Статті в журналах: "Molecular Structural Dynamics"

1

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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2

Krukenberg, Kristin A., Timothy O. Street, Laura A. Lavery, and David A. Agard. "Conformational dynamics of the molecular chaperone Hsp90." Quarterly Reviews of Biophysics 44, no. 2 (March 18, 2011): 229–55. http://dx.doi.org/10.1017/s0033583510000314.

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AbstractThe ubiquitous molecular chaperone Hsp90 makes up 1–2% of cytosolic proteins and is required for viability in eukaryotes. Hsp90 affects the folding and activation of a wide variety of substrate proteins including many involved in signaling and regulatory processes. Some of these substrates are implicated in cancer and other diseases, making Hsp90 an attractive drug target. Structural analyses have shown that Hsp90 is a highly dynamic and flexible molecule that can adopt a wide variety of structurally distinct states. One driving force for these rearrangements is the intrinsic ATPase activity of Hsp90, as seen with other chaperones. However, unlike other chaperones, studies have shown that the ATPase cycle of Hsp90 is not conformationally deterministic. That is, rather than dictating the conformational state, ATP binding and hydrolysis only shift the equilibria between a pre-existing set of conformational states. For bacterial, yeast and human Hsp90, there is a conserved three-state (apo–ATP–ADP) conformational cycle; however; the equilibria between states are species specific. In eukaryotes, cytosolic co-chaperones regulate the in vivo dynamic behavior of Hsp90 by shifting conformational equilibria and affecting the kinetics of structural changes and ATP hydrolysis. In this review, we discuss the structural and biochemical studies leading to our current understanding of the conformational dynamics of Hsp90, as well as the roles that nucleotide, co-chaperones, post-translational modification and substrates play. This view of Hsp90's conformational dynamics was enabled by the use of multiple complementary structural methods including, crystallography, small-angle X-ray scattering (SAXS), electron microscopy, Förster resonance energy transfer (FRET) and NMR. Finally, we discuss the effects of Hsp90 inhibitors on conformation and the potential for developing small molecules that inhibit Hsp90 by disrupting the conformational dynamics.

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3

Apostolov, Rossen, Yasushige Yonezawa, Yu Takano, and Haruki Nakamura. "3P116 Structural Fundamentals for Monoamine Oxidase A Inhibition Control Revealed by Molecular Dynamics Simulations." Seibutsu Butsuri 45, supplement (2005): S232. http://dx.doi.org/10.2142/biophys.45.s232_4.

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4

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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5

Yan, Wang, and Dong Shun-Le. "Molecular dynamics study of ice structural evolution." Chinese Physics B 17, no. 6 (June 2008): 2175–79. http://dx.doi.org/10.1088/1674-1056/17/6/039.

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6

Chergui, Y., N. Nehaoua, B. Telghemti, S. Guemid, N. E. Deraddji, H. Belkhir, and D. E. Mekki. "The structural properties of PbF2by molecular dynamics." European Physical Journal Applied Physics 51, no. 2 (July 22, 2010): 20502. http://dx.doi.org/10.1051/epjap/2010096.

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7

Cailleau, Hervé, Maciej Lorenc, Laurent Guérin, Marina Servol, Eric Collet, and Marylise Buron-Le Cointe. "Structural dynamics of photoinduced molecular switching in the solid state." Acta Crystallographica Section A Foundations of Crystallography 66, no. 2 (February 18, 2010): 189–97. http://dx.doi.org/10.1107/s0108767309051046.

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Fast and ultra-fast time-resolved diffraction is a fantastic tool for directly observing the structural dynamics of a material rearrangement during the transformation induced by an ultra-short laser pulse. The paper illustrates this ability using the dynamics of photoinduced molecular switching in the solid state probed by 100 ps X-ray diffraction. This structural information is crucial for establishing the physical foundations of how to direct macroscopic photoswitching in materials. A key feature is that dynamics follow a complex pathway from molecular to material scales through a sequence of processes. Not only is the pathway indirect, the nature of the dynamical processes along the pathway depends on the timescale. This dictates which types of degrees of freedom are involved in the subsequent dynamics or kinetics and which are frozen or statistically averaged. We present a recent investigation of the structural dynamics in multifunctional spin-crossover materials, which are prototypes of molecular bistability in the solid state. The time-resolved X-ray diffraction results show that the dynamics span from subpicosecond molecular photoswitching followed by volume expansion (on a nanosecond timescale) and additional thermoswitching (on a microsecond timescale).

