相关论文: Folding Lennard-Jones proteins by a contact potent…

The behavior of energy polydisperse $2d$ Lennard-Jones fluid (in thin-film geometry) is studied subjected to linear flow field using molecular dynamics simulations. By considering neutral and selective substrates we systematically explore…

In this paper, we utilized generative models, and reformulate it for problems in molecular dynamics (MD) simulation, by introducing an MD potential energy component to our generative model. By incorporating potential energy as calculated…

The crucial problem for better understanding the nature of glass transition and related relaxation phenomena is to find proper interrelations between molecular dynamics and thermodynamics of viscous systems. To gain this aim the recently…

Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which…

Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to…

Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…

We have considered the problem of protein design based on a model where the contact energy between amino acid residues is fitted phenomenologically using the Miyazawa--Jernigan matrix. Due to the simple form of the contact energy function,…

In this paper we analyze a two-dimensional discrete model of nearest-neighbour Lennard-Jones interactions under the microscopical constraint that points on a lattice triangle maintain their order. This can be understood as a microscopical…

We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…

In a recent article, Wang et al (Phys. Chem. Chem. Phys., 22, 10624 (2020)) introduced a new class of interparticle potential for molecular simulations. The potential is defined by a single range parameter, eliminating the need to decide…

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…

We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…

Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend…

Based on the concept of energy landscape a picture of the mismatch between the reduced interaction matrix of residues and the matrix of statistical contact potentials is presented. For the Miyazawa and Jernigan (MJ) matrix, rational…

The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…

Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…

One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…

The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the…

Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…

In this two part series, we present a contact model able to capture the response of interacting adhesive elastic-perfectly plastic particles under a variety of loadings. In Part I, we focus on elastic through fully-plastic contact with and…