Related papers: Model for processive movement of dynein
The cytoskeleton protein actin assembles into large bundles when supporting stresses in the cell, but grows into a fine branched network to induce cell motion. Such self-organization processes are studied in artificial networks of…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
In this paper we report, clarify and broaden various recent efforts to complement the chemistry-centered models of force generation in muscles by mechanics-centered models. The physical mechanisms of interest can be grouped into two…
We discuss the influence of external forces on the motion of the tip in dynamic atomic force microscopy (AFM). First, a compact solution for the steady-state problem is derived employing a Fourier approach. Founding on this solution, we…
Active filaments, such as microtubules with attached cargo-carrying motor proteins, are important dynamic structures for fluid transport in and around living cells. The mathematical models of active filaments appearing in the literature…
A discrete-state model of the F1-ATPase molecular motor is developed which describes not only the dependences of the rotation and ATP consumption rates on the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on…
The cellular cytoskeleton is an active material, driven out of equilibrium by molecular motor proteins. It is not understood how the collective behaviors of cytoskeletal networks emerge from the properties of the network's constituent motor…
Transport at microscopic length scales is essential in biological systems and various technologies, including microfluidics. Recent experiments achieved self-organized transport phenomena in microtubule active matter using light to modulate…
We propose a generic model for thin films and shallow drops of a polar active liquid that have a free surface and are in contact with a solid substrate. The model couples evolution equations for the film height and the local polarization…
Observations of single epidermal cells on flat adhesive substrates have revealed two distinct morphological and functional states, namely a non-migrating symmetric unpolarized state and a migrating asymmetric polarized state. These states…
We present a model study of gliding assays in which actin filaments are moved by non-processive myosin motors. We show that even if the power stroke of the motor protein has no lateral component, the filaments will rotate around their axis…
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is implicated in many membrane severing processes in eukaryotic cells. Setting the grounds for a better understanding of this biological function, we develop a generalized…
Several theoretical models based on totally asymmetric simple exclusion process (TASEP) have been extensively utilized to study various non-equilibrium transport phenomena. Inspired by the the role of microtubule-transported vesicles in…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different…
Solid-solid phase transitions are ubiquitous in nature, but the kinetic pathway of anisotropic particle systems remains elusive, where the coupling between translational and rotational motions plays a critical role in various kinetic…
The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in…
Experiments suggest that the migration of some cells in the three-dimensional extra cellular matrix bears strong resemblance to one-dimensional cell migration. Motivated by this observation, we construct and study a minimal one-dimensional…
We develop a model of amoeboid cell motility based on active gel theory. Modeling the motile apparatus of a eukaryotic cell as a confined layer of finite length of poroelastic active gel permeated by a solvent, we first show that, due to…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…