相关论文: Refolding dynamics of stretched biopolymers upon f…

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…

Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of…

Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…

Predicting the time and temperature dependent behavior of polymer networks under complex loading is essential for the design of advanced elastomeric materials. Many practical applications involve combinations of deformation modes, such as…

This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…

We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…

We carry out uniaxial continuous and step stretching of various crosslinked polymer networks to demonstrate how characteristics of rupture (from continuous stretching) and delayed rupture (from step stretching) can be used to probe the…

Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…

We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…

We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…

Folding and unfolding of biopolymers are often manipulated in experiment by tuning pH, temperature, single-molecule force or shear field. Here we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting…

A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…

We present an extremely simplified model of multiple-domains polymer stretching in an atomic force microscopy experiment. We portray each module as a binary set of contacts and decompose the system energy into a harmonic term (the…

We present force-clamp data on the collapse of ubiquitin polyproteins in response to a quench in the force. These nonequilibrium trajectories are analyzed using a general method based on a diffusive assumption of the end-to-end length to…

Drawing an analogy to the paradigm of quasi-elastic neutron scattering, we present a general approach for quantitatively investigating the spatiotemporal dependence of structural anisotropy relaxation in deformed polymers by using…

We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments. The force is applied along the end to end vector at one extremity of the filament,…

Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…

A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…

The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…