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8

Tsegaye, Solomon, Gobena Dedefo, and Mohammed Mehdi. "Biophysical applications in structural and molecular biology." Biological Chemistry 402, no. 10 (July 7, 2021): 1155–77. http://dx.doi.org/10.1515/hsz-2021-0232.

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Abstract The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn’t be solved by X-ray crystallography or NMR. Now a day’s low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.

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9

Balasubramanian, Sangeetha, Muthukumaran Rajagopalan, and Amutha Ramaswamy. "Structural dynamics of full-length retroviral integrase: a molecular dynamics analysis." Journal of Biomolecular Structure and Dynamics 29, no. 6 (April 2012): 1163–74. http://dx.doi.org/10.1080/07391102.2011.672630.

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10

Takada, Akira, Kathryn J. Glaser, Robert G. Bell, and C. Richard A. Catlow. "Molecular dynamics study of tridymite." IUCrJ 5, no. 3 (April 17, 2018): 325–34. http://dx.doi.org/10.1107/s2052252518004803.

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Structural changes in tridymite have been investigated by molecular dynamics simulation. Two thermal processes were carried out, one cooling from the high-temperature hexagonal structure of tridymite (HP-tridymite) and the other heating from the low-temperature monoclinic structure of tridymite (MX1-tridymite). The former process showed that HP, LHP (low-temperature hexagonal structure), OC (orthorhombic structure withC2221symmetry) and OP (orthorhombic structure withP212121symmetry)-like structures appeared in sequence. In contrast, the latter process showed that MX1, OP, OC, LHP and HP-like structures appeared in sequence. Detailed analysis of the calculated structures showed that the configuration underwent stepwise changes associated with several characteristic modes. First, the structure of HP-tridymite determined from diffraction experiments was identified as a time-averaged structure in a similar manner to β-cristobalite, thus indicating the important role of floppy modes of oxygen atoms at high temperature – one of the common features observed in silica crystals and glass. Secondly, the main structural changes were ascribed to a combination of distortion of the six-membered rings in the layers and misalignment between layers. We suggest that the slowing down of floppy oxygen movement invokes the multistage emergence of structures with lower symmetry on cooling. This study therefore not only reproduces the sequence of the main polymorphic transitions in tridymite, except for the appearance of the monoclinic phase, but also explains the microscopic dynamic structural changes in detail.

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11

Furuta, Tadaomi. "Structural dynamics of ABC transporters: molecular simulation studies." Biochemical Society Transactions 49, no. 1 (February 26, 2021): 405–14. http://dx.doi.org/10.1042/bst20200710.

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The biological activities of living organisms involve various inputs and outputs. The ATP-driven substances (biomolecules) responsible for these kinds of activities through membrane (i.e. uptake and efflux of substrates) include ATP-binding cassette (ABC) transporters, some of which play important roles in multidrug resistance. The basic architecture of ABC transporters comprises transmembrane domains (TMDs) and nucleotide-binding domains (NBDs). The functional dynamics (substrate transport) of ABC transporters are realized by concerted motions, such as NBD dimerization, mechanical transmission via coupling helices (CHs), and the translocation of substrates through TMDs, which are induced by the binding and/or hydrolysis of ATP molecules and substrates. In this mini-review, we briefly discuss recent progresses in the structural dynamics as revealed by molecular simulation studies at all-atom (AA), coarse-grained (CG), and quantum mechanics/molecular mechanics (QM/MM) levels.

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12

Bodo, Enrico. "Structural Features of Triethylammonium Acetate through Molecular Dynamics." Molecules 25, no. 6 (March 21, 2020): 1432. http://dx.doi.org/10.3390/molecules25061432.

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I have explored the structural features and the dynamics of triethylammonium acetate by means of semi-empirical (density functional tight binding, DFTB) molecular dynamics. I find that the results from the present simulations agree with recent experimental determinations with only few minor differences in the structural interpretation. A mixture of triethylamine and acetic acid does not form an ionic liquid, but gives rise to a very complex system where ionization is only a partial process affecting only few molecules (1 over 4 experimentally). I have also found that the few ionic couples are stable and remain mainly embedded inside the AcOH neutral moiety.

