Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena

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

Series: Nanotechnology Science and Technology, Computer Science, Technology and Applications
BISAC: TEC027000

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In this book, chapters from multiple experts have been collected that demonstrate the efficient use of the computer molecular dynamics (MD) simulation methods for the studying of nanoscale phenomena in materials and life sciences. This volume contains the Proceedings of the International Symposium KSCMBS-2016 Khujand Symposium on Computational Materials and Biological Sciences (10th Japan-Russia Workshop on Molecular Simulation Studies in Materials and Biological Sciences), which was organized by the Frank Laboratory of Neutron Physics (FLNP), Joint Institute for Nuclear Research (JINR), Dubna, Russian Federation and Khujand State University named after Academician B. Gafurov, The Ministry of Education and Science of The Republic of Tajikistan (HGU, RT) from September 24-28, 2016 in Khujand, Tajikistan. It is remarkable that the first chapter opening this book is contributed by C. Arnarez and S.J. Marrink, representatives of the same faculty from the University of Groningen in the Netherlands, where Prof. Bernard L. Feringa won the 2016 Nobel Prize in Chemistry “for the design and synthesis of molecular machines” (nanomotors and nanorobots), which are the actual topics of the current KSCMBS-2016 Japan-Russia-Tajikistan International Symposium. In the first chapter, C. Arnarez and S.J. Marrink have developed a computational “microscopy” approach based on a coarse-grained molecular dynamics simulation to study the mitochondrial membranes. The developed method is capable of simulating the cell membranes and efficiently capturing the interplay between the lipids and proteins at a spatio-temporal resolution, which is unmatched by other methods. The other interesting chapters of the book provide very broad and useful information to the readers by demonstrating the clear examples of how modern state-of-the-art molecular dynamics modeling can provide a molecular level of insight into the organization and dynamics of the atomic/molecular processes in nanosystems, cell membranes, lipids, and proteins through new materials, exploring and new drug design. (Imprint: Nova)

Preface

Introduction

Chapter 1. Computational Microscopy of Mitochondrial Membranes
Clement Arnarez and Siewert J. Marrink

Chapter 2. Integrative Method for Finding Antimalarials Using In Silico Approach
Pawan Kumar, Ashutosh Shandilya, Bhyravabhotla Jayaram and Indira Ghosh

Chapter 3. Mesoscale Modelling for the Lubrication Mechanism of Human Joints
Mitsuhiro Matsumoto, Kojiro Sano and Kisuke Inoue

Chapter 4. The Structural and Dynamic Properties of Lipid Bilayers Exhibit Concordant Changes: MD Simulations
Daria V. Pyrkova and Roman G. Efremov

Chapter 5. A Molecular Basis of Protein-Protein Interactions in Membranes: A Computational Investigation
Andrey S. Kuznetsov, Pavel E. Volynsky and Roman G. Efremov

Chapter 6. MD Simulation of Sandwiched Liquid Evaporation
Takashi Ao and Mitsuhiro Matsumoto

Chapter 7. Molecular Dynamic Simulations of Hybrid Halide Perovskites: The Effect of Bond Rigidness and Heating on Structural Properties
Kholmirzo Kholmurodov, Khaiyom Rahmonov, Mekhrdod Subhoni Qurboniyon, Elkhan Hamzin, Meir Erdauletov, Mahabbat Nurqasimova, Tatyana Zelenyak, Alexander Doroschkevich, Pavel Gladishev and Tomoyuki Yamamoto

Chapter 8. Pyrimidine-Purine and CPD-Purine Interactions in the DNA Repairing Process
Ermuhammad B. Dushanov and Kholmirzo T. Kholmurodov

Chapter 9. Nonlinear Dynamics of One-Dimensional Anisotropic Heisenberg Ferromagnetics
Mekhrdod Subhoni Qurboniyon and Farhod Rahimi

Chapter 10. Modelling of Nonequilibrium Chemo-Electronic Conversion of Water Adsorption on the Surface of Yttria-Stabilized Zirconia: Experimental Preparation and Problem Overview
A. S. Doroshkevich, A. I. Lyubchyk, A. K. Islamov, A. A. Nabiyev, V. A. Turchenko, V. A. Glazunova, T. Yu. Zelenyak, V. V. Burkhovetskiy, A. V. Shylo, A. V. Saprykina, O. S. Lygina, S. B. Lyubchyk, T. E. Konstantinova, V. I. Bodnarchuk, S. Ohmura and Kh. T. Kholmurodov

Chapter 11. Brownian Dynamics Study of the Complex Formation of Proteins Plastocyanin and Cytochrome f
Ilya B. Kovalenko, Anna M. Abaturova, Olga S. Knyazeva, Vladimir V. Fedorov, Sergei S. Khruschev, Galina Yu. Riznichenko and Andrei B. Rubin

Chapter 12. X-Ray Absorption Near-Edge Structure Measurements and First-Principles Density Functional Theory Calculations for Local Environment Analysis of Trace Elements in Bioceramics
Kazuhiko Kawabata and Tomoyuki Yamamoto

About the Editor

Index

Audience: The university MSc and graduate students; researchers and professors; the people working in the industrial nanobiotechnologies and new drugs development areas

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