Related papers: Undulations in a weakly interacting mechanically g…
Motivated by recent advances in single molecule manipulation techniques that enabled several groups to tie knots in individual polymer strands and to monitor their dynamics, we have used computer simulations to study "friction knots"…
Movements of molecular motors on cytoskeletal filaments are described by directed walks on a line. Detachment from this line is allowed to occur with a small probability. Motion in the surrounding fluid is described by symmetric random…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
Contractility in animal cells is often generated by molecular motors such as myosin, which require polar substrates for their function. Motivated by recent experimental evidence of motor-independent contractility, we propose a robust…
This article studies the fundamental problem of separating two adhesive elastic fibers based on numerical simulation employing a recently developed finite element model for molecular interactions between curved slender fibers. Specifically,…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
The motility of a cell can be triggered or inhibited not only by an applied force but also by a mechanically neutral force couple. This type of loading, represented by an applied stress and commonly interpreted as either squeezing or…
Soft elastic filaments that can be stretched, bent and twisted exhibit a range of topologically and geometrically complex morphologies that include plectonemes, solenoids, knot-like and braid-like structures. We combine numerical…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
The consolidation of suspended particulate matter under external forces such as pressure or gravity is of widespread interest. In this work, we derive a constitutive relation to describe the deformation of a {\it two-dimensional} strongly…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Stiff forces, which bind objects together or otherwise confine motion, are found widely in soft-matter systems - colloids with short range attractions, ligand-receptor contacts, particles in optical traps, fibres that resist stretching,…
A theoretical model is proposed for low temperature friction between two smooth rigid solid surfaces separated by lubricant molecules, admitting their deformations and rotations. Appearance of different modes of energy dissipation (by…
The influence of an external field acting differently on the two constituents of a binary colloidal mixture performing Brownian dynamics is investigated by computer simulations and a simple theory. In our model, one half of the particles…