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13

Makino, Takehiko, Koichi Okouchi, and Shoichi Matsuda. "Molecular Dynamics Analysis of Nucleation in Structural Transformation." Materials Transactions, JIM 40, no. 5 (1999): 435–38. http://dx.doi.org/10.2320/matertrans1989.40.435.

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14

Tahara, Shuta, Hiroshi Toyama, Hironori Shimakura, and Takanori Fukami. "Structural Analysis of Molten NaNO3by Molecular Dynamics Simulation." EPJ Web of Conferences 151 (2017): 01004. http://dx.doi.org/10.1051/epjconf/201715101004.

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15

Wentzcovitch, Renata M. "Invariant molecular-dynamics approach to structural phase transitions." Physical Review B 44, no. 5 (August 1, 1991): 2358–61. http://dx.doi.org/10.1103/physrevb.44.2358.

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16

Gutiérrez, Gonzalo, A. B. Belonoshko, Rajeev Ahuja, and Börje Johansson. "Structural properties of liquidAl2O3:A molecular dynamics study." Physical Review E 61, no. 3 (March 1, 2000): 2723–29. http://dx.doi.org/10.1103/physreve.61.2723.

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17

CHRISTENSEN, A. "ACCELERATING CONVERGENCE OF MOLECULAR DYNAMICS-BASED STRUCTURAL RELAXATION." International Journal of Modern Physics C 16, no. 02 (February 2005): 193–223. http://dx.doi.org/10.1142/s0129183105007042.

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We describe strategies to accelerate the terminal stage of molecular dynamics (MD)-based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from an MD trajectory, as another route for final phase acceleration. Our suggestions may be implemented within most MD quench implementations with a few, straightforward lines of code, thus maintaining the appealing simplicity of the MD quench algorithms. In this paper, we also bridge the conceptual gap between the MD quench algorithms inspired from physics and the mathematically rooted line search algorithms.

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18

Centurion, Martin. "Molecular Structural Dynamics Captured with Ultrafast Electron Diffraction." Microscopy and Microanalysis 26, S2 (July 30, 2020): 918. http://dx.doi.org/10.1017/s1431927620016311.

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19

ERKOÇ, ŞAKIR, and OSMAN BARIŞ MALCIOĞLU. "STRUCTURAL PROPERTIES OF CARBON NANORODS: MOLECULAR-DYNAMICS SIMULATIONS." International Journal of Modern Physics C 13, no. 03 (March 2002): 367–73. http://dx.doi.org/10.1142/s0129183102003188.

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The formation of carbon nanorods from various types of carbon nanotubes has been investigated by performing molecular-dynamics computer simulations. Calculations have been realized by using an empirical many-body potential energy function for carbon. It has been found that carbon nanorod formed from carbon nanotubes with different chirality is not stable even at low temperature.

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20

MALCIOĞLU, OSMAN BARIŞ, and ŞAKIR ERKOÇ. "STRUCTURAL PROPERTIES OF DIAMOND NANORODS: MOLECULAR-DYNAMICS SIMULATIONS." International Journal of Modern Physics C 14, no. 04 (May 2003): 441–47. http://dx.doi.org/10.1142/s0129183103004644.

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The structural properties of carbon nanorods obtained from diamond crystal have been investigated by performing molecular-dynamics computer simulations. Calculations have been realized by using an empirical many-body potential energy function for carbon. Diamond nanorods have been generated from three low-index planes of diamond crystal. It has been found that the average coordination number, cross-section geometry, and surface orientation from which the nanorod is generated play a role in the stability of diamond nanorods under heat treatment. The most stable diamond nanorod has been obtained from the (111) surface.

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21

Kitazawa, Hideaki, Kenjiro Hashi, Tuerxun Wuernisha, Kayoko Hotta, Cherry L. Ringor, Takao Furubayashi, Atsushi Goto, Tadashi Shimizu, and Kun'ichi Miyazawa. "Molecular dynamics and structural phase transition in C60nanowhiskers." Journal of Physics: Conference Series 159 (April 1, 2009): 012022. http://dx.doi.org/10.1088/1742-6596/159/1/012022.

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22

Matsunaga, Shigeki. "Structural features in molten RbAg4I5by molecular dynamics simulation." Molecular Simulation 39, no. 2 (February 2013): 119–22. http://dx.doi.org/10.1080/08927022.2012.706711.

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23

Kihara, K., and M. Matsui. "Molecular dynamics study of structural changes in berlinite." Physics and Chemistry of Minerals 26, no. 7 (August 16, 1999): 601–14. http://dx.doi.org/10.1007/s002690050224.

