Experimental study of work fluctuations in a harmonic oscillator

The work fluctuations of a harmonic oscillator in contact with a thermostat and driven out of equilibrium by an external force are studied experimentally. For the work both the transient and stationary state fluctuation theorems hold. The finite time corrections are very different from those of a first order Langevin equation. The heat and work fluctuations are studied when a periodic forcing is applied to the oscillator. The importance of the choice of the ''good work'' to compute the free energy from the Jarzinsky equality is discussed

Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev.

Experimental study of work fluctuations in a harmonic oscillator

International audienceThe work fluctuations of a harmonic oscillator in contact with a thermostat and driven out of equilibrium by an external force are studied experimentally. For the work both the transient and stationary state fluctuation theorems hold. The finite time corrections are very different from those of a first order Langevin equation. The heat and work fluctuations are studied when a periodic forcing is applied to the oscillator. The importance of the choice of the ''good work'' to compute the free energy from the Jarzinsky equality is discussed

Modélisation d'expériences permettant la manipulation de molécules biologiques uniques

Thèse commencée en octobre 2002 au Laboratoire de Dynamique des Fluides Complexes (LDFC) de l'université Louis Pasteur (ULP, Strasbourg 1). Terminée au Laboratoire de Physique Statistique (LPS) de l'Ecole Normale Supérieure (ENS), université Pierre et Marie Curie (UPMC, Paris 6).Modelization of mechanisms regulating gene expression is the main topic of this manuscript which is divided in two parts. Looping of the DNA molecule is studied from the static point of view. Size of proteins clamping the loop is taken into account as well as mechanisms inducing stiffness loss - additional proteins binding for instance - or stretching of the molecule thanks to an external force. End-to-end distance distributions including the cyclization factor of the "Worm-Like Chain" (WLC) have been computed using numerical methods. This semiflexible polymer model includes only bending stiffness all along this work. The analytical expression Shimada and Yamakawa derived in 1984 is furthermore extended. Follows a brief report on numerical stochastic algorithms which allow the dynamical simulation of the plasmid ColE1 Copy Number Control (CNC) mechanism. These should shortly complement futher theoretical and experimental studies on robustness with respect to noise.Le manuscrit concerne la modélisation de mécanismes de régulation de l'expression génétique. Il se divise en deux parties. Une étude statique de la formation de boucles dans la molécule d'ADN par exemple observable lors de la répression, à l'étape de transcription, de l'opéron Lac. Sont pris en compte : les effets liés à la taille des protéines fixant la boucle, des mécanismes entraînant une perte de rigidité du double brin - typiquement l'accrochage d'autres protéines - ainsi que son étirement au moyen d'une force extérieure. Nous avons calculé numériquement les diverses distributions en extension, ainsi que le facteur de cyclisation du modèle de polymère semi-flexible, dit "du ver". Seule la rigidité de courbure de l'ADN a été considérée. Nous avons adapté l'expression analytique obtenue par Shimada et Yamakawa en 1984. Suit un bilan posant les bases d'une simulation stochastique du mécanisme permettant, à l'étape de réplication, le Contrôle du Nombre de Copie (CNC) du plasmide ColE1. Ce travail numérique devrait compléter une future caractérisation tant théorique qu'expérimentale, de la robustesse au bruit

Motility and aerotaxis in Sinorhizobium melilotiSinorhizobium\ meliloti, a soil bacterium

International audienceAerotaxis is the ability of motile cells to move towards oxygen. Bacteria tracking and in-situ oxygen concentration measurements are used to characterize aerotaxis in Sinorhizobium meliloti, a motile nitrogen-fixing bacterium naturally present in the soil. Aerotaxis takes place in a sealed glass capillary closed at one end with an oxygen-permeable plug. Our results suggest that the oxygen dependence of the aerotactic velocity, ∝ ∇c/c$^2$ , is stronger than the "logarithmic sensing" response (∝ ∇c/c) found in other chemoattractants