Related papers: Sequence heterogeneity and the dynamics of molecul…
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
We introduce and analyze a model for the transport of particles or energy in extended lattice systems. The dynamics of the model acts on a discrete phase space at discrete times but has nonetheless some of the characteristic properties of…
We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics…
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…
Two approaches to incorporate heterogeneity in discrete models are compared. In the first, standard approach, the heterogeneity is dictated by geometrical structure of the discrete system. In the second approach, the heterogeneity is…
Linear bio-molecular motors move unidirectionally along a track by coordinating several different processes, such as fuel (ATP) capture, hydrolysis, conformational changes, binding and unbinding from a track, and center-of-mass diffusion. A…
The collective behavior of molecular motor proteins have been investigated in the literature using models to describe the long-time dynamics of a unidimensional continuum motor distribution. Here, we consider the phenomena related to the…
Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show that this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in…
We introduce a multi-species lattice gas model for motor protein driven collective cargo transport on cellular filaments. We use this model to describe and analyze the collective motion of interacting vesicle cargoes being carried by…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period $N$ are developed. Theoretical analysis that allows to calculate explicitly the steady-state…
The transportation of the cargoes in biological cells is primarily driven by the motor proteins on filamentous protein tracks. The stochastic nature of the motion of motor protein often leads to its spontaneous detachment from the track.…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
The energetics and efficiency of a linear molecular motor model proposed by Mogilner et al. (Phys. Lett. 237, 297 (1998)) is analyzed from an analytical point of view. The model which is based on protein friction with a track is described…
In this paper we investigate the ability of some recently introduced discrete kinetic models of vehicular traffic to catch, in their large time behavior, typical features of theoretical fundamental diagrams. Specifically, we address the…
Nanochains of atoms, molecules and polymers have gained recent interest in the experimental sciences. This article contributes to an advanced mathematical modeling of the mechanical properties of nanochains that allow for heterogenities,…
Molecular motors interacting with cytoskeletal filaments undergo peculiar random walks consisting of alternating sequences of directed movements along the filaments and diffusive motion in the surrounding solution. An ensemble of motors is…
The dynamics of a spherical chemically-powered synthetic colloidal motor that operates by a self-diffusiophoretic mechanism and has a catalytic domain of arbitrary shape is studied using both continuum theory and particle-based simulations.…