Nonlinear soil-structure interaction calculations simulating the SIMQUAKE experiment using STEALTH 2D

Transient, nonlinear soil-structure interaction simulations of an Electric Power Research Institute, SIMQUAKE experiment were performed using the large strain, time domain STEALTH 2D code and a cyclic, kinematically hardening cap soil model. Results from the STEALTH simulations were compared to identical simulations performed with the TRANAL code and indicate relatively good agreement between all the STEALTH and TRANAL calculations. The differences that are seen can probably be attributed to: (1) large (STEALTH) vs. small (TRANAL) strain formulation and/or (2) grid discretization differences

Nucleation of quark matter in neutron stars cores

We consider the general conditions of quark droplets formation in high density neutron matter. The growth of the quark bubble (assumed to contain a sufficiently large number of particles) can be described by means of a Fokker-Planck equation. The dynamics of the nucleation essentially depends on the physical properties of the medium it takes place. The conditions for quark bubble formation are analyzed within the frameworks of both dissipative and non-dissipative (with zero bulk and shear viscosity coefficients) approaches. The conversion time of the neutron star to a quark star is obtained as a function of the equation of state of the neutron matter and of the microscopic parameters of the quark nuclei. As an application of the obtained formalism we analyze the first order phase transition from neutron matter to quark matter in rapidly rotating neutron stars cores, triggered by the gravitational energy released during the spinning down of the neutron star. The endothermic conversion process, via gravitational energy absorption, could take place, in a very short time interval, of the order of few tens seconds, in a class of dense compact objects, with very high magnetic fields, called magnetars.Comment: 31 pages, 2 figures, to appear in Ap

Localization of Denaturation Bubbles in Random DNA Sequences

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to \AT-rich segments. In the localized regime, the bubbles exhibit ``aging'' and move around sub-diffusively with continuously varying dynamic exponents. These properties are derived using results of large-deviation theory together with scaling arguments, and are verified by Monte-Carlo simulations.Comment: TeX file with postscript figure

The chemotherapeutic agent DMXAA as a unique IRF3-dependent type-2 vaccine adjuvant

5,6-Dimethylxanthenone-4-acetic acid (DMXAA), a potent type I interferon (IFN) inducer, was evaluated as a chemotherapeutic agent in mouse cancer models and proved to be well tolerated in human cancer clinical trials. Despite its multiple biological functions, DMXAA has not been fully characterized for the potential application as a vaccine adjuvant. In this report, we show that DMXAA does act as an adjuvant due to its unique property as a soluble innate immune activator. Using OVA as a model antigen, DMXAA was demonstrated to improve on the antigen specific immune responses and induce a preferential Th2 (Type-2) response. The adjuvant effect was directly dependent on the IRF3-mediated production of type-I-interferon, but not IL-33. DMXAA could also enhance the immunogenicity of influenza split vaccine which led to significant increase in protective responses against live influenza virus challenge in mice compared to split vaccine alone. We propose that DMXAA can be used as an adjuvant that targets a specific innate immune signaling pathway via IRF3 for potential applications including vaccines against influenza which requires a high safety profile

Simulation and analysis of in vitro DNA evolution

We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic simulations of evolution starting from a single DNA sequence. We identify different parameter regimes characterized by distinct evolutionary behaviors. For each regime we find analytical estimates which agree well with simulation results. For small population sizes, the DNA evolutional path is a random walk on a smooth landscape. While for large population sizes, the evolution dynamics can be well described by a mean-field theory. We also study how the details of the DNA-protein interaction affect the evolution.Comment: 11 pages, 11 figures. Submitted to PNA

Multi-Modes Phonon Softening in Two-Dimensional Electron-Lattice System

Phonon dispersion in a two-dimensional electron-lattice system described by a two-dimensional square-lattice version of Su-Schrieffer-Heeger's model and having the half-filled electronic band is studied theoretically at temperatures higher than the mean field critical temperature of the Peierls transition. When the temperature is lowered from the higher region down to the critical one, softening of multi phonon modes which have wave vectors equal to the nesting vector \vv{Q}=(\pi/a,\pi/a) with $a$ the lattice constant or parallel to \vv{Q} is observed. Although both of the transverse and longitudinal modes are softened at the critical temperature in the case of the wave vector equal to \vv{Q}, only the transverse modes are softened for other wave vectors parallel to \vv{Q}. This behavior is consistent with the Peierls distortions at lower temperatures.Comment: 10 pages, 5 Figure

Fulde-Ferrell-Larkin-Ovchinnikov State in the absence of a Magnetic Field

We propose that in a system with pocket Fermi surfaces, a pairing state with a finite total momentum q_tot like the Fulde-Ferrell-Larkin-Ovchinnikov state can be stabilized even without a magnetic field. When a pair is composed of electrons on a pocket Fermi surface whose center is not located at Gamma point, the pair inevitably has finite q_tot. To investigate this possibility, we consider a two-orbital model on a square lattice that can realize pocket Fermi surfaces and we apply fluctuation exchange approximation. Then, by changing the electron number n per site, we indeed find that such superconducting states with finite q_tot are stabilized when the system has pocket Fermi surfaces.Comment: 4 pages, 5 figure