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Journal articles on the topic 'Molecular dynamics'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Gough, Craig A., Takashi Gojobori, and Tadashi Imanishi. "1P563 Consistent dynamic phenomena in amyloidogenic forms of transthyretin : a molecular dynamics study(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S287. http://dx.doi.org/10.2142/biophys.46.s287_3.

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2

Biyani, Manish, T. Aoyama, and K. Nishigaki. "1M1330 Solution structure dynamics of single-stranded oligonucleotides : Experiments and molecular dynamics." Seibutsu Butsuri 42, supplement2 (2002): S76. http://dx.doi.org/10.2142/biophys.42.s76_2.

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3

Okumura, Hisashi, Satoru G. Itoh, and Yuko Okamoto. "1P585 Explicit Symplectic Molecular Dynamics Simulation for Rigid-Body Molecules in the Canonical Ensemble(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S293. http://dx.doi.org/10.2142/biophys.46.s293_1.

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4

Sugiyama, Ayumu, Tetsunori Yamamoto, Hidemi Nagao, et al. "1P567 Molecular dynamics study of dynamical structure stability of giant hemoglobin from Oligobrachia mashikoi(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_3.

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5

Slavgorodska, Maria, and Alexander Kyrychenko. "Structure and Dynamics of Pyrene-Labeled Poly(acrylic acid): Molecular Dynamics Simulation Study." Chemistry & Chemical Technology 14, no. 1 (2020): 76–80. http://dx.doi.org/10.23939/chcht14.01.076.

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6

Davies, Matt. "Molecular dynamics." Biochemist 26, no. 4 (2004): 53–54. http://dx.doi.org/10.1042/bio02604053.

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7

Bergstra, J. A., and I. Bethke. "Molecular dynamics." Journal of Logic and Algebraic Programming 51, no. 2 (2002): 193–214. http://dx.doi.org/10.1016/s1567-8326(02)00021-8.

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8

Goodfellow, Julia M., and Mark A. Williams. "Molecular dynamics." Current Biology 2, no. 5 (1992): 257–58. http://dx.doi.org/10.1016/0960-9822(92)90373-i.

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9

Goodfellow, Julia M., and Mark A. Williams. "Molecular dynamics." Current Opinion in Structural Biology 2, no. 2 (1992): 211–16. http://dx.doi.org/10.1016/0959-440x(92)90148-z.

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10

Alder, Berni J. "Slow dynamics by molecular dynamics." Physica A: Statistical Mechanics and its Applications 315, no. 1-2 (2002): 1–4. http://dx.doi.org/10.1016/s0378-4371(02)01220-7.

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11

Williams, Sarah L., César Augusto F. de Oliveira, and J. Andrew McCammon. "Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics." Journal of Chemical Theory and Computation 6, no. 2 (2010): 560–68. http://dx.doi.org/10.1021/ct9005294.

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12

Righini, R. "Molecular dynamics and lattice dynamics calculations in molecular crystals." Physica B+C 131, no. 1-3 (1985): 234–48. http://dx.doi.org/10.1016/0378-4363(85)90156-1.

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13

Zakharov, A. Yu, M. A. Zakharov, and V. V. Zubkov. "PRINCIPLES OF RELATIVISTIC MOLECULAR DYNAMICS." Vestnik NovSU, no. 3 (2024): 425–35. https://doi.org/10.34680/2076-8052.2024.3(137).425-435.

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A relativistic dynamic theory of a system of interacting atoms is constructed based on the concept of an auxiliary field. Variational formulation of problems of relativistic molecular dynamics. An exact closed relativistic system of equations is obtained that describes the evolution of the system of atoms and the auxiliary field. An analysis of the qualitative properties of solutions to the system dynamics equations has been carried out.

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14

Phares, Denis J., and Arun R. Srinivasa. "Molecular Dynamics with Molecular Temperature." Journal of Physical Chemistry A 108, no. 29 (2004): 6100–6108. http://dx.doi.org/10.1021/jp037910y.

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15

Wagner, Geri, Eirik Flekkøy, Jens Feder, and Torstein Jøssang. "Coupling molecular dynamics and continuum dynamics." Computer Physics Communications 147, no. 1-2 (2002): 670–73. http://dx.doi.org/10.1016/s0010-4655(02)00371-5.

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16

Erban, Radek. "From molecular dynamics to Brownian dynamics." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 470, no. 2167 (2014): 20140036. http://dx.doi.org/10.1098/rspa.2014.0036.

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Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors

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17

Brooks, Charles L., David A. Case, Steve Plimpton, Benoît Roux, David van der Spoel, and Emad Tajkhorshid. "Classical molecular dynamics." Journal of Chemical Physics 154, no. 10 (2021): 100401. http://dx.doi.org/10.1063/5.0045455.

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18

SHINTO, Hiroyuki. "Molecular Dynamics Simulation." Journal of the Japan Society of Colour Material 86, no. 10 (2013): 380–85. http://dx.doi.org/10.4011/shikizai.86.380.

