Related papers: CSAW: a dynamical model of protein folding
In the present paper, we consider the interacting partially-directed self-avoiding walk (IPDSAW) attracted by a vertical wall. The IPDSAW was introduced by Zwanzig and Lauritzen (J. Chem. Phys., 1968) as a manner of investigating the…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
A surgical world model capable of generating realistic surgical action videos with precise control over tool-tissue interactions can address fundamental challenges in surgical AI and simulation -- from data scarcity and rare event synthesis…
Anomalous diffusion, in particular subdiffusion, is frequently invoked as a mechanism of motion in dense biological media, and may have a significant impact on the kinetics of binding/unbinding events at the cellular level. In this work we…
Using the continuous-time random walk (CTRW) approach, we study the phenomenon of relaxation of two-state systems whose elements evolve according to a dichotomous process. Two characteristics of relaxation, the probability density function…
Coagulation-flocculation, the physicochemical process widely used for purification a wastewater, is affected both by chemical details of involved polymers and by the statistics of their conformations on a large scale. The latter aspect is…
Membrane proteins move in heterogeneous environments with spatially (sometimes temporally) varying friction and with biochemical interactions with various partners. It is important to reliably distinguish different modes of motion to…
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…
Self-propelled particles serve as minimal models for emulating the dynamic self-organization of microorganisms, yet most synthetic systems remain limited to a single mode of motion, namely active Brownian particles (ABPs). Here, we present…
Several kinds of walks on complex networks are currently used to analyze search and navigation in different systems. Many analytical and computational results are known for random walks on such networks. Self-avoiding walks (SAWs) are…
We study the conformational properties of polymers in presence of extended columnar defects of parallel orientation. Two classes of macromolecules are considered: the so-called partially directed polymers with preferred orientation along…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on…
We consider a model of semi-flexible interacting self-avoiding trails (sISAT's) on a lattice, where the walks are constrained to visit each lattice edge at most once. Such models have been studied as an alternative to the self-attracting…
We show that the dynamics of supercooled liquids, analyzed from computer simulations of the binary mixture Lennard-Jones system, can be described in terms of a continuous time random walk (CTRW). The required discretization comes from…
We present a nonlinear and non-Markovian random walk model for stochastic movement and the spatial aggregation of living organisms that have the ability to sense population density. We take into account social crowding effects for which the…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
Self-attracting walks (SATW) with attractive interaction u > 0 display a swelling-collapse transition at a critical u_{\mathrm{c}} for dimensions d >= 2, analogous to the \Theta transition of polymers. We are interested in the structure of…
Continuous time random walks impose a random waiting time before each particle jump. Scaling limits of heavy tailed continuous time random walks are governed by fractional evolution equations. Space-fractional derivatives describe heavy…
We consider random walks (RWs) and self-avoiding walks (SAWs) on disordered lattices directly at the percolation threshold. Applying numerical simulations, we study the scaling behavior of the models on the incipient percolation cluster in…
Understanding how biological and synthetic systems achieve robust function in noisy environments remains a fundamental challenge across the physical and life sciences. To connect robust behavior with non-trivial topological features present…