Related papers: Excluded Volume in Protein Sidechain Packing
In this paper, we construct an effective model for the dynamics of an excluded-volume chain under confinement, by extending the formalism of Rouse modes. We make specific predictions about the behavior of the modes for a single polymer…
We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves…
When the local intrinsic stiffness of a polymer chain varies over a wide range, one can observe both a crossover from rigid-rod-like behavior to (almost) Gaussian random coils and a further crossover towards self-avoiding walks in good…
The behavior of a system of two-dimensional elongated particles (discorectangles) packed into a slit between two parallel walls was analyzed using a simulation approach. The packings were produced using the random sequential adsorption…
We characterise the entropy profiles of 32 very high mass ($M_{500}>7.75\times10^{14}~M_{\odot}$) galaxy clusters (HIGHMz), selected from the CHEX-MATE sample, to study the intracluster medium (ICM) entropy distribution in a regime where…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak…
Characteristics of relaxed density profile and conformation of polymer chains are studied by a Monte Carlo simulation on a discrete lattice in three dimensions using different segmental (kink-jump $K$, crank-shaft $C$, reptation $R$)…
This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…
The nature of randomness in disordered packings of frictional and frictionless spheres is investigated using theory and simulations of identical spherical grains. The entropy of the packings is defined through the force and volume ensemble…
It has been shown that under high cylindrical confinement, two ring polymers with excluded volume interactions between monomers, segregate to two halves of the cylinder to maximize their entropy. In contrast, two ring polymers remain mixed…
In the present work, four series of simulations are analyzed: entangled model networks of a) mono-disperse or b) poly-disperse weight distribution between the crosslinks, c) non-entangled phantom model networks and d) non-entangled model…
Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. When these systems are confined their structural properties…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
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…
The entropic effects of anchored polymers on biomembranes are studied using simulations of a meshless membrane model combined with anchored linear polymer chains. The bending rigidity and spontaneous curvature are investigated for anchored…
Efficient and accurate estimation of multivariate empirical probability distributions is fundamental to the calculation of information-theoretic measures such as mutual information and transfer entropy. Common techniques include variations…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
Monodisperse circular disks have been collectively packed in confined geometries using a Monte Carlo method where the compaction is propelled by two- dimensional stochastic agitation. We have found that confinement (i.e., finite-size plus…