ABSTRACT

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.

chapter 1|30 pages

Introduction to Molecular Dynamics and Enhanced Sampling Algorithms

ByXuhui Huang, Ruhong Zhou, Bruce J. Berne

chapter 2|50 pages

Toward Quantitative Analysis of Metalloenzyme Function Using MM and Hybrid QM/MM Methods: Challenges, Methods, and Recent Applications

ByMichael Gaus, Puja Goyal, Guanhua Hou, Xiya Lu, Xueqin Pang, Jan Zienau, Xin Xu, Marcus Elstner, and Qiang Cui

chapter 3|28 pages

Development of AMOEBA Force Field with Advanced Electrostatics

ByZhen Xia, Qiantao Wang, Xiaojia Mu, Pengyu Ren

chapter 4|30 pages

Molecular Simulations of Protein Folding Dynamics and Thermodynamics

ByDeepak R. Canchi, Charles English, Camilo A. Jimenez-Cruz, and Angel E. Garcia

chapter 5|24 pages

Minimal Models for the Structure and Dynamics of Nucleic Acids

ByChangbong Hyeon and Devarajan (Dave) Thirumalai

chapter 7|26 pages

Lipid Bilayers: Structure, Dynamics, and Interactions with Antimicrobial Peptides

ByYi Wang, J. Andrew McCammon

chapter 8|26 pages

Protein and Nucleic Acid Interactions with Molecular Dynamics Simulations

ByZhen Xia, Ruhong Zhou

chapter 9|34 pages

Simulating Membranes and Membrane Proteins

ByNicholas Leioatts, Alan Grossfield

chapter 10|34 pages

Protein and Nanoparticle Interactions: Perspectives of Nanomedicine and Nanotoxicity

BySeung-gu Kang and Ruhong Zhou

chapter 11|18 pages

Modeling of DNA Sequencing with Solid-State Nanopores

ByBinquan Luan

chapter 12|32 pages

Biological Water under Confinement: Nanoscale Dewetting

ByRuhong Zhou