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

A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

/pdf/pattern-formation-outside-of-equilibrium-1601b9znum.pdf

Pattern formation outside of equilibrium

The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Reaction-rate theory: fifty years after Kramers

It has often been remarked that turbulence is a subject of great scientific and technological importance, and yet one of the least understood (e.g. McComb 1990). To an outsider this may seem strange, since the basic physical laws of fluid mechanics are well established, an excellent mathematical model is available in the Navier-Stokes equations, and the results of well over a century of increasingly sophisticated experiments are at our disposal. One major difficulty, of course, is that the governing equations are nonlinear and little is known about their solutions at high Reynolds number, even in simple geometries. Even mathematical questions as basic as existence and uniqueness are unsettled in three spatial dimensions (cf Temam 1988). A second problem, more important from the physical viewpoint, is that experiments and the available mathematical evidence all indicate that turbulence involves the interaction of many degrees of freedom over broad ranges of spatial and temporal scales. One of the problems of turbulence is to derive this complex picture from the simple laws of mass and momentum balance enshrined in the NavierStokes equations. It was to this that Ruelle & Takens (1971) contributed with their suggestion that turbulence might be a manifestation in physical

/pdf/the-proper-orthogonal-decomposition-in-the-analysis-of-44vs42u998.pdf

The Proper Orthogonal Decomposition in the Analysis of Turbulent Flows

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

The Navier–Stokes equations are a set of nonlinear partial differential equations comprising the fundamental dynamical description of fluid motion. They are applied routinely to problems in engineering, geophysics, astrophysics, and atmospheric science. This book is an introductory physical and mathematical presentation of the Navier–Stokes equations, focusing on unresolved questions of the regularity of solutions in three spatial dimensions, and the relation of these issues to the physical phenomenon of turbulent fluid motion. Intended for graduate students and researchers in applied mathematics and theoretical physics, results and techniques from nonlinear functional analysis are introduced as needed with an eye toward communicating the essential ideas behind the rigorous analyses.

Applied analysis of the Navier-Stokes equations

We consider the problem of thermally activated potential barrier crossing in the presence of fluctuations of the barrier itself. For piecewise linear barrier switching between two values as a Markov process, exact and Monte Carlo results reveal a novel resonantlike phenomenon as a function of the barrier fluctuation rate. For very slow variations the average crossing time is the average of the times required to diffuse over each of the barriers separately; for very fast variations the mean crossing time is that required to cross the average barrier. At intermediate rates the crossing is strongly correlated with the potential variation and the escape rate exhibits a local maximum at a ``resonant'' fluctuation rate.

Resonant activation over a fluctuating barrier.

Ratchetlike devices can rectify symmetric, unbiased nonequilibrium noise resulting in fluctuation-induced currents. We study some simple models to investigate the dependence of a nonequilibrium steady-state current on the characteristic features of the ratchet and the applied noise. It turns out that the magnitude and the direction of the induced current depend not only on the shape of the ratchet, but also on the statistics of the fluctuations.

Nonequilibrium fluctuation-induced transport

The Navier-Stokes equations are utilized to derive upper bounds on the turbulent energy dissipation rate for an incompressible Newtonian fluid confined between parallel comoving plates. These estimates provide a rigorous foundation for one of the basic scaling ideas of turbulence theory, namely, the independence of the dissipation rate and the viscosity at high Reynolds number. The bounds are compared to experiments on turbulence in the Couette-Taylor system.

Energy dissipation in shear driven turbulence.

Building on a method of analysis for the Navier-Stokes equations introduced by Hopf [Math. Ann. 117, 764 (1941)], a variational principle for upper bounds on the largest possible time averaged convective heat flux is derived from the Boussinesq equations of motion. When supplied with appropriate test background fields satisfying a spectral constraint, reminiscent of an energy stability condition, the variational formulation produces rigorous upper bounds on the Nusselt number (Nu) as a function of the Rayleigh number (Ra). For the case of vertical heat convection between parallel plates in the absence of sidewalls, a simplified (but rigorous) formulation of the optimization problem yields the large Rayleigh number bound Nu\ensuremath{\le}0.167 ${\mathrm{Ra}}^{1/2}$-1. Nonlinear Euler-Lagrange equations for the optimal background fields are also derived, which allow us to make contact with the upper bound theory of Howard [J. Fluid Mech. 17, 405 (1963)] for statistically stationary flows. The structure of solutions of the Euler-Lagrange equations are elucidated from the geometry of the variational constraints, which sheds light on Busse's [J. Fluid Mech. 37, 457 (1969)] asymptotic analysis of general solutions to Howard's Euler-Lagrange equations. The results of our analysis are discussed in the context of theory, recent experiments, and direct numerical simulations. \textcopyright{} 1996 The American Physical Society.

Charles R. Doering

Papers

Applied analysis of the Navier-Stokes equations

Resonant activation over a fluctuating barrier.

Nonequilibrium fluctuation-induced transport

Energy dissipation in shear driven turbulence.

Variational bounds on energy dissipation in incompressible flows. III. Convection