相关论文: New force replica exchange method and protein fold…
In this communication, we propose a model to study the non-equilibrium process by which actin stress fibers develop force in contractile cells. The emphasis here is on the non-equilibrium thermodynamics, which is necessary to address the…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
The resolution of Brownian motion in simulations of micro-particle suspensions can be crucial to reproducing the correct dynamics of individual particles, as well as providing an accurate characterisation of suspension properties. Including…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
Actin and myosin drive many instances of force generation, deformation, and shape change in cells, tissues, and organisms. In particular, cytoskeletal actomyosin is remarkable in its adaptive architecture, responding to a host of…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
We discuss the use of a structure based C$\alpha$-Go model and Langevin dynamics to study in detail the mechanical properties and unfolding pathway of the titin I27 domain. We show that a simple Go-model does detect correctly the origin of…
Elastocaloric cooling has been identified as a promising alternative to high global warming potential vapor compression cooling. Two key bottlenecks to adoption are the need for bulky/expensive actuators to provide sufficient uniaxial…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
We present an analysis of a partially directed walk model of a polymer which at one end is tethered to a sticky surface and at the other end is subjected to a pulling force at fixed angle away from the point of tethering. Using the kernel…
The study of rigid protein-protein docking plays an essential role in a variety of tasks such as drug design and protein engineering. Recently, several learning-based methods have been proposed for the task, exhibiting much faster docking…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in…
We study theoretically ultracold collisions in quasi one-dimensional optical traps for bosonic and fermionic reactive molecules in the presence of a periodic potential along the trap axis. Elastic, reactive, and umklapp processes due to…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity…
Employing ab-initio electronic structure calculations combined with the non-equilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series…