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Journal articles on the topic 'MOLECULAR DYNAMCS'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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1

Mori, K., Y. Seki, and K. Soda. "Volume Fluctuation Dynamcs of Lysozyme by Molecular Dynamics Simulation." Seibutsu Butsuri 43, supplement (2003): S54. http://dx.doi.org/10.2142/biophys.43.s54_3.

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2

WANG, Yu. "A STEERED MOLECULAR DYNAMCS STUDY OF ADSORBED POLYMER CHAIN." Acta Polymerica Sinica 008, no. 3 (September 15, 2008): 216–20. http://dx.doi.org/10.3724/sp.j.1105.2008.00216.

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3

Tse, John. "Structure, bonding and dynamcs under extreme conditions." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1534. http://dx.doi.org/10.1107/s2053273314084654.

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Knowledge on the composition and structure of a material are essential to the understanding of the properties. Recent advances in structural prediction techniques from first-principles calculations have greatly enhanced the perspective on the large variety of new crystal types, particularly, under extreme conditions at high pressure and high temperature. The structural information helps to develop a new understanding on the change in chemical bonding in highly compressed solids. I will present the results and experience in the use of several structural prediction methods with examples drawn from recent studies on the outstanding problems in pressure-induced amorphization of SnI4, structural transformations, atomic dynamics and structural chemistry of simple elemental and molecular solids at high pressure and high temperature. Our results will highlight the successes, challenges and future development on the practical applications of these methods.
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4

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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5

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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6

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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7

Tilokani, Lisa, Shun Nagashima, Vincent Paupe, and Julien Prudent. "Mitochondrial dynamics: overview of molecular mechanisms." Essays in Biochemistry 62, no. 3 (July 20, 2018): 341–60. http://dx.doi.org/10.1042/ebc20170104.

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Mitochondria are highly dynamic organelles undergoing coordinated cycles of fission and fusion, referred as ‘mitochondrial dynamics’, in order to maintain their shape, distribution and size. Their transient and rapid morphological adaptations are crucial for many cellular processes such as cell cycle, immunity, apoptosis and mitochondrial quality control. Mutations in the core machinery components and defects in mitochondrial dynamics have been associated with numerous human diseases. These dynamic transitions are mainly ensured by large GTPases belonging to the Dynamin family. Mitochondrial fission is a multi-step process allowing the division of one mitochondrion in two daughter mitochondria. It is regulated by the recruitment of the GTPase Dynamin-related protein 1 (Drp1) by adaptors at actin- and endoplasmic reticulum-mediated mitochondrial constriction sites. Drp1 oligomerization followed by mitochondrial constriction leads to the recruitment of Dynamin 2 to terminate membrane scission. Inner mitochondrial membrane constriction has been proposed to be an independent process regulated by calcium influx. Mitochondrial fusion is driven by a two-step process with the outer mitochondrial membrane fusion mediated by mitofusins 1 and 2 followed by inner membrane fusion, mediated by optic atrophy 1. In addition to the role of membrane lipid composition, several members of the machinery can undergo post-translational modifications modulating these processes. Understanding the molecular mechanisms controlling mitochondrial dynamics is crucial to decipher how mitochondrial shape meets the function and to increase the knowledge on the molecular basis of diseases associated with morphology defects. This article will describe an overview of the molecular mechanisms that govern mitochondrial fission and fusion in mammals.
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8

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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9

Srinivasan, S. G., I. Ashok, Hannes Jônsson, Gretchen Kalonji, and John Zahorjan. "Dynamic-domain-decomposition parallel molecular dynamics." Computer Physics Communications 102, no. 1-3 (May 1997): 44–58. http://dx.doi.org/10.1016/s0010-4655(97)00016-7.

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10

Paolini, Gaia V. "Dynamic approach to nonequilibrium molecular dynamics." Nuclear Physics B - Proceedings Supplements 5, no. 1 (September 1988): 272–77. http://dx.doi.org/10.1016/0920-5632(88)90054-0.

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11

Zhou, S. J., P. S. Lomdahl, R. Thomson, and B. L. Holian. "Dynamic Crack Processes via Molecular Dynamics." Physical Review Letters 76, no. 13 (March 25, 1996): 2318–21. http://dx.doi.org/10.1103/physrevlett.76.2318.

