分子動力学法分子動力学法の概要

単純な系における分子動力学シミュレーションの例: 単一のCu 原子のCu (001) 表面への堆積。それぞれの円は単一原子の位置を示す。現在のシミュレーションにおいて用いられる実際の原子的相互作用は図中の2次元剛体球の相互作用よりも複雑である。

分子動力学法は生物物理学的系をシミュレーションするためにしばしば用いられる。ここで描かれているのは水の100 psシミュレーションである。

分子の系は莫大な数の粒子から構成されるため、このような複雑系の性質を解析的に探ることは不可能である。MDシミュレーションは数値的手法を用いることによってこの問題を回避する。しかしながら、長いMDシミュレーションは数学的に悪条件であり、数値積分において累積誤差を生成してしまう。これはアルゴリズムとパラメータの適切な選択によって最小化することができるが、完全に取り除くことはできない。

エルゴード仮説に従う系では、単一の分子動力学シミュレーションの展開は系の巨視的熱力学的性質を決定するために使うことができる。エルゴード系の時間平均はミクロカノニカルアンサンブル（小正準集団）平均に対応する。MDは自然の力をアニメーションすることによって未来を予測する、原子スケールの分子の運動についての理解を可能にする「数による統計力学」や「ニュートン力学のラプラス的視点」とも称されている^[3]^[4]。

MDシミュレーションでは等温、定圧、等温・定圧、定エネルギー、定積、定ケミカルポテンシャル、グランドカノニカルといった様々なアンサンブル（統計集団）の計算が可能である。また、結合長や位置の固定など様々な拘束条件を付加することもできる。計算対象は、バルク、表面、界面、クラスターなど多様な系を扱える。

MD法で扱える系の規模としては、最大で数億原子からなる系の計算例がある。通常の計算規模は数百から数万原子（分子、粒子）程度である。

通常、ポテンシャル関数は、原子-原子の二体ポテンシャルを組み合わせて表現し、これを計算中に変更しない。そのため化学反応のように、原子間結合の生成・開裂を表現するには、何らかの追加の工夫が必要となる。また、ポテンシャルは経験的・半経験的なパラメータから求められる。

こうしたポテンシャル面の精度の問題を回避するため、ポテンシャル面を電子状態の第一原理計算から求める手法もある。このような方法は、第一原理分子動力学法〔量子（ab initio）分子動力学法〕と呼ばれる。この方法では、ポテンシャル面がより正確なものになるが、扱える原子数は格段に減る（スーパーコンピュータを利用しても、最大で約千個程度）。

また第一原理分子動力学法の多くは、電子状態が常に基底状態であることを前提としているものが多く、電子励起状態や電子状態間の非断熱遷移を含む現象の記述は、こうした手法であってもなお困難である。

脚注

^ ^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.

[前の解説]

[続きの解説]

「分子動力学法」の続きの解説一覧

[a&w-1] 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.rahman-2] 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.

[3] 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

[4] Laplace, P. S. (1820) (French). Oeuveres Completes de Laplace, Theorie Analytique des Probabilites. Paris, France: Gauthier-Villars

[5] 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.

[6] Steve Plimpton. “Molecular Dynamics - Parallel Algorithms”. 2015年7月22日閲覧。

[Streett-7] 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.

[Tuckerman1991-8] 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.

[Tuckerman1992-9] 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.

[10] 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.

[11] 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.

[12] 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.

[13] 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.

[14] 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.

[15] 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.

[16] 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.

[17] 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.

[18] 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.

[19] 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.

[Lamoureux3-20] 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.

[Patel2004b-21] 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.

[22] 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。

[23] 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.

[24] 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.

[25] 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.

[26] 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.

[27] 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-28] Nienhaus, Gerd Ulrich (2005). Protein-ligand interactions: methods and applications. pp. 54–56. ISBN 978-1-61737-525-5

[Leszczyński-29] Leszczyński, Jerzy (2005). Computational chemistry: reviews of current trends, Volume 9. pp. 54–56. ISBN 978-981-256-742-0

[30] 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.

[31] 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.

[32] 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.

[33] 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.

[Ave98-34] 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

[Smith-35] R. Smith, ed (1997). Atomic & ion collisions in solids and at surfaces: theory, simulation and applications. Cambridge, UK: Cambridge University Press

[36] 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.

[37] 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.

[38] 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.

[39] 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.

[40] 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。

[41] The Folding@Home Project and recent papers published using trajectories from it. Vijay Pande Group. Stanford University

[DESRES-Science2011-42] 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.

[43] 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.

[44] 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.

[Jaya2011-45] 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.

[46] 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.

[3]

[4]

分子動力学法 分子動力学法の概要

分子動力学法

急上昇のことば

「分子動力学法」の関連用語

分子動力学法分子動力学法の概要