Related papers: Sequence heterogeneity and the dynamics of molecul…
Molecular motors of the kinesin-1 family move in a directed and processive fashion along microtubules (MTs). It is generally accepted that steric hindrance of motors leads to crowding effects; however, little is known about the specific…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
We study the effect of a coupling between two motor domains in highly-processive motor protein complexes. A simple stochastic discrete model, in which the two parts of the protein molecule interact through some energy potential, is…
We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different…
Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically…
RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input…
A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the…
We study a model of synthetic molecular motor - a [3]-catenane consisting of two small macrocycles mechanically interlocked with a bigger one - subjected to a time-dependent driving using stochastic thermodynamics. The model presents…
We study the behavior of the stationary velocity of a driven particle in an environment of mobile hard-core obstacles. Based on a lattice gas model, we demonstrate analytically that the drift velocity can exhibit a nonmonotonic dependence…
Molecular motor proteins such as Myosin V, Dynein or Kinesin are no ratchets, at least not with a flashing asymmetric potential; the crucial asymmetry is in the dynamical activity. We make that explicit in terms of a simple Markov model,…
Here we study a driven lattice gas model for microtubule depolymerizing molecular motors, where traffic jams of motors induce stochastic switching between microtubule growth and shrinkage. We term this phenomenon \enquote{traffic dynamic…
We study a kinetically constrained lattice glass model in which continuous local densities are randomly redistributed on neighbouring sites with a kinetic constraint that inhibits the process at high densities, and a random bias accounting…
Very small synthetic motors that make use of chemical reactions to propel themselves in solution hold promise for new applications in the development of new materials, science and medicine. The prospect of such potential applications, along…
Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and…
In this paper we investigate the use of path-integral formalism and the concepts of entropy and traffic in the context of molecular motors. We show that together with time-reversal symmetry breaking arguments one can find bounds on…
We study a continuum model of dislocation transport in order to investigate the formation of heterogeneous dislocation patterns. We propose a physical mechanism which relates the formation of heterogeneous patterns to the dynamics of a…
Biological functions in each animal cell depend on coordinated operations of a wide variety of molecular motors. Some of the these motors transport cargo to their respective destinations whereas some others are mobile workshops which…
One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which…
We numerically investigate the dynamic heterogeneity and its length scale found in the coarse-grained ionic liquid model systems. In our ionic liquid model systems, cations are modeled as dimers with positive charge, while anions are…
A fundamental challenge in car-following modeling lies in accurately representing the multi-scale complexity of driving behaviors, particularly the intra-driver heterogeneity where a single driver's actions fluctuate dynamically under…