Author

# John Bechhoefer

Other affiliations: University of Chicago, University of British Columbia

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

##### Papers published on a yearly basis

##### Papers

More filters

••

[...]

TL;DR: In this article, the authors 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 AU tip.

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.

3,720 citations

••

[...]

TL;DR: In this paper, a tutorial essay aims to give enough of the formal elements of control theory to satisfy the experimentalist designing or running a typical physics experiment and enough to satisfy a theorist wishing to understand its broader intellectual context.

Abstract: Feedback and control theory are important ideas that should form part of the education of a physicist but rarely do. This tutorial essay aims to give enough of the formal elements of control theory to satisfy the experimentalist designing or running a typical physics experiment and enough to satisfy the theorist wishing to understand its broader intellectual context. The level is generally simple, although more advanced methods are also introduced. Several types of applications are discussed, as the practical uses of feedback extend far beyond the simple regulation problems where it is most often employed. Sketches are then provided of some of the broader implications and applications of control theory, especially in biology, which are topics of active research.

265 citations

••

[...]

TL;DR: In this article, the authors confirm Landauer's 1961 hypothesis that reducing the number of possible macroscopic states in a system by a factor of 2 requires work of at least kT ln2.

Abstract: We confirm Landauer’s 1961 hypothesis that reducing the number of possible macroscopic states in a system by a factor of 2 requires work of at least kT ln2. Our experiment uses a colloidal particle in a timedependent, virtual potential created by a feedback trap to implement Landauer’s erasure operation. In a control experiment, similar manipulations that do not reduce the number of system states can be done reversibly. Erasing information thus requires work. In individual cycles, the work to erase can be below the Landauer limit, consistent with the Jarzynski equality.

253 citations

••

[...]

TL;DR: In this article, the frequency response of the optical-detection electronics of an atomic-force microscope cantilever was corrected for a high frequency cut-off, which, in our case, was higher than the resonant frequency of the cantilevers.

Abstract: In our calibration of atomic-force microscope cantilevers, we neglected to correct for the frequency response of the optical-detection electronics. The response to cantilever vibrations will have a high-frequency cut-off, which, in our case, was higher than the resonant frequency of the cantilever. Our results were not affected, but for higher resonant frequencies, one should calibrate the detector response. We thank V. Croquette for raising this point.

218 citations

••

[...]

TL;DR: This model is the first to suggest a detailed, testable, biochemically plausible mechanism for the regulation of replication timing in eukaryotes and demonstrates how initiation can be stochastic and yet occur at defined times during S phase, without an explicit timing program.

Abstract: Microarrays are powerful tools to probe genome-wide replication kinetics. The rich data sets that result contain more information than has been extracted by current methods of analysis. In this paper, we present an analytical model that incorporates probabilistic initiation of origins and passive replication. Using the model, we performed least-squares fits to a set of recently published time course microarray data on Saccharomyces cerevisiae. We extracted the distribution of firing times for each origin and found that the later an origin fires on average, the greater the variation in firing times. To explain this trend, we propose a model where earlier-firing origins have more initiator complexes loaded and a more accessible chromatin environment. The model demonstrates how initiation can be stochastic and yet occur at defined times during S phase, without an explicit timing program. Furthermore, we hypothesize that the initiators in this model correspond to loaded minichromosome maintenance complexes. This model is the first to suggest a detailed, testable, biochemically plausible mechanism for the regulation of replication timing in eukaryotes.

119 citations

##### Cited by

More filters

[...]

28 Jul 2005

TL;DR: PfPMP1）与感染红细胞、树突状组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�ly.

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。

18,940 citations

••

[...]

TL;DR: A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented in this article, with emphasis on comparisons between theory and quantitative experiments, and a classification of patterns in terms of the characteristic wave vector q 0 and frequency ω 0 of the instability.

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.

5,723 citations

••

[...]

TL;DR: In this article, the authors 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 AU tip.

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.

3,720 citations

••

[...]

TL;DR: Van Kampen as mentioned in this paper provides an extensive graduate-level introduction which is clear, cautious, interesting and readable, and could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes.

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.

3,620 citations

••

[...]

TL;DR: The atomic force microscope (AFM) is not only used to image the topography of solid surfaces at high resolution but also to measure force-versus-distance curves as discussed by the authors, which provide valuable information on local material properties such as elasticity, hardness, Hamaker constant, adhesion and surface charge densities.

Abstract: The atomic force microscope (AFM) is not only a tool to image the topography of solid surfaces at high resolution. It can also be used to measure force-versus-distance curves. Such curves, briefly called force curves, provide valuable information on local material properties such as elasticity, hardness, Hamaker constant, adhesion and surface charge densities. For this reason the measurement of force curves has become essential in different fields of research such as surface science, materials engineering, and biology. Another application is the analysis of surface forces per se. Some of the most fundamental questions in colloid and surface science can be addressed directly with the AFM: What are the interactions between particles in a liquid? How can a dispersion be stabilized? How do surfaces in general and particles in particular adhere to each other? Particles and surfaces interactions have major implications for friction and lubrication. Force measurements on single molecules involving the rupture of single chemical bonds and the stretching of polymer chains have almost become routine. The structure and properties of confined liquids can be addressed since force measurements provide information on the energy of a confined liquid film. After the review of Cappella [B. Cappella, G. Dietler, Surf. Sci. Rep. 34 (1999) 1–104] 6 years of intense development have occurred. In 1999, the AFM was used only by experts to do force measurements. Now, force curves are used by many AFM researchers to characterize materials and single molecules. The technique and our understanding of surface forces has reached a new level of maturity. In this review we describe the technique of AFM force measurements. Important experimental issues such as the determination of the spring constant and of the tip radius are discussed. Current state of the art in analyzing force curves obtained under different conditions is presented. Possibilities, perspectives but also open questions and limitations are discussed.

3,024 citations