Web Release Date: November 9,
Method for Efficient Computation of the Density of States in Water-Explicit Biopolymer
Simulations on a Lattice
and
Department of Chemical Engineering, and Department of Chemistry, Princeton University, Princeton, New Jersey 08544
Received: August 2, 2007
In Final Form: October 3, 2007
Abstract:
We present a method for fast computation of the density of states of binary systems. The contributions of each of the components to the density of states can be separated based on the conditional independence of the individual components' degrees of freedom. The conditions establishing independence are the degrees of freedom of the interfacial region between the two components. The separate contributions of the components to the density of states can then be calculated using the Wang-Landau algorithm [Wang, F.; Landau, D. P. Phys. Rev. Lett. 2001, 86, 2050]. We apply this method to a 2D lattice model of a hydrophobic homopolymer in water that exhibits protein-like cold, pressure, and thermal unfolding. The separate computation of the protein and water density of states contributions is faster and more accurate than the combined simulation of both components and allows for the investigation of larger systems.
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