John Bechhoefer

Bio: John Bechhoefer is an academic researcher from Simon Fraser University. The author has contributed to research in topics: DNA replication & Liquid crystal. The author has an hindex of 36, co-authored 133 publications receiving 7487 citations. Previous affiliations of John Bechhoefer include University of Chicago & University of British Columbia.

Particle dynamics in a virtual harmonic potential

Abstract: Feedback traps can create arbitrary virtual potentials for exploring the dynamics of small Brownian particles. In a feedback trap, the particle position is measured periodically and, after each measurement, one applies the force that would be produced by the gradient of the “virtual potential,” at the particle location. Virtual potentials differ from real ones in that the feedback loop introduces dynamical effects not present in ordinary potentials. These dynamical effects are caused by small time scales associated with the feedback, including the delay between the measurement of a particle’s position and the feedback response, the feedback response that is applied for a finite update time, and the finite camera exposure from integrating motion. Here, we characterize the relevant experimental parameters and compare to theory the observed power spectra and variance for a particle in a virtual harmonic potential. We show that deviations from the dynamics expected of a continuous potential are measured by the ratio of these small time scales to the relaxation time scale of the virtual potential.

Curve fits in the presence of random and systematic error

Abstract: From the autocovariance function of residual errors in least-square curve fits, one can estimate the random error present in experimental data, along with the relative proportion of systematic to statistical error. The methods outlined here have important implications for teaching error analysis.

Plagiarism: text-matching program offers an answer.

Abstract: SIR — The accusations made by arXiv that my colleagues and I have plagiarized the works of others, reported in your News story ‘Turkish physicists face accusations of plagiarism’ (Nature 449, 8; 2007) are upsetting and unfair. It’s inappropriate to single out my colleagues and myself on this issue. For those of us whose mother tongue is not English, using beautiful sentences from other studies on the same subject in our introductions is not unusual. I imagine that if all articles from specialist fields of research were checked, similarities with other texts and papers would easily be found. In my case, I aimed to cite all the references from which I had sourced information, although I may have missed some of them. Borrowing sentences in the part of a paper that simply helps to better introduce the problem should not be seen as plagiarism. Even if our introductions are not entirely original, our results are — and these are the most important part of any scientific paper. In the current climate of ‘publish or perish’, we are under pressure to publish our findings along with an introduction that reads well enough for the paper to be published and read, so that our research will be noticed and inspire further work. Ihsan Yilmaz Physics Department, Çanakkale Onsekiz Mart University, Çanakkale, Turkey

Feedback trap with scattering-based illumination

Abstract: Feedback traps can explore particle dynamics in virtual potentials. They periodically measure particle position and, after each measurement, apply a force imposed by the potential. Here, a scattering-based illumination improves particle position measurements and bandwidth.

Effect of order parameter fluctuations on the Halperin-Lubensky-Ma first-order transition in superconductors and liquid crystals

Abstract: We show that order parameter fluctuations in a good type-I superconductor or a liquid crystal always increase the size of the first-order transition. This behavior is eventually changed when the system crosses over to an inverted-XY critical behavior, with the size of the first-order transition vanishing as a power law with a crossover exponent. We find good agreement between our theory and a recent experiment on the nematic-smectic-A first-order transition in 8CB-10CB mixtures of liquid crystals.

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

Abstract: 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。

Pattern formation outside of equilibrium

Abstract: 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.

Calibration of atomic‐force microscope tips

Abstract: 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.

Stochastic Processes in Physics and Chemistry

Abstract: 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.