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Novel Monte Carlo algorithms and their applications

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS 2003年第1-2期321卷 340-350页

作者： Okabe, Y Tomita, Y Yamaguchi, C Tokyo Metropolitan Univ Dept Phys Hachioji Tokyo 1920397 Japan

We describe a generalized scheme for the probability-changing cluster (PCC) algorithm, based on the study of the finite-size scaling property of tile correlation ratio, the ratio of the correlation functions with different distances, We apply this generalized PCC algorithm to the two-dimensional 6-state clock model. We also discuss the combination of the cluster algorithm and the extended ensemble method. We derive a rigorous broad histogram relation for the bond number. A Monte Carlo dynamics based on the number of potential moves for the bond number is proposed. and applied to the three-dimensional Ising and 3-state Potts models. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： cluster algorithm finite-size scaling correlation ratio broad histogram relation

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Universal amplitude ratios in the critical two-dimensional Ising model on a torus

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JOURNAL OF STATISTICAL PHYSICS 2000年第3-4期98卷 551-588页

作者： Salas, J Sokal, AD Univ Zaragoza Fac Ciencias Dept Fis Teor Zaragoza 50009 Spain Univ Zaragoza Fac Ciencias Dept Fis Mat Condensada Zaragoza 50009 Spain NYU Dept Phys New York NY 10003 USA

Using results from conformal field theory, we compute several universal amplitude ratios for the two-dimensional Ising model at criticality on a symmetric torus. These include the correlation-length ratio x* = lim(L-->infinity) xi(L)/L and the first four magnetization moment ratios V(2n) = [M(2n)]/[M(2)](n). As a corollary we get the first four renormalized 2n-point coupling constants for the massless theory on a symmetric torus, G(2n)*. We confirm these predictions by a high-precision Monte Carlo simulation.

关键词： Ising model universal amplitude ratios conformal field theory torus finite-size scaling corrections to scaling Monte Carlo Swendsen-Wang algorithm cluster algorithm

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THE LUND MONTE-CARLO FOR JET FRAGMENTATION AND E+E- PHYSICS - JETSET VERSION 6.3 - AN UPDATE

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COMPUTER PHYSICS COMMUNICATIONS 1987年第3期43卷 367-379页

作者： SJOSTRAND, T BENGTSSON, M Department of Theoretical Physics University of Lund Sölvegatan 14A S-223 62 Lund Sweden

Title of program: JETSET 6.3 Catalogue number: AATJ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland (see application form in this issue) Computer for which the program is designed and others on which it is operable: ND, VAX, IBM, CDC and others with a FORTRAN 77 compiler Computer: ND-570; Installation: University of Lund, Lund, Sweden Operating system: SINTRAN III - VSX/500 Programming language used: FORTRAN 77 High speed storage required: 50 Kwords No. of bits in word: 32 Peripherals used: terminal for input, terminal or line printer for output No. of lines in combined program and test deck: 6173

关键词： cluster algorithm e+ e- annihilation event analysis gluon jet hadronization jet fragmentation leading log evolution Monte Carlo event simulation multiparticle production onium decays parton showers quark jet

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Bayesian Ising Graphical Model for Variable Selection

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JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS 2016年第2期25卷 589-605页

作者： Fang, Zaili Kim, Inyoung Virginia Polytech Inst & State Univ Dept Stat Blacksburg VA 24061 USA

In this article, we propose a new Bayesian variable selection (BVS) approach via the graphical model and the Ising model, which we refer to as the "Bayesian Ising graphical model" (BIGM). The BIGM is developed by showing that the BVS problem based on the linear regression model can be considered as a complete graph and described by an Ising model with random interactions. There are several advantages of our BIGM: it is easy to (i) employ the single-site updating and cluster updating algorithm, both of which are suitable for problems with small sample sizes and a larger number of variables, (ii) extend this approach to nonparametric regression models, and (iii) incorporate graphical prior information. In our BIGM, the interactions are determined by the linear model coefficients, so we systematically study the performance of different scale normal mixture priors for the model coefficients by adopting the global-local shrinkage strategy. Our results indicate that the best prior for the model coefficients in terms of variable selection should place substantial weight on small, nonzero shrinkage. The methods are illustrated with simulated and real data. Supplementary materials for this article are available online.

