Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology, 1st Edition (Hardback) book cover

Molecular Modeling at the Atomic Scale

Methods and Applications in Quantitative Biology, 1st Edition

Edited by Ruhong Zhou

CRC Press

388 pages | 48 B/W Illus.

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pub: 2014-08-21
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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

Biomolecular Interactions

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


About the Series

Series in Computational Biophysics

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Subject Categories

BISAC Subject Codes/Headings:
SCIENCE / Life Sciences / Biology / General
SCIENCE / Chemistry / Physical & Theoretical
SCIENCE / Physics