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12

Fukae, Kazuki, Kazuo Sutoh, and Takuo Yasunaga. "1P575 Potential structure changes of dynein stalk by molecular dynamics calculation(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S290. http://dx.doi.org/10.2142/biophys.46.s290_3.

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13

Terada, Tohru, and Kentaro Shimizu. "1P581 Improving efficiency of conformation sampling in multicanonical molecular dynamics simulation(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S292. http://dx.doi.org/10.2142/biophys.46.s292_1.

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14

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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15

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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16

Yamamori, Yu, and Akio Kitao. "1P072 Large time step molecular dynamics using Torsion Angle Molecular Dynamics(01D. Protein : Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))." Seibutsu Butsuri 54, supplement1-2 (2014): S152. http://dx.doi.org/10.2142/biophys.54.s152_6.

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17

Fuchigami, Sotaro, Mitsunori Ikeguchi, and Akinori Kidera. "1P564 All-Atom Molecular Dynamics Simulation of Conformational Changes in Adenylate Kinase(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_4.

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18

Bolesta, Alexey. "Calculation of Dynamic Hardness by Molecular Dynamics." EPJ Web of Conferences 221 (2019): 01005. http://dx.doi.org/10.1051/epjconf/201922101005.

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Based on the molecular-dynamic simulation of the impact of a solid ball on the surface of polycrystalline copper, a method for calculating the dynamic hardness of nanocrystalline materials is proposed. It is proposed to carry out the calculation of hardness by dividing the impact work by the squeezed volume. It is shown that this expression of dynamic hardness is consistent with Meyer hardness in the case of quasistatic indentation. As a result of this simulation, it is shown that under conditions when the diameter of the impactor decreases and approaches the crystal lattice constant of the target, the dynamic hardness increases. Also, in the calculations, the impactor density varied approximately twice, which was equal to the density of steel and the density of tungsten carbide. For a striker diameter of 5 nm, dynamic hardness increases with the speed of the striker and does not depend on its density.
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19

Gumbsch, P., S. J. Zhou, and B. L. Holian. "Molecular dynamics investigation of dynamic crack stability." Physical Review B 55, no. 6 (February 1, 1997): 3445–55. http://dx.doi.org/10.1103/physrevb.55.3445.

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20

Rashid, Aijaz, and Shazia Ahad. "Molecular Mechanism of Microtubules Dynamics and its Precise Regulation Inside Cells." International Journal of Trend in Scientific Research and Development Volume-1, Issue-4 (June 30, 2017): 714–22. http://dx.doi.org/10.31142/ijtsrd2214.

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21

Lima, M., Victor Volkov, P. Foggi, Riccardo Chelli, and Roberto Righini. "1P216 Two-dimensional Infrared Spectroscopy and Molecular Dynamics of Liquid Formamide." Seibutsu Butsuri 45, supplement (2005): S85. http://dx.doi.org/10.2142/biophys.45.s85_4.

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22

CHIKASAKO, Yuzuru, Kentaro DOI, and Satoyuki KAWANO. "F1-2 Molecular fluid dynamics of Li^+ ions forming solvation structures." Proceedings of The Computational Mechanics Conference 2010.23 (2010): _F—3_—_F—4_. http://dx.doi.org/10.1299/jsmecmd.2010.23._f-3_.

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23

Liubysh, O. O., A. V. Vlasiuk, and S. M. Perepelytsya. "Structurization Of Counterions Around DNA Double Helix: A Molecular Dynamics Study." Ukrainian Journal of Physics 60, no. 5 (May 2015): 433–42. http://dx.doi.org/10.15407/ujpe60.05.0433.

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24

Khairudin, Nurul Bahiyah Ahmad, and Fatahiya Mohamed Tap. "Molecular Dynamics Folding Simulation of Amyloid A4 Peptide in Implicit Solvent." International Journal of Bioscience, Biochemistry and Bioinformatics 4, no. 5 (2014): 351–54. http://dx.doi.org/10.7763/ijbbb.2014.v4.369.

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25

Lehn, Jean-Marie. "Dynamers: dynamic molecular and supramolecular polymers." Progress in Polymer Science 30, no. 8-9 (August 2005): 814–31. http://dx.doi.org/10.1016/j.progpolymsci.2005.06.002.

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26

Lehn, Jean-Marie. "Dynamers: Dynamic Molecular and Supramolecular Polymers." Australian Journal of Chemistry 63, no. 4 (2010): 611. http://dx.doi.org/10.1071/ch10035.

