Models in Bioscience and Materials Research: Molecular Dynamics and Related Techniques

Kholmirzo T. Kholmurodov (Editor)
Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia

Series: Microbiology Research Advances, Materials Science and Technologies
BISAC: MED052000

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Volume 10

Issue 1

Volume 2

Volume 3

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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This book provides an overview on different aspects of materials science and biological research. It outlines the current state and prospects of computer molecular simulation studies covering a broad spectrum of problems in modern physics, biochemistry, and nanotechnology. Topics discussed include molecular dynamics simulations of proteins mutation transition effects in protein structures and Monte-Carlo simulations of radiation-induced mutations. Novel MD computing methods and modern communication architectures are also mentioned. (Imprint: Nova Biomedical )

Preface

Introduction

Chapter 1. Ab Initio Molecular-Dynamics Study of Nonequilibrium Phenomena in Disordered Materials
(Satoshi Ohmura, Kiyonobu Nagaya, Fuyuki Shimojo, Makoto Yao, Department of Physics, Faculty of Science, Kyoto University
Kyoto, Japan, and others)

Chapter 2. MD Studies of the Structural and Diffusion Properties of Formamide/Water and Ethanol/Water Mixtures on Titanium and Platinum Surfaces
(Ermuhammad Dushanov, Kholmirzo Kholmurodov, Kenji Yasuoka and Evgenii Krasavin, Laboratory of Radiation Biology, JINR, Moscow Region, Russia, and others)

Chapter 3. Salt Effects on Folding of Villin Headpiece Subdomain HP36 Studied by Generalized-Ensemble Simulations
(Takao Yoda, Yuji Sugita, Yuko Okamoto, Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology
Tamura, Nagahama, Shiga, Japan, and others)

Chapter 4. Anisotropic Electrostatics Approaches in Description of Halogen Bonding within Intermolecular Potentials
(Oleg I. Titov, Dmitry A. Shulga, Vladimir A. Palyulin, Nikolai S. Zefirov, Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia)

Chapter 5. The Study of Phase Diagram of the Surfactant/Water System by Molecular Dynamics Simulation
(Aram A. Shahinyan, L.H. Arsenyan and A.H. Poghosyan, International Scientific-Educational Center, National Academy of Sciences, Yerevan
Republic of Armenia, and others)

Chapter 6. All-Atom Multibaric-Multithermal Molecular Dynamics Simulations of Proteins
(Hisashi Okumura, Research Center for Computational Science,
Institute for Molecular Science, Aichi, Japan and others)

Chapter 7. Probing Free Energy of Transmembrane Helix-Helix Association via a Novel Single-Residue Based Approach
(Andrey S. Kuznetsov, Pavel E. Volynsky, Roman G. Efremov, M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry,
Russian Academy of Sciences, Moscow, Russia, and others)

Chapter 8. Hydrogen-Bond Networks as Structure-Determining Conjugated Systems
(Yulia V. Novakovskaya, Chemistry Department, Moscow State University, Moscow, Russia)

Chapter 9. Development and Application of Fragment-Based Electronic Structure Calculation Method for Biomolecules
(Tomoki Kobori, Takao Otsuka, Shinji Tsuneyuki, Makoto Taiji, Quantitative Biology Center (QBiC), RIKEN (The Institute of Physical and Chemical Research), Hyogo, Japan, and others)

Chapter 10. Molecular Dynamics Simulations for Small-Angle Neutron Scattering: Scattering Length Density Spatial Distributions for Mono-Carboxylic Acids in d-Decalin
(Roman A. Eremin, Kholmirzo T. Kholmurodov, Viktor I. Petrenko, Laszio Rosta and Mikhail V. Avdeev, Joint Institute for Nuclear Research, Moscow Region, Russia, and others)

Chapter 11. Computational Design of Small Peptide Inhibitors of Protein-Protein Interactions in CRK-SH2 Mediated Intracellular Signaling
(Junya Yamagishi, Noriaki Okimoto, Takuma Kasai, Atsushi Suenaga, Mariko Okada, Akira Imamoto, Makoto Taiji, Department of Computational Biology, Graduate School of Frontier Sciences
The University of Tokyo, Japan, and others)

Chapter 12. Molecular Dynamics Simulations of the DNA Interaction with Metallic Nanoparticles and TiO2 Surfaces
(Kholmirzo T. Kholmurodov, Ermuhammad B. Dushanov, Evgenii A. Krasavin, Hagar K. Hassan, Hadeer A. ElHabashy, Ahmed Galal, Nasser H. Sweilam and Kenji Yasuoka, Laboratory of Radiation Biology, Moscow Region, Russia, and others)

Index

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