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

We study theoretically the effect of an external field on the nematic–smectic-A transition close to the
tricritical point, where fluctuation effects govern the qualitative behavior of the transition. An external
field suppresses nematic-director fluctuations by making them massive. For a fluctuation-driven firstorder
transition, we show that an external field can drive the transition second order. In an appropriate
liquid-crystal system, we predict the required magnetic field to be of order 10 T. The equivalent electric
field is of order 1 V�mm.

/pdf/external-field-induced-tricritical-point-in-a-fluctuation-719d7jzzvg.pdf

External-Field-Induced Tricritical Point in a Fluctuation-Driven Nematic–Smectic-ATransition

We present an alternate version of the undergraduate laboratory experiment developed by Dixon [Am. J. Phys. 75, 1038–1045 (2007)] that is suitable for second-year students. We study the temperature variation of the capacitance of a ferroelectric ceramic derived from barium titanate, the Ba(Ti0.9Sn0.1)O3 solid solution. The ratio of tin to titanium is chosen to provide a convenient Curie temperature near 50°C. Using careful temperature control and real-time capacitance measurements, we track the time evolution of the capacitance in response to temperature changes at 5Hz for runs that last up to a day. At temperatures well above the Curie temperature, TC, the capacitance relaxation is well-described by a single exponential decay. Near TC, the relaxation is linear in the logarithm of time over more than three decades. For T>TC, the permittivity deviates from the Curie–Weiss law and follows another phenomenological form commonly used to describe relaxor perovskite-ceramic capacitors.

Temperature dependence of the capacitance of a ferroelectric material

We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation rates from experimental data concerning replication in cell populations. Previous work based on curve fitting depended on arbitrarily chosen functional forms for the initiation rate, with free parameters that were constrained by the data. We introduce a nonparametric method of inference that is based on Gaussian process regression. The method replaces specific assumptions about the functional form of the initiation rate with more general prior expectations about the smoothness of variation of this rate, along the genome and in time. Using this inference method, we recover, with high precision, simulated replication schemes from noisy data that are typical of current experiments.

Inferring the spatiotemporal DNA replication program from noisy data.

Liquid crystals, discovered just a century ago, have wide application to electrooptic displays and thermography. Their physical properties have also made them fascinating materials for more fundamental research.The name “liquid crystals” is actually a misnomer for what are more properly termed “mesophases,” that is, phases having symmetries intermediate between ordinary solids and liquids. There are three major classes of liquid crystals: nematics, smectics, and columnar mesophases. In nematics, although there is no correlation between positions of the rodlike molecules, the molecules tend to lie parallel along a common axis, labeled by a unit vector (or director) n. Smectics are more ordered. The molecules are also rodlike and are in layers. Different subtypes of smectics (labeled, for historical reasons, smectic A, smectic B,…) have layers that are more or less organized. In the smectic A phase, the layers are fluid and can glide easily over each other. In the smectic B phase, the layers have hexagonal ordering and strong interlayer correlations. Indeed, the smectic B phase is more a highly anisotropic plastic crystal than it is a liquid crystal. Finally, columnar mesophases are obtained with disklike molecules. These molecules can stack up in columns which are themselves organized in a two-dimensional array. There is no positional correlation between molecules in one column and molecules in the other columns.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0883769400057894

Pattern Formation During the Growth of Liquid Crystal Phases

Control theory, an interdisciplinary concept dealing with the behaviour of dynamical systems, is an important but often overlooked aspect of physics. This is the first broad and complete treatment of the topic tailored for physicists, one which goes from the basics right through to the most recent advances. Simple examples develop a deep understanding and intuition for the systematic principles of control theory, beyond the recipes given in standard engineering-focused texts. Up-to-date coverage of control of networks and complex systems, and a thorough discussion of the fundamental limits of control, including the limitations placed by causality, information theory, and thermodynamics are included. In addition it explores important recent advances in stochastic thermodynamics on the thermodynamic costs of information processing and control. For all students of physics interested in control theory, this classroom-tested, comprehensive approach to the topic with online solutions and further materials delivers both fundamental principles and current developments.

John Bechhoefer

Papers

External-Field-Induced Tricritical Point in a Fluctuation-Driven Nematic–Smectic-ATransition

Temperature dependence of the capacitance of a ferroelectric material

Inferring the spatiotemporal DNA replication program from noisy data.

Pattern Formation During the Growth of Liquid Crystal Phases

Control Theory for Physicists