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24

Kihara, K. "Molecular dynamics interpretation of structural changes in quartz." Physics and Chemistry of Minerals 28, no. 6 (July 1, 2001): 365–76. http://dx.doi.org/10.1007/s002690100168.

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25

Smolin, Nikolai, and Seth Robia. "Molecular Dynamics Simulations of Calcium Pump Structural Disorder." Biophysical Journal 108, no. 2 (January 2015): 147a. http://dx.doi.org/10.1016/j.bpj.2014.11.811.

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26

Post, Carol Beth, Christopher M. Dobson, and Martin Karplus. "A molecular dynamics analysis of protein structural elements." Proteins: Structure, Function, and Genetics 5, no. 4 (1989): 337–54. http://dx.doi.org/10.1002/prot.340050409.

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27

SCHOMMERS, W., P. VON BLANCKENHAGEN, and U. ROMAHN. "THE EFFECT OF PREMELTING STUDIED BY MOLECULAR DYNAMICS." Modern Physics Letters B 02, no. 10 (November 1988): 1131–36. http://dx.doi.org/10.1142/s0217984988001028.

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The effect of premelting is investigated by four molecular-dynamics models. It is shown that premelting is initiated by a disorder (roughening) normal to the surface. Also the interlayer spacings strongly influence the structural and dynamical properties of the outermost surface layer.

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28

Liu, Hangxin, Shuqing Xiang, Haomiao Zhu, and Li Li. "The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation." Molecules 26, no. 17 (September 5, 2021): 5403. http://dx.doi.org/10.3390/molecules26175403.

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The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

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29

Kojima, Masaki, Alexander A. Timchenko, Junichi Higo, Kazuki Ito, Kazumoto Kimura, Shigeru Yanagi, and Hiroshi Kihara. "S3d2-3 Structural refinement with molecular dynamics using SAXS constraints(S3-d2: "Structural approach to protein dynamics using solution scattering",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S142. http://dx.doi.org/10.2142/biophys.46.s142_4.

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30

Nienhaus, Karin, Pengchi Deng, John S. Olson, Joshua J. Warren, and G. Ulrich Nienhaus. "Structural Dynamics of Myoglobin." Journal of Biological Chemistry 278, no. 43 (August 7, 2003): 42532–44. http://dx.doi.org/10.1074/jbc.m306888200.

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31

Lamb, Don C., Karin Nienhaus, Alessandro Arcovito, Federica Draghi, Adriana E. Miele, Maurizio Brunori, and G. Ulrich Nienhaus. "Structural Dynamics of Myoglobin." Journal of Biological Chemistry 277, no. 14 (January 15, 2002): 11636–44. http://dx.doi.org/10.1074/jbc.m109892200.

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32

Soares, Rosemberg O., Pedro H. M. Torres, Manuela L. da Silva, and Pedro G. Pascutti. "Unraveling HIV protease flaps dynamics by Constant pH Molecular Dynamics simulations." Journal of Structural Biology 195, no. 2 (August 2016): 216–26. http://dx.doi.org/10.1016/j.jsb.2016.06.006.

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33

Li, Ao, Jeffrey W. Schertzer, and Xin Yong. "Molecular dynamics modeling ofPseudomonas aeruginosaouter membranes." Physical Chemistry Chemical Physics 20, no. 36 (2018): 23635–48. http://dx.doi.org/10.1039/c8cp04278k.

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34

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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35

Černý, Jiří, Paulína Božíková, Aleš Balík, Sérgio M. Marques, and Ladislav Vyklický. "NMDA Receptor Opening and Closing—Transitions of a Molecular Machine Revealed by Molecular Dynamics." Biomolecules 9, no. 10 (September 28, 2019): 546. http://dx.doi.org/10.3390/biom9100546.

