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,
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 kTln2. Our experiment uses a colloidal particle in a time-dependent, 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.
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.
We developed analytical models of DNA replication that include probabilistic initiation of origins, fork progression, passive replication, and asynchrony.We fit the model to budding yeast genome-wide microarray data probing the replication fraction and found that initiation times correlate with the precision of timing.We extracted intrinsic origin properties, such as potential origin efficiency and firing-time distribution, which cannot be done using phenomenological approaches.We propose that origin timing is controlled by stochastically activated initiators bound to origin sites rather than explicit time-measuring mechanisms.
Replication timing is a crucial aspect of genome regulation that is strongly correlated with chromatin structure, gene expression, DNA repair, and genome evolution. Replication timing is determined by the timing of replication origin firing, which involves activation of MCM helicase complexes loaded at replication origins. Nonetheless, how the timing of such origin firing is regulated remains mysterious. Here, we show that the number of MCMs loaded at origins regulates replication timing. We show for the first time in vivo that multiple MCMs are loaded at origins. Because early origins have more MCMs loaded, they are, on average, more likely to fire early in S phase. Our results provide a mechanistic explanation for the observed heterogeneity in origin firing and help to explain how defined replication timing profiles emerge from stochastic origin firing. These results establish a framework in which further mechanistic studies on replication timing, such as the strong effect of heterochromatin, can be pursued.
(J.B.) and abensim@pasteur.fr (A.B.) We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of different data within a simple theoretical framework. This allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.
We measure the threshold accelerations necessary to excite surface waves in a vertically vibrated fluid container (the Faraday instability). Under the proper conditions, the thresholds and onset wavelengths agree with recent theoretical predictions for a laterally infinite, finite-depth container filled with a viscous fluid. Experimentally, we show that by using a viscous, non-polar fluid, the finite-size effects of sidewalls and the effects of surface contamination can be made negligible. We also show that finite-size corrections are of order h/L, where h is the fluid depth and L the container size. Based on these measurements, one can more easily interpret certain unexpected observations from previous experimental studies of the Faraday instability.
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