Dynamic mean-field and cavity methods for diluted Ising systems

We compare dynamic mean-field and dynamic cavity as methods to describe the stationary states of dilute kinetic Ising models. We compute dynamic mean-field theory by expanding in interaction strength to third order, and compare to the exact dynamic mean-field theory for fully asymmetric networks. We show that in diluted networks the dynamic cavity method generally predicts magnetizations of individual spins better than both first order ("naive") and second order ("TAP") dynamic mean field theory

Dispersion control for matter waves and gap solitons in optical superlattices

We present a numerical study of dispersion manipulation and formation of matter-wave gap solitons in a Bose-Einstein condensate trapped in an optical superlattice. We demonstrate a method for controlled generation of matter-wave gap solitons in a stationary lattice by using an interference pattern of two condensate wavepackets, which mimics the structure of the gap soliton near the edge of a spectral band. The efficiency of this method is compared with that of gap soliton generation in a moving lattice recently demonstrated experimentally by Eiermann et al. [Phys. Rev. Lett. 92, 230401 (2004)]. We show that, by changing the relative depths of the superlattice wells, one can fine-tune the effective dispersion of the matter waves at the edges of the mini-gaps of the superlattice Bloch-wave spectrum and therefore effectively control both the peak density and the spatial width of the emerging gap solitons.Comment: 8 pages, 9 figures; modified references in Section 2; minor content changes in Sections 1 and 2 and Fig. 9 captio

Crystal structure of the catalytic fragment of murine poly(ADP-ribose) polymerase-2.

Poly(ADP-ribose) polymerase-1 (PARP-1) has become an important pharmacological target in the treatment of cancer due to its cellular role as a 'DNA-strand break sensor', which leads in part to resistance to some existing chemo- and radiological treatments. Inhibitors have now been developed which prevent PARP-1 from synthesizing poly(ADP-ribose) in response to DNA-breaks and potentiate the cytotoxicity of DNA damaging agents. However, with the recent discoveries of PARP-2, which has a similar DNA-damage dependent catalytic activity, and additional members containing the 'PARP catalytic' signature, the isoform selectivity and resultant pharmacological effects of existing inhibitors are brought into question. We present here the crystal structure of the catalytic fragment of murine PARP-2, at 2.8 A resolution, and compare this to the catalytic fragment of PARP-1, with an emphasis on providing a possible framework for rational drug design in order to develop future isoform-specific inhibitors

Atmosphere, Interior, and Evolution of the Metal-Rich Transiting Planet HD 149026b

We investigate the atmosphere and interior of the new transiting planet HD 149026b, which appears to be very rich in heavy elements. We first compute model atmospheres at metallicities ranging from solar to ten times solar, and show how for cases with high metallicity or inefficient redistribution of energy from the day side, the planet may develop a hot stratosphere due to absorption of stellar flux by TiO and VO. The spectra predicted by these models are very different than cooler atmosphere models without stratospheres. The spectral effects are potentially detectable with the Spitzer Space Telescope. In addition the models with hot stratospheres lead to a large limb brightening, rather than darkening. We compare the atmosphere of HD 149026b to other well-known transiting planets, including the recently discovered HD 189733b, which we show have planet-to-star flux ratios twice that of HD 209458 and TrES-1. The methane abundance in the atmosphere of HD 189733b is a sensitive indicator of atmospheric temperature and metallicity and can be constrained with Spitzer IRAC observations. We then turn to interior studies of HD 149026b and use a grid of self-consistent model atmospheres and high-pressure equations of state for all components to compute thermal evolution models of the planet. We estimate that the mass of heavy elements within the planet is in the range of 60 to 93 M_earth. Finally, we discuss trends in the radii of transiting planets with metallicity in light of this new member of the class.Comment: Accepted to the Astrophysical Journal. 18 pages, including 10 figures. New section on the atmosphere of planet HD 189733b. Enhanced discussion of atmospheric Ti chemistry and core mass for HD 149026

Ignorance based inference of optimality in thermodynamic processes

We derive ignorance based prior distribution to quantify incomplete information and show its use to estimate the optimal work characteristics of a heat engine.Comment: Latex, 10 pages, 3 figure

Dynamical replica analysis of disordered Ising spin systems on finitely connected random graphs

We study the dynamics of macroscopic observables such as the magnetization and the energy per degree of freedom in Ising spin models on random graphs of finite connectivity, with random bonds and/or heterogeneous degree distributions. To do so we generalize existing implementations of dynamical replica theory and cavity field techniques to systems with strongly disordered and locally tree-like interactions. We illustrate our results via application to the dynamics of e.g. $\pm J$ spin-glasses on random graphs and of the overlap in finite connectivity Sourlas codes. All results are tested against Monte Carlo simulations.Comment: 4 pages, 14 .eps file

Finding a needle in an exponential haystack: Discrete RRT for exploration of implicit roadmaps in multi-robot motion planning

We present a sampling-based framework for multi-robot motion planning which combines an implicit representation of a roadmap with a novel approach for pathfinding in geometrically embedded graphs tailored for our setting. Our pathfinding algorithm, discrete-RRT (dRRT), is an adaptation of the celebrated RRT algorithm for the discrete case of a graph, and it enables a rapid exploration of the high-dimensional configuration space by carefully walking through an implicit representation of a tensor product of roadmaps for the individual robots. We demonstrate our approach experimentally on scenarios of up to 60 degrees of freedom where our algorithm is faster by a factor of at least ten when compared to existing algorithms that we are aware of.Comment: Kiril Solovey and Oren Salzman contributed equally to this pape

Binary Models for Marginal Independence

Log-linear models are a classical tool for the analysis of contingency tables. In particular, the subclass of graphical log-linear models provides a general framework for modelling conditional independences. However, with the exception of special structures, marginal independence hypotheses cannot be accommodated by these traditional models. Focusing on binary variables, we present a model class that provides a framework for modelling marginal independences in contingency tables. The approach taken is graphical and draws on analogies to multivariate Gaussian models for marginal independence. For the graphical model representation we use bi-directed graphs, which are in the tradition of path diagrams. We show how the models can be parameterized in a simple fashion, and how maximum likelihood estimation can be performed using a version of the Iterated Conditional Fitting algorithm. Finally we consider combining these models with symmetry restrictions

An efficient CDMA decoder for correlated information sources

We consider the detection of correlated information sources in the ubiquitous Code-Division Multiple-Access (CDMA) scheme. We propose a message-passing based scheme for detecting correlated sources directly, with no need for source coding. The detection is done simultaneously over a block of transmitted binary symbols (word). Simulation results are provided demonstrating a substantial improvement in bit-error-rate in comparison with the unmodified detector and the alternative of source compression. The robustness of the error-performance improvement is shown under practical model settings, including wrong estimation of the generating Markov transition matrix and finite-length spreading codes.Comment: 11 page