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

While particle trajectories encode information on their governing potentials, potentials can be challenging to robustly extract from trajectories. Measurement errors may corrupt a particle’s position, and sparse sampling of the potential limits data in higher-energy regions such as barriers. We develop a Bayesian method to infer potentials of arbitrary shape alongside measurement noise. As an alternative to Gaussian process priors over potentials, we introduce structured kernel interpolation to the Natural Sciences which allows us to extend our analysis to large data sets. Our method is validated on 1D and 2D experimental trajectories for particles in a feedback trap.

Inferring potential landscapes from noisy trajectories

Feedback traps are tools for trapping single charged objects in solution. They periodically measure an object’s position and apply a feedback force to counteract Brownian motion. The feedback force can be calculated as a gradient of a potential function, effectively creating a “virtual potential.” Its flexibility regarding the choice of form of the potential gives an opportunity to explore various fundamental questions in stochastic thermodynamics. Here, we review the theory behind feedback traps and apply it to measuring the average work required to erase a fraction of a bit of information. The results agree with predictions based on the nonequilibrium system entropy. With this example, we also show how a feedback trap can easily implement the complex erasure protocols required to reach ultimate thermodynamic limits.

Direct measurement of a nonequilibrium system entropy using a feedback trap

https://physicstoday.scitation.org/doi/pdf/10.1063/PT.3.4711

Repulsive Casimir forces

We design and implement a feedback tracking system to study the correlated diffusive properties of a Brownian colloidal sphere near a flat wall. A feedback-controlled piezo vertical stage tracks the sphere’s position.

When Wall-hindered Diffusion Dynamics Becomes Non-Gaussian

Thermal systems are an attractive setting for exploring the connections between the lumped-element approximations of elementary circuit theory and the partial-differential field equations of mathematical physics, a topic that has been neglected in physics curricula. In a calculation suitable for an undergraduate course in mathematical physics, we show that the response function between an oscillating heater and temperature probe has a smooth crossover between a low-frequency, "lumped-element" regime where the system behaves as an electrical capacitor and a high-frequency regime dominated by the spatial dependence of the temperature field. Undergraduates can easily (and cheaply) explore these ideas experimentally in a typical advanced laboratory course. Because the characteristic frequencies are low, ($\approx$ 30 s)$^{-1}$, measuring the response frequency by frequency is slow and challenging; to speed up the measurements, we introduce a useful, if underappreciated experimental technique based on a multisine power signal that sums carefully chosen harmonic components with random phases. Strikingly, we find that the simple model of a one-dimensional, finite rod predicts a temperature response in the frequency domain that closely approximates experimental measurements from an irregular, blob-shaped object. The unexpected conclusion is that the frequency response of this irregular thermal system is nearly independent of its geometry, an example of---and justification for---the "spherical cow" approximations so beloved of physicists.

John Bechhoefer

Papers

Inferring potential landscapes from noisy trajectories

Direct measurement of a nonequilibrium system entropy using a feedback trap

Repulsive Casimir forces

When Wall-hindered Diffusion Dynamics Becomes Non-Gaussian

From rods to blobs: When geometry is irrelevant for heat diffusion