Related papers: Equilibrium Blocking Model of Isometric Tension
Heterogeneous mechanical dyskinesis during acute myocardial ischaemia is thought to contribute to arrhythmogenic alterations to cardiac electrophysiology. Various forms of mechano-electric coupling (MEC) mechanisms have been suggested to…
The purpose of this study was to report numerical validation of a 3D finite element model of contracting muscle. The model was based on continuum theory for fibre-reinforced composite materials. Here we simulated contractions for an…
The presynaptic free calcium dynamics of neurons due to various stimulation protocols is investigated in a mathematical model. The model includes calcium influx through voltage-dependent calcium channels, calcium buffering by endogenous and…
Predicting the rheological behavior of associative polymers bridging colloidal particles into transient networks is fundamentally challenging because the coupled spatiotemporal scales prevent efficient molecular-fidelity modeling. We…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Mineralized collagen microfibrils in human bone provide its mechanical properties (stiffness, elasticity, ductility, energy dissipation and strength). However, detailed 3D finite element models describing the mechanical behaviour of the…
We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…
In this work, we study in detail the distribution of stochastic forces generated by the molecular motors activity, in the actin cortex of pre-muscular cells. By combining active and passive rheology experiments, performed on the same…
The physics of critical phenomena in a many-body system far from thermal equilibrium is an interesting and important issue to be addressed both experimentally and theoretically. The trapped cold atoms have been actively used as a clean and…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
Modeling deformation twin nucleation in magnesium has proven to be a challenging task. In particular, the absence of a heterogeneous twin nucleation model which provides accurate energetic descriptions for twin-related structures belies a…
Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…
The tight binding model is a minimal electronic structure model for molecular modelling and simulation. We show that the total energy in this model can be decomposed into site energies, that is, into contributions from each atomic site…
The article presents new model of equilibrium in open chemical systems suggesting a linear dependence of the reaction shift from equilibrium in presence of the external thermodynamic force. Basic equation of this model contains traditional…
We present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often…
Protein assembly plays an important role in the regulation of biological systems. The cytoskeleton assembly activity is provided by the binding cofactors GTP (guanidine triphosphate) or ATP(adenosine triphosphate) to monomeric protein, and…
Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse…
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…
The structural reorganization of the actin cytoskeleton is facilitated through the action of motor proteins that crosslink the actin filaments and transport them relative to each other. Here, we present a combined experimental-computational…