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Books on the topic 'Molecular dynamics simulations (MD)'

Author: Grafiati

Published: 4 June 2025

Last updated: 15 July 2025

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1

Yonezawa, Fumiko, ed. Molecular Dynamics Simulations. Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-84713-4.

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2

Shuichi, Nosé, ed. Molecular dynamics simulations. Progress of theoretical physics, 1991.

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3

Heinecke, Alexander, Wolfgang Eckhardt, Martin Horsch, and Hans-Joachim Bungartz. Supercomputing for Molecular Dynamics Simulations. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17148-7.

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4

Massobrio, Carlo, Jincheng Du, Marco Bernasconi, and Philip S. Salmon, eds. Molecular Dynamics Simulations of Disordered Materials. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-15675-0.

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5

Heyes, David M. The liquid state: Applications of molecular simulations. Wiley, 1998.

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6

Kamberaj, Hiqmet. Molecular Dynamics Simulations in Statistical Physics: Theory and Applications. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-35702-3.

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7

1944-, Binder K., ed. Monte Carlo and molecular dynamics simulations in polymer sciences. Oxford University Press, 1995.

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8

1944-, Binder K., ed. Monte Carlo and molecular dynamics simulations in polymer science. Oxford University Press, 1995.

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9

Greenspan, Donald. Molecular mechanics simulations of the three dimensional cavity problem. Dept. of Mathematics, University of Texas at Arlington, 1999.

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10

service), SpringerLink (Online, ed. First Principles Modelling of Shape Memory Alloys: Molecular Dynamics Simulations. Springer Berlin Heidelberg, 2012.

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11

Postma, Johannes Petrus Maria. MD of H₂O: A molecular dynamics study of water. [s.n.], 1985.

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12

Sansom, M. S. P., and Philip Charles Biggin. Molecular simulations and biomembranes: From biophysics to function. Royal Society of Chemistry, 2010.

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13

Al-Hilli, Safaa. ZnO nano-structures for biosensing applications: Molecular dynamic simulations. Nova Science Publishers, 2010.

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14

Lim, Melvin Choon Giap. Carbon Nanotubes as Nanodelivery Systems: An Insight Through Molecular Dynamics Simulations. Springer Singapore, 2013.

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15

1959-, Nielaba P., Mareschal Michel, and Ciccotti Giovanni, eds. Bridging time scales: Molecular simulations for the next decade. Springer, 2002.

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16

Hoare, Neil Edward. The use of molecular dynamics simulations in QSAR studies of pyrethroid insecticides. University of Portsmouth, School of Biological Sciences, 1995.

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17

Uwe, Burghaus, ed. A practical guide to Monte Carlo simulations and classical molecular dynamics simulations by captain cook: An example booklet. Nova Science Publishers, 2005.

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18

Steven, Brawer. Relaxation in viscous liquids and glasses: Review of phenomenology, molecular dynamics simulations, and theoretical treatment. American Ceramic Society, 1985.

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19

F, Yonezawa, ed. Molecular dynamics simulations: Proceedings of the 13th Taniguchi Symposium, Kashikojima, Japan, November 6-9, 1990. Springer-Verlag, 1992.

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20

Timothy, Cygan Randall, U.S. Nuclear Regulatory Commission. Division of Systems Analysis and Regulatory Effectiveness., and Sandia National Laboratories, eds. Large-scale molecular dynamics simulations of metal sorption onto the basal surfaces of clay minerals. Division of Systems Analysis and Regulatory Effectiveness, Office of Nuclear Regulatory Research, U.S. Nuclear Regulatory Commission, 2002.

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21

Zeiske, Tim. Understanding complex biomolecular systems through the synergy of molecular dynamics simulations, NMR spectroscopy and X-Ray crystallography. [publisher not identified], 2016.

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22

Joint International Conference of IBM and Division de Chimie Physique (SFC) (1991 Obernai, France). Advances in biomolecular simulations: Joint International Conference of IBM and Division de Chimie Physique (SFC), Obernai, France, 1991. Edited by Lavery Richard, Rivail J. L, Smith Jeremy, IBM France, Société française de chimie. Division de chimie physique., and American Institute of Physics. American Institute of Physics, 1991.

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23

Mathew, Shyno. Molecular Dynamics Simulations of Microtubule-associated protein 1A/1B-light chain 3 (LC3) and its membrane associated form(LC3-II). [publisher not identified], 2017.

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24

Martin, James Arthur. Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography. [publisher not identified], 2020.

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25

Kostyukov, Viktor. Molecular mechanics of biopolymers. INFRA-M Academic Publishing LLC., 2020. http://dx.doi.org/10.12737/1010677.

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The monograph is devoted to molecular mechanics simulations of biologically important polymers like proteins and nucleic acids. It is shown that the algorithms based on the classical laws of motion of Newton, with high-quality parameterization and sufficient computing resources is able to correctly reproduce and predict the structure and dynamics of macromolecules in aqueous solution. Summarized the development path of biopolymers molecular mechanics, its theoretical basis, current status and prospects for further progress.  It may be useful to researchers specializing in molecular Biophysics and molecular biology, as well as students of senior courses of higher educational institutions, studying the biophysical and related areas of training.

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26

Coveney, Peter V., and Shunzhou Wan. Molecular Dynamics: Probability and Uncertainty. Oxford University PressOxford, 2025. https://doi.org/10.1093/9780198893479.001.0001.

