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Symposium on Progress and Future Prospects in Molecular Dynamics Simulation

作者： Itoh, Satoru G. Okumura, Hisashi Okamoto, Yuko Nagoya Univ Sch Sci Dept Phys Nagoya Aichi 4648602 Japan

In complex systems with many degrees of freedom such as biomolecular systems, conventional Monte Carlo and molecular dynamics simulations in canonical ensemble or isobaric-isothermal ensemble suffer from the multiple-minima problem, resulting in entrapment in states of energy local minima. A simulation in generalized ensemble performs a random walk in specified variables and overcomes this difficulty. In this article we review the generalized-ensemble algorithms. Multicanonical algorithm is described first. In this method, a random walk in potential energy space is realized and the simulation can avoid the multiple-minima problem. We then present two new generalized-ensemble algorithms, namely multioverlap algorithm and multibaric-multithermal algorithm, which are multi-variable/multi-dimensional extensions of the multicanonical algorithm. In the former method, a random walk in overlap space is realized, and in the latter that in both potential energy space and volume space is obtained. Emphasis is laid in the description of the molecular dynamics versions of these algorithms.

关键词： molecular dynamics simulation generalized-ensemble algorithms multicanonical algorithm multioverlap algorithm multibaric-multithermal algorithm

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Tackling the multiple-minima problem in protein folding by Monte Carlo simulated annealing and generalized-ensemble algorithms

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INTERNATIONAL JOURNAL OF MODERN PHYSICS C 1999年第8期10卷 1571-1582页

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

Monte Carlo simulations based on simulated annealing and multicanonical algorithm have been performed to predict the secondary and tertiary structures of oligopeptide systems. Two oligopeptides, C-peptide of ribonuclease A and the fragment BPTI(16-36) of bovine pancreatic trypsin inhibitor, were studied. Only the amino-acid sequence information was used as input and initial conformations were randomly generated. The lowest-energy conformations obtained have alpha-helix structure and beta-sheet structure for C-peptide and BPTI(16-36), respectively, in remarkable agreement with experimental results.

关键词： simulated annealing generalized-ensemble algorithms multicanonical algorithm replica-exchange method parallel tempering simulated tempering

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generalized-ensemble algorithms for molecular dynamics simulations

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MOLECULAR SIMULATION 2007年第1-2期33卷 47-56页

作者： Itoh, Satoru G. Okumura, Hisashi Okamoto, Yuko Nagoya Univ Sch Sci Dept Phys Nagoya Aichi 4648602 Japan

关键词： molecular dynamics simulation generalized-ensemble algorithms multicanonical algorithm multioverlap algorithm multibaric-multithermal algorithm

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Free energy landscape analysis of two-dimensional dipolar solvent model at temperatures below and above the rotational freezing point

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JOURNAL OF CHEMICAL PHYSICS 2006年第12期124卷 24508-1-24508-页

作者： Suzuki, Y Tanimura, Y Kyoto Univ Dept Chem Sakyo Ku Kyoto 6068502 Japan

Ionic solvation in a polar solvent is modeled by a central charge surrounded by dipolar molecules posted on two-dimensional distorted lattice sites with simple rotational dynamics. Density of states is calculated by applying the Wang-Landau algorithm to both the energy and polarization states. The free energy landscapes of solvent molecules as a function of polarization are depicted to explore the competition between the thermal fluctuation and solvation energy. Without a central charge, for temperatures higher than the energy scale of the dipole-dipole interactions, the energy landscape for the small polarization region exhibits a parabolic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] for electron transfer reaction, while there is an additional quartic contribution to the landscape for the large polarization region. When the temperature drops, the simulated free energy landscapes are no longer smooth due to the presence of multiple local minima arising from the frustrated interaction among the dipoles. The parabolic contribution becomes negligible and the energy landscape becomes quartic in shape. For a strong central charge, the energy landscape exhibits an asymmetric profile due to the contributions of linear and cubic terms that arise from the charge-dipole interactions.

关键词： ELECTRON-TRANSFER REACTIONS generalized-ensemble algorithms DIELECTRIC-RELAXATION COMPUTER-SIMULATION MOLECULAR-DYNAMICS SOLVATION DYNAMICS PHASE-TRANSITIONS MONTE-CARLO LATTICE LIMIT

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Combining elastic network analysis and molecular dynamics simulations by Hamiltonian replica exchange

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JOURNAL OF CHEMICAL THEORY AND COMPUTATION 2008年第3期4卷 477-487页

作者： Zacharias, Martin Jacobs Univ Bremen Sch Sci & Engn D-28759 Bremen Germany

Coarse-grained elastic network models (ENM) of proteins can be used efficiently to explore the global mobility of a protein around a reference structure. A new Hamiltonian-replica exchange molecular dynamics (H-RexMD) method has been designed that effectively combines information extracted from an ENM analysis with atomic-resolution MD simulations. The ENM analysis is used to construct a distance-dependent penalty (flooding or biasing) potential that can drive the structure away from its current conformation in directions compatible with the ENM model. Various levels of the penalty or biasing potential are added to the force field description of the MD simulation along the replica coordinate. One replica runs at the original force field. By focusing the penalty potential on the relevant soft degrees of freedom the method avoids the rapid increase of the replica number with increasing system size to cover a desired temperature range in conventional (temperature) RexMD simulations. The application to domain motions in lysozyme of bacteriophage T4 and to peptide folding indicates significantly improved conformational sampling compared to conventional MD simulations.

关键词： FREE-ENERGY LANDSCAPE generalized-ensemble algorithms NORMAL-MODE CALCULATIONS BETA-HAIRPIN MONTE-CARLO BACTERIOPHAGE-T4 LYSOZYME STRUCTURE PREDICTION EXPLICIT SOLVENT FOLDING SIMULATIONS STRUCTURAL BIOLOGY

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

Multi-dimensional multicanonical algorithm, simulated temper...

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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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All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations

All-Atom Molecular Dynamics Simulation Methods for the Aggre...

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作者： Satoru G. Itoh Hisashi Okumura

Protein aggregates are associated with more than 40 serious human diseases. To understand the formation mechanism of protein aggregates at atomic level, all-atom molecular dynamics (MD) simulation is a powerful computational tool. In this chapter, we review the all-atom MD simulation methods that are useful for study on the protein aggregation. We first explain conventional MD simulation methods in physical statistical ensembles, such as the canonical and isothermal-isobaric ensembles. We then describe the generalized-ensemble algorithms such as replica-exchange and replica-permutation MD methods. These methods can overcome a difficulty, in which simulations tend to get trapped in local-minimum free-energy states. Finally we explain the nonequilibrium MD method. Some simulation results based on these methods are also presented. less

关键词： Molecular Dynamics Simulation NMR Atomic Force Microscopy (AFM) Statistical Calculation Amyloid fibril Amyloid-β peptide Oligomer generalized-ensemble algorithms Nonequilibrium

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