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TEXTBOOK : MOLECULAR DYNAMICS – STUDIES OF SYNTHETIC AND BIOLOGICAL MACROMOLECULES

MOLECULAR DYNAMICS – STUDIES OF SYNTHETIC AND BIOLOGICAL MACROMOLECULES

Edited by Lichang Wang .

444 pages .
Open Access .
ISBN 978-953-51-0444-5 .

Molecular dynamics (MD) simulations have played increasing roles in our understanding of physical and chemical processes of complex systems and in advancing science and technology. Over the past forty years, MD simulations have made great progress from developing sophisticated theories for treating complex systems to broadening applications to a wide range of scientific and technological fields. The chapters of Molecular Dynamics are a reflection of the most recent progress in the field of MD simulations.
This is the second book of Molecular Dynamics that focuses on the MD studies of synthetic and biological macromolecules. This book is divided into five parts. The first part deals with the molecular dynamics simulations of polymers. Steinhauser provides a general introduction of MD simulations, both equilibrium and nonequilibrium, on the studies of macromolecules of hard and soft matters in Chapter 1.
In Chapter 2, Sandoval presents the MD results to understand various phenomena of synthetic polymers, three amphiphilic polymers at the air-water interface and two polymers in condensed phase. Ma & Hu discuss in Chapter 3 the MD simulations on the backbone connectivity of polymer chains and the aggregation process or phase separation. In Chapter 4, Islami & Mehdipour provide a summary of MD methods to investigate the solubility and diffusion of gaseous molecules, such as Ar, N2, CO2, CH4, and C3H8, in polymers.
The second part consists of five chapters that employ MD simulations to study biomolecules. Laaksonen et al. describe in Chapter 5 their MD simulation package M.DynaMix as well as its application to study lipid bilayers and the hydration and coordination of counterions around DNA. In Chapter 6, Tsurui & Takahashi give a description of dielectric and coarse-grained models and use TCR-pMHC complexes as examples to illustrate the application of these models. Chapter 7 provides a MD study of the conformational profile of Neuromedin B by Sharma, et al. Chapter 8 summarizes the MD studies of Fis protein, tvMyb1 transcriptional factor, and BACE1 enzyme by Gutiérrez et al. In Chapter 9, Hayes & Archontis present a review of calculations in the study of protein-ligand binding events. 
Part III is about the MD studies of plasmas. In Chapter 10, Perera et al. provide a description of micro-structure and micro-heterogeneity of liquid mixtures. Eriguchi presents MD studies of plasma etch damage mechanism in Chapter 11. Chapter 12 by Durniak & Samsonov gives a description of the MD simulations of dusty plasmas on the structure, linear and nonlinear waves, shocks, and other related phenomena.
The fourth part is on the MD simulations of interfaces that play important roles in the development of biomaterials, implant biocompatibility, and biosensors. In Chapter 13, Hung et al. describe the MD studies of cardio toxin protein adsorption on selfassembled monolayers. In Chapter 14, Nakamura & Ohno provide the MD results of water behavior inside of carbon nanotubes. In Chapter 15, Chinappi provides a summary of MD results on the study of nanofluids.
In the last part of the book, MD studies of nanomachines are discussed. The study of nanomachines is important in our understanding of how biological systems work and in the technological development of nano-instruments. In Chapter 16, Chun-Lang describes the dynamics of fluid from nanojets and provides the analysis of the atomization process based on the MD simulation results. Oluwajobi gives a detailed description of MD simulations of nanomachines and presents the MD results in the studies of cutting processes in Chapter 17. The last chapter of this book is written by Weinzierl, which deals with protein dynamics in molecular machines.
With strenuous and continuing efforts, a greater impact of MD simulations will be made on understanding various processes and on advancing many scientific and technological areas in the foreseeable future.
In closing I would like to thank all the authors taking primary responsibility to ensure the accuracy of the contents covered in their respective chapters. I also want to thank my publishing process manager Ms. Daria Nahtigal for her diligent work and for keeping the book publishing progress in check.

Lichang Wang
Department of Chemistry and Biochemistry
Southern Illinois University
Carbondale
USA
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CONTENTS : 

Part 1 Dynamics of Polymers .


 1 Introduction to Molecular Dynamics Simulations: Applications in Hard and Soft Condensed Matter Physics 3 Martin Oliver Steinhauser

 2 Molecular Dynamics Simulation of Synthetic Polymers 29 Claudia Sandoval

 3 Backbone Connectivity and Collective Aggregation Phenomena in Polymer Systems 45 Wen-Jong Ma and Chin-Kun Hu

 4 Molecular Dynamics Simulation of Permeation in Polymers 61 Hossein Eslami and Nargess Mehdipour

Part 2 Dynamics of Biomolecules .


 5 M.DynaMix Studies of Solvation, Solubility and Permeability 85 Aatto Laaksonen, Alexander Lyubartsev and Francesca Mocci

 6 Practical Estimation of TCR-pMHC Binding Free-Energy Based on the Dielectric Model and the Coarse-Grained Model 107 Hiromichi Tsurui and Takuya Takahashi

 7 An Assessment of the Conformational Profile of Neuromedin B Using Different Computational Sampling Procedures 135 Parul Sharma, Parvesh Singh, Krishna Bisetty and Juan J Perez

 8 Essential Dynamics on Different Biological Systems: Fis Protein, tvMyb1 Transcriptional Factor and BACE1 Enzyme 151 Lucas J. Gutiérrez, Ricardo D. Enriz and Héctor A. Baldoni

 9 MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies 171 Joseph M. Hayes and Georgios Archontis

Part 3 Dynamics of Plasmas .


 10 Micro-Heterogeneity in Complex Liquids 193 Aurélien Perera, Bernarda Kežić, Franjo Sokolić and Larisa Zoranić

 11 Application of Molecular Dynamics Simulations to Plasma Etch Damage in Advanced Metal-Oxide-Semiconductor Field-Effect Transistors 221 Koji Eriguchi

 12 Molecular Dynamics Simulations of Complex (Dusty) Plasmas 245 Céline Durniak and Dmitry Samsonov

Part 4 Dynamics at the Interface .


 13 Studies of Cardio Toxin Protein Adsorption on Mixed Self-Assembled Monolayers Using Molecular Dynamics Simulations 275 Shih-Wei Hung, Pai-Yi Hsiao and Ching-Chang Chieng

 14 Simulations of Unusual Properties of Water Inside Carbon Nanotubes 297 Yoshimichi Nakamura and Takahisa Ohno

 15 Applications of All-Atom Molecular Dynamics to Nanofluidics 319 Mauro Chinappi

Part 5 Dynamics of Nanomachines .


 16 Analysis of the Atomization Process by Molecular Dynamics Simulation 341 Yeh Chun-Lang

 17 Molecular Dynamics Simulation of Nanoscale Machining 389 Akinjide Oluwajobi

 18 High-Throughput Simulations of Protein Dynamics in Molecular Machines: The ‘Link’ Domain of RNA Polymerase 419 Robert O. J. Weinzierl .



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