分子動力学法
出典: フリー百科事典『ウィキペディア（Wikipedia）』 (2024/05/10 14:33 UTC 版)
分子動力学法（ぶんしどうりきがくほう、英: molecular dynamics、MD法）は、原子ならびに分子の物理的な動きのコンピューターシミュレーション手法である。原子および分子はある時間の間相互作用することが許され、これによって原子の動的発展の光景が得られる。最も一般的なMD法では、原子および分子のトラクジェクトリは、相互作用する粒子の系についての古典力学におけるニュートンの運動方程式を数値的に解くことによって決定される。この系では粒子間の力およびポテンシャルエネルギーは原子間ポテンシャル（分子力学力場）によって定義される。MD法は元々は1950年代末に理論物理学分野で考え出されたが[1][2]、今日では主に化学物理学、材料科学、生体分子のモデリングに適用されている。系の静的、動的安定構造や、動的過程（ダイナミクス）を解析する手法。
- ^ a b c Alder, B. J.; T. E. Wainwright (1959). “Studies in Molecular Dynamics. I. General Method”. J. Chem. Phys. 31 (2): 459. Bibcode: 1959JChPh..31..459A. doi:10.1063/1.1730376.
- ^ a b c Rahman, A. (19 October 1964). “Correlations in the Motion of Atoms in Liquid Argon”. Physical Review 136 (2A): A405–A411. Bibcode: 1964PhRv..136..405R. doi:10.1103/PhysRev.136.A405.
- ^ Schlick, T. (1996). “Pursuing Laplace's Vision on Modern Computers”. In J. P. Mesirov, K. Schulten and D. W. Sumners. Mathematical Applications to Biomolecular Structure and Dynamics, IMA Volumes in Mathematics and Its Applications. 82. New York: Springer-Verlag. pp. 218–247. ISBN 978-0-387-94838-6
- ^ de Laplace, P. S. (1820) (French). Oeuveres Completes de Laplace, Theorie Analytique des Probabilites. Paris, France: Gauthier-Villars
- ^ Gibson, J B; Goland, A N; Milgram, M; Vineyard, G H (1960). “Dynamics of Radiation Damage”. Phys. Rev. 120: 1229–1253. Bibcode: 1960PhRv..120.1229G. doi:10.1103/PhysRev.120.1229.
- ^ Steve Plimpton. “Molecular Dynamics - Parallel Algorithms”. 2015年7月22日閲覧。
- ^ Streett WB, Tildesley DJ, Saville G; Tildesley; Saville (1978). “Multiple time-step methods in molecular dynamics”. Mol Phys 35 (3): 639–648. Bibcode: 1978MolPh..35..639S. doi:10.1080/00268977800100471.
- ^ Tuckerman ME, Berne BJ, Martyna GJ; Berne; Martyna (1991). “Molecular dynamics algorithm for multiple time scales: systems with long range forces”. J Chem Phys 94 (10): 6811–6815. Bibcode: 1991JChPh..94.6811T. doi:10.1063/1.460259.
- ^ Tuckerman ME, Berne BJ, Martyna GJ; Berne; Martyna (1992). “Reversible multiple time scale molecular dynamics”. J Chem Phys 97 (3): 1990–2001. Bibcode: 1992JChPh..97.1990T. doi:10.1063/1.463137.
- ^ Sugita, Yuji; Yuko Okamoto (1999). “Replica-exchange molecular dynamics method for protein folding”. Chem Phys Letters 314: 141–151. Bibcode: 1999CPL...314..141S. doi:10.1016/S0009-2614(99)01123-9.
- ^ Sinnott, S. B.; Brenner, D. W. (2012). “Three decades of many-body potentials in materials research”. MRS Bulletin 37 (5): 469–473. doi:10.1557/mrs.2012.88.
- ^ Albe, K.; Nordlund, K.; Averback, R. S. (2002). “Modeling metal-semiconductor interaction: Analytical bond-order potential for platinum-carbon”. Phys. Rev. B 65 (19): 195124. Bibcode: 2002PhRvB..65s5124A. doi:10.1103/physrevb.65.195124.
- ^ Brenner, D. W. (1990). “Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films”. Phys. Rev. B 42 (15): 9458–9471. Bibcode: 1990PhRvB..42.9458B. doi:10.1103/PhysRevB.42.9458.
- ^ Keith Beardmore and Roger Smith. (1996) Empirical potentials for c-si-h systems with application to C60 interactions with Si crystal surfaces. Phil. Mag. A 74:1439--1466.
