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

Images and force measurements taken by an atomic‐force microscope (AFM) depend greatly on the properties of the spring and tip used to probe the sample’s surface. In this article, we describe a simple, nondestructive procedure for measuring the force constant, resonant frequency, and quality factor of an AFM cantilever spring and the effective radius of curvature of an AFM tip. Our procedure uses the AFM itself and does not require additional equipment.

Calibration of atomic‐force microscope tips

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

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

The formalism of state estimation and hidden Markov models (HMMs) can simplify and clarify the discussion of stochastic thermodynamics in the presence of feedback and measurement errors. After reviewing the basic formalism, we use it to shed light on a recent discussion of phase transitions in the optimized response of an information engine, for which measurement noise serves as a control parameter. The HMM formalism also shows that the value of additional information shows a maximum at intermediate signal-to-noise ratios. Finally, we discuss how systems open to information flow can apparently violate causality; the HMM formalism can quantify the performance gains due to such violations.

Hidden Markov models for stochastic thermodynamics

We have developed a new, extremely sensitive real-space technique (intensity fluctuation microscopy) to probe the order of the nematic-smectic-A (NA) transition Using this technique, we show that the NA transition in 4'-n-octyl-4-cyanobiphenyl (8CB) is clearly first order, contrary to calorimetric studies but in agreement with conclusions drawn from front-velocity measurements We characterize the strength of the discontinuity at the first-order transition by the dimensionless quantity t(0)=(T(NA)-T*)/T(*) By precisely measuring t(0), we have made the first detailed tests of predictions based on the Halperin-Lubensky-Ma (HLM) theory of fluctuation-induced, first-order phase transitions First, we explore the effect of an external magnetic field on the NA transition Although modest fields (of order 10 T) are predicted to drive the weakly first-order transition in pure 8CB second order, we observe no such effect; we establish instead that the lower bound on this critical field is approximately 30 T Likewise, we observe no effect in mixtures of 8CB with its longer chemical homolog 4'-n-decyl-4-cyanobiphenyl (10CB) Second, we examine the dependence of t(0) as a function of 8CB-10CB mixture concentration and find that the data in mixtures with small nematic temperature range are well-fit by the parameters derived by Anisimov et al based on calorimetric measurements As we increase the nematic range (by using concentrations closer to pure 8CB), the measured t(0) deviates more and more from the HLM predictions Smectic fluctuations, which are neglected in the HLM calculation, are an obvious candidate to explain such a discrepancy, but one's naive expectation is that they would reduce t(0) below the HLM levels, whereas the observed values are too large However, a recent renormalization-group calculation concludes that smectic fluctuations, surprisingly, should indeed increase t(0), explaining the observations presented here

Two experimental tests of a fluctuation-induced first-order phase transition: intensity fluctuation microscopy at the nematic-smectic-A transition.

Joule or free expansion of an ideal gas into a volume with a lower pressure is an example of an irreversible isothermal process. This nonequilibrium example is often used in traditional thermodynamics text books to demonstrate that an arbitrarily slow process need not be reversible. Cyclic operation of any engine that involves a free expansion is therefore necessary dissipative. Here, we explore experimentally the origin of the thermodynamic irreversibility at the level of a single-particle gas. A feedback trap is used to confine a silica particle in a virtual bistable potential, creating a system analogous to two vessels connected by a valve, where volume of one vessel is adjustable via piston. We operate two types of cyclic transformations, both start and end in the same equilibrium state, and both use the same basic operations—but in different order. One transformation required no work, while the other required work, no matter how slowly it was carried out. A statistical analysis and a recently derived formula are used to show that the difference traces back to the observation that when time is reversed the two protocols have different outcomes. This property is not possible to notice in a single repetition, unlike in a macroscopic system where free expansion is followed by a “whoosh”.

http://iopscience.iop.org/article/10.1209/0295-5075/114/50002/pdf

Arbitrarily slow, non-quasistatic, isothermal transformations

Secondary instabilities of Faraday waves show three regimes: 1) As seen previously, low-viscosity (ν) fluids destabilize first into squares. At higher driving accelerations a, squares show low-frequency modulations corresponding to the motion of phase defects, while theory predicts a stationary transverse amplitude modulation (TAM). 2) High-ν fluids destabilize first to stripes. Stripes then show an oscillatory TAM whose frequency is incommensurate with the driving frequency. At higher a, the TAM undergoes a phase instability. At still higher a, edge dislocations form and fluid droplets are ejected. 3) Intermediate-ν fluids show a complex coexistence of squares and stripes, as well as stationary and oscillatory TAM instabilities of the stripes.

http://iopscience.iop.org/article/10.1209/0295-5075/32/4/005/pdf

Secondary Instabilities of Surface Waves on Viscous Fluids in the Faraday Instability

We study experimentally the patterns behind a moving cholesteric--smectic-A interface. There are three interface types, each of which corresponds to one of the three basic topologically possible configurations.

John Bechhoefer

Papers

Hidden Markov models for stochastic thermodynamics

Two experimental tests of a fluctuation-induced first-order phase transition: intensity fluctuation microscopy at the nematic-smectic-A transition.

Arbitrarily slow, non-quasistatic, isothermal transformations

Secondary Instabilities of Surface Waves on Viscous Fluids in the Faraday Instability

Pattern formation behind a moving cholesteric – smectic- A interface