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。

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

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

Chemistry of Carbon Nanotubes

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.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

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.

/pdf/stochastic-thermodynamics-fluctuation-theorems-and-molecular-2epwyvmpf0.pdf

Stochastic thermodynamics, fluctuation theorems and molecular machines

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.

/pdf/anomalous-diffusion-models-and-their-properties-non-50bjeilyc7.pdf

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

Diffusive escape and reentry through a channel in the cavity wall

Single-molecule experiments have now achieved a time resolution allowing observation of transition paths, the brief trajectory segments where the molecule undergoing an unfolding or folding transition enters the energetically or entropically unfavorable barrier region from the folded/unfolded side and exits to the unfolded/folded side, thereby completing the transition. This resolution, however, is yet insufficient to identify the precise entrance/exit events that mark the beginning and the end of a transition path: the nature of the diffusive dynamics is such that a molecular trajectory will recross the boundary between the barrier region and the folded/unfolded state, multiple times, at a time scale much shorter than that of the typical experimental resolution. Here we use theory and Brownian dynamics simulations to show that, as a result of such recrossings, the apparent transition path times are generally longer than the true ones. We quantify this effect using a simple model where the observed dynamics is a moving average of the true dynamics and discuss experimental implications of our results.

https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.2c05550

The Effect of Time Resolution on Apparent Transition Path Times Observed in Single-Molecule Studies of Biomolecules

The activationless escape of a free Brownian particle from a unit interval is analyzed over the entire range of friction coefficient $\ensuremath{\gamma}$. Approximate analytic expressions that compare favorably with simulations are derived for the effective and asymptotic rate constants $k$ and $\ensuremath{\Gamma}$ that describe the escape kinetics. Both rate constants show a turnover behavior as functions of $\ensuremath{\gamma}$, qualitatively similar to the rate constant in the Kramers theory of activated rate processes. It is found that $k\ensuremath{\sim}1/\mathrm{ln}(1/\ensuremath{\gamma})$ and $\ensuremath{\Gamma}\ensuremath{\sim}{\ensuremath{\gamma}}^{1/3}$ as $\ensuremath{\gamma}\ensuremath{\rightarrow}0$ while both rate constants vanish as ${\ensuremath{\gamma}}^{\ensuremath{-}1}$ as $\ensuremath{\gamma}\ensuremath{\rightarrow}\ensuremath{\infty}$.

Kramers-like turnover in activationless rate processes

First-passage times in phase space for the strong collision model

This paper deals with the effect of stochastic gating on the flux of solute molecules through a membrane channel. According to the conventional approach, this flux is given by the product of the flux through the open channel and the probability of finding the channel in the open state. Recently we derived an expression for the flux through a stochastically gated channel (Berezhkovskii and Bezrukov 2017 J. Chem. Phys. 147 084109) that showed that the conventional approach may underestimate the flux at fast gating by orders of magnitude. The present work proposes a novel approach to the problem: while our initial derivation of the expression for the flux focuses on the molecule propagator in the channel, here we treat the problem by considering the steady-state flux through an ensemble of identical stochastically gated channels. We show now that the effect of gating on the flux is independent of the gate position, i.e. whether the gate is located at the channel entrance or exit.

Alexander M. Berezhkovskii

Papers

Diffusive escape and reentry through a channel in the cavity wall

The Effect of Time Resolution on Apparent Transition Path Times Observed in Single-Molecule Studies of Biomolecules

Kramers-like turnover in activationless rate processes

First-passage times in phase space for the strong collision model

Effect of stochastic gating on the flux through a membrane channel: a steady-state approach.