相关论文: Excluded Volume in Protein Sidechain Packing

Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…

Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…

In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…

Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the…

The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…

The interplay of topological constraints, excluded volume interactions, persistence length and dynamical entanglement length in solutions and melts of linear chains and ring polymers is investigated by means of kinetic Monte Carlo…

Single-chain elasticity of polyethylene at $\theta$ point up to 90% of stretching with respect to its contour length is computed by Monte-Carlo simulation of an atomistic model in continuous space. The elasticity law together with the…

Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…

The efficiency of Monte Carlo samplers is dictated not only by energetic effects, such as large barriers, but also by entropic effects that are due to the sheer volume that is sampled. The latter effects appear in the form of an entropic…

Redshift-space clustering anisotropies caused by cosmic peculiar velocities provide a powerful probe to test the gravity theory on large scales. However, to extract unbiased physical constraints, the clustering pattern has to be modelled…

We present numerical simulations that allow us to compute the number of ways in which $N$ particles can pack into a given volume $V$. Our technique modifies the method of Xu et al. (Phys. Rev. Lett. 106, 245502 (2011)) and outperforms…

Following the Flory ideality hypothesis intrachain and interchain excluded volume interactions are supposed to compensate each other in dense polymer systems. Multi-chain effects should thus be neglected and polymer conformations may be…

The most efficient way to pack equally sized spheres isotropically in 3D is known as the random close packed state, which provides a starting point for many approximations in physics and engineering. However, the particle size distribution…

Side chain flexibility is an important factor in ligand binding. In order to determine the extent to which side chain flexibility is involved in ligand binding, a knowledge-based approach was taken. A database composed of examples of…

We review a recently proposed theory of random packings. We describe the volume fluctuations in jammed matter through a volume function, amenable to analytical and numerical calculations. We combine an extended statistical mechanics…

We report the results of extensive Dynamic Monte Carlo simulations of systems of self-assembled Equilibrium Polymers without rings in good solvent. Confirming recent theoretical predictions, the mean-chain length is found to scale as $\Lav…

Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…

A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…

We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used…

We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyse their range of validity by means of comprehensive Molecular…