Statistical theory of any physical process needs a formulation of possibly simple but adequate models of the phenomena underlying microscopic dynamics. Remarkable progress in studies of internal dynamics of biomolecules acomplished in the recent years has made it possible to formulate such...

Molecular dynamics simulations of plastocyanin, an electron transfer copper containing protein involved in the photosynthetic process, have been performed in both the hydrated and dry state. An analysis of the potential energy fluctuations during a 500 ps dynamical evolution of the macromolecule...

A realistic physical model for the so-called rate-promoting vibration (RPV) at enzyme action is constructed. The origin of the RPV is assumed to be an oscillating electric field produced by long-lived localized vibrational modes in protein dynamics, namely, by the so-called discrete breather...

Protein activities may exhibit oscillations which often occur due to the existence of a negative feedback loop with an effective time delay. Many biological systems are, however, not limited to one feedback loop but consist of multiple loops on different regulatory levels. Here, we analyze the...

Identification of proton-conducting pathways in a protein is a key to understanding the mechanisms of biomolecular proton transfer. Starting from a known protein structure, proton pathways are modeled here as hydrogen bonded networks of proton conducting groups, including proton-exchanging...

We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion process (ASEP). The model is formulated to account for (i) excluded-volume interactions, (ii) the observed asymmetry of the stochastic movement of individual...

Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion observed in experiments depends on the nature of the force...

By analytical methods we study the large time properties of the solution of a simple one-dimensional model of stochastic Stokes’ drift. Semi-explicit formulae allow us to characterize the behaviour of the solutions and compute global quantities such as the asymptotic speed of the center of...

We present a novel method of computing the asymptotic drift velocity V and the diffusion coefficient D of a particle diffusing in an arbitrary periodic medium. We focus on a particular case of 1D systems with the nearest-neighbor transition rates and explain in detail how our method works in...

Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density–density correlations in fluctuating ratchet models for interacting molecular motors is...