The Journal of Chemical Physics · 2005 · 52 citations · 25 references
Natural SciencesBiophysicsPhysicsComputational BiophysicsCondensed Matter PhysicsStructural BiophysicsCoarse-grained ModelingConformational SamplingGlobular ProteinsLiquid CrystalsMacromolecular FoldingMacromolecular StructureChain StiffnessChain Stiffness EffectsCoarse-grained SimulationConformational EnsemblesMonte Carlo SamplingProtein Conformational SamplingSolid-liquid Phase TransitionStiffness
Using a coarse-grained model we perform a Monte Carlo simulation of the state behavior of an individual semiflexible macromolecule. Chains consisting of N = 256 and 512 monomer units have been investigated. A recently proposed enhanced sampling Monte Carlo technique for the bond fluctuation model in an expanded ensemble in four-dimensional coordinate space was applied. The algorithm allows one to accelerate the sampling of statistically independent three-dimensional conformations in a dense globular state. We found that the temperature of the intraglobular liquid-solid transition decreases with increasing chain stiffness. We have investigated the possible intraglobular orientationally ordered (i.e., liquid-crystalline) structures and obtained a diagram of states for chains consisting of N = 256 monomer units. This diagram contains regions of stability of coil, two spherical globules (liquid and solid), and rod-like globule conformations. Transitions between the globular states are rounded first-order ones since the states of liquid, solid, and cylinder-like globules do have different internal symmetry.
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Fugao Wang, D. P. Landau · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · 2001 · 1.2K citations · Full text