Computational Materials and Biological Sciences

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

Series: Materials Science and Technologies
BISAC: SCI013070

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In this book, original papers have been collected to demonstrate the efficient use of computer molecular dynamics simulation methods for the studying of nanoscale phenomena in the materials and life sciences. This book discusses modern molecular simulation methods for the study of molecular shape and properties in protein and polymer engineering, drugs and materials design, structure-function relationships, and related issues.

This book contains the Proceedings of the MSSMBS-2014 and DSCMBS-2014 International Workshops which have been organized by the Joint Institute for Nuclear Research, the Institute of Bioorganic Chemistry of the Russian Academy of Sciences and S.U. Umarov Physical-Technical Institute of the Academy of Sciences of the Republic of Tajikistan. The research topics discussed in the MSSMBS’14 & DSCMBS’14 International Workshops are as follows: computer molecular simulation methods and approaches; molecular dynamics and Monte-Carlo techniques; modeling of biological molecules; physical and biochemical systems; material fabrication and design; drug design in medicine; computational and computing physics, chemistry, biology and medicine; GPU accelerated molecular dynamics and related techniques.

(Imprint: Nova)

Preface

Lubrication Mechanism in Joints—Role of Biopolymers
(Mitsuhiro Matsumoto, Mitsuho Ide, Department of Mechanical Engineering and Science, Graduate School of Engineering, Kyoto University, Kyoto, Japan, and others)

Using the Molecular Dynamics Simulation and Neutron Scattering Methods to Study Structural and Functional Properties of Biological Macromolecules
(Alexey Shvetsov, Dmitry Lebedev, Vladimir Isaev-Ivanov, FSBI ”Petersburg Nuclear Physics Institute”, NRC ”Kurchatov Institute”, Gatchina, Russia, and other)

Oleic Acid in Benzene and Decalin Solutions: Solvation Shell Effect on Small-Angle Neutron Scattering
(Roman A. Eremin, Kholmirzo T. Kholmurodov, Viktor I. Petrenko and
Mikhail V. Avdeev, Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia, and other)

Coherent Control of Ultrafast Reversible Photoreaction of Rhodopsin
(Olga Smitienko, Victor Nadtochenko, Tatiana Feldman, Maria Balatskaya, Ivan Shelaev, Fedor Gostev, Oleg Sarkisov, and Mikhail Ostrovsky, Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia, and others)

Mechanism of Interaction of Macromolecules with Surfactant Micelles in Aqueous Solution: A Molecular Dynamic Simulation
(Aram A. Shahinyan, Levon H. Arsenyan, Armen H. Poghosyan, International Scientific-Educational Center, National Academy of Sciences, Yerevan, Republic of Armenia)

Quadrupole Excitation in Spin Tunneling in Magnetic Nano-Particles
(Khikmat Kh. Muminov, Yousef Yousefi, Physical-Technical Institute named after S.U.Umarov, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan)

A Simulation Study on Conformations of an Anti-Microbial Peptid
(Takao Yoda, Toshiyuki Tsuji, Department of Computer Bioscience,
Nagahama Institute of Bio-Science and Technology, Tamura, Nagahama,
Shiga, Japan, and other)

Mathematical Modeling of the Efficiency Gadolinium Based Neutron Converters
(Djamshed A. Abdushukurov, Physical-Technical Institute named after S.U.Umarov, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan)

Atomistic Basis for Unique Physical Properties of Archaeal–Like Membranes (Discovered by Computer Simulations)
(Anton O. Chugunov, Pavel E. Volynsky, Nicolay A. Krylov, Ivan A. Boldyrev and Roman G. Efremov, M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia)

The Structural Behavior of the DNA and CPD in the Repairing Molecular System
(Ermuhammad B. Dushanov, Kholmirzo T. Kholmurodov, Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia, and others)

Local Environment Analysis of Magnetic Elements in Functional Materials by X-Ray Absorption Near-Edge Structure Measurements and First-Principles Calculations
(Tomoyuki Yamamoto, Kazuma Nishimura, and Tsuyoshi Yoshioka, Faculty of Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan, and other)

The Small Nucleotide Chain and Gold Nanoparticles Interaction inside Carbon Nanotube: Molecular Dynamics Study
(Mirzoziz A. Khusenov, Ermuhammad B. Dushanov, Kholmirzo T. Kholmurodov, Tajik Technical University named after M.S. Osimi, Dushanbe, Republic of Tajikistan, and others)

Lipid Environment Promotes Dimerization of Transmembrane Helices
(Andrey S. Kuznetsov, Anton A. Polyansky, Pavel E. Volynsky, Roman G. Efremov, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry,
Russian Academy of Sciences, Moscow, Russia, and others)

Protein–Protein Interaction in Photosynthetic Electron Transfer Chain: Computer Simulation
(Ilya B. Kovalenko, Anna M. Abaturova, Aleksandra N. Diakonova, Dmitry M. Ustinin, Sergei S. Khruschev, G.alina Yu. Riznichenko and
Andrei B. Rubin, Biological Faculty, Lomonosov Moscow State University, Leninskye Gory, Moscow, Russia, and other)

Molecular–Dynamics Based Insights into the Problem of Graphite Melting
(Nikita D. Orekhov, Vladimir V. Stegailov, Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russia, and others)

Phase Diagrams of Gas Hydrates: Molecular Simulation Studies
(Grigory S. Smirnov, Vladimir V. Stegailov, Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow, Russia, and others)

Index

Audience: University students, the young and leading researcher of the institutes and universities, companies on the electronic, pharmaceutical and related industries.

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