Phase diagram of a Bose gas near a wide Feshbach resonance

In this paper, we study the phase diagram of a homogeneous Bose gas with a repulsive interaction near a wide Feshbach resonance at zero temperature. The Bose-Einstein-condensation (BEC) state of atoms is a metastable state. When the scattering length $a$ exceeds a critical value depending on the atom density $n$, $na^3>0.035$, the molecular excitation energy is imaginary and the atomic BEC state is dynamically unstable against molecule formation. The BEC state of diatomic molecules has lower energy, where the atomic excitation is gapped and the molecular excitation is gapless. However when the scattering length is above another critical value, $na^3>0.0164$, the molecular BEC state becomes a unstable coherent mixture of atoms and molecules. In both BEC states, the binding energy of diatomic molecules is reduced due to the many-body effect.Comment: 5 pages, 4 figure

Controllability and controller-observer design for a class of linear time-varying systems

“The final publication is available at Springer via http://dx.doi.org/10.1007/s10852-012-9212-6"In this paper a class of linear time-varying control systems is considered. The time variation consists of a scalar time-varying coefficient multiplying the state matrix of an otherwise time-invariant system. Under very weak assumptions of this coefficient, we show that the controllability can be assessed by an algebraic rank condition, Kalman canonical decomposition is possible, and we give a method for designing a linear state-feedback controller and Luenberger observer

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth

<p>Abstract</p> <p>Background</p> <p>Bifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with exogenous bifidobacteria show they don't remain in the intestine, suggesting they may lose competitive fitness when grown outside the gut.</p> <p>Results</p> <p>To further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate, <it>Bifidobacterium longum </it>DJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain, <it>B. longum </it>NCC2705. This comparison revealed colinear genomes that exhibited high sequence identity, except for the presence of 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While the majority of these unique regions encoded proteins of diverse function, eight from the DJO10A genome and one from NCC2705, encoded gene clusters predicted to be involved in diverse traits pertinent to the human intestinal environment, specifically oligosaccharide and polyol utilization, arsenic resistance and lantibiotic production. Seven of these unique regions were suggested by a base deviation index analysis to have been precisely deleted from strain NCC2705 and this is substantiated by a DNA remnant from within one of the regions still remaining in the genome of NCC2705 at the same locus. This targeted loss of genomic regions was experimentally validated when growth of the intestinal <it>B. longum </it>in the laboratory for 1,000 generations resulted in two large deletions, one in a lantibiotic encoding region, analogous to a predicted deletion event for NCC2705. A simulated fecal growth study showed a significant reduced competitive ability of this deletion strain against <it>Clostridium difficile </it>and <it>E. coli</it>. The deleted region was between two IS<it>30 </it>elements which were experimentally demonstrated to be hyperactive within the genome. The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.</p> <p>Conclusion</p> <p>Deletion of genomic regions, often facilitated by mobile elements, allows bifidobacteria to adapt to fermentation environments in a very rapid manner (2 genome deletions per 1,000 generations) and the concomitant loss of possible competitive abilities in the gut.</p

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

<p>Abstract</p> <p>Background</p> <p>Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level.</p> <p>Results</p> <p>We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models.</p> <p>Conclusion</p> <p>By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.</p

Combustion in thermonuclear supernova explosions

Type Ia supernovae are associated with thermonuclear explosions of white dwarf stars. Combustion processes convert material in nuclear reactions and release the energy required to explode the stars. At the same time, they produce the radioactive species that power radiation and give rise to the formation of the observables. Therefore, the physical mechanism of the combustion processes, as reviewed here, is the key to understand these astrophysical events. Theory establishes two distinct modes of propagation for combustion fronts: subsonic deflagrations and supersonic detonations. Both are assumed to play an important role in thermonuclear supernovae. The physical nature and theoretical models of deflagrations and detonations are discussed together with numerical implementations. A particular challenge arises due to the wide range of spatial scales involved in these phenomena. Neither the combustion waves nor their interaction with fluid flow and instabilities can be directly resolved in simulations. Substantial modeling effort is required to consistently capture such effects and the corresponding techniques are discussed in detail. They form the basis of modern multidimensional hydrodynamical simulations of thermonuclear supernova explosions. The problem of deflagration-to-detonation transitions in thermonuclear supernova explosions is briefly mentioned.Comment: Author version of chapter for 'Handbook of Supernovae,' edited by A. Alsabti and P. Murdin, Springer. 24 pages, 4 figure

