Molecular modeling at the atomic scale : methods and applications in quantitative biology

Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts.

The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage.

This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.

Xuhui Huang and Rahong Zhou and Bruce J. BerneMichael Gaus and Puja Goyal and Guanhua Hou and Xiya Lu and Xueqin Pang and Jan Zienau and Xin Xu and Marcus Elstner and Qiang CuiZhen Xia and Qiantao Wang and Xiaojia Mu and Pengyu RenDeepak R. Canchi and Charles English and Camilo A. Jimenez-Cruz and Angel E. GarciaChangbong Hyeon and Devarajan (Dave) ThirumalaiLuca Larini and Joan-Emma SheaYi Wang and J. Andrew McCammonZhen Xia and Ruhong ZhouNicholas Leioatts and Alan GrossfieldSeung-gu Kang and Ruhong ZhouBinquan LuanRuhong Zhou

Series Preface	p. xi
Preface	p. xiii
Editor	p. xv
Contributors	p. xvii
Section I Advanced Simulation Techniques
1 Introduction to Molecular Dynamics and Enhanced Sampling Algorithms	p. 3
2 Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods: Challenges, Methods, and Recent Applications	p. 33
3 Development of AMOEBA Force Field with Advanced Electrostatics	p. 83
Section II Self-Assembly of Biomolecules
4 Molecular Simulations of Protein Folding Dynamics and Thermodynamics	p. 111
5 Minimal Models for the Structure and Dynamics of Nucleic Acids	p. 141
6 Amyloid Peptide Aggregation: Computational Techniques to Deal with Multiple Time and Length Scales	p. 165
7 Lipid Bilayers: Structure, Dynamics, and Interactions with Antimicrobial Peptides	p. 191
Section III Biomolecular Interactions
8 Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations	p. 217
9 Simulating Membranes and Membrane Proteins	p. 243
10 Protein and Nanoparticle Interactions: Perspectives of Nanomedicine and Nanotoxicity	p. 277
Section IV More Applications in Molecular Biology
11 Modeling of DNA Sequencing with Solid-State Nanopores	p. 311
12 Biological Water under Confinement: Nanoscale Dewetting	p. 329
Index	p. 353

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