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EN
A new model for characterizing the free volume of a glassy polymer-gas systems is proposed. An improved method for the calculation of occupied volume per monomer unit was developed within the limits of this model. The model assumptions, error estimates and algorithm efficiencies are described. Using the example of polyvinyltrimethylsilane, it is shown that linear dependences of logarithms of the diffusion and the permeability coefficients on specific accessible volume for inert gases exist.
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Monte Carlo simulations of protein-like heteropolymers.

88%
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2001
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vol. 48
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issue 1
77-81
EN
Properties of a simple model of polypeptide chains were studied by the means of the Monte Carlo method. The chains were built on the (310) hybrid lattice. The residues interacted with long-range potential. There were two kinds of residues: hydrophobic and hydrophilic forming a typical helical pattern -HHPPHPP-. Short range potential was used to prefer helical conformations of the chain. It was found that at low temperatures the model chain formes dense and partially ordered structures (non-unique). The presence of the local potential led to an increase of helicity. The effect of the interplay between the two potentials was studied. After the collapse of the chain further annealing caused rearrangement of helical structures. Dynamic properties of the chain at low temperature depended strongly on the local chain ordering.
Open Physics
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2009
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vol. 7
|
issue 3
490-502
EN
In this paper we discuss how partial knowledge of the density of states for a model can be used to give good approximations of the energy distributions in a given temperature range. From these distributions one can then obtain the statistical moments corresponding to e.g. the internal energy and the specific heat. These questions have gained interest apropos of several recent methods for estimating the density of states of spin models. As a worked example we finally apply these methods to the 3-state Potts model for cubic lattices of linear order up to 128. We give estimates of e.g. latent heat and critical temperature, as well as the micro-canonical properties of interest.
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2002
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vol. 49
|
issue 3
683-692
EN
A high coordination lattice model was used to represent the protein chain. Lattice points correspond to amino-acid side groups. A complicated force field was designed in order to reproduce a protein-like behavior of the chain. Long-distance tertiary restraints were also introduced into the model. The Replica Exchange Monte Carlo method was applied to find the lowest energy states of the folded chain and to solve the problem of multiple minima. In this method, a set of replicas of the model chain was simulated independently in different temperatures with the exchanges of replicas allowed. The model chains, which consisted of up to 100 residues, were folded to structures whose root-mean-square deviation (RMSD) from their native state was between 2.5 and 5 Å. Introduction of restrain based on the positions of the backbone hydrogen atoms led to an improvement in the number of successful simulation runs. A small improvement (about 0.5 Å) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data.
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