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

Giant enhanced optical nonlinearity of colloidal nanocrystals with a graded-index host

The effective linear and third-order nonlinear optical properties of metallic colloidal crystal immersed in a graded-index host fluid are investigated theoretically. The local electric fields are extracted self-consistently based on the layer-to-layer interactions, which are readily given by the Lekner summation method. The resultant optical absorption and nonlinearity enhancement show a series of sharp peaks, which merge in a broadened resonant band. The sharp peaks become a continuous band for increasing packing density and number of layers. We believe that the sharp peaks arise from the in-plane dipolar interactions and the surface plasmon resonance, whereas the continuous band is due to the presence of the gradient in the host refractive index. These results have not been observed in homogeneous and randomly-dispersed colloids, and thus would be of great interest in optical nanomaterial engineering.Comment: Submitted to Applied Physics Letter

Temperature-dependent Cross Sections for Charmonium Dissociation in Collisions with Pions and Rhos in Hadronic Matter

Meson-charmonium dissociation reactions governed by the quark interchange are studied with temperature-dependent quark potentials. Quark-antiquark relative-motion wave functions and masses of charmonia and charmed mesons are determined by the central spin-independent part of the potentials or by the central spin-independent part and a smeared spin-spin interaction. The prominent temperature dependence of the masses is found. Based on the potentials, the wave functions, and the meson masses, we obtain temperature-dependent cross sections for fifteen pion-charmonium and rho-charmonium dissociation reactions. The numerical cross sections are parametrized for future applications in hadronic matter. The particular temperature dependence of the J/psi bound state leads to unusual behavior of the cross sections for endothermic J/psi dissociation reactions. The quantum numbers of psi' and chi_c can not make their difference in mass in the temperature region 0.6T_c < T < T_c, but can make the psi' dissociation different from the chi_c dissociation.Comment: 52 pages, 23 figures, 6 table

Competition between Phase Separation and Spin Density Wave or Charge Density Wave Order: Role of Long-Range Interactions

Recent studies of pairing and charge order in materials such as FeSe, SrTiO$_3$, and 2H-NbSe$_2$ have suggested that momentum dependence of the electron-phonon coupling plays an important role in their properties. Initial attempts to study Hamiltonians which either do not include or else truncate the range of Coulomb repulsion have noted that the resulting spatial non-locality of the electron-phonon interaction leads to a dominant tendency to phase separation. Here we present Quantum Monte Carlo results for such models in which we incorporate both on-site and intersite electron-electron interactions. We show that these can stabilize phases in which the density is homogeneous and determine the associated phase boundaries. As a consequence, the physics of momentum dependent electron-phonon coupling can be determined outside of the trivial phase separated regime.Comment: 9 pages, 7 figure