Game Dynamics. Bulletin of Mathematical Biology 2007, 69 (4) , 1377-1399. https://doi.org/10.1007/s11538-006-9170-0
5072. Azi Lipshtat. “All possible steps” approach to the accelerated use of Gillespie’s algorithm. The Journal of Chemical Physics 2007, 126 (18) , 184103. https://doi.org/10.1063/1.2730507
5073. Ibrahim M. Maafa, João B. P. Soares, Ali Elkamel. Prediction of Chain Length Distribution of Polystyrene Made in Batch Reactors with Bifunctional Free-Radical Initiators Using Dynamic Monte Carlo Simulation. Macromolecular Reaction Engineering 2007, 1 (3) , 364-383. https://doi.org/10.1002/mren.200700007
5074. Mitsumasa Yoda, Kohei Eguchi, Tomoki P. Terada, Masaki Sasai, . Monomer-Shuffling and Allosteric Transition in KaiC Circadian Oscillation. PLoS ONE 2007, 2 (5) , e408. https://doi.org/10.1371/journal.pone.0000408
5075. Chrisantha Fernando, Günter Von Kiedrowski, Eörs Szathmáry. A Stochastic Model of Nonenzymatic Nucleic Acid Replication: “Elongators” Sequester Replicators. Journal of Molecular Evolution 2007, 64 (5) , 572-585. https://doi.org/10.1007/s00239-006-0218-4
5076. Marco A. Huertas, Gregory D. Smith. The dynamics of luminal depletion and the stochastic gating of -activated channels and release sites. Journal of Theoretical Biology 2007, 246 (2) , 332-354. https://doi.org/10.1016/j.jtbi.2007.01.003
5077. R Ewald, C Maus, A Rolfs, A Uhrmacher. Discrete event modelling and simulation in systems biology. Journal of Simulation 2007, 1 (2) , 81-96. https://doi.org/10.1057/palgrave.jos.4250018
5078. Jeroen S. van Zon, David K. Lubensky, Pim R. H. Altena, Pieter Rein ten Wolde. An allosteric model of circadian KaiC phosphorylation. Proceedings of the National Academy of Sciences 2007, 104 (18) , 7420-7425. https://doi.org/10.1073/pnas.0608665104
5079. M. Scott, T. Hwa, B. Ingalls. Deterministic characterization of stochastic genetic circuits. Proceedings of the National Academy of Sciences 2007, 104 (18) , 7402-7407. https://doi.org/10.1073/pnas.0610468104
5080. Refael Abta, Nadav M. Shnerb. Angular velocity variations and stability of spatially explicit prey-predator systems. Physical Review E 2007, 75 (5) https://doi.org/10.1103/PhysRevE.75.051914
5081. Luis G. Morelli, Frank Jülicher. Precision of Genetic Oscillators and Clocks. Physical Review Letters 2007, 98 (22) https://doi.org/10.1103/PhysRevLett.98.228101
5082. Christopher R. Myers, James P. Sethna. Python for Education: Computational Methods for Nonlinear Systems. Computing in Science & Engineering 2007, 9 (3) , 75-79. https://doi.org/10.1109/MCSE.2007.56
5083. Daniel T. Gillespie. Stochastic Simulation of Chemical Kinetics. Annual Review of Physical Chemistry 2007, 58 (1) , 35-55. https://doi.org/10.1146/annurev.physchem.58.032806.104637
5084. Peter Rowat. Interspike Interval Statistics in the Stochastic Hodgkin-Huxley Model: Coexistence of Gamma Frequency Bursts and Highly Irregular Firing. Neural Computation 2007, 19 (5) , 1215-1250. https://doi.org/10.1162/neco.2007.19.5.1215
5085. D. Milutinović, R.J. De Boer. Process Noise: An Explanation for the Fluctuations in the Immune Response during Acute Viral Infection. Biophysical Journal 2007, 92 (10) , 3358-3367. https://doi.org/10.1529/biophysj.106.094508
5086. Matthew R. Bennett, Dmitri Volfson, Lev Tsimring, Jeff Hasty. Transient Dynamics of Genetic Regulatory Networks. Biophysical Journal 2007, 92 (10) , 3501-3512. https://doi.org/10.1529/biophysj.106.095638
5087. Hao Song, Paul Smolen, Evyatar Av-Ron, Douglas A. Baxter, John H. Byrne. Dynamics of a Minimal Model of Interlocked Positive and Negative Feedback Loops of Transcriptional Regulation by cAMP-Response Element Binding Proteins. Biophysical Journal 2007, 92 (10) , 3407-3424. https://doi.org/10.1529/biophysj.106.096891
5088. E. Libby, T. J. Perkins, P. S. Swain. Noisy information processing through transcriptional regulation. Proceedings of the National Academy of Sciences 2007, 104 (17) , 7151-7156. https://doi.org/10.1073/pnas.0608963104
5089. Radek Erban, Thomas A. Frewen, Xiao Wang, Timothy C. Elston, Ronald Coifman, Boaz Nadler, Ioannis G. Kevrekidis. Variable-free exploration of stochastic models: A gene regulatory network example. The Journal of Chemical Physics 2007, 126 (15) , 155103. https://doi.org/10.1063/1.2718529
5090. Weinan E, Di Liu, Eric Vanden-Eijnden. Response to “Comment on ‘Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates’ [J. Chem. Phys. 123, 194107 (2005)]”. The Journal of Chemical Physics 2007, 126 (13) , 137102. https://doi.org/10.1063/1.2567071
5091. Yu-Pin Luo, Ming-Chang Huang, Jinn-Wen Wu, Tsong-Ming Liaw, Simon C. Lin. Master equation approach to folding kinetics of lattice polymers based on conformation networks. The Journal of Chemical Physics 2007, 126 (13) , 134907. https://doi.org/10.1063/1.2711816
5092. Tihamer Geyer, Florian Lauck, Volkhard Helms. Molecular stochastic simulations of chromatophore vesicles from Rhodobacter sphaeroides. Journal of Biotechnology 2007, 129 (2) , 212-228. https://doi.org/10.1016/j.jbiotec.2006.12.018
5093. Stefan Braunewell, Stefan Bornholdt. Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. Journal of Theoretical Biology 2007, 245 (4) , 638-643. https://doi.org/10.1016/j.jtbi.2006.11.012
5094. P. Ghosh, S. Ghosh, K. Basu, S. Das. Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes. 2007,,, 439-446. https://doi.org/10.1109/CIBCB.2007.4221254
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