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19

Hoover. "Nonequilibrium molecular dynamics." Condensed Matter Physics 8, no. 2 (2005): 247. http://dx.doi.org/10.5488/cmp.8.2.247.

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20

Binder, Kurt, Jürgen Horbach, Walter Kob, Wolfgang Paul, and Fathollah Varnik. "Molecular dynamics simulations." Journal of Physics: Condensed Matter 16, no. 5 (2004): S429—S453. http://dx.doi.org/10.1088/0953-8984/16/5/006.

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21

Ashfold, M. N. R., and D. H. Parker. "Imaging molecular dynamics." Phys. Chem. Chem. Phys. 16, no. 2 (2014): 381–82. http://dx.doi.org/10.1039/c3cp90161k.

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22

Thomas, David D. "Molecular dynamics resolved." Nature 321, no. 6069 (1986): 539–40. http://dx.doi.org/10.1038/321539a0.

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23

STADLER, BÄRBEL M. R., and PETER F. STADLER. "MOLECULAR REPLICATOR DYNAMICS." Advances in Complex Systems 06, no. 01 (2003): 47–77. http://dx.doi.org/10.1142/s0219525903000724.

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Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability to multi-stability and chaotic dynamics. Nevertheless, there are some general principles that govern t

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24

Rapaport, D. C. "Interactive molecular dynamics." Physica A: Statistical Mechanics and its Applications 240, no. 1-2 (1997): 246–54. http://dx.doi.org/10.1016/s0378-4371(97)00148-9.

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25

Tidor, Bruce. "Molecular dynamics simulations." Current Biology 7, no. 9 (1997): R525—R527. http://dx.doi.org/10.1016/s0960-9822(06)00269-7.

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26

Hansson, Tomas, Chris Oostenbrink, and WilfredF van Gunsteren. "Molecular dynamics simulations." Current Opinion in Structural Biology 12, no. 2 (2002): 190–96. http://dx.doi.org/10.1016/s0959-440x(02)00308-1.

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27

Matthews, G. Peter. "Molecular dynamics simulator." Journal of Chemical Education 70, no. 5 (1993): 387. http://dx.doi.org/10.1021/ed070p387.2.

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28

Krienke, Hartmut. "Molecular dynamics simulation." Journal of Molecular Liquids 75, no. 3 (1998): 271–72. http://dx.doi.org/10.1016/s0167-7322(97)00106-2.

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29

Bandrauk, André D., Jörn Manz, and M. J. J. Vrakking. "Attosecond molecular dynamics." Chemical Physics 366, no. 1-3 (2009): 1. http://dx.doi.org/10.1016/j.chemphys.2009.10.023.

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30

DUMITRICA, T., and R. JAMES. "Objective molecular dynamics." Journal of the Mechanics and Physics of Solids 55, no. 10 (2007): 2206–36. http://dx.doi.org/10.1016/j.jmps.2007.03.001.

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31

Mitchell, P. J., and D. Fincham. "Multicomputer molecular dynamics." Future Generation Computer Systems 9, no. 1 (1993): 5–10. http://dx.doi.org/10.1016/0167-739x(93)90020-p.

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32

Casavecchia, Piergiorgio, Mark Brouard, Michel Costes, David Nesbitt, Evan Bieske, and Scott Kable. "Molecular collision dynamics." Physical Chemistry Chemical Physics 13, no. 18 (2011): 8073. http://dx.doi.org/10.1039/c1cp90049h.

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33

Schroeder, Daniel V. "Interactive molecular dynamics." American Journal of Physics 83, no. 3 (2015): 210–18. http://dx.doi.org/10.1119/1.4901185.

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34

Straatsma, T. P. "Scalable molecular dynamics." Journal of Physics: Conference Series 16 (January 1, 2005): 287–99. http://dx.doi.org/10.1088/1742-6596/16/1/040.

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35

Hoffman, Mark B., and Peter V. Coveney. "Lattice Molecular Dynamics." Molecular Simulation 27, no. 3 (2001): 157–68. http://dx.doi.org/10.1080/08927020108023021.

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36

Rapaport, D. C. "Molecular dynamics simulation." Computing in Science & Engineering 1, no. 1 (1999): 70–71. http://dx.doi.org/10.1109/5992.743625.

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37

D.P. "Molecular photodissociation dynamics." Journal of Molecular Structure 213 (October 1989): 321. http://dx.doi.org/10.1016/0022-2860(89)85133-6.

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38

Feldmeier, H. "Fermionic molecular dynamics." Nuclear Physics A 515, no. 1 (1990): 147–72. http://dx.doi.org/10.1016/0375-9474(90)90328-j.

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39

Ritchie, Burke. "Quantum molecular dynamics." International Journal of Quantum Chemistry 111, no. 1 (2010): 1–7. http://dx.doi.org/10.1002/qua.22371.