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Dynamers are defined as constitutional dynamic polymers, i.e. polymeric entities whose monomeric components are linked through reversible connections and have therefore the capacity to modify their constitution by exchange and reshuffling of their components. They may be either of supramolecular or molecular nature depending on whether the connections are non-covalent interactions or reversible covalent bonds. They are formed respectively either by polyassociation with interactional recognition or by polycondensation with functional recognition between the connecting subunits. Both types are illustrated by specific examples implementing hydrogen bonding on one hand and formation of imine-type bonds on the other. The dynamic properties confer to dynamers the ability to undergo adaptation and driven evolution under the effect of external chemical or physical triggers. Dynamers thus are constitutional dynamic materials resulting from the application of the principles of constitutional dynamic chemistry to polymer science.
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27

Miyagawa, Hiroh, and Kunihiro Kitamura. "1P565 Molecular dynamics simulations of association and docking between an inhibitor and an enzyme.(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_1.

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28

Higuchi, Mariko, and Miroslav Pinak. "1P566 Molecular dynamics simulation of clustered DNA damage site with DNA repair enzyme MutM(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_2.

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29

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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30

Nishikawa, Keigo, Ayumu Sugiyama, Tetsunori Yamamoto, Hidemi Nagao, Nobutaka Numoto, Kunio Miki, and Yoshihiro Fukumori. "1P569 Molecular dynamics study of solvent water behavior in giant hemoglobin of Oligobrachia mashikoi(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S289. http://dx.doi.org/10.2142/biophys.46.s289_1.

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31

Hirano, Yoshinori, Noriaki Okimoto, Atsushi Suenaga, Makoto Taiji, Naoko Imamoto, Masato Yasui, and Toshikazu Ebisuzaki. "1P590 Investigation of The Structure-Function Relationship of Importin-β by Molecular Dynamics Simulations(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S294. http://dx.doi.org/10.2142/biophys.46.s294_2.

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32

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 (March 13, 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 resulted in liposome size of 71.22 ± 2.54 nm, which was located within the range of the liposome size resulted from the empirical observations (95.99 ± 43.02 nm). Moreover, similar liposome forms were observed on both results of molecular dynamics simulations and empirical approaches.
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33

Chikenji, George. "1P592 All atom molecular dynamics simulations of short peptides for De Novo protein structure prediction(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S294. http://dx.doi.org/10.2142/biophys.46.s294_4.

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34

Koga, Tsuyoshi, and Chen Li. "Shear-Induced Network Formation in Colloid/Polymer Mixtures: A Molecular Dynamics Study." Nihon Reoroji Gakkaishi 42, no. 2 (2014): 123–27. http://dx.doi.org/10.1678/rheology.42.123.

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35

Raksha, Elena, Aleksandr Eresko, Yuliya Berestneva, Aleksey Muratov, and Gennadiy Zaikov. "Molecular Modeling of the 2-(Pyridin-2-Yl)-1H-Benzimidazole Intramolecular Dynamics." Vestnik Volgogradskogo gosudarstvennogo universiteta. Serija 10. Innovatcionnaia deiatel’nost’, no. 4 (December 2015): 33–39. http://dx.doi.org/10.15688/jvolsu10.2015.4.5.

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36

Voronkov, V. V., and E. N. Voronkova. "Investigation of Static Properties of Strongly Coupled Plasma with Molecular Dynamics Method." International Journal of Mathematics and Physics 6, no. 1 (2015): 48–52. http://dx.doi.org/10.26577/2218-7987-2015-6-1-48-52.

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37

Otajonov, Sh, B. Eshchanov, and A. Isamatov. "Study of Molecular Dynamics of Condensed States of a Substance by Spectroscopy." Ukrainian Journal of Physics 59, no. 3 (March 2014): 254–56. http://dx.doi.org/10.15407/ujpe59.03.0254.

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38

Wen Jincheng, 闻锦程, 张琳 Zhang Lin, 吴寒 Wu Han, 李萌 Li Meng, and 马修泉 Ma Xiuquan. "飞秒激光作用铝-玻璃界面的分子动力学模拟研究." Laser & Optoelectronics Progress 60, no. 1 (2023): 0114011. http://dx.doi.org/10.3788/lop222640.

