References analysis of the Wikipedia article "分子動力学法" in the Japanese version

doi.org

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

harvard.edu

ui.adsabs.harvard.edu

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.

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.

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.

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.

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.

nih.gov

pubmed.ncbi.nlm.nih.gov

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.

ncbi.nlm.nih.gov

分子動力学法 (Japanese Wikipedia)

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