关键词： cluster algorithm Global-local shrinkage Graphical model Ising model Mixture normals Variable selection

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Antiferromagnetic potts models on the square lattice: A high-precision Monte Carlo study

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JOURNAL OF STATISTICAL PHYSICS 1999年第3-4期96卷 461-530页

作者： Ferreira, SJ Sokal, AD Univ Fed Minas Gerais Dept Estatist ICEx BR-30161970 Belo Horizonte MG Brazil NYU Dept Phys New York NY 10003 USA

study the antiferromagnetic q-state Potts model on the square lattice for q = 3 and q = 4, using the Wang-Swendsen-Kotecky (WSK) Monte Carlo algorithm and a powerful finite-size-scaling extrapolation method. For q=3 we obtain good control up to correlation length xi similar to 5000;the data are consistent with xi(B)=Ae(2 beta)beta(P)(1 + a(1)e(-beta) + ...) as beta--> infinity, with p approximate to 1. The staggered susceptibility behaves as chi(stagg) similar to xi(5/3). For q = 4 the model is disordered (xi less than or similar to 2) even at zero temperature. In appendices we prove a correlation inequality for Potts antiferromagnets on a bipartite lattice, and we prove ergodicity of the WSK algorithm at zero temperature for Potts antiferromagnets on a bipartite lattice.

关键词： Potts model antiferromagnet square lattice phase transition zero-temperature critical point Monte Carlo cluster algorithm Swendsen-Wang algorithm Wang-Swendsen-Kotecky algorithm finite-size scaling

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A systematic method for analysing the protein hydration structure of T4 lysozyme

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JOURNAL OF MOLECULAR RECOGNITION 2013年第10期26卷 479-487页

作者： Kysilka, J. Vondrasek, J. Acad Sci Czech Republic Inst Organ Chem & Biochem CR-16610 Prague Czech Republic Charles Univ Prague Fac Nat Sci Prague 12000 Czech Republic

A systematic method for the analysis of the hydration structure of proteins is demonstrated on the case study of lysozyme. The method utilises multiple structural data of the same protein deposited in the protein data bank. clusters of high water occupancy are localised and characterised in terms of their interaction with protein. It is shown that they constitute a network of interconnected hydrogen bonds anchored to the protein molecule. The high occupancy of the clusters does not directly correlate with water-protein interaction energy as was originally hypothesised. The highly occupied clusters rather correspond to the nodes of the hydration network that have the maximum number of hydrogen bonds including both the protein atoms and the surrounding water clusters. Copyright (c) 2013 John Wiley & Sons, Ltd.

关键词： protein hydration structure water X-ray crystallography cluster algorithm interaction enthalpy

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RECENT EVOLUTIONARY HISTORY OF AMERICAN ONCHOCERCA-VOLVULUS, BASED ON ANALYSIS OF A TANDEMLY REPEATED DNA-SEQUENCE FAMILY

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MOLECULAR BIOLOGY AND EVOLUTION 1994年第3期11卷 384-392页

作者： ZIMMERMAN, PA KATHOLI, CR WOOTEN, MC LANGUNNASCH, N UNNASCH, TR UNIV ALABAMA DEPT MED DIV GEOG MED BIRMINGHAM AL 35294 USA UNIV ALABAMA DEPT BIOSTAT & BIOMATH BIRMINGHAM AL 35294 USA CASE WESTERN RESERVE UNIV DEPT BIOL CLEVELAND OH USA AUBURN UNIV DEPT ZOOL AUBURN AL USA

Polymerase chain reaction (PCR) products were characterized for a repeated sequence family (designated ''O-150'') of the human filarial parasite Onchocerca volvulus. In phylogenetic inferences, the O-150 sequences clustered into closely related groups, suggesting that concerted evolution maintains sequence homology in this family. Using a novel mathematical model based on a nested application of an analysis of variance, we demonstrated that African rainforest and savannah strain parasite populations are significantly different. In contrast, parasites collected in the New World are indistinguishable from African savannah strains of O. volvulus. This finding supports the hypothesis that onchocerciasis was recently introduced into the New World, possibly as a result of the slave trade.

