An Introduction to Molecular Dynamics

Mark S. Kemp (Editor)

Series: Physics Research and Technology
BISAC: SCI074000

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Volume 10

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Special issue: Resilience in breaking the cycle of children’s environmental health disparities
Edited by I Leslie Rubin, Robert J Geller, Abby Mutic, Benjamin A Gitterman, Nathan Mutic, Wayne Garfinkel, Claire D Coles, Kurt Martinuzzi, and Joav Merrick

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In the opening chapter of An Introduction to Molecular Dynamics, the method of statistical geometry, based on the construction of a Voronoi polyhedral, is applied to the pattern recognition of atomic environments and to the investigation of the local order in molecular dynamics-simulated materials.

Next, the authors discuss the methodology of bimolecular simulations and their advancements, as well as their applications in the field of nanoparticle-biomolecular interactions. The theory of molecular dynamics simulation and some of the recent molecular dynamics methods such as steered molecular dynamics, umbrella sampling, and coarse-grained simulation are also discussed.

The use of auxiliary programs in the cases of modified cyclodextrins is discussed. Additionally, results from molecular dynamics studies on cases of inclusion compounds of molecules of different sizes and shapes encapsulated in the same host cyclodextrin have been examined and compared.

In closing, the authors discuss the methodology of molecular dynamics simulation with a non-constant force field. In the context of molecular simulations, the term “force field” refers to a set of equations and parameters for the calculation of forces acting on the particles of the system and its potential energy.
(Imprint: Nova)

Preface

Chapter 1. Application of the Method of Statistical Geometry in Molecular Dynamic Calculations
(Alexander Galashev, Institute of High Temperature Electrochemistry, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia)

Chapter 2. Molecular Dynamics Simulations: A Tool to Investigate the Interactions between Biomolecules and Nanoparticles
(Sanchaita Rajkhowa and Anupam Nath Jha, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India)

Chapter 3. Molecular Dynamics Studies of Cyclodextrin Inclusion Compounds
(Elias Christoforides and Kostas Bethanis, Department of Biotechnology, Agricultural University of Athens, Athens, Greece)

Chapter 4. Non-Constant Force Field Molecular Dynamics
(Anton Raskovalov, Laboratory of Electrochemical Materials Science, Institute of High Temperature Electrochemistry of UB of RAS, Yekaterinburg, Russia)

Index

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