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Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics

作者： Mitsutake, Ayori Mori, Yoshiharu Okamoto, Yuko Nagoya Univ Dept Phys Aichi 4648602 Japan Keio Univ Dept Phys Kanagawa 2238522 Japan Nagoya Univ Dept Phys Nagoya Aichi 4648602 Japan Nagoya Univ Struct Biol Res Ctr Nagoya Aichi 4648602 Japan

We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E-0 by adding any physical quantity V of interest as a new energy term with a coupling constant lambda. We then perform a multi-dimensional multicanonical simulation where a random walk in E-0 and V space is realized. We can alternately perform a multi-dimensional simulated-tempering simulation where a random walk in temperature T and parameter lambda is realized. The results of the multi-dimensional replica-exchange simulations can be used to determine the weight factors for these multi-dimensional multicanonical and simulated tempering simulations. Two examples of the above methods are presented for biomoleculr systems where the parameter lambda corresponds to the solvation parameter and the pressure. In the former, a random walk in the conformational energy and solvation free energy is performed, and in the latter, a random walk in the potential energy and volume is realized. (C) 2010 Published by Elsevier B.V.

关键词： Generalized-ensemble algorithms multicanonical algorithm simulated tempering replica-exchange method parallel tempering Mont Carlo molecular dynamics

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Multi-dimensional multicanonical algorithm, simulated tempering, replica-exchange method, and all that

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Physics Procedia 2010年 4卷 89-105页

作者： Ayori Mitsutake Yoshiharu Mori Yuko Okamoto Department of Physics Keio University Yokohama Kanagawa 223-8522 Japan Department of Physics Nagoya University Nagoya Aichi 464-8602 Japan Structural Biology Research Center Nagoya University Nagoya Aichi 464-8602 Japan

We discuss multi-dimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential energy function E 0 by adding any physical quantity V of interest as a new energy term with a coupling constant λ . We then perform a multi-dimensional multicanonical simulation where a random walk in E 0 and V space is realized. We can alternately perform a multi-dimensional simulated-tempering simulation where a random walk in temperature T and parameter λ is realized. The results of the multi-dimensional replica-exchange simulations can be used to determine the weight factors for these multi-dimensional multicanonical and simulated tempering simulations. Two examples of the above methods are presented for biomoleculr systems where the parameter λ corresponds to the solvation parameter and the pressure. In the former, a random walk in the conformational energy and solvation free energy is performed, and in the latter, a random walk in the potential energy and volume is realized.

关键词： Generalized-ensemble algorithms multicanonical algorithm Simulated tempering Replica-exchange method Parallel tempering Mont Carlo Molecular dynamics

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THE SURFACE TENSION AND A multicanonical algorithm FOR SU(3) PURE GAUGE THEORY

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International Journal of Modern Physics C 1992年第5期3卷 1147-1154页

作者： B. GROSSMANN M.L. LAURSEN HLRZ c/o Kfa Juelich D-5170 Juelich Gemany

We present a multicanonical algorithm for the SU(3) pure gauge theory at the deconfinement phase transition. We measure the tunneling times for lattices of size L 2 ×2 for L=8, 10, and 12. In contrast to the canonical algorithm the tunneling time increases only moderately with L. Finally, we determine the interfacial free energy applying the multicanonical algorithm.

关键词： multicanonical algorithm Interface Tension SU(3) Gauge Theory

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multicanonical simulations step by step

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COMPUTER PHYSICS COMMUNICATIONS 2003年第3期153卷 397-406页

作者： Berg, BA Florida State Univ Dept Phys Tallahassee FL 32306 USA

The purpose of this article is to provide a starter kit for multicanonical simulations in statistical physics. Fortran code for the q-state Potts model in d = 2, 3,... dimensions can be downloaded from the Web and this paper describes simulation results, which are in all details reproducible by running prepared programs. To allow for comparison with exact results, the internal energy, the specific heat, the free energy and the entropy are calculated for the d = 2 Ising (q = 2) and the q = 10 Potts model. Analysis programs, relying on an all-log jackknife technique, which is suitable for handling sums of very large numbers, are introduced to calculate our final estimators. (C) 2003 Elsevier B.V. All rights reserved.

关键词： multicanonical algorithm Fortran code all-log jackknife technique internal energy free energy entropy

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Residual entropy of ordinary ice calculated from multicanonical Monte Carlo simulations

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MOLECULAR SIMULATION 2012年第11期38卷 856-860页

作者： Berg, Bernd A. Muguruma, Chizuru Okamoto, Yuko Nagoya Univ Grad Sch Sci Dept Phys Nagoya Aichi 4648602 Japan Nagoya Univ Grad Sch Sci Struct Biol Res Ctr Nagoya Aichi 4648602 Japan Nagoya Univ Grad Sch Engn Ctr Computat Sci Nagoya Aichi 4648603 Japan Chukyo Univ Dept Int Liberal Studies Toyota Aichi 4700393 Japan Florida State Univ Dept Phys Tallahassee FL 32306 USA

In this article, we calculated the residual entropy of ice I (ordinary ice) by multicanonical Monte Carlo simulations of two simple models with nearest neighbour interactions on 3D hexagonal lattices. Our estimate is found to be within 0.13% of an analytical approximation by Nagle, which is an improvement of Pauling's result from 1935. We pose it as a challenge to experimentalists to improve on the accuracy of a 1936 measurement by Giauque and Stout by about one order of magnitude, which would allow one to identify corrections to Pauling's value unambiguously. It is straightforward to transfer our methods to other crystal systems.

