Modulation of HU-DNA interactions by salt concentration and applied force.

HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression

Saturation and Confinement: Analyticity, Unitarity and AdS/CFT Correspondence

In $1/N_c$ expansion, analyticity and crossing lead to crossing even and odd ($C=\pm 1$) vacuum exchanges at high-energy, the {\em Pomeron} and the {\em Odderon}. We discuss how, using {\em String/Gauge duality}, these can be identified with a reggeized {\em Graviton} and the anti-symmetric {\em Kalb-Ramond fields} in $AdS$ background. With confinement, these Regge singularities interpolate with glueball states. We also discuss unitarization based on eikonal sum in $AdS$.Comment: more references added. presented at ISMD 2008, 15-20 Sept. 200

Continuum model for polymers with finite thickness

We consider the continuum limit of a recently-introduced model for discretized thick polymers, or tubes. We address both analytically and numerically how the polymer thickness influences the decay of tangent-tangent correlations and find how the persistence length scales with the thickness and the torsional rigidity of the tube centerline. At variance with the worm-like chain model, the phase diagram that we obtain for a continuous tube is richer; in particular, for a given polymer thickness there exists a threshold value for the centerline torsional rigidity separating a simple exponential decay of the tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.

The AGN dusty torus as a clumpy two-phase medium: radiative transfer modeling with SKIRT

We modeled the AGN dusty torus as a clumpy two-phase medium, with high-density clumps embedded in a low-density interclump dust. To obtain spectral energy distributions and images of the torus at different wavelengths, we employed the 3D Monte Carlo radiative transfer code SKIRT. Apart from the grid of two-phase models, we calculated the corresponding sets of clumps-only models and models with a smooth dust distribution for comparison. We found that the most striking feature of the two-phase model is that it might offer a natural solution to the common issue reported in a number of papers -- the observed excess of the near-infrared emission.Comment: Proceedings of the Torus Workshop 2012 held at the University of Texas at San Antonio, 5-7 December 2012. C. Packham, R. Mason, and A. Alonso-Herrero (eds.). 8 pages, 5 figures. A grid of model SEDs available at https://sites.google.com/site/skirtorus