Related papers: Spontaneous sarcomere dynamics
The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
We present the first molecular dynamics study to probe the mechanisms of anomalous diffusion in cationic surfactant micelles in the presence of explicit salt and solvent-mediated interactions. Simulations show that when the counter ion…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
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…
A simple model that replicates the dynamics of spiking and spiking-bursting activity of real biological neurons is proposed. The model is a two-dimensional map which contains one fast and one slow variable. The mechanisms behind generation…
In analogy to nanoscopic molecules that are composed of individual atoms, we consider an active "microswimmer molecule". It is built up from three individual magnetic colloidal microswimmers that are connected by harmonic springs and…
The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
We present self-organizing control principles for simulated robots actuated by synthetic muscles. Muscles correspond to linear motors exerting force only when contracting, but not when expanding, with joints being actuated by pairs of…
The study of motor protein dynamics within cytoskeletal networks is of high interest to physicists and biologists to understand how the dynamics and properties of individual motors lead to cooperative effects and control of overall network…
Using shear wave elastography, we measure the changes in the wave speed with the stress produced by a striated muscle during isometric voluntary contraction. To isolate the behaviour of an individual muscle from complementary or…
We study the high-frequency micro-mechanical response of suspensions composed by cardiac and skeletal muscle myosin by optical trapping interferometry. We observe that in low ionic strength solutions upon the addition of magnesium adenosine…
Coordination of cytoplasmic flows on large scales in space and time are at the root of many cellular processes, including growth, migration or division. These flows are driven by organized contractions of the actomyosin cortex. In order to…
We have developed numerical simulations of three dimensional suspensions of active particles to characterize the capabilities of the hydrodynamic stresses induced by active swimmers to promote global order and emergent structures in active…
Mechanical cues like the rigidity of the substrate are main determinants for the decision making of adherent cells. Here we use a mechano-chemical model to predict the cellular response to varying substrate stiffness. The model equations…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
The adhesive and frictional response of an AFM tip connected to a substrate through supramolecular host-guest complexes is investigated by dynamic Monte Carlo simulations. The variation of the pull-off force with the unloading rate recently…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…