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.

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Pattern formation outside of equilibrium

Since the review of periodic flow phenomena by Berger & Wille (1972) in this journal, over twenty years ago, there has been a surge of activity regarding bluff body wakes. Many of the questions regarding wake vortex dynamics from the earlier review have now been answered in the literature, and perhaps an essential key to our new understandings (and indeed to new questions) has been the recent focus, over the past eight years, on the three-dimensional aspects of nominally two-dimensional wake flows. New techniques in experiment, using laser-induced fluorescence and PIV (Particle-Image-Velocimetry), are vigorously being applied to wakes, but interestingly, several of the new discoveries have come from careful use of classical methods. There is no question that strides forward in understanding of the wake problem are being made possible by ongoing three- dimensional direct numerical simulations, as well as by the surprisingly successful use of analytical modeling in these flows, and by secondary stability analyses. These new developments, and the discoveries of several new phenomena in wakes, are presented in this review.

Vortex Dynamics in the Cylinder Wake

The boundary layer equations for plane, incompressible, and steady flow are 

$$\matrix{ {u{{\partial u} \over {\partial x}} + v{{\partial u} \over {\partial y}} = - {1 \over \varrho }{{\partial p} \over {\partial x}} + v{{{\partial ^2}u} \over {\partial {y^2}}},} \cr {0 = {{\partial p} \over {\partial y}},} \cr {{{\partial u} \over {\partial x}} + {{\partial v} \over {\partial y}} = 0.} \cr }$$

Boundary Layer Theory

Numerical Initial Value Problems in Ordinary Differential Equations

Results are reported from a highly accurate, global numerical stability analysis of the periodic wake of a circular cylinder for Reynolds numbers between 140 and 300 The analysis shows that the two-dimensional wake becomes (absolutely) linearly unstable to three-dimensional perturbations at a critical Reynolds number of 1885±10 The critical spanwise wavelength is 396 ± 002 diameters and the critical Floquet mode corresponds to a ‘Mode A’ instability At Reynolds number 259 the two-dimensional wake becomes linearly unstable to a second branch of modes with wavelength 0822 diameters at onset Stability spectra and corresponding neutral stability curves are presented for Reynolds numbers up to 300

/pdf/three-dimensional-floquet-stability-analysis-of-the-wake-of-4r1lk83e37.pdf

Three-dimensional Floquet stability analysis of the wake of a circular cylinder

Shear flows undergo a sudden transition from laminar to turbulent motion as the velocity increases, and the onset of turbulence radically changes transport efficiency and mixing properties. Even for the well-studied case of pipe flow, it has not been possible to determine at what Reynolds number the motion will be either persistently turbulent or ultimately laminar. We show that in pipes, turbulence that is transient at low Reynolds numbers becomes sustained at a distinct critical point. Through extensive experiments and computer simulations, we were able to identify and characterize the processes ultimately responsible for sustaining turbulence. In contrast to the classical Landau-Ruelle-Takens view that turbulence arises from an increase in the temporal complexity of fluid motion, here, spatial proliferation of chaotic domains is the decisive process and intrinsic to the nature of fluid turbulence.

/pdf/the-onset-of-turbulence-in-pipe-flow-5d241paxp3.pdf

The onset of turbulence in pipe flow

/pdf/a-model-for-fast-computer-simulation-of-waves-in-excitable-36h8yqz3gc.pdf

A model for fast computer simulation of waves in excitable media

A highly accurate 2D linear stability analysis is performed on the mean flow of laminar vortex shedding from a circular cylinder for Reynolds numbers between 46 and 180. Consistent with past studies of mean profiles, the analysis shows that the eigenfrequency of the mean flow tracks almost exactly the Strouhal number of vortex shedding. The linear growth rate reveals that the wake mean flow is a marginally stable state over the whole range of Reynolds numbers for stable 2D vortex shedding. This is contrasted with 2D stability analysis about the unstable steady base flow. The relevance to nonlinear saturation and frequency selection are discussed.

/pdf/linear-analysis-of-the-cylinder-wake-mean-flow-4b94lbbo3f.pdf

Linear analysis of the cylinder wake mean flow

Results are reported from a three-dimensional computational stability analysis of flow over a backward-facing step with an expansion ratio (outlet to inlet height) of 2 at Reynolds numbers between 450 and 1050. The analysis shows that the first absolute linear instability of the steady two-dimensional flow is a steady three-dimensional bifurcation at a critical Reynolds number of 748. The critical eigenmode is localized to the primary separation bubble and has a flat roll structure with a spanwise wavelength of 6.9 step heights. The system is further shown to be absolutely stable to two-dimensional perturbations up to a Reynolds number of 1500. Stability spectra and visualizations of the global modes of the system are presented for representative Reynolds numbers.

/pdf/three-dimensional-instability-in-flow-over-a-backward-facing-r5hwlqsxxq.pdf

Dwight Barkley

Papers

Three-dimensional Floquet stability analysis of the wake of a circular cylinder

The onset of turbulence in pipe flow

A model for fast computer simulation of waves in excitable media

Linear analysis of the cylinder wake mean flow

Three-dimensional instability in flow over a backward-facing step