Related papers: Properties of modified periodic one-dimensional ho…
Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…
We have investigated the motion characteristics of a movable piston immersed in a one dimensional gas of hard rods by event-oriented molecular dynamics in the absence of thermal noise. Periodic and reflecting boundary conditions are…
We examine the dependence of the physical quantities of the rotatory molecular motor, such as the rotation velocity and the proton translocation rate, on the chemical reaction rate using the model based only on diffusion process. A peculiar…
In this work we examine a system consisting of a confined one-dimensional arrangement of atoms that we describe by using the 2-dimensional ${\mathbb C}P^{N-1}$ model, restricted to an interval and at finite temperature. We develop a method…
We study a one-dimensional exclusion process with a fixed jump length $I \ge 1$ in which a particle may advance or retreat $I$ sites provided all intermediate sites are vacant, with hopping rates of Arrhenius type depending on the local…
We investigate the mean first passage time of an active Brownian particle in one dimension using numerical simulations. The activity in one dimension is modeled as a two state model; the particle moves with a constant propulsion strength…
The movement of motor particles consisting of one or several molecular motors bound to a cargo particle is studied theoretically. The particles move on patterns of immobilized filaments. Several patterns are described for which the motor…
In this doctoral thesis we have studied the quantum properties of several models which have been classified as statical and dynamical systems. The first part has been devoted to investigate the properties of the statical models including…
We describe a two-dimensional model for active particles whose self-propulsion speed is not fixed, but varies in time, and whose motion is subject to both translational and rotational diffusion. In the conventional treatment of active…
We analyse a one-dimensional model of hard particles, within ensembles of trajectories that are conditioned (or biased) to atypical values of the time-averaged dynamical activity. We analyse two phenomena that are associated with these…
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…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
Large-scale three dimensional molecular dynamics simulations of hopper flow are presented. The flow rate of the system is controlled by the width of the aperture at the bottom. As the steady-state flow rate is reduced, the force…
We consider a basic one-dimensional model of diffusion which allows to obtain a diversity of diffusive regimes whose speed depends on the moments of the per-site trapping time. This model is closely related to the continuous time random…
We study a driven zero range process which models a closed system of attractive particles that hop with site-dependent rates and whose steady state shows a condensation transition with increasing density. We characterise the dynamical…
We study dynamic behavior of Potts model with invisible states near the first-order phase transition temperature. We focus on melting process starting from the perfect ordered state. This model is regarded as a standard model to analyze…
We study a frequency-dependent damping model of hyper-diffusion within the generalized Langevin equation. The model allows for the colored noise defined by its spectral density, assumed to be proportional to $\omega^{\delta-1}$ at low…
It is known that exact traveling wave solutions exist for families of (n+1)-states stochastic one-dimensional non-equilibrium lattice models with open boundaries provided that some constraints on the reaction rates are fulfilled. These…
We introduce and explore a family of self-dual models of single-particle motion in quasiperiodic potentials, with hopping amplitudes that fall off as a power law with exponent $p$. These models are generalizations of the familiar…