Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach

We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows that it can be either double or mono-peaked, depending on the system parameters. We show that the most probable translocation time is proportional to the polymer length, and inversely proportional to the first or second power of the voltage, depending on the initial conditions. The model recovers experimental observations on hetro-polymers when using their properties inside the pore, such as stiffness and polymer-pore interaction.Comment: 7 pages submitted to PR

Phase space reduction of the one-dimensional Fokker-Planck (Kramers) equation

A pointlike particle of finite mass m, moving in a one-dimensional viscous environment and biased by a spatially dependent force, is considered. We present a rigorous mapping of the Fokker-Planck equation, which determines evolution of the particle density in phase space, onto the spatial coordinate x. The result is the Smoluchowski equation, valid in the overdamped limit, m->0, with a series of corrections expanded in powers of m. They are determined unambiguously within the recurrence mapping procedure. The method and the results are interpreted on the simplest model with no field and on the damped harmonic oscillator.Comment: 13 pages, 1 figur

Pascal Principle for Diffusion-Controlled Trapping Reactions

"All misfortune of man comes from the fact that he does not stay peacefully in his room", has once asserted Blaise Pascal. In the present paper we evoke this statement as the "Pascal principle" in regard to the problem of survival of an "A" particle, which performs a lattice random walk in presence of a concentration of randomly moving traps "B", and gets annihilated upon encounters with any of them. We prove here that at sufficiently large times for both perfect and imperfect trapping reactions, for arbitrary spatial dimension "d" and for a rather general class of random walks, the "A" particle survival probability is less than or equal to the survival probability of an immobile target in the presence of randomly moving traps.Comment: 4 pages, RevTex, appearing in PR

Survival and residence times in disordered chains with bias

We present a unified framework for first-passage time and residence time of random walks in finite one-dimensional disordered biased systems. The derivation is based on exact expansion of the backward master equation in cumulants. The dependence on initial condition, system size, and bias strength is explicitly studied for models with weak and strong disorder. Application to thermally activated processes is also developed.Comment: 13 pages with 2 figures, RevTeX4; v2:minor grammatical changes, typos correcte

A continuous time random walk model for financial distributions

We apply the formalism of the continuous time random walk to the study of financial data. The entire distribution of prices can be obtained once two auxiliary densities are known. These are the probability densities for the pausing time between successive jumps and the corresponding probability density for the magnitude of a jump. We have applied the formalism to data on the US dollar/Deutsche Mark future exchange, finding good agreement between theory and the observed data.Comment: 14 pages, 5 figures, revtex4, submitted for publicatio

Diffusion Time-Scale Invariance, Markovization Processes and Memory Effects in Lennard-Jones Liquids

We report the results of calculation of diffusion coefficients for Lennard-Jones liquids, based on the idea of time-scale invariance of relaxation processes in liquids. The results were compared with the molecular dynamics data for Lennard-Jones system and a good agreement of our theory with these data over a wide range of densities and temperatures was obtained. By calculations of the non-Markovity parameter we have estimated numerically statistical memory effects of diffusion in detail.Comment: 10 pages, 3 figure

Lattice theory of trapping reactions with mobile species

We present a stochastic lattice theory describing the kinetic behavior of trapping reactions $A + B \to B$, in which both the $A$ and $B$ particles perform an independent stochastic motion on a regular hypercubic lattice. Upon an encounter of an $A$ particle with any of the $B$ particles, $A$ is annihilated with a finite probability; finite reaction rate is taken into account by introducing a set of two-state random variables - "gates", imposed on each $B$ particle, such that an open (closed) gate corresponds to a reactive (passive) state. We evaluate here a formal expression describing the time evolution of the $A$ particle survival probability, which generalizes our previous results. We prove that for quite a general class of random motion of the species involved in the reaction process, for infinite or finite number of traps, and for any time $t$, the $A$ particle survival probability is always larger in case when $A$ stays immobile, than in situations when it moves.Comment: 12 pages, appearing in PR

Kinetics of active surface-mediated diffusion in spherically symmetric domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: Published online in J. Stat. Phy

On the applicability of entropy potentials in transport problems

Transport in confined structures of varying geometry has become the subject of growing attention in recent years since such structures are ubiquitous in biology and technology. In analyzing transport in systems of this type, the notion of entropy potentials is widely used. Entropy potentials naturally arise in one-dimensional description of equilibrium distributions in multidimensional confined structures. However, their application to transport problems requires some caution. In this article we discuss such applications and summarize the results of recent studies exploring the limits of applicability. We also consider an example of a transport problem in a system of varying geometry, where the conventional approach is inapplicable since the geometry changes abruptly. In addition, we demonstrate how the entropy potential can be used to analyze optimal transport through a three-dimensional cosine-shaped channel