相关论文: New force replica exchange method and protein fold…

We study a discrete-time asynchronous midpoint dynamics on the circle in which, at each step, a uniformly chosen neighboring pair moves to the midpoint along the shortest arc. Although the update rule is locally contractive, we show that…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

At finite temperature and in presence of disorder, a one-dimensional elastic interface displays different scaling regimes at small and large lengthscales. Using a replica approach and a Gaussian Variational Method (GVM), we explore the…

We present both analytical and numerical results for the behaviour of the Casimir force in a Ginzburg-Landau type model of a film of a simple fluid or binary liquid mixture in which the confining surfaces are strongly adsorbing but…

Pattern formation and the mechanics of a mixture of actin filaments and myosin motors that is confined by a rigid membrane is investigated. By using a coarse-grained molecular dynamics model, we demonstrate that the competition between the…

Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed…

Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…

Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures.…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

In this paper, adhesive contact of a rigid cylinder on an elastic power-law graded half-space is studied analytically with the theory of weakly singular integral equation and orthogonal polynomial method. Emphasis is placed on the coupling…

In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…

Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…

The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…

The tribology between surfaces can have a profound impact on the response of a mechanical system, such as how granular particles are driven to flow. In this work, we perform experiments that time-resolve the tangential and normal components…

Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…

The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…

We propose a simple friction model for isolated polymer chains on a solid substrate. The chains are pulled at constant velocity by one end, the other end can be trapped on the solid substrate on localised sites. We focus on the energy…

A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…

Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…