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Abstract This book explores the intersection of molecular dynamics (MD) simulation with advanced probabilistic methodologies to address the inherent uncertainties in the approach. Beginning with a clear and comprehensible introduction to classical mechanics, the book transitions into the probabilistic formulation of MD, highlighting the importance of ergodic theory, kinetic theory, and unstable periodic orbits, concepts which are largely unknown to current practitioners within the domain. It discussed ensemble-based simulations, free energy calculations and the study of polymer nanocomposites using multi-scale modelling, providing detailed guidance on performing reliable and reproducible computations. A thorough discussion on Verification, Validation, and Uncertainty Quantification (VVUQ) lays out a definitive approach to formulating the uncertainty of MD modelling and simulation. Its interaction with artificial intelligence is examined in the light of these issues. While machine learning (ML) methods offer some advantages and less often-noted drawbacks, the integration of ML with physics-based MD simulations may in future enhance our ability to predict new drugs and advanced materials. The final chapter, ‘The End of Certainty’, synthesizes these themes, advocating a systematic and careful approach to computational research and the embrace of uncertainty as an integral part of innovation. This book serves as a highly original, conceptual and comprehensible guide for researchers and practitioners, emphasizing the need for rapid, accurate, precise and actionable techniques in the rapidly-evolving field of molecular dynamics.

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27

The Critical Assessment of Protein Dynamics using Molecular Dynamics (MD) Simulations and Nuclear Magnetic Resonance (NMR) Spectroscopy Experimentation. [publisher not identified], 2020.

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28

Velinova, Maria. Molecular Dynamics Simulations. Arcler Education Inc, 2017.

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29

Beu, Titus A. Introduction to Molecular Dynamics Simulations. Taylor & Francis Group, 2023.

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30

Mioduszewski, Lukasz, and Marek Cieplak. Gluten Simulations: With Molecular Dynamics. Eliva Press, 2021.

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31

Köhler, Steffen. Advances in Molecular Dynamics Simulations Research. Nova Science Publishers, Incorporated, 2021.

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32

Köhler, Steffen. Advances in Molecular Dynamics Simulations Research. Nova Science Publishers, Incorporated, 2021.

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33

Bonomi, Massimiliano, and Carlo Camilloni. Biomolecular Simulations: Methods and Protocols. Springer New York, 2019.

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34

Bonomi, Massimiliano, and Carlo Camilloni. Biomolecular Simulations: Methods and Protocols. Springer New York, 2020.

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35

Mongelli, Guy Francis. Molecular Dynamics Simulations: Key Operations in GROMACS. de Gruyter GmbH, Walter, 2099.

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36

Mongelli, Guy Francis. Molecular Dynamics Simulations: Key Operations in GROMACS. de Gruyter GmbH, Walter, 2099.

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37

Mongelli, Guy Francis. Molecular Dynamics Simulations: Key Operations in GROMACS. de Gruyter GmbH, Walter, 2099.

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38

Succi, Sauro. Numerical Methods for the Kinetic Theory of Fluids. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780199592357.003.0010.

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This chapter provides a bird’s eye view of the main numerical particle methods used in the kinetic theory of fluids, the main purpose being of locating Lattice Boltzmann in the broader context of computational kinetic theory. The leading numerical methods for dense and rarified fluids are Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC), respectively. These methods date of the mid 50s and 60s, respectively, and, ever since, they have undergone a series of impressive developments and refinements which have turned them in major tools of investigation, discovery and design. However, they are both very demanding on computational grounds, which motivates a ceaseless demand for new and improved variants aimed at enhancing their computational efficiency without losing physical fidelity and vice versa, enhance their physical fidelity without compromising computational viability.

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39

Biomolecular Simulations Methods And Protocols. Humana Press, 2012.

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40

Holian, Brad Lee, and Michel Mareschal. Microscopic Simulations of Complex Hydrodynamic Phenomena. Springer London, Limited, 2013.

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41

Becker, Oren M., and Martin Karplus. Guide to Biomolecular Simulations. Springer, 2008.

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42

Becker, Oren M., and Martin Karplus. Guide to Biomolecular Simulations. Springer London, Limited, 2007.

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43

Becker, Oren M., and Martin Karplus. Guide to Biomolecular Simulations. Springer, 2016.

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44

Computer Simulations in Molecular Biology: From Quantum Mechanics to Molecular Dynamics. Springer, 2023.

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45

Meunier, Marc. Industrial Applications of Molecular Simulations. Taylor & Francis Group, 2019.

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46

Meunier, Marc. Industrial Applications of Molecular Simulations. Taylor & Francis Group, 2016.

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47

Hu, Yi. Internal motions of peptides: Experiments, theory, and simulations. 1992.

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48

Ciccotti, Giovanni, Michel Mareschal, and Peter Nielaba. Bridging the Time Scales: Molecular Simulations for the Next Decade. Springer, 2010.

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49

Ciccotti, Giovanni, Michel Mareschal, and Peter Nielaba. Bridging the Time Scales: Molecular Simulations for the Next Decade. Springer London, Limited, 2007.

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50

Chemistry, Royal Society of. Molecular Simulations and Visualization: Faraday Discussion 169. Royal Society of Chemistry, The, 2014.

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