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The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
Recently, the Brownian dynamics of self-propelled (active) rod-like particles was explored to model the motion of colloidal microswimmers, catalytically-driven nanorods, and bacteria. Here, we generalize this description to biaxial…
We study the movement of the living organism in a band form towards the presence of chemical substrates based on a system of partial differential evolution equations. We incorporate Einstein's method of Brownian motion to deduce the…
A classical model of Brownian motion consists of a heavy molecule submerged into a gas of light atoms in a closed container. In this work we study a 2D version of this model, where the molecule is a heavy disk of mass M and the gas is…
We present an exact solution of the discrete wormlike chain (DWLC) model describing a single semiflexible polymer under arbitrary external force. Through exact closure relations between pair angular correlations and single-site angular…
The paper contains mathematical justification of basic facts concerning the Brownian motor theory. The homogenization theorems are proved for the Brownian motion in periodic tubes with a constant drift. The study is based on an application…
The interplay between Coulomb friction and random excitations is studied experimentally by means of a rotating probe in contact with a stationary granular gas. The granular material is independently fluidized by a vertical shaker, acting as…
Dynamics of array of coupled self-excited oscillators is considered. Model of Franklin bell is adopted as a mechanism for the self-excitation. The model allows derivation of exact analytic solutions for discrete breathers (DBs), and…
We present a tensor constitutive model for predicting stress and flow-induced structure formation in dilute wormlike micellar solutions. The micellar solution is treated as a dilute suspension of rigid Brownian rods whose length varies…
We investigate the translational motion of rotating colloidal systems at moderate Reynolds numbers (Re), focusing on particle dimers in snowman-like configurations under three scenarios: (i) two co-rotating spheres driven by an external…
We investigate a two-dimensional system of active Brownian dumbbells using molecular dynamics simulations. In this model, each dumbbell is driven by an active force oriented perpendicular to the axis connecting its two constituent beads. We…
In this paper we present a new method for determining optimal designs for enzyme inhibition kinetic models, which are used to model the influence of the concentration of a substrate and an inhibition on the velocity of a reaction. The…
This paper is based on the talk in "Probability Symposium" at Research Institute of Mathematical Sciences (Kyoto University) on 2013/12/18, and gives an announcement of some parts of the results in [1,8,10,11]. We show two instances of…
We give an overview over recent studies on the model of Active Brownian Motion (ABM) coupled to reservoirs providing free energy which may be converted into kinetic energy of motion. First, we present an introduction to a general concept of…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Using a Brownian dynamics simulation, we numerically studied the interaction of DNA with histone and proposed an octamer-rotation model to describe the process of nucleosome formation. Nucleosome disruption under stretching was also…
The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…
Brownian motion is essential for describing diffusion in systems ranging from simple to complex liquids. Unlike simple liquids, which consist of only a solvent, complex liquids, such as colloidal suspensions or the cytoplasm of a cell, are…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…