Unraveling the Beautiful Complexity of Simple Lattice Model Polymers and Proteins Using Wang-Landau Sampling
نویسندگان
چکیده
منابع مشابه
Unraveling the beautiful complexity of simple lattice model polymers and proteins using Wang-Landau sampling
We describe a class of “bare bones” models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the temperature is lowered. We then show how, with the use of a properly chosen trial move set, Wang-Landau Monte Carlo sampling can be used to study the rough free energ...
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Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results are in good agreement with those obtained using Metropolis importance sampling. This algorithm enables one to accurately simulate the usually hardly accessibl...
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Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very demanding and the quest for efficient algorithms is as old as the models themselves. Expanding on our previous work [T. Wüst and D. P. Landau, Phys. Rev. Lett....
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Abstract Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a short HP sequence consisting of only 36 monomers interacting with a substrate which attracts all monomers in the sequence. The conformational “phase t...
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We demonstrate how Wang-Landau simulations may be used in an efficient manner to investigate the statistical mechanics of lattice polymers adsorbed at a planar surface, and confined in slit geometry between two parallel surfaces. For nearest neighbour interactions, we show that one or two Wang-Landau simulations, recording the density of states as a function of numbers of internal contacts and ...
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ژورنال
عنوان ژورنال: Journal of Statistical Physics
سال: 2011
ISSN: 0022-4715,1572-9613
DOI: 10.1007/s10955-011-0266-z