相关论文: Statistical Geometry of Packing Defects of Lattice…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Proteins form a very important class of polymers. In spite of major advances in the understanding of polymer science, the protein problem has remained largely unsolved. Here, we show that a polymer chain viewed as a tube not only captures…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
One of the basic problems in discrete geometry is to determine the most efficient packing of congruent replicas of a given convex set $K$ in the plane or in space. The most commonly used measure of efficiency is density. Several types of…
We present a Monte Carlo algorithm that provides efficient and unbiased sampling of polymer melts consisting of two chains of equal length that jointly visit all the sites of a cubic lattice with rod geometry L x L x rL and non-periodic…
Histogram-reweighting grand canonical Monte Carlo simulations are used to obtain the critical properties of lattice chains composed of solvophilic and solvophobic monomers. The model is a modification of one proposed by Larson \emph{et al.}…
A fast and accurate grid-based method with low memory requirement is presented to calculate volume characteristics in molecular systems. The distribution of volume and packing density is characterized in globular proteins, where void space…
CONTEXT: Cosmic voids are observed in the distribution of galaxies and, to some extent, in the dark matter distribution. If these distributions have fractal geometry, it must be reflected in the geometry of voids; in particular, we expect…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Monte Carlo dynamics of the lattice 48 monomers toy protein is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability $P(T)$, which is the…
In this paper we study the shape characteristics of a polymer chain in a good solvent using a mesoscopic level of modelling. The dissipative particle dynamics simulations are performed in the $3D$ space at a range of chain lengths $N$. The…
We propose new polymer models for Monte Carlo simulation and apply them to a polymer chain confined in a relatively thin box which has both curved and flat sides, and show that either an ideal or an excluded-volume chain spends more time in…
The effect of different Monte Carlo move sets on the the folding kinetics of lattice polymer chains is studied from the geometry of the conformation-network. The networks have the characteristics of small- world. The Monte Carlo move, rigid…
Maximum-density dimer packings (maximum matchings) of non-bipartite site-diluted lattices, such as the triangular and Shastry-Sutherland lattices in $d=2$ dimensions and the stacked-triangular and corner-sharing octahedral lattices in…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
The large-scale structure of the universe can only be observed via luminous tracers of the dark matter. However, the clustering statistics of tracers are biased and depend on various properties, such as their host-halo mass and assembly…