关键词： residual entropy ice ice rules multicanonical algorithm generalised-ensemble algorithms

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APPLICATION OF THE multicanonical MULTIGRID MONTE-CARLO METHOD TO THE 2-DIMENSIONAL PHI(4)-MODEL - AUTOCORRELATIONS AND INTERFACE TENSION

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JOURNAL OF STATISTICAL PHYSICS 1995年第3-4期78卷 759-798页

作者： JANKE, W SAUER, T FREE UNIV BERLIN INST THEORET PHYS D-14195 BERLIN GERMANY

We discuss the recently proposed multicanonical multigrid Monte Carlo method and apply it to the scalar phi(4)-model on a square lattice. To investigate the performance of the new algorithm at the field-driven first-order phase transitions between the two ordered phases we carefully analyze the autocorrelations of the Monte Carlo process. Compared with standard multicanonical simulations a real-time improvement of about one order of magnitude is established. The interface tension between the two ordered phases is extracted from high-statistics histograms of the magnetization applying histogram reweighting techniques.

关键词： LATTICE FIELD THEORY FIRST-ORDER PHASE TRANSITIONS INTERFACES MONTE CARLO SIMULATIONS multicanonical algorithm MULTIGRID TECHNIQUES AUTOCORRELATIONS

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Generalized-ensemble algorithms for molecular simulations of biopolymers

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BIOPOLYMERS 2001年第2期60卷 96-123页

作者： Mitsutake, A Sugita, Y Okamoto, Y Inst Mol Sci Dept Theoret Studies Okazaki Aichi 4448585 Japan Grad Univ Adv Studies Dept Funct Mol Sci Okazaki Aichi 4448585 Japan

In complex systems with many degrees of freedom such cis peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. lit this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The, effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems. (C) 2001 John Wiley & Sons, Inc.

关键词： protein folding generalized-ensemble algorithm multicanonical algorithm simulated tempering replica-exchange method parallel tempering

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Structural phase transition of di-block polyampholyte

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MOLECULAR SIMULATION 1999年第4-5期22卷 285-301页

作者： Shimizu, H Uehara, K Yamamoto, K Hiwatari, Y Kanazawa Univ Fac Sci Dept Computat Sci Kanazawa Ishikawa 9201192 Japan Natl Res Council Canada Steacie Inst Mol Sci Ottawa ON K1A 0R6 Canada

We have performed both conventional canonical molecular dynamics (MD) and multicanonical MD (MMD) simulations for a single di-block polyampholyte in vacuum to investigate possible structural phase transitions. The conventional canonical MD simulation for temperature T* > 0.05 gives reliable results, since these are independent of the initial conformation. The MMD simulation results for temperature T* > 0.05 are in good agreement with those of the conventional canonical MD simulation. Glassy-like states are obtained when quenched into temperatures below T* similar to 0.05 with a straight chain structure as an initial conformation. On the other hand a spherical double helical structure is obtained when the temperature is gradually lowered to T* similar to 0.01. Also we find a stretched double helical structure at T* similar to 0.01 which changes to the spherical double helical structure by annealing and quenching.

关键词： molecular dynamics simulation multicanonical algorithm constraint dynamics charged polymer Coulomb interaction structural transition

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Comparisons of force fields for proteins by generalized-ensemble simulations

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CHEMICAL PHYSICS LETTERS 2004年第4-6期386卷 460-467页

作者： Yoda, T Sugita, Y Okamoto, Y Inst Mol Sci Dept Theoret Studies Bunkyo Ku Okazaki Aichi 4448585 Japan Inst Mol Sci Dept Therapeut Studies Tokyo Japan Grad Univ Adv Studies Dept Funct Mol Sci Okazaki Aichi 4448585 Japan

Secondary structural characteristics of six commonly used force fields for protein systems developed by different research groups have been compared. We performed molecular dynamics simulations of an alpha-helical polypeptide and a beta-hairpin polypeptide with explicit water molecules. Two generalized-ensemble algorithms, replica-exchange multicanonical algorithm and multicanonical replica-exchange method, for efficient sampling of configurational space have been employed. Comparisons of the secondary structure content of polypeptides for different force fields highlighted differences of their structural tendency. The results imply that a-helix is favored for AMBER94 and AMBER99 and that beta-hairpin is favored for GROMOS96, while CHARNIM22, AMBER96, and OPLS-AA/L have intermediate tendency. (C) 2004 Published by Elsevier B.V.

关键词： Molecular-dynamics simulations Beta-hairpin formation Energy landscape multicanonical algorithm Solution conformations Phase-transitions Aqueous-solution Ribonuclease-a C-peptide Thermodynamics

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Peptide folding simulations

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CURRENT OPINION IN STRUCTURAL BIOLOGY 2003年第2期13卷 168-174页

作者： Gnanakaran, S Nymeyer, H Portman, J Sanbonmatsu, KY García, AE Los Alamos Natl Lab Theoret Biol & Biophys Grp Div Theoret Los Alamos NM 87545 USA

Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics. Two newly implemented simulation techniques, parallel replica dynamics and replica exchange molecular dynamics, can now describe directly from simulations the kinetics and thermodynamics of peptide formation, respectively. Given these developments, the simulation community now has the tools to verify and validate simulation protocols and models (forcefields).

关键词： Molecular-dynamics simulations Intramolecular contact formation Free-energy landscape Implicit solvent models Beta-hairpin formation Explicit water multicanonical algorithm Hydrogen-bonds Side-chain Protein time-resolved spectroscopy development design simulating Protein hydrogen bonds Peptides Molecular Dynamics Simulation Parallel Lines Free energy Simulation models dynamics Peptide Biosynthesis Molecular Dynamics Thermodynamics

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