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39

Lee, In Ho, Sukky Jun, Hanchul Kim, Seung Yeon Kim, and Jooyoung Lee. "Exploring dynamic pathways by action-derived molecular dynamics." International Journal of Nanotechnology 3, no. 2/3 (2006): 334. http://dx.doi.org/10.1504/ijnt.2006.009587.

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40

Rambaut, C., H. Jobic, H. Jaffrezic, J. Kohanoff, and S. Fayeulle. "Molecular dynamics simulation of the lattice: dynamic properties." Journal of Physics: Condensed Matter 10, no. 19 (May 18, 1998): 4221–29. http://dx.doi.org/10.1088/0953-8984/10/19/010.

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41

Qiu, Chao, and Hui Сhen Zhang. "Molecular Dynamics Simulation on Dynamic Properties of Bubble." Advanced Materials Research 705 (June 2013): 150–56. http://dx.doi.org/10.4028/www.scientific.net/amr.705.150.

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Development of a single bubble in free space under the canonical ensemble was studied by using molecular dynamics simulation method. The detailed dynamic characteristics in the evolution process were analyzed by calculating the displacement of molecules, density, diffusion coefficient, pressure and potential energy of bubble. The results indicate that the evolution is divided into three stages according to the change of bubble potential energy, which are expansion, compression and balance state respectively. The temperature and density have significant influences on the final state of bubbles. The bubble in the liquid with larger density has a higher transition rate. The collapsing speed of bubble becomes faster with temperature increasing.
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42

Wang, Yeng-Tseng, and Heng-Chuan Kan. "1P562 Force-Induced Human Lysozyme with Camelid VHH HL6 Antibody Fragment : Dissociation 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_2.

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43

Kikugawa, Gota, Yasushige Yonezawa, Haruki Nakamura, and Ryutaro Himeno. "1P579 Large-scale molecular dynamics simulations with the pairwise electrostatic interaction method for protein-solvent systems(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S291. http://dx.doi.org/10.2142/biophys.46.s291_3.

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44

Kinosita, Kazuhiko. "S2h1-1 Probing motor dynamics with huge and small tags(S2-h1: "Single Molecule Analysis of Molecular Motor",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S126. http://dx.doi.org/10.2142/biophys.46.s126_4.

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45

Shimbo, Yudai, Yasutaka Seki, Hiroki Matsumoto, and Kunitsugu Soda. "2P402 Structural and Thermodynamic Analysis of Hydrophobic Hydration by Molecular Dynamics Simulation(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S396. http://dx.doi.org/10.2142/biophys.46.s396_2.

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46

Kawasaki, Naoko, Takao Furuki, and Minoru Sakurai. "2P406 Molecular Dynamics Simulation on the Glassy States of Trehalose and Neotrehalose(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S397. http://dx.doi.org/10.2142/biophys.46.s397_2.

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47

Fujii, Satoshi, Hidetoshi Kono, Shigenori Takenaka, Nobuhiro Go, and Akinori Sarai. "2P422 Sequence Context Dependent Flexibility of DNA Studied by Molecular Dynamics Simulation(46. Water and bio-molecule,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S401. http://dx.doi.org/10.2142/biophys.46.s401_2.

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48

SAITOH, Ken-ichi, Hiroshi KITAGAWA, Akihiro NAKATANI, and Shigenobu OGATA. "Molecular Dynamics Simulations. Molecular Dynamic Study on Strength of Coincidence Grain Boundaries." Journal of the Society of Materials Science, Japan 46, no. 3 (1997): 238–43. http://dx.doi.org/10.2472/jsms.46.238.

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49

Ohmura, Satoshi, Hironori Shimakura, Yukinobu Kawakita, Fuyuki Shimojo, and Makoto Yao. "Dynamic Structure of a Molecular Liquid S0.5Cl0.5: Ab initio Molecular-Dynamics Simulations." Journal of the Physical Society of Japan 82, no. 7 (July 15, 2013): 074602. http://dx.doi.org/10.7566/jpsj.82.074602.

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50

ISKANDAROV, Albert, Atsushi KUBO, and Yoshitaka UMENO. "OS1608 Molecular dynamics study of oxygen diffusion near surface in yttria-stabilized zirconia." Proceedings of the Materials and Mechanics Conference 2014 (2014): _OS1608–1_—_OS1608–2_. http://dx.doi.org/10.1299/jsmemm.2014._os1608-1_.

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