Elementary simulation of tethered Brownian motion

We describe a simple numerical simulation, suitable for an undergraduate project (or graduate problem set), of the Brownian motion of a particle in a Hooke-law potential well. Understanding this physical situation is a practical necessity in many experimental contexts, for instance in single molecule biophysics; and its simulation helps the student to appreciate the dynamical character of thermal equilibrium. We show that the simulation succeeds in capturing behavior seen in experimental data on tethered particle motion.Comment: Submitted to American Journal of Physic

Tethered Particle Motion as a Diagnostic of DNA Tether Length

The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping

DNA Looping Kinetics Analyzed Using Diffusive Hidden Markov Model

Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this method is used to measure rate constants of DNA loop formation and breakdown mediated by repressor protein that binds to the DNA. We report a new technique for measuring these rates using a modified hidden Markov analysis that directly incorporates the diffusive motion of the bead, which is an inherent complication of tethered particle motion because it occurs on a time scale between the sampling frequency and the looping time. We compare looping lifetimes found with our method, which are consistent over a range of sampling frequencies, to those obtained via the traditional threshold-crossing analysis, which vary depending on how the raw data are filtered in the time domain. Our method does not involve such filtering, and so can detect short-lived looping events and sudden changes in looping behavior.Comment: 3 page pdf including 3 figures corrections: 2nd page, 1st column, values of diffusion coefficient, spring constant and the decay time were typed incorrectly. No conlcusions were affecte

Regionalization strategies in the historiography of argentine drama

La historiografía del teatro argentino posee actualmente un importante desafío disciplinar: historiar los complejos procesos de regionalización del “teatro nacional” para evitar la homogeneización y el reduccionismo poético-conceptual de las diversidades escé- nicas registradas en las zonas periféricas. Por lo tanto, en este artículo se propone una reflexión crítica sobre estos debates epistemológicos, mediante una revisión conceptual de herramientas operativas procedentes de la geografía humana y los estudios culturales contemporáneos que, entre otros resultados, permiten formular una estrategia teóricometodológica eficaz para la historiografía de los teatros regionales.The historiography of Argentine theater has, at present, an important disciplinary challenge: to chronicle the complex processes of regionalization of the “national drama” to avoid the homogenization and the poetic-conceptual reductionism of the scenic diversities registered in the peripheral zones. Therefore, in this article I propose a critical reflection on these epistemological debates, through a conceptual review of operational tools from human geography and contemporary cultural studies that, among other results, allow us to formulate an effective theoretical-methodological strategy for historiography of regional theater.Fil: Tossi, Mauricio Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Argentina de la Empresa; Argentin