Alexander M. Berezhkovskii

Bio: Alexander M. Berezhkovskii is an academic researcher from Center for Information Technology. The author has contributed to research in topics: Brownian motion & Diffusion (business). The author has an hindex of 40, co-authored 264 publications receiving 5740 citations. Previous affiliations of Alexander M. Berezhkovskii include National Institutes of Health & Academia Sinica.

Single-file transport of water molecules through a carbon nanotube

Abstract: Recent molecular dynamics simulations of water transport through the interior channel of a carbon nanotube in contact with an aqueous reservoir showed that conduction occurred in bursts with collective water motion. A continuous-time random-walk model is used to describe concerted transport through channels densely filled with molecules in a single-file arrangement, as also found in zeolites, as well as ion channels and aquaporins in biological membranes. Theoretical predictions for different collective properties of the single-file transport agree with the simulation results.

One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions

Abstract: For multidimensional activated rate processes controlled by diffusive crossing of a saddle point region, we show that a one-dimensional reaction coordinate can be constructed even when the diffusion anisotropy is arbitrary. The rate constant, found using the potential of mean force along this coordinate, is identical to that predicted by the multidimensional Kramers–Langer theory. This reaction coordinate minimizes the one-dimensional rate constant obtained using a trial reaction coordinate and is orthogonal to the stochastic separatrix, the transition state that separates reactants from products.

Reactive flux and folding pathways in network models of coarse-grained protein dynamics.

Abstract: The reactive flux between folded and unfolded states of a two-state protein, whose coarse-grained dynamics is described by a master equation, is expressed in terms of the commitment or splitting probabilities of the microstates in the bottleneck region This allows one to determine how much each transition through a dividing surface contributes to the reactive flux By repeating the analysis for a series of dividing surfaces or, alternatively, by partitioning the reactive flux into contributions of unidirectional pathways that connect reactants and products, insight can be gained into the mechanism of protein folding Our results for the flux in a network with complex connectivity, obtained using the discrete counterpart of Kramers’ theory of activated rate processes, show that the number of reactive transitions is typically much smaller than the total number of transitions that cross a dividing surface at equilibrium

Kinetics of escape through a small hole

Abstract: We study the time dependence of the survival probability of a Brownian particle that escapes from a cavity through a round hole. When the hole is small the escape is controlled by an entropy barrier and the survival probability decays as a single exponential. We argue that the rate constant is given by k=4Da/V, where a and V are the hole radius and the cavity volume and D is the diffusion constant of the particle. Brownian dynamics simulations for spherical and cubic cavities confirmed both the exponential decay of the survival probability and the expression for the rate constant for sufficiently small values of a.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Chemistry of Carbon Nanotubes

Abstract: Department of Materials Science, University of Patras, 26504 Rio Patras, Greece, Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. Constantinou Avenue, 116 35 Athens, Greece, Institut de Biologie Moleculaire et Cellulaire, UPR9021 CNRS, Immunologie et Chimie Therapeutiques, 67084 Strasbourg, France, and Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste, Italy

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

Stochastic thermodynamics, fluctuation theorems and molecular machines

Abstract: Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (Some figures may appear in colour only in the online journal) This article was invited by Erwin Frey.

Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Abstract: Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.