Intercalation and buckling instability of DNA linker within locked chromatin fiber

The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the nucleosomes are strongly end constrained. Longitudinal thermal fluctuations in these linkers allow intercalative mode of protein binding. We show that mechanical constraints generated in the first stage of the binding process induce linker DNA buckling; buckling in turn modifies the binding energies and activation barriers and creates a force of decondensation at the chromatin fiber level. The unique structure and properties of DNA thus yield a novel physical mechanism of buckling instability that might play a key role in the regulation of gene expression.Comment: 5 pages, 4 figures. To appear in Physical Review E (Rapid Communication

The carbon dioxide solubility in alkali basalts: an experimental study

International audienceExperiments were conducted to determine CO2 solubilities in alkali basalts from Vesuvius, Etna and Stromboli volcanoes. The basaltic melts were equilibrated with nearly pure CO2 at 1,200°C under oxidizing conditions and at pressures ranging from 269 to 2,060 bars. CO2 solubility was determined by FTIR measurements. The results show that alkalis have a strong effect on the CO2 solubility and confirm and refine the relationship between the compositional parameter Π devised by Dixon (Am Mineral 82:368-378, 1997) and the CO2 solubility

The H2O solubility of alkali basaltic melts: an experimental study

International audienceExperiments were conducted to determine the water solubility of alkali basalts from Etna, Stromboli and Vesuvius volcanoes, Italy. The basaltic melts were equilibrated at 1,200°C with pure water, under oxidized conditions, and at pressures ranging from 163 to 3,842 bars. Our results show that at pressures above 1 kbar, alkali basalts dissolve more water than typical mid-ocean ridge basalts (MORB). Combination of our data with those from previous studies allows the following simple empirical model for the water solubility of basalts of varying alkalinity and fO2 to be derived: {\text{H}}_{ 2} {\text{O}}\left( {{\text{wt}}\% } \right) = {\text{ H}}_{ 2} {\text{O}}_{\text{MORB}} \left( {{\text{wt}}\% } \right) + \left( {5.84 \times 10^{ - 5} *{\text{P}} - 2.29 \times 10^{ - 2} } \right) \times \left( {{\text{Na}}_{2} {\text{O}} + {\text{K}}_{2} {\text{O}}} \right)\left( {{\text{wt}}\% } \right) + 4.67 \times 10^{ - 2} \times \Updelta {\text{NNO}} - 2.29 \times 10^{ - 1} where H2OMORB is the water solubility at the calculated P, using the model of Dixon et al. (1995). This equation reproduces the existing database on water solubilities in basaltic melts to within 5%. Interpretation of the speciation data in the context of the glass transition theory shows that water speciation in basalt melts is severely modified during quench. At magmatic temperatures, more than 90% of dissolved water forms hydroxyl groups at all water contents, whilst in natural or synthetic glasses, the amount of molecular water is much larger. A regular solution model with an explicit temperature dependence reproduces well-observed water species. Derivation of the partial molar volume of molecular water using standard thermodynamic considerations yields values close to previous findings if room temperature water species are used. When high temperature species proportions are used, a negative partial molar volume is obtained for molecular water. Calculation of the partial molar volume of total water using H2O solubility data on basaltic melts at pressures above 1 kbar yields a value of 19 cm3/mol in reasonable agreement with estimates obtained from density measurements

Constructing and exploring wells of energy landscapes

Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic explorations of the relief and introduce as basic topographic features ``wells of duration $T$ and altitude $y$''. We determine an intrinsic exploration mechanism governing the evolutions from an initial state in the well up to its rim in a prescribed time, whose finite-difference approximations on finite grids yield a constructive algorithm for determining the wells. Our main results are thus (i) a quantitative characterization of landscape topography rooted in a dynamic exploration of the landscape, (ii) an alternative to stochastic gradient dynamics for performing such an exploration, (iii) a constructive access to the wells and (iv) the determination of some bare dynamic features inherent to the landscape. The mathematical tools used here are not familiar in physics: They come from set-valued analysis (differential calculus of set-valued maps and differential inclusions) and viability theory (capture basins of targets under evolutionary systems) which have been developed during the last two decades; we therefore propose a minimal appendix exposing them at the end of this paper to bridge the possible gap.Comment: 28 pages, submitted to J. Math. Phys -

Visions de la complexité. Le démon de Laplace dans tous ses états

Nous distinguons trois visions de la complexité afin de clarifier les contours de la recherche dans ce domaine. Nous utilisons le démon de Laplace comme référence pour présenter ces visions. La vision 1 brise le rêve du démon de Laplace en identifiant des systèmes particuliers qui lui résistent en mathématiques, physique et informatique. La vision 2 propose une nouvelle version du rêve de Laplace fondée sur la disponibilité récente de grandes quantités de données et de nouvelles technologies de programmation, de stockage et de calcul. La vision 3 met le démon face au défi de simuler la subjectivité et ses effets collectifs. (Résumé d'auteur