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40

Heermann, Dieter W., Peter Nielaba, and Mauro Rovere. "Hybrid molecular dynamics." Computer Physics Communications 60, no. 3 (1990): 311–18. http://dx.doi.org/10.1016/0010-4655(90)90030-5.

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41

Hoover, Wm G. "Nonequilibrium molecular dynamics." Nuclear Physics A 545, no. 1-2 (1992): 523–36. http://dx.doi.org/10.1016/0375-9474(92)90490-b.

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42

Tully, John C. "Nonadiabatic molecular dynamics." International Journal of Quantum Chemistry 40, S25 (1991): 299–309. http://dx.doi.org/10.1002/qua.560400830.

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43

Schulman, Stephen J. "Molecular Photodissociation Dynamics." Journal of Pharmaceutical Sciences 78, no. 5 (1989): 435. http://dx.doi.org/10.1002/jps.2600780520.

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44

Braeckmans, Kevin, Dries Vercauteren, Jo Demeester, and Stefaan C. De Smedt. "Measuring Molecular Dynamics." Imaging & Microscopy 11, no. 2 (2009): 26–28. http://dx.doi.org/10.1002/imic.200990033.

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45

Proctor, Elizabeth A., Feng Ding, and Nikolay V. Dokholyan. "Discrete molecular dynamics." WIREs Computational Molecular Science 1, no. 1 (2011): 80–92. http://dx.doi.org/10.1002/wcms.4.

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46

VASHISHTA, PRIYA, RAJIV K. KALIA, AIICHIRO NAKANO, and JIN YU. "MOLECULAR DYNAMICS AND QUANTUM MOLECULAR DYNAMICS SIMULATIONS ON PARALLEL ARCHITECTURES." International Journal of Modern Physics C 05, no. 02 (1994): 281–83. http://dx.doi.org/10.1142/s0129183194000325.

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Efficient parallel molecular dynamics (MD) algorithm based on the multiple-time-step (MTS) approach is developed. The MTS-MD algorithm is used to study structural correlations in porous silica at densities 2.2 g/cm3 to 1.6 g/cm3. Nature of phonons and effects of hydrostatic pressure in solid C60 is studied using the tight-binding MD method within a unified interaction model which includes intermolecular and intra-molecular interactions.

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47

Narumi, Tetsu, Ryutaro Susukita, Toshikazu Ebisuzaki, Geoffrey McNiven, and Bruce Elmegreen. "Molecular Dynamics Machine: Special-Purpose Computer for Molecular Dynamics Simulations." Molecular Simulation 21, no. 5-6 (1999): 401–15. http://dx.doi.org/10.1080/08927029908022078.

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48

Wu, Jian-Bo, Shu-Jia Li, Hong Liu, Hu-Jun Qian, and Zhong-Yuan Lu. "Dynamics and reaction kinetics of coarse-grained bulk vitrimers: a molecular dynamics study." Physical Chemistry Chemical Physics 21, no. 24 (2019): 13258–67. http://dx.doi.org/10.1039/c9cp01766f.

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We used the hybrid molecular dynamics–Monte Carlo (MD–MC) algorithm to establish a molecular dynamics model that can accurately reflect bond exchange reactions, and reveal the intrinsic mechanism of the dynamic behavior of the vitrimer system.

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49

Anam, Muhammad Syaekhul, and S. Suwardi. "Hydration Structures and Dynamics of Ga3+ Ion Based on Molecular Mechanics Molecular Dynamics Simulation (Classical DM)." Indonesian Journal of Chemistry and Environment 4, no. 2 (2022): 49–56. http://dx.doi.org/10.21831/ijoce.v4i2.48401.

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The structure and hydration dynamics of Ga3+ ion have been studied using classical Molecular Dynamics (MD) simulations. The data collection procedure includes determining the best base set, constructing 2-body and 3-body potential equations, classical molecular dynamics simulations based on 2-body potentials, classical molecular dynamics simulations based on 2-body + 3 potential-body. The trajectory file data analysis was done to obtain structural properties parameters such as RDF, CND, ADF, and dynamic properties, namely the movement of H2O ligands between hydrations shells. The results of th

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50

Dwiastuti, Rini, Muhammad Radifar, Marchaban Marchaban, Sri Noegrohati, and Enade Perdana Istyastono. "Molecular Dynamics Simulations and Empirical Observations on Soy Lecithin Liposome Preparation." Indonesian Journal of Chemistry 16, no. 2 (2018): 222. http://dx.doi.org/10.22146/ijc.21167.

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Soy lecithin is a phospholipid often used in liposome formulations. Determination of water and phospholipid composition is one of the problems in the liposome formulation. This study is using molecular dynamics simulation and empirical observation in producing liposome preparations. Phospholipids 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine (DLPE) were objected in molecular dynamics simulations using Coarse Grained Molecular Dynamics (CGMD) approaches. The result showed that the molecular dynamic simulations could be employed to predict the liposome size. The molecular dynamic simulations re

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