975 research outputs found

    A review of Monte Carlo simulations of polymers with PERM

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    In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the Θ\Theta point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

    Non-spherical shapes of capsules within a fourth-order curvature model

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    We minimize a discrete version of the fourth-order curvature based Landau free energy by extending Brakke's Surface Evolver. This model predicts spherical as well as non-spherical shapes with dimples, bumps and ridges to be the energy minimizers. Our results suggest that the buckling and faceting transitions, usually associated with crystalline matter, can also be an intrinsic property of non-crystalline membranes.Comment: 6 pages, 4 figures (LaTeX macros EPJ), accepted for publication in EPJ

    Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl

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    Background: Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don) Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Results: Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2), glycine-rich RNA-binding protein (RNP), and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK) was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Conclusion: Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens

    Deposition of earth-abundant p-type CuBr films with high hole conductivity and realization of p-CuBr/n-Si heterojunction solar cell

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    We present details of the deposition of transparent and earth-abundant p-type CuBr films with high hole conductivity and the fabrication and characterization of a prototype solar cell based on p-CuBr/n-Si heterojunctions. p-type CuBr films with typical resistivities and hole concentrations of 7×10-1 Ωcm and 7.5×1019 cm-3, respectively, are deposited by thermal evaporation followed by oxygen plasma treatment. The transparent p-type films show strong room temperature photoluminescence at ~2.97 eV. The current voltage (I-V) characteristics of the heterojunctions show good diode behaviour. Power conversion efficiency of ~ 2 % was achieved for the heterojunction device without any optimization of the cell structure under AM 1.5 illumination condition with a short circuit current (Jsc) and open circuit voltage (Voc) of 13.2 mA/cm2 and 0.44 V, respectively

    Interacting Three Fluid System and Thermodynamics of the Universe Bounded by the Event Horizon

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    The work deals with the thermodynamics of the universe bounded by the event horizon. The matter in the universe has three constituents namely dark energy, dark matter and radiation in nature and interaction between then is assumed. The variation of entropy of the surface of the horizon is obtained from unified first law while matter entropy variation is calculated from the Gibbss' law. Finally, validity of the generalized second law of thermodynamics is examined and conclusions are written point wise.Comment: 7 page

    Racetrack Inflation

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    We develop a model of eternal topological inflation using a racetrack potential within the context of type IIB string theory with KKLT volume stabilization. The inflaton field is the imaginary part of the K\"ahler structure modulus, which is an axion-like field in the 4D effective field theory. This model does not require moving branes, and in this sense it is simpler than other models of string theory inflation. Contrary to single-exponential models, the structure of the potential in this example allows for the existence of saddle points between two degenerate local minima for which the slow-roll conditions can be satisfied in a particular range of parameter space. We conjecture that this type of inflation should be present in more general realizations of the modular landscape. We also consider `irrational' models having a dense set of minima, and discuss their possible relevance for the cosmological constant problem.Comment: 23 pages 7 figures. The final version with minor modifications, to appear in JHE

    Asymptotics for products of characteristic polynomials in classical β\beta-Ensembles

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    We study the local properties of eigenvalues for the Hermite (Gaussian), Laguerre (Chiral) and Jacobi β\beta-ensembles of N×NN\times N random matrices. More specifically, we calculate scaling limits of the expectation value of products of characteristic polynomials as NN\to\infty. In the bulk of the spectrum of each β\beta-ensemble, the same scaling limit is found to be ep11F1e^{p_{1}}{}_1F_{1} whose exact expansion in terms of Jack polynomials is well known. The scaling limit at the soft edge of the spectrum for the Hermite and Laguerre β\beta-ensembles is shown to be a multivariate Airy function, which is defined as a generalized Kontsevich integral. As corollaries, when β\beta is even, scaling limits of the kk-point correlation functions for the three ensembles are obtained. The asymptotics of the multivariate Airy function for large and small arguments is also given. All the asymptotic results rely on a generalization of Watson's lemma and the steepest descent method for integrals of Selberg type.Comment: [v3] 35 pages; this is a revised and enlarged version of the article with new references, simplified demonstations, and improved presentation. To be published in Constructive Approximation 37 (2013

    Explicit differential characterization of the Newtonian free particle system in m > 1 dependent variables

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    In 1883, as an early result, Sophus Lie established an explicit necessary and sufficient condition for an analytic second order ordinary differential equation y_xx = F(x,y,y_x) to be equivalent, through a point transformation (x,y) --> (X(x,y), Y(x,y)), to the Newtonian free particle equation Y_XX = 0. This result, preliminary to the deep group-theoretic classification of second order analytic ordinary differential equations, was parachieved later in 1896 by Arthur Tresse, a French student of S. Lie. In the present paper, following closely the original strategy of proof of S. Lie, which we firstly expose and restitute in length, we generalize this explicit characterization to the case of several second order ordinary differential equations. Let K=R or C, or more generally any field of characteristic zero equipped with a valuation, so that K-analytic functions make sense. Let x in K, let m > 1, let y := (y^1, ..., y^m) in K^m and let y_xx^j = F^j(x,y,y_x^l), j = 1,...,m be a collection of m analytic second order ordinary differential equations, in general nonlinear. We provide an explicit necessary and sufficient condition in order that this system is equivalent, under a point transformation (x, y^1, ..., y^m) --> (X(x,y), Y^1(x,y),..., Y^m(x, y)), to the Newtonian free particle system Y_XX^1 = ... = Y_XX^m = 0. Strikingly, the (complicated) differential system that we obtain is of first order in the case m > 1, whereas it is of second order in S. Lie's original case m = 1.Comment: 76 pages, no figur
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