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.
Table of Contents
Advanced Simulation Techniques
Introduction to Molecular Dynamics and Enhanced Sampling Algorithms, Xuhui Huang, Ruhong Zhou, and Bruce J. Berne
Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods: Challenges, Methods, and Recent Applications, Michael Gaus, Puja Goyal, Guanhua Hou, Xiya Lu, Xueqin Pang, Jan Zienau, Xin Xu, Marcus Elstner, and Qiang Cui
Development of AMOEBA Force Field with Advanced Electrostatics, Zhen Xia, Qiantao Wang, Xiaojia Mu, and Pengyu Ren
Self-Assembly of Biomolecules
Molecular Simulations of Protein Folding Dynamics and Thermodynamics, Deepak R. Canchi, Charles English, Camilo A. Jimenez-Cruz, and Angel E. Garcia
Minimal Models for the Structure and Dynamics of Nucleic Acids, Changbong Hyeon and Devarajan (Dave) Thirumalai
Amyloid Peptide Aggregation: Computational Techniques to Deal with Multiple Time and Length Scales, Luca Larini and Joan-Emma Shea
Lipid Bilayers: Structure, Dynamics, and Interactions with Antimicrobial Peptides, Yi Wang and J. Andrew McCammon
Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations, Zhen Xia and Ruhong Zhou
Simulating Membranes and Membrane Proteins, Nicholas Leioatts and Alan Grossfield
Protein and Nanoparticle Interactions: Perspectives of Nanomedicine and Nanotoxicity, Seung-gu Kang and Ruhong Zhou
IV More Applications in Molecular Biology
Modeling of DNA Sequencing with Solid-State Nanopores, Binquan Luan
Biological Water under Confinement: Nanoscale Dewetting, Ruhong Zhou