Parton Fragmentation within an Identified Jet at NNLL

The fragmentation of a light parton i to a jet containing a light energetic hadron h, where the momentum fraction of this hadron as well as the invariant mass of the jet is measured, is described by "fragmenting jet functions". We calculate the one-loop matching coefficients J_{ij} that relate the fragmenting jet functions G_i^h to the standard, unpolarized fragmentation functions D_j^h for quark and gluon jets. We perform this calculation using various IR regulators and show explicitly how the IR divergences cancel in the matching. We derive the relationship between the coefficients J_{ij} and the quark and gluon jet functions. This provides a cross-check of our results. As an application we study the process e+ e- to X pi+ on the Upsilon(4S) resonance where we measure the momentum fraction of the pi+ and restrict to the dijet limit by imposing a cut on thrust T. In our analysis we sum the logarithms of tau=1-T in the cross section to next-to-next-to-leading-logarithmic accuracy (NNLL). We find that including contributions up to NNLL (or NLO) can have a large impact on extracting fragmentation functions from e+ e- to dijet + h.Comment: expanded introduction, typos fixed, journal versio

Matrix interpretation of multiple orthogonality

In this work we give an interpretation of a (s(d + 1) + 1)-term recurrence relation in terms of type II multiple orthogonal polynomials.We rewrite this recurrence relation in matrix form and we obtain a three-term recurrence relation for vector polynomials with matrix coefficients. We present a matrix interpretation of the type II multi-orthogonality conditions.We state a Favard type theorem and the expression for the resolvent function associated to the vector of linear functionals. Finally a reinterpretation of the type II Hermite- Padé approximation in matrix form is given

Dispersive charge density wave excitations and temperature dependent commensuration in Bi2Sr2CaCu2O8+{\delta}

Experimental evidence on high-Tc cuprates reveals ubiquitous charge density wave (CDW) modulations, which coexist with superconductivity. Although the CDW had been predicted by theory, important questions remain about the extent to which the CDW influences lattice and charge degrees of freedom and its characteristics as functions of doping and temperature. These questions are intimately connected to the origin of the CDW and its relation to the mysterious cuprate pseudogap. Here, we use ultrahigh resolution resonant inelastic x-ray scattering (RIXS) to reveal new CDW character in underdoped Bi2Sr2CaCu2O8+{\delta} (Bi2212). At low temperature, we observe dispersive excitations from an incommensurate CDW that induces anomalously enhanced phonon intensity, unseen using other techniques. Near the pseudogap temperature T*, the CDW persists, but the associated excitations significantly weaken and the CDW wavevector shifts, becoming nearly commensurate with a periodicity of four lattice constants. The dispersive CDW excitations, phonon anomaly, and temperature dependent commensuration provide a comprehensive momentum space picture of complex CDW behavior and point to a closer relationship with the pseudogap state

Silver nanowire-based transparent, flexible, and conductive thin film

The fabrication of transparent, conductive, and uniform silver nanowire films using the scalable rod-coating technique is described in this study. Properties of the transparent conductive thin films are investigated, as well as the approaches to improve the performance of transparent silver nanowire electrodes. It is found that silver nanowires are oxidized during the coating process. Incubation in hydrogen chloride (HCl) vapor can eliminate oxidized surface, and consequently, reduce largely the resistivity of silver nanowire thin films. After HCl treatment, 175 Ω/sq and approximately 75% transmittance are achieved. The sheet resistivity drops remarkably with the rise of the film thickness or with the decrease of transparency. The thin film electrodes also demonstrated excellent flexible stability, showing < 2% resistance change after over 100 bending cycles