关键词： ONCHOCERCA VOLVULUS AFRICAN RIVER BLINDNESS TANDEM REPEAT FAMILY cluster algorithm PHENETICS

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Study of phase separation in a first-order phase transition:: Nucleation versus spinodal decomposition

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INTERNATIONAL JOURNAL OF MODERN PHYSICS C 1999年第7期10卷 1261-1269页

作者： Arkin, H Çelik, T Berg, BA Meyer-Ortmanns, H Hacettepe Univ Dept Phys Ankara Turkey Florida State Univ Dept Phys Tallahassee FL 32306 USA Univ Gesamthsch Wuppertal Fachbereich Phys Wuppertal Germany

Studies of dynamical properties of first-order phase transition for a scalar field theory indicate that the phase conversion mechanism itself depends on the strength of the first-order transition: if the transition is strongly (weakly) first-order, bubble nucleation (spinodal decomposition) are favored conversion mechanisms, respectively. These distinct scenarios are of phenomenological impact. In order to see which phase conversion mechanism takes place depending on the strength of transition, we have simulated the q = 5 state Potts model in two dimensions with an external magnetic field. The transition gets weakened in its first-order as the external field increases. Our results indicate that the phase conversion mechanism changes from nucleation to spinodal decomposition.

关键词： phase separation Potts model spinodal decomposition cluster algorithm bubble nucleation deconfinement transition

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Large-scale calculation of ferromagnetic spin systems on the pyrochlore lattice

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PHYSICS LETTERS A 2017年第7期381卷 707-712页

作者： Soldatov, Konstantin Nefedev, Konstantin Komura, Yukihiro Okabe, Yutaka Far Eastern Fed Univ Sch Nat Sci Vladivostok Russia Russian Acad Sci Inst Appl Math Far Eastern Branch Vladivostok Russia CIJ Solut Chuo Ku Tokyo 1030023 Japan Tokyo Metropolitan Univ Dept Phys Hachioji Tokyo 1920397 Japan

We perform the high-performance computation of the ferromagnetic Ising model on the pyrochlore lattice. We determine the critical temperature accurately based on the finite-size staling of the Binder ratio. Comparing with the data on the simple cubic lattice, we argue the universal finite-size scaling. We also calculate the classical XY model and the classical Heisenberg model on the pyrochlore lattice. (C) 2016 Elsevier B.V. All rights reserved.

关键词： Monte Carlo simulation cluster algorithm Ising model Classical XY model Classical Heisenberg model Pyrochlore lattice

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Dynamic critical behavior of the Swendsen-Wang algorithm: The two-dimensional three-state Potts model revisited

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JOURNAL OF STATISTICAL PHYSICS 1997年第1-2期87卷 1-36页

作者： Salas, J Sokal, AD NYU DEPT PHYS NEW YORK NY 10003 USA

We have performed a high-precision Monte Carlo study of the dynamic critical behavior of the Swendsen-Wang algorithm for the two-dimensional three-state Ports model. We find that the Li-Sokal bound (tau(int,E) greater than or equal to const x C-H) is almost but not quite sharp. The ratio tau(int,E)/C-H Seems to diverge either as a small power (approximate to 0.08) or as a logarithm.

关键词： Potts model Swendsen-Wang algorithm cluster algorithm Monte Carlo Li-Sokal bound dynamic critical phenomena

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