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

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

■ Abstract The phase-field method has recently emerged as a powerful computational approach to modeling and predicting mesoscale morphological and microstructure evolution in materials. It describes a microstructure using a set of conserved and nonconserved field variables that are continuous across the interfacial regions. The temporal and spatial evolution of the field variables is governed by the Cahn-Hilliard nonlinear diffusion equation and the Allen-Cahn relaxation equation. With the fundamental thermodynamic and kinetic information as the input, the phase-field method is able to predict the evolution of arbitrary morphologies and complex microstructures without explicitly tracking the positions of interfaces. This paper briefly reviews the recent advances in developing phase-field models for various materials processes including solidification, solid-state structural phase transformations, grain growth and coarsening, domain evolution in thin films, pattern formation on surfaces, dislocation microstructures, crack propagation, and electromigration.

/pdf/phase-field-models-for-microstructure-evolution-espg8ri45v.pdf

Phase-Field Models for Microstructure Evolution

Transactions of the Institute of British Geographers

A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to time scales much larger than conventional atomic methods. The model is shown to be consistent with the predictions of Read and Shockley for grain boundary energy, and Matthews and Blakeslee for misfit dislocations in epitaxial growth.

/pdf/modeling-elasticity-in-crystal-growth-46mxf8f9ls.pdf

Modeling elasticity in crystal growth.

A continuum field theory approach is presented for modeling elastic and plastic deformation, free surfaces, and multiple crystal orientations in nonequilibrium processing phenomena. Many basic properties of the model are calculated analytically, and numerical simulations are presented for a number of important applications including, epitaxial growth, material hardness, grain growth, reconstructive phase transitions, and crack propagation.

/pdf/modeling-elastic-and-plastic-deformations-in-nonequilibrium-4qj5n9x40c.pdf

Modeling elastic and plastic deformations in nonequilibrium processing using phase field crystals.

In this paper the relationship between the classical density functional theory of freezing and phase-field modeling is examined. More specifically a connection is made between the correlation functions that enter density functional theory and the free energy functionals used in phase-field crystal modeling and standard models of binary alloys (i.e., regular solution model). To demonstrate the properties of the phase-field crystal formalism a simple model of binary alloy crystallization is derived and shown to simultaneously model solidification, phase segregation, grain growth, elastic and plastic deformations in anisotropic systems with multiple crystal orientations on diffusive time scales.

/pdf/phase-field-crystal-modeling-and-classical-density-513lp2zikw.pdf

Phase-field crystal modeling and classical density functional theory of freezing

A theoretical approach to the Ostwald ripening of droplets is presented in dimension D\ensuremath{\ge}2. A mean-field theory is constructed to incorporate screening effects in the competing many-droplet system. The mean-field equations are solved to infinite order in the volume fraction and provide analytic expressions for the coarsening rate, the time-dependent droplet-distribution function, and the time evolution of the total number of droplets. These results are in good agreement with experiments in three dimensions and with a very large scale and extensive numerical study in both two and three dimensions presented in this paper. The numerical study also provides the time evolution of the structure factors, which scale with the only length scale, the average droplet radius.

Theory and simulation of Ostwald ripening.

We model friction acting on the tip of an atomic force microscope as it is dragged across a surface at nonzero temperatures. We find that stick-slip motion occurs and that the average frictional force follows $|\mathrm{ln}v{|}^{2/3}$, where $v$ is the tip velocity. This compares well to recent experimental work, permitting the quantitative extraction of all microscopic parameters. We calculate the scaled form of the average frictional force's dependence on both temperature and tip speed as well as the form of the friction-force distribution function.

/pdf/thermal-effects-on-atomic-friction-3ekedzxq7t.pdf

Martin Grant

Papers

Modeling elasticity in crystal growth.

Modeling elastic and plastic deformations in nonequilibrium processing using phase field crystals.

Phase-field crystal modeling and classical density functional theory of freezing

Theory and simulation of Ostwald ripening.

Thermal effects on atomic friction.