- ^ Boris Ni, Ki-Ho Lee, and Susan B Sinnott. (2004) A reactive empirical bond order (rebo) potential for hydrocarbon oxygen interactions. J. Phys.: Condens. Matter 16:7261--7275.
- ^ van Duin, A.; Siddharth Dasgupta, François Lorant and William A. Goddard III; Lorant, Francois; Goddard, William A. (2001). “ReaxFF: A Reactive Force Field for Hydrocarbons”. J. Phys. Chem. A 105 (41): 9398. doi:10.1021/jp004368u.
- ^ Tersoff, J. (1989). “Modeling solid-state chemistry: Interatomic potentials for multicomponent systems”. Phys. Rev. B 39 (8): 5566–5568. Bibcode: 1989PhRvB..39.5566T. doi:10.1103/PhysRevB.39.5566.
- ^ Daw, M. S.; S. M. Foiles and M. I. Baskes (1993). “The embedded-atom method: a review of theory and applications”. Mat. Sci. And Engr. Rep. 9 (7–8): 251–310. doi:10.1016/0920-2307(93)90001-U.
- ^ Cleri, F.; V. Rosato (1993). “Tight-binding potentials for transition metals and alloys”. Phys. Rev. B 48: 22–33. Bibcode: 1993PhRvB..48...22C. doi:10.1103/PhysRevB.48.22.
- ^ Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD; Harder; Vorobyov; Roux; MacKerell (2006). “A polarizable model of water for molecular dynamics simulations of biomolecules”. Chem Phys Lett 418: 245–249. Bibcode: 2006CPL...418..245L. doi:10.1016/j.cplett.2005.10.135.
- ^ Patel, S.; MacKerell, Jr. AD; Brooks III, Charles L (2004). “CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model”. J Comput Chem 25 (12): 1504–1514. doi:10.1002/jcc.20077. PMID 15224394.
- ^ こういった手法のための方法論はウォーシェルと共同研究者らによって発表された。近年、アリー・ウォーシェル（南カリフォルニア大学）、Weitao Yang（デューク大学）、Sharon Hammes-Schiffer（ペンシルベニア州立大学）、ドナルド・トゥルーラーおよびJiali Gao（ミネソタ大学）、Kenneth Merz（フロリダ大学）を含む複数のグループによって開拓された。
- ^ Billeter, SR; SP Webb; PK Agarwal; T Iordanov; S Hammes-Schiffer (2001). “Hydride Transfer in Liver Alcohol Dehydrogenase: Quantum Dynamics, Kinetic Isotope Effects, and Role of Enzyme Motion”. J Am Chem Soc 123 (45): 11262–11272. doi:10.1021/ja011384b. PMID 11697969.
- ^ Smith, A; CK Hall (2001). “Alpha-Helix Formation: Discontinuous Molecular Dynamics on an Intermediate-Resolution Protein Model”. Proteins 44 (3): 344–360. doi:10.1002/prot.1100. PMID 11455608.
- ^ Ding, F; JM Borreguero; SV Buldyrey; HE Stanley; NV Dokholyan (2003). “Mechanism for the alpha-helix to beta-hairpin transition”. J Am Chem Soc 53 (2): 220–228. doi:10.1002/prot.10468. PMID 14517973.
- ^ Paci, E; M Vendruscolo; M Karplus (2002). “Validity of Go Models: Comparison with a Solvent-Shielded Empirical Energy Decomposition”. Biophys J 83 (6): 3032–3038. Bibcode: 2002BpJ....83.3032P. doi:10.1016/S0006-3495(02)75308-3. PMC 1302383. PMID 12496075.
- ^ Chakrabarty, A; T Cagin (2010). “Coarse grain modeling of polyimide copolymers”. Polymer 51 (12): 2786–2794. doi:10.1016/j.polymer.2010.03.060.
- ^ Nienhaus, Gerd Ulrich (2005). Protein-ligand interactions: methods and applications. pp. 54–56. ISBN 978-1-61737-525-5
- ^ Leszczyński, Jerzy (2005). Computational chemistry: reviews of current trends, Volume 9. pp. 54–56. ISBN 978-981-256-742-0
- ^ Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal; Swendsen, Robert H.; Kollman, Peter A. (1992). “The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method”. J. Comput. Chem. 13 (8): 1011–1021. doi:10.1002/jcc.540130812.
- ^ Bartels, Christian (2000). “Analyzing biased Monte Carlo and molecular dynamics simulations”. Chem. Phys. Lett. 331 (5–6): 446–454. Bibcode: 2000CPL...331..446B. doi:10.1016/S0009-2614(00)01215-X.