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We report the first complete description of the molecular mechanisms behind the transition of the N-methyl-d-aspartate (NMDA) receptor from the state where the transmembrane domain (TMD) and the ion channel are in the open configuration to the relaxed unliganded state where the channel is closed. Using an aggregate of nearly 1 µs of unbiased all-atom implicit membrane and solvent molecular dynamics (MD) simulations we identified distinct structural states of the NMDA receptor and revealed functionally important residues (GluN1/Glu522, GluN1/Arg695, and GluN2B/Asp786). The role of the “clamshell” motion of the ligand binding domain (LBD) lobes in the structural transition is supplemented by the observed structural similarity at the level of protein domains during the structural transition, combined with the overall large rearrangement necessary for the opening and closing of the receptor. The activated and open states of the receptor are structurally similar to the liganded crystal structure, while in the unliganded receptor the extracellular domains perform rearrangements leading to a clockwise rotation of up to 45 degrees around the longitudinal axis of the receptor, which closes the ion channel. The ligand-induced rotation of extracellular domains transferred by LBD–TMD linkers to the membrane-anchored ion channel is responsible for the opening and closing of the transmembrane ion channel, revealing the properties of NMDA receptor as a finely tuned molecular machine.

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36

Reddy, Th Dhileep N., and Bhabani S. Mallik. "Heterogeneity in the microstructure and dynamics of tetraalkylammonium hydroxide ionic liquids: insight from classical molecular dynamics simulations and Voronoi tessellation analysis." Physical Chemistry Chemical Physics 22, no. 6 (2020): 3466–80. http://dx.doi.org/10.1039/c9cp06796e.

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Microscopic structural and dynamic heterogeneities were investigated for three ionic liquids (ILs), tetraethylammonium hydroxide, tetrapropylammonium hydroxide, and tetrabutylammonium hydroxide employing classical molecular dynamics (MD) simulations.

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37

Bux, Khair, Thomas S. Hofer, and Syed Tarique Moin. "Exploring interfacial dynamics in homodimeric S-ribosylhomocysteine lyase (LuxS) from Vibrio cholerae through molecular dynamics simulations." RSC Advances 11, no. 3 (2021): 1700–1714. http://dx.doi.org/10.1039/d0ra08809a.

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To the best of our knowledge, this is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae to evaluate its structural and dynamical properties including the dynamics of the interface formed by the two monomeric chains of the enzyme.

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38

Wang, W. Y., J. J. Han, H. Z. Fang, J. Wang, Y. F. Liang, S. L. Shang, Y. Wang, et al. "Anomalous structural dynamics in liquid Al80Cu20: An ab initio molecular dynamics study." Acta Materialia 97 (September 2015): 75–85. http://dx.doi.org/10.1016/j.actamat.2015.07.001.

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39

Netz, Paulo A. "Molecular dynamics simulations of structural and dynamical aspects of DNA hydration water." Journal of Physics: Condensed Matter 34, no. 16 (February 21, 2022): 164002. http://dx.doi.org/10.1088/1361-648x/ac5198.

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Abstract Water is a remarkable liquid, both because of it is intriguing but also because of its importance. Water plays a key role on the structure and function of biological molecules, but on the other hand also the structure and dynamics of water are deeply influenced by its interactions with biological molecules, specially at low temperatures, where water’s anomalies are enhanced. Here we present extensive molecular dynamics simulations of water hydrating a oligonucleotide down to very low temperatures (supercooled water), comparing four water models and analyzing the water structure and dynamics in different domains: water in the minor groove, water in the major groove and bulk water. We found that the water in the grooves is slowed down by the interactions with the nucleic acid and a hints of a dynamic transition regarding translational and orientational dynamics were found, specially for the water models TIP4P/2005 and TIP4P-Ew, which also showed the closest agreement with available experimental data. The behavior of water in such extreme conditions is relevant for the study of cryopreservation of biological tissues.

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40

Bühler, Christine C., Michael P. Minitti, Sanghamitra Deb, Jie Bao, and Peter M. Weber. "Ultrafast Dynamics of 1,3-Cyclohexadiene in Highly Excited States." Journal of Atomic, Molecular, and Optical Physics 2011 (August 25, 2011): 1–6. http://dx.doi.org/10.1155/2011/637593.

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The ultrafast dynamics of 1,3-cyclohexadiene has been investigated via structurally sensitive Rydberg electron binding energies and shown to differ upon excitation to the 1B state and the 3p Rydberg state. Excitation of the molecule with 4.63 eV photons into the ultrashort-lived 1B state yields the well-known ring opening to 1,3,5-hexatriene, while a 5.99 eV photon lifts the molecule directly into the 3p-Rydberg state. Excitation to 3p does not induce ring opening. In both experiments, time-dependent shifts of the Rydberg electron binding energy reflect the structural dynamics of the molecular core. Structural distortions associated with 3p-excitation cause a dynamical shift in the - and -binding energies by 10 and 26 meV/ps, respectively, whereas after excitation into 1B, more severe structural transformations along the ring-opening coordinate produce shifts at a rate of 40 to 60 meV/ps. The experiment validates photoionization-photoelectron spectroscopy via Rydberg states as a powerful technique to observe structural dynamics of polyatomic molecules.

