相关论文: Excluded Volume in Protein Sidechain Packing
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue participation in folding nucleus and sequence conservation…
We present a reduced-dimension, ballistic deposition, Monte Carlo particle packing algorithm and discuss its application to the analysis of the microstructure of hard-sphere systems with broad particle size distributions. We extend our…
Using molecular dynamics simulation of a standard bead-spring model we investigate the density crossover scaling of strictly two-dimensional self-avoiding polymer chains focusing on properties related to the contact exponent set by the…
A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules.…
The region of entropic vectors is a convex cone that has been shown to be at the core of many fundamental limits for problems in multiterminal data compression, network coding, and multimedia transmission. This cone has been shown to be…
Small-angle scattering is a commonly used tool to analyze the dispersion of nanoparticles in all kinds of matrices. Besides some obvious cases, the associated structure factor is often complex and cannot be reduced to a simple interparticle…
Using the concepts of mixed volumes and quermassintegrals of convex geometry, we derive an exact formula for the exclusion volume for a general convex body that applies in any space dimension, including both the rotationally-averaged…
An analytically solvable model of unsaturated lipid bilayer is derived by introducing finite bending angle of the unsaturated bond relative to straight part of the lipid chain considered previously in our model of semi-flexible strings. It…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
It has been recently suggested that a totally asymmetric exclusion process with two species on an open chain could exhibit spontaneous symmetry breaking in some range of the parameters defining its dynamics. The symmetry breaking is…
We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and…
The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…
Using an athermal quasistatic simulation protocol, we study the distribution of free volumes in sheared hard-particle packings close to, but below, the random-close packing threshold. We show that under shear, and independent of volume…
We investigate the nature of randomness in disordered packings of frictional spheres. We calculate the entropy of 3D packings through the force and volume ensemble of jammed matter, a mesoscopic ensemble and numerical simulations using…
We present a statistical mechanical description of randomly packed spherical particles, where the average coordination number is treated as a macroscopic thermodynamic variable. The overall packing entropy is shown to have two…
The current literature on sandpile models mainly deals with the abelian sandpile model (ASM) and its variants. We treat a less known - but equally interesting - model, namely Zhang's sandpile. This model differs in two aspects from the ASM.…
Obtaining reliable estimates of the statistical properties of complex macromolecules by computer simulation is a task that requires high computational effort as well as the development of highly efficient simulation algorithms. We present…
Nano-scale confinement of polymer in cone-shaped geometries occurs in many experimental situations. A flexible polymer confined in a cone-shaped nano-channel is studied theoretically and using molecular dynamics simulations. Distribution of…
Ladder polymers, known for their rigid, ladder-like structures, exhibit exceptional thermal stability and mechanical strength, positioning them as candidates for advanced applications. However, accurately determining their structure from…
We study equilibrium statistics of single semi-flexible polymer chain in the presence of defects. The defects are lying along a line in the two and three dimensions and the monomers are interacting with the onsite potential of the defects.…