- ^ Levitt, M; A Warshel (1975). “Computer Simulations of Protein Folding”. Nature 253 (5494): 694–8. Bibcode: 1975Natur.253..694L. doi:10.1038/253694a0. PMID 1167625.
- ^ Warshel, A (1976). “Bicycle-pedal Model for the First Step in the Vision Process”. Nature 260 (5553): 679–683. Bibcode: 1976Natur.260..694B. doi:10.1038/260679a0.
- ^ Averback, R. S.; Diaz de la Rubia, T. (1998). “Displacement damage in irradiated metals and semiconductors”. In H. Ehrenfest and F. Spaepen. Solid State Physics. 51. New York: Academic Press. pp. 281–402
- ^ R. Smith, ed (1997). Atomic & ion collisions in solids and at surfaces: theory, simulation and applications. Cambridge, UK: Cambridge University Press
- ^ Offman, MN; M Krol; I Silman; JL Sussman; AH Futerman (2010). “Molecular basis of reduced glucosylceramidase activity in the most common Gaucher disease mutant, N370S”. J. Biol. Chem. 285 (53): 42105–42114. doi:10.1074/jbc.M110.172098. PMC 3009936. PMID 20980259.
- ^ Offman, MN; M Krol; B Rost; I Silman; JL Sussman; AH Futerman (2011). “Comparison of a molecular dynamics model with the X-ray structure of the N370S acid-beta-glucosidase mutant that causes Gaucher disease”. Protein Eng. Des. Sel. 24 (10): 773–775. doi:10.1093/protein/gzr032. PMID 21724649.
- ^ Hu, Han; Sun, Ying. “Molecular dynamics simulations of disjoining pressure effect in ultra-thin water film on a metal surface”. Appl. Phys. Lett. 14: 263110. Bibcode: 2013ApPhL.103z3110H. doi:10.1063/1.4858469.
- ^ David A Welch, B Layla Mehdi, Hannah J Hatchell, Roland Faller, James E Evans and Nigel D Browning (2015). “Using molecular dynamics to quantify the electrical double layer and examine the potential for its direct observation in the in-situ TEM”. Advanced Structural and Chemical Imaging 1: 1. doi:10.1186/s40679-014-0002-2.
- ^ Freddolino P, Arkhipov A, Larson SB, McPherson A, Schulten K. “Molecular dynamics simulation of the Satellite Tobacco Mosaic Virus (STMV)”. Theoretical and Computational Biophysics Group. University of Illinois at Urbana Champaign. 2015年8月26日閲覧。
- ^ The Folding@Home Project and recent papers published using trajectories from it. Vijay Pande Group. Stanford University
- ^ a b Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O.; Shaw, David E. (2011). “How Fast-Folding Proteins Fold”. Science 334 (6055): 517–520. Bibcode: 2011Sci...334..517L. doi:10.1126/science.1208351. PMID 22034434.
- ^ Shaw, David E.; Maragakis, Paul; Lindorff-Larsen, Kresten; Piana, Stefano; Dror, Ron O.; Eastwood, Michael P.; Bank, Joseph A.; Jumper, John M. et al. (2010). “Atomic-Level Characterization of the Structural Dynamics of Proteins”. Science 330 (6002): 341–346. Bibcode: 2010Sci...330..341S. doi:10.1126/science.1187409. PMID 20947758.
- ^ Goel S, Luo; Reuben R L. “Molecular dynamics simulation model for the quantitative assessment of tool wear during single point diamond turning of cubic silicon carbide”. Comput. Mater. Sci 51.
- ^ Jayasena, Buddhika; Subbiah Sathyan (2011). “A novel mechanical cleavage method for synthesizing few-layer graphenes”. Nanoscale Research Letters 6 (1): 95. Bibcode: 2011NRL.....6...95J. doi:10.1186/1556-276X-6-95. PMC 3212245. PMID 21711598.
- ^ Jayasena, B; Reddy C.D; Subbiah S. “Separation, folding and shearing of graphene layers during wedge-based mechanical exfoliation”. Nanotechnology. 24 (20): 205301. Bibcode: 2013Nanot..24t5301J. doi:10.1088/0957-4484/24/20/205301.
[続きの解説]
「分子動力学法」の続きの解説一覧
このページでは「ウィキペディア」から分子動力学法を検索した結果を表示しています。
Weblioに収録されているすべての辞書から分子動力学法を検索する場合は、下記のリンクをクリックしてください。
全ての辞書から分子動力学法 を検索
Weblioに収録されているすべての辞書から分子動力学法を検索する場合は、下記のリンクをクリックしてください。
全ての辞書から分子動力学法 を検索 - 分子動力学法のページへのリンク
