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Journal articles on the topic 'Molecular dynamics'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 November 2024

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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, Keigo Nishikawa, Nobutaka Numoto, Kunio Miki, and Yoshihiro Fukumori. "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 (February 20, 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 (August 1, 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 (June 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 (May 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 (April 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 (November 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 (January 14, 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 (August 1985): 234–48. http://dx.doi.org/10.1016/0378-4363(85)90156-1.

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13

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

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14

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

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15

Erban, Radek. "From molecular dynamics to Brownian dynamics." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 470, no. 2167 (July 8, 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 on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.

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16

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 (March 14, 2021): 100401. http://dx.doi.org/10.1063/5.0045455.

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17

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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18

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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19

Binder, Kurt, Jürgen Horbach, Walter Kob, Wolfgang Paul, and Fathollah Varnik. "Molecular dynamics simulations." Journal of Physics: Condensed Matter 16, no. 5 (January 23, 2004): S429—S453. http://dx.doi.org/10.1088/0953-8984/16/5/006.

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20

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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21

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

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22

STADLER, BÄRBEL M. R., and PETER F. STADLER. "MOLECULAR REPLICATOR DYNAMICS." Advances in Complex Systems 06, no. 01 (March 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 their overall behavior. We focus on the question to what extent the dynamics of replication can explain the accumulation of genetic information that eventually leads to the emergence of the first cell and hence the origin of life as we know it. A large class of ligation-based replication systems, which includes the experimentally available model systems for template directed self-replication, is of particular interest because its dynamics bridges the gap between the survival of a single fittest species to the global coexistence of everthing. In this intermediate regime the selection is weak enough to allow the coexistence of genetically unrelated replicators and strong enough to limit the accumulation of disfunctional mutants.

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23

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

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24

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

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25

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

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26

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

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27

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

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28

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

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29

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

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30

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

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31

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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32

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

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33

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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34

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

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35

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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36

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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37

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

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38

Ritchie, Burke. "Quantum molecular dynamics." International Journal of Quantum Chemistry 111, no. 1 (October 26, 2010): 1–7. http://dx.doi.org/10.1002/qua.22371.

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39

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

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40

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

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41

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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42

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

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43

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

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44

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

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45

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 (April 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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46

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 (January 1999): 401–15. http://dx.doi.org/10.1080/08927029908022078.

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47

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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48

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 (March 10, 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 the research indicated that the hydration complex structure of Ga(H2O)83+ and Ga(H2O)63+ was observed in molecular dynamics simulations (MM-2 body) and (MM-2 body + 3-body), respectively. The movement of H2O ligands occurs between the first and second shell or vice versa in the MD simulation of MM-2 bodies but does not occur in MD simulations of (MM-2 bodies + MM-3 bodies). Therefore, the water ligands in the first hydrated shell are stable.

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49

Sivak, A. B., D. N. Demidov, and P. A. Sivak. "DIFFUSION CHARACTERISTICS OF RADIATION DEFECTS IN IRON: MOLECULAR DYNAMICS DATA." Problems of Atomic Science and Technology, Ser. Thermonuclear Fusion 44, no. 2 (2021): 148–57. http://dx.doi.org/10.21517/0202-3822-2021-44-2-148-157.

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50

Inoue, Yasuhiro, Shinji Matsushita, and Taiji Adachi. "BC-JP-6 Molecular dynamics simulations of an actin filament." Proceedings of Mechanical Engineering Congress, Japan 2012 (2012): _BC—JP—6–1—_BC—JP—6–1. http://dx.doi.org/10.1299/jsmemecj.2012._bc-jp-6-1.

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