相关论文: Does changing the pulling direction give better in…

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…

Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins.…

The mechanical stretching of single poly-proteins is an emerging tool for the study of protein (un)folding, chemical catalysis and polymer physics at the single molecule level. The observed processes i.e unfolding or reduction events, are…

The coupled dynamics of entangled polymers which span a broad time and length scales govern the unique viscoelastic properties of polymers. To follow chain mobility by numerical simulations from the intermediate Rouse and reptation regimes…

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…

The dynamical phase diagrams for vortices in clean films, driven by an uniform force, and interacting with periodic pinning resulting from a columnar-defect lattice are investigated by numerical simulations of a London model, and other…

By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…

Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to…

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…

Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…

The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…

The conditions under which biological cells switch from a static to a motile state are fundamental to the understanding of many healthy and pathological processes. In this paper, we show that even in the presence of a fully symmetric…

We investigate the mechanical properties of amorphous polymers by means of coarse-grained simulations and nonaffine lattice dynamics theory. A small increase of polymer chain bending stiffness leads first to softening of the material, while…

Many open problems in biology, as in the physical sciences, display nonlinear and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably understood. Moreover, mathematical models which aim to predict/estimate unknown…

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…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

We investigate polymers pulled away from an interacting surface, where the force is applied to the untethered endpoint and at an angle $\theta$ to the surface. We use the canonical self-avoiding walk model of polymers and obtain the phase…

We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible…

Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…