MOLECULAR DYNAMICS STUDIES OF SYNTHETIC AND BIOLOGICAL MACROMOLECULES Edited by Lichang Wang MOLECULAR DYNAMICS – STUDIES OF SYNTHETIC AND BIOLOGICAL MACROMOLECULES Edited by Lichang Wang Molecular Dynamics – Studies of Synthetic and Biological Macromolecules Edited by Lichang Wang Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work Any republication, referencing or personal use of the work must explicitly identify the original source As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher No responsibility is accepted for the accuracy of information contained in the published chapters The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book Publishing Process Manager Daria Nahtigal Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published April, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechopen.com Molecular Dynamics – Studies of Synthetic and Biological Macromolecules, Edited by Lichang Wang p cm ISBN 978-953-51-0444-5 Contents Preface IX Part Chapter Dynamics of Polymers Introduction to Molecular Dynamics Simulations: Applications in Hard and Soft Condensed Matter Physics Martin Oliver Steinhauser Chapter Molecular Dynamics Simulation of Synthetic Polymers Claudia Sandoval Chapter Backbone Connectivity and Collective Aggregation Phenomena in Polymer Systems Wen-Jong Ma and Chin-Kun Hu Chapter Part Molecular Dynamics Simulation of Permeation in Polymers Hossein Eslami and Nargess Mehdipour 29 45 61 Dynamics of Biomolecules 83 Chapter M.DynaMix Studies of Solvation, Solubility and Permeability 85 Aatto Laaksonen, Alexander Lyubartsev and Francesca Mocci Chapter Practical Estimation of TCR-pMHC Binding Free-Energy Based on the Dielectric Model and the Coarse-Grained Model 107 Hiromichi Tsurui and Takuya Takahashi Chapter 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 VI Contents Chapter Chapter Part Essential Dynamics on Different Biological Systems: Fis Protein, tvMyb1 Transcriptional Factor and BACE1 Enzyme Lucas J Gutiérrez, Ricardo D Enriz and Héctor A Baldoni 151 MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies 171 Joseph M Hayes and Georgios Archontis Dynamics of Plasmas 191 Chapter 10 Micro-Heterogeneity in Complex Liquids 193 Aurélien Perera, Bernarda Kežić, Franjo Sokolić and Larisa Zoranić Chapter 11 Application of Molecular Dynamics Simulations to Plasma Etch Damage in Advanced Metal-Oxide-Semiconductor Field-Effect Transistors 221 Koji Eriguchi Chapter 12 Molecular Dynamics Simulations of Complex (Dusty) Plasmas 245 Céline Durniak and Dmitry Samsonov Part Dynamics at the Interface 273 Chapter 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 Chapter 14 Simulations of Unusual Properties of Water Inside Carbon Nanotubes 297 Yoshimichi Nakamura and Takahisa Ohno Chapter 15 Applications of All-Atom Molecular Dynamics to Nanofluidics Mauro Chinappi Part 319 Dynamics of Nanomachines 339 Chapter 16 Analysis of the Atomization Process by Molecular Dynamics Simulation 341 Yeh Chun-Lang Chapter 17 Molecular Dynamics Simulation of Nanoscale Machining 389 Akinjide Oluwajobi Contents Chapter 18 High-Throughput Simulations of Protein Dynamics in Molecular Machines: The ‘Link’ Domain of RNA Polymerase 419 Robert O J Weinzierl VII Preface 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 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 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 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 provides a MD study of the conformational profile of Neuromedin B by Sharma, et al Chapter 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 X Preface 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 ... methods Usually, one Molecular Dynamics – Studies of Synthetic and Biological Macromolecules Will-be-set-by-IN-TECH considers the internal degrees of freedom of polymers and biomacromolecules... total number of subcells is N/ ρ r and particles in each one of the subcells is ρ rcut cut 12 10 Molecular Dynamics – Studies of Synthetic and Biological Macromolecules Will-be-set-by-IN-TECH Fig.. .MOLECULAR DYNAMICS – STUDIES OF SYNTHETIC AND BIOLOGICAL MACROMOLECULES Edited by Lichang Wang Molecular Dynamics – Studies of Synthetic and Biological Macromolecules