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

We present an overview of the lattice Boltzmann method (LBM), a parallel and efficient algorithm for simulating single-phase and multiphase fluid flows and for incorporating additional physical complexities. The LBM is especially useful for modeling complicated boundary conditions and multiphase interfaces. Recent extensions of this method are described, including simulations of fluid turbulence, suspension flows, and reaction diffusion systems.

Lattice boltzmann method for fluid flows

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.

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Pattern formation outside of equilibrium

Couplings and changes of variables.- Three examples of coupling techniques.- The founding fathers of optimal transport.- Qualitative description of optimal transport.- Basic properties.- Cyclical monotonicity and Kantorovich duality.- The Wasserstein distances.- Displacement interpolation.- The Monge-Mather shortening principle.- Solution of the Monge problem I: global approach.- Solution of the Monge problem II: Local approach.- The Jacobian equation.- Smoothness.- Qualitative picture.- Optimal transport and Riemannian geometry.- Ricci curvature.- Otto calculus.- Displacement convexity I.- Displacement convexity II.- Volume control.- Density control and local regularity.- Infinitesimal displacement convexity.- Isoperimetric-type inequalities.- Concentration inequalities.- Gradient flows I.- Gradient flows II: Qualitative properties.- Gradient flows III: Functional inequalities.- Synthetic treatment of Ricci curvature.- Analytic and synthetic points of view.- Convergence of metric-measure spaces.- Stability of optimal transport.- Weak Ricci curvature bounds I: Definition and Stability.- Weak Ricci curvature bounds II: Geometric and analytic properties.

Optimal Transport: Old and New

Physical and numerical experiments show that deterministic noise, or chaos, is ubiquitous. While a good understanding of the onset of chaos has been achieved, using as a mathematical tool the geometric theory of differentiable dynamical systems, moderately excited chaotic systems require new tools, which are provided by the ergodic theory of dynamical systems. This theory has reached a stage where fruitful contact and exchange with physical experiments has become widespread. The present review is an account of the main mathematical ideas and their concrete implementation in analyzing experiments. The main subjects are the theory of dimensions (number of excited degrees of freedom), entropy (production of information), and characteristic exponents (describing sensitivity to initial conditions). The relations between these quantities, as well as their experimental determination, are discussed. The systematic investigation of these quantities provides us for the first time with a reasonable understanding of dynamical systems, excited well beyond the quasiperiodic regimes. This is another step towards understanding highly turbulent fluids.

Ergodic theory of chaos and strange attractors

Finite-dimensional, inviscid equations of hydrodynamics, such as the zero-viscosity, one-dimensional Burgers equation or the three-dimensional incompressible Euler equation, obtained through a Fourier-Galerkin projection, thermalise---mediated through structures known as tygers [Ray et al., Phys. Rev. E 84, 016301 (2011)]---with an energy equipartition. Therefore, numerical solutions of inviscid partial differential equations, which typically have to be Galerkin-truncated, show a behaviour at odds with the parent equation. We now propose, by using the one-dimensional Burgers equation as a testing ground, a novel numerical recipe, named tyger purging, to arrest the onset of thermalisation and hence recover the true dissipative solution.

Constructing weak solutions by tyger purging in the Burgers equation

This is the first book entirely devoted to magnetohydrodynamic (MHD) turbulence, a most welcome event for many physicists, astrophysicists and plasma physicists. Contrary to ordinary hydrodynamic t...

Book Review of Magnetohydrodynamic Turbulence, by Dieter Biskamp, Cambridge University Press, 2003, XII+297 pp., £65.00, $95, hardback (ISBN 0-521-81011-6).

The multifractal theory of turbulence uses a saddle-point evaluation in determining the power-law behaviour of structure functions. Without suitable precautions, this could lead to the presence of logarithmic corrections, thereby violating known exact relations such as the four-fifths law. Using the theory of large deviations applied to the random multiplicative model of turbulence and calculating subdominant terms, we explain here why such corrections cannot be present.

Does multifractal theory of turbulence have logarithms in the scaling relations

The existence of two-dimensional flows having an isotropic and negative eddy viscosity is demonstrated. Such flows, when subject to a very weak large-scale perturbation of wavenumber k will amplify it with a rate proportional to k 2 , independent of the direction.

Two-Dimensional Isotropic Negative Eddy Viscosity: A Common Phenomenon

Stretched exponential probability density functions (pdf), having the form of the exponential of minus a fractional power of the argument, are commonly found in turbulence and other areas. They can arise because of an underlying random multiplicative process. For this, a theory of extreme deviations is developed, devoted to the far tail of the pdf of the sum $X$ of a finite number $n$ of independent random variables with a common pdf $e^{-f(x)}$. The function $f(x)$ is chosen (i) such that the pdf is normalized and (ii) with a strong convexity condition that $f''(x)>0$ and that $x^2f''(x)\to +\infty$ for $|x|\to\infty$. Additional technical conditions ensure the control of the variations of $f''(x)$. The tail behavior of the sum comes then mostly from individual variables in the sum all close to $X/n$ and the tail of the pdf is $\sim e^{-nf(X/n)}$. This theory is then applied to products of independent random variables, such that their logarithms are in the above class, yielding usually stretched exponential tails. An application to fragmentation is developed and compared to data from fault gouges. The pdf by mass is obtained as a weighted superposition of stretched exponentials, reflecting the coexistence of different fragmentation generations. For sizes near and above the peak size, the pdf is approximately log-normal, while it is a power law for the smaller fragments, with an exponent which is a decreasing function of the peak fragment size. The anomalous relaxation of glasses can also be rationalized using our result together with a simple multiplicative model of local atom configurations. Finally, we indicate the possible relevance to the distribution of small-scale velocity increments in turbulent flow.

Uriel Frisch

Papers

Constructing weak solutions by tyger purging in the Burgers equation

Book Review of Magnetohydrodynamic Turbulence, by Dieter Biskamp, Cambridge University Press, 2003, XII+297 pp., £65.00, $95, hardback (ISBN 0-521-81011-6).

Does multifractal theory of turbulence have logarithms in the scaling relations

Two-Dimensional Isotropic Negative Eddy Viscosity: A Common Phenomenon

Extreme deviations and applications