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41

van Gunsteren, Wilfred F. "Molecular dynamics studies of proteins." Current Opinion in Structural Biology 3, no. 2 (April 1993): 277–81. http://dx.doi.org/10.1016/s0959-440x(05)80164-2.

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42

Beveridge, David L., and Ganesan Ravishanker. "Molecular dynamics studies of DNA." Current Opinion in Structural Biology 4, no. 2 (January 1994): 246–55. http://dx.doi.org/10.1016/s0959-440x(94)90316-6.

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43

Itoh, S., M. Konagai, and K. Takahashi. "Molecular Dynamics Study of Molten Lithium Iodide." Zeitschrift für Naturforschung A 46, no. 1-2 (February 1, 1991): 155–59. http://dx.doi.org/10.1515/zna-1991-1-225.

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AbstractThe structural and dynamic properties of molten lithium iodide are investigated at two pressures (334 MPa at 784 K and 1054 MPa at 915 K), using molecular dynamics simulations with Born- Mayer-Huggins type pair potentials. On increasing the pressure, the local packing of the ions changes from tetrahedral to octahedral, the self-exchange velocity in the coordination shells decreases by a factor of 0.031, DLi by a factor of 0.033 and D1 by a factor of 0.021.

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44

Drabowicz, W. "Molecular Dynamics Study of the Structural and Dynamical Properties of Liquid Tetrahydrofuran." Zeitschrift für Naturforschung A 45, no. 11-12 (December 1, 1990): 1342–44. http://dx.doi.org/10.1515/zna-1990-11-1218.

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AbstractA molecular dynamics simulation has been performed to investigate the structural and dynamical properties of liquid tetrahydrofuran. In particular, we have calculated six radial distribution functions, translational and rotational autocorrelation functions and their associated frequency spectra.

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45

Yadav, Rajat, and Aman Sharma. "Structural dynamics of peptide nanotube and their conformational implication investigation by molecular modeling, molecular mechanics and molecular dynamics." Materials Today: Proceedings 45 (2021): 2934–37. http://dx.doi.org/10.1016/j.matpr.2020.11.942.

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46

Athanasiou, N. S. "Structural and Dynamical Properties of Nanocrystalline Krypton." Modern Physics Letters B 11, no. 15 (June 30, 1997): 681–90. http://dx.doi.org/10.1142/s0217984997000839.

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In this paper we discuss structural and dynamical properties of nano-clusters. The study is based on molecular dynamics calculations. In particular, the behavior of the following functions have been studied: single-particle distribution function, velocity autocorrelation function and the generalized phonon density of states (PDOS). The calculations have been done for krypton since for this material a realistic pair potential is available (Barker et al. potential). In order to have more informations about the nano-cluster properties, we also performed molecular dynamics calculations for the bulk. The comparison of the bulk results with the nano-cluster results shows that the shift of the cluster PDOS to low frequencies, caused from the different number of particles.

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47

Vant, John W., Daipayan Sarkar, Jonathan Nguyen, Alexander T. Baker, Josh V. Vermaas, and Abhishek Singharoy. "Exploring cryo-electron microscopy with molecular dynamics." Biochemical Society Transactions 50, no. 1 (February 25, 2022): 569–81. http://dx.doi.org/10.1042/bst20210485.

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Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

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48

Goldsmith, Zachary K., Marcos F. Calegari Andrade, and Annabella Selloni. "Effects of applied voltage on water at a gold electrode interface from ab initio molecular dynamics." Chemical Science 12, no. 16 (2021): 5865–73. http://dx.doi.org/10.1039/d1sc00354b.

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49

Grubmüller, Helmut, and Klaus Schulten. "Special issue: Advances in molecular dynamics simulations." Journal of Structural Biology 157, no. 3 (March 2007): 443. http://dx.doi.org/10.1016/j.jsb.2007.02.002.

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Guvench, Olgun. "Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes." Molecules 27, no. 21 (October 26, 2022): 7276. http://dx.doi.org/10.3390/molecules27217276.

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This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan’s flexibility and capacity for intra- and intermolecular non-covalent interactions.

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