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

The large-scale dynamics of the Kolmogorov flow near its threshold of instability is studied in the presence of the β-effect (Rossby waves). The governing equation, obtained by a multiscale technique, fails the Painleve test of integrability when β ≠ 0. This “β-Cahn-Hilliard” equation with cubic nonlinearity is simulated numerically in various regimes. The dispersive action of the waves modifies the inverse cascade associated with the Kolmogorov flow [1]. For small values of β the inverse cascade is interrupted at a wavenumber which increases with β. For large values of β only resonant wave interactions (RWI) survive. An original approach to RWI is developed, based on a reduction to normal form, of the sort used in celestial mechanics [2]. Otherwise, wavenumber discreteness effects, which are dramatic in the present case, are not captured. The method is extendable to arbitrary RWI problems of the kind encountered in plasma physics, spin waves, oceanography, etc. (See, e.g., Ref [3]). The Only four-wave reasonances present involve two pairs of opposite wavenumbers. This allows leading-order decoupling of moduli and phases of the varios Fourier modes, so that an exact kinetic equation is obtained for the energies of the modes. It has a Lyapunov function (gredient) formulation and multiple attracting steady-states. each with a single mode excited.

Large-Scale Kolmogorov Flow on the Beta-Plane, Resonant Wave Interactions and Scale Selection

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.

Suppressing thermalization and constructing weak solutions in truncated inviscid equations of hydrodynamics: Lessons from the Burgers equation

A brief introduction to fully developed turbulence is given (cf. Refs. 1-2). We then report results obtained from numerical simulations of the Taylor-Green three dimensional vortex flow 3. This flow is perhaps the simplest system in which one can study the generation of small scales by three-dimensional vortex stretching and the resulting turbulence. The problem is studied by both direct spectral numerical solution of the Navier-Stokes equations (with up to 2563 modes) and by power series analysis in time.

The taylor-green vortex : Fully developed turbulence and transition to spatial chaos

Significant efforts have recently been made in order to explain the spontaneous formation of large scale structures in hydrodynamical systems. Most of the theoretical works are based on the idea that instabilities are the source of the phenomenon. We are here interested in situations where structures develop at scales much larger than those of the instability and result from an inverse cascade. Classical examples are the inverse energy cascade in two-dimensional turbulence, which is driven by a negative viscosity (Kraichnan 1967,1976) and the inverse cascade of magnetic helicity in MHD flows, which is driven by the α-effect (Frisch, Leorat, Mazure and Pouquet 1975). A known deterministic example is the two-dimensional Kolmogorov flow (She 1987).

On the Possibility of an Inverse Cascade in Three-Dimensional Anisotropic Flows Lacking Parity Invariance

Burgers turbulence subject to a force $f(x,t)=\sum_jf_j(x)\delta(t-t_j)$, where the $t_j$'s are ``kicking times'' and the ``impulses'' $f_j(x)$ have arbitrary space dependence, combines features of the purely decaying and the continuously forced cases. With large-scale forcing this ``kicked'' Burgers turbulence presents many of the regimes proposed by E, Khanin, Mazel and Sinai (1997) for the case of random white-in-time forcing. It is also amenable to efficient numerical simulations in the inviscid limit, using a modification of the Fast Legendre Transform method developed for decaying Burgers turbulence by Noullez and Vergassola (1994). For the kicked case, concepts such as ``minimizers'' and ``main shock'', which play crucial roles in recent developments for forced Burgers turbulence, become elementary since everything can be constructed from simple two-dimensional area-preserving Euler--Lagrange maps. 
One key result is for the case of identical deterministic kicks which are periodic and analytic in space and are applied periodically in time: the probability densities of large negative velocity gradients and of (not-too-large) negative velocity increments follow the power law with -7/2 exponent proposed by E {\it et al}. (1997) in the inviscid limit, whose existence is still controversial in the case of white-in-time forcing. (More in the full-length abstract at the beginning of the paper.)

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Uriel Frisch

Papers

Large-Scale Kolmogorov Flow on the Beta-Plane, Resonant Wave Interactions and Scale Selection

Suppressing thermalization and constructing weak solutions in truncated inviscid equations of hydrodynamics: Lessons from the Burgers equation

The taylor-green vortex : Fully developed turbulence and transition to spatial chaos

On the Possibility of an Inverse Cascade in Three-Dimensional Anisotropic Flows Lacking Parity Invariance

Kicked Burgers Turbulence