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Showing papers by "John Bechhoefer published in 2009"


Journal ArticleDOI
TL;DR: In this article, a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions was proposed, and it was shown that the interaction between DNA and the rate-limiting protein must be subdiffusive.
Abstract: We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.

31 citations


Journal ArticleDOI
TL;DR: An algorithm for calculating, offline or in real time and with no explicit system characterization, the feedforward input required for repetitive motions of a system gives accurate motion at frequencies limited only by the signal-to-noise ratio and the actuator power and range.
Abstract: We introduce an algorithm for calculating, offline or in real time and with no explicit system characterization, the feedforward input required for repetitive motions of a system. The algorithm is based on the secant method of numerical analysis and gives accurate motion at frequencies limited only by the signal-to-noise ratio and the actuator power and range. We illustrate the secant-solver algorithm on a stage used for atomic force microscopy.

21 citations


Book ChapterDOI
TL;DR: This chapter describes methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized origins--from such data.
Abstract: New technologies such as DNA combing have led to the availability of large quantities of data that describe the state of DNA while undergoing replication in S phase. In this chapter, we describe methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized origins--from such data. We first present a version of the technique that applies to "ideal" data. We then show how to deal with, a number of real-world complications, such as the asynchrony of starting times of a population of cells, the finite length of fragments used in the analysis, and the finite amount of DNA in a chromosome.

7 citations