Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Nonuniversal correlations in multiple scattering

We show that intensity of a wave created by a source embedded inside a three-dimensional disordered medium exhibits a non-universal space-time correlation which depends explicitly on the short-distance properties of disorder, source size, and dynamics of disorder in the immediate neighborhood of the source. This correlation has an infinite spatial range and is long-ranged in time. We suggest that a technique of "diffuse microscopy" might be developed employing spatially-selective sensitivity of the considered correlation to the disorder properties.Comment: 15 pages, 3 postscript figures, accepted to Phys. Rev.

Quantum-Noise Reduction in a Driven Cavity with Feedback

We show that amplitude-squeezed states may be produced by driving a feedback-controlled cavity with a coherent input signal. The feedback controls the transmissivity of one output from the cavity and is essentially equivalent to nonlinear absorption. The cavity effectively acts as a nonlinear reflector. Hence, amplitude-squeezed states with arbitrarily strong coherent intensities can be obtained

Mode-Locking in Driven Disordered Systems as a Boundary-Value Problem

We study mode-locking in disordered media as a boundary-value problem. Focusing on the simplest class of mode-locking models which consists of a single driven overdamped degree-of-freedom, we develop an analytical method to obtain the shape of the Arnol'd tongues in the regime of low ac-driving amplitude or high ac-driving frequency. The method is exact for a scalloped pinning potential and easily adapted to other pinning potentials. It is complementary to the analysis based on the well-known Shapiro's argument that holds in the perturbative regime of large driving amplitudes or low driving frequency, where the effect of pinning is weak.Comment: 6 pages, 7 figures, RevTeX, Submitte

Spiral Galaxies Rotation Curves with a Logarithmic Corrected Newtonian Gravitational Potential

We analyze the rotation curves of 10 spiral galaxies with a newtonian potential corrected with an extra logarithmic term, using a disc modelization for the spiral galaxies. There is a new constant associated with the extra term in the potential. The rotation curve of the chosen sample of spiral galaxies is well reproduced for a given range of the new constant. It is argued that this correction can have its origin from string configurations. The compatibility of this correction with local physics is discussed.Comment: Latex file, 6 pages, 20 figure

Phase-Locking of Vortex Lattices Interacting with Periodic Pinning

We examine Shapiro steps for vortex lattices interacting with periodic pinning arrays driven by AC and DC currents. The vortex flow occurs by the motion of the interstitial vortices through the periodic potential generated by the vortices that remain pinned at the pinning sites. Shapiro steps are observed for fields B_{\phi} < B < 2.25B_{\phi} with the most pronouced steps occuring for fields where the interstitial vortex lattice has a high degree of symmetry. The widths of the phase-locked current steps as a function of the magnitude of the AC driving are found to follow a Bessel function in agreement with theory.Comment: 5 pages 5 postscript figure

A Hedged Monte Carlo Approach to Real Option Pricing

In this work we are concerned with valuing optionalities associated to invest or to delay investment in a project when the available information provided to the manager comes from simulated data of cash flows under historical (or subjective) measure in a possibly incomplete market. Our approach is suitable also to incorporating subjective views from management or market experts and to stochastic investment costs. It is based on the Hedged Monte Carlo strategy proposed by Potters et al (2001) where options are priced simultaneously with the determination of the corresponding hedging. The approach is particularly well-suited to the evaluation of commodity related projects whereby the availability of pricing formulae is very rare, the scenario simulations are usually available only in the historical measure, and the cash flows can be highly nonlinear functions of the prices.Comment: 25 pages, 14 figure

The Relativistic Factor in the Orbital Dynamics of Point Masses

There is a growing population of relativistically relevant minor bodies in the Solar System and a growing population of massive extrasolar planets with orbits very close to the central star where relativistic effects should have some signature. Our purpose is to review how general relativity affects the orbital dynamics of the planetary systems and to define a suitable relativistic correction for Solar System orbital studies when only point masses are considered. Using relativistic formulae for the N body problem suited for a planetary system given in the literature we present a series of numerical orbital integrations designed to test the relevance of the effects due to the general theory of relativity in the case of our Solar System. Comparison between different algorithms for accounting for the relativistic corrections are performed. Relativistic effects generated by the Sun or by the central star are the most relevant ones and produce evident modifications in the secular dynamics of the inner Solar System. The Kozai mechanism, for example, is modified due to the relativistic effects on the argument of the perihelion. Relativistic effects generated by planets instead are of very low relevance but detectable in numerical simulations

Temporal fluctuations of waves in weakly nonlinear disordered media

We consider the multiple scattering of a scalar wave in a disordered medium with a weak nonlinearity of Kerr type. The perturbation theory, developed to calculate the temporal autocorrelation function of scattered wave, fails at short correlation times. A self-consistent calculation shows that for nonlinearities exceeding a certain threshold value, the multiple-scattering speckle pattern becomes unstable and exhibits spontaneous fluctuations even in the absence of scatterer motion. The instability is due to a distributed feedback in the system "coherent wave + nonlinear disordered medium". The feedback is provided by the multiple scattering. The development of instability is independent of the sign of nonlinearity.Comment: RevTeX, 15 pages (including 5 figures), accepted for publication in Phys. Rev.

Dynamics of an anisotropic Haldane antiferromagnet in strong magnetic field

We report the results of elastic and inelastic neutron scattering experiments on the Haldane gap quantum antiferromagnet Ni(C5D14N2)2N3(PF6) performed at mK temperatures in a wide range of magnetic field applied parallel to the S = 1 spin chains. Even though this geometry is closest to an ideal axially symmetric configuration, the Haldane gap closes at the critical field Hc~4T, but reopens again at higher fields. The field dependence of the two lowest magnon modes is experimentally studied and the results are compared with the predictions of several theoretical models. We conclude that of several existing theories, only the recently proposed model [Zheludev et al., cond-mat/0301424 ] is able to reproduce all the features observed experimentally for different field orientations.Comment: 11 pages 8 figures submitted to Phys. Rev.