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

Critical Behavior of the Banded-Unbanded Spherulite Transition in a Mixture of Ethylene Carbonate with Polyacrylonitrile

In a recent Letter [1], Joykutty et al. claim to observe parametric resonance in an optical trap. They use the observation of a peak in the position variance of a trapped particle as a function of modulation frequency to give a new, precise method for calibrating trap stiffness. We found this result extremely surprising. Intuitively, to show a resonant effect, the particle must ‘‘remember’’ its dynamics over at least one oscillation period. In the extremely overdamped conditions of an optical trap, the effects of any outside influence decay in a small fraction of a period, preventing the buildup of coherent motion, which must be present in order to affect the variance. Although the discussion in [1] is qualitative and based on the behavior of the underdamped system, the solution to the Brownian parametric oscillator with arbitrary damping has been previously derived [2]. In the accompanying Comment, Pedersen and Flyvbjerg discuss in detail the overdamped limit and conclude that, indeed, there should be no finite-frequency peak in the position variance versus the trap modulation frequency [3]. To experimentally test these ideas, we repeated the experiment of Joykutty et al., here modulating the laser power P by direct control of the laser current. We set the trap stiffness to be 9:27 pN= m for a 3:17 m polystyrene bead and measured the variance of the position from a 10 s time series sampled at 16 kHz at different modulation frequencies. Because of the long measurement time, the result may be affected by drift and ambient noise. In our experiment, we compensated for these effects by following each measurement with another where no modulation was present. We report the ratio of the two variances, xx= 0, as a function of the frequency near twice the natural frequency !0, in Fig. 1. We see no sign of a resonance peak. In response to a first version of this Comment, Venkataraman et al. [4] suggest that their observations could be explained by their use of an acousto-optic modulator (AOM) for varying the trap strength. They propose that the AOM modulates inadvertently either the beam position or the beam shape. However, neither effect leads to a variance peak. In modulating the laser-diode current, we also observed a periodic, linear shift in beam position. In the data reported in Fig. 1, we set our position-sensitive detector’s axis normal to the beam-modulation direction. Because motion is linear for small modulations, the two axes are uncoupled, and we recovered the expected results. Analyzing the motion along the modulation direction, we saw an artificially increased variance because the trap drags the particle back and forth. But we observed no peak in variance at any finite frequency. Theoretically, a periodic shift in beam location can be accounted for by changing coordinates to x1 t x t xbeam t , where xbeam t is the time-dependent beam position. In the new coordinates x1 t , the modulation simply adds an ordinary inhomogeneous driving term. Since the oscillator is overdamped, no resonant response is expected. As for a modulation of the beam shape, since only the linear regime is probed, the effect can be simply absorbed into the overall magnitude of the modulation. [One expands V x V 0 1=2 V 00 0 x2. Shape changes then modulate V 00 0 at lowest order, but that is exactly the same effect as changing the overall laser power.] To conclude, our experimental evidence shows no peak in the variance, in contrast to the observations of Joykutty et al.. In addition, their proposed explanations that the effect is somehow linked to modulation of the beam position or shape can also be ruled out. Thus, we conclude that their observations are not due to parametric resonance and suggest that some other feature of their apparatus must be responsible for the data that they present.

Comment on "direct measurement of the oscillation frequency in an optical-tweezers trap by parametric excitation".

We have experimentally realized an information engine consisting of an optically trapped, heavy bead in water. The device raises the trap center after a favorable "up" thermal fluctuation, thereby increasing the bead's average gravitational potential energy. In the presence of measurement noise, poor feedback decisions degrade its performance; below a critical signal-to-noise ratio, the engine shows a phase transition and cannot store any gravitational energy. However, using Bayesian estimates of the bead's position to make feedback decisions can extract gravitational energy at all measurement noise strengths and has maximum performance benefit at the critical signal-to-noise ratio.

Bayesian Information Engine that Optimally Exploits Noisy Measurements.

We present a new, extremely sensitive optical method to study the nematic-smectic-A (NA) phase transition in liquid crystals. In this new technique, we monitor nematic director fluctuations as a function of temperature as we approach the NA transition. We show that the NA transition in the liquid crystal 8CB (which has a small nematic range) is clearly first order, well within the resolution of the experiment. This is contrary to previous calorimetric measurements but confirms an earlier dynamical measurement. We characterize the strength of the phase transition by a dimensionless, technique-independent quantity t 0 = (T NA - T*)/T NA. For 8CB, we measure t 0 = (6 ± 2) × 10−6.

Using Nematic Director Fluctuations as a Sensitive Probe of the Nematic-Smectic-a Phase Transition in Liquid Crystals

https://doi.org/10.1016/j.isci.2022.104731

John Bechhoefer

Papers

Critical Behavior of the Banded-Unbanded Spherulite Transition in a Mixture of Ethylene Carbonate with Polyacrylonitrile

Comment on "direct measurement of the oscillation frequency in an optical-tweezers trap by parametric excitation".

Bayesian Information Engine that Optimally Exploits Noisy Measurements.

Using Nematic Director Fluctuations as a Sensitive Probe of the Nematic-Smectic-a Phase Transition in Liquid Crystals

Inferring potential landscapes from noisy trajectories of particles within an optical feedback trap