1st Edition

Many-Body Effects and Electrostatics in Biomolecules

Edited By Qiang Cui, Markus Meuwly, Pengyu Ren Copyright 2016
    596 Pages 23 Color & 61 B/W Illustrations
    by Jenny Stanford Publishing

    As computational hardware continues to develop at a rapid pace, quantitative computations are playing an increasingly essential role in the study of biomolecular systems. One of the most important challenges that the field faces is to develop the next generation of computational models that strike the proper balance of computational efficiency and accuracy, so that the problems of increasing complexity can be tackled in a systematic and physically robust manner. In particular, properly treating intermolecular interactions is fundamentally important for the reliability of all computational models. In this book, contributions by leading experts in the area of biomolecular simulations discuss cutting-edge ideas regarding effective strategies to describe many-body effects and electrostatics at quantum, classical, and coarse-grained levels. The goal of the book is to not only provide an up-to-date snapshot of the current simulation field but also stimulate exchange of ideas across different sub-fields of modern computational (bio)chemistry. The text will be a useful reference for the biomolecular simulation community and help attract talented young students into this exciting frontier of research.

    QM and QM/MM Methods
    Polarizable continuum models for (bio)molecular electrostatics: Basic theory and recent developments for macromolecules and simulations, J. M. Herbert, A. W. Lange
    A modified divide-and-conquer linear-scaling quantum force field with multipolar charge densities, T. J. Giese, D. M. York
    Explicit polarization theory, Y. Wang, M. J. M. Mazack, D. G. Truhlar, J. Gao
    Effective fragment potential method, L. Slipchenko
    Quantum mechanical methods for quantifying and analyzing non-covalent interactions and for force-field development, D. Sherrill, K. Merz
    Force field development with density-based energy decomposition analysis, N. Zhou, Q. Wu, Y. Zhang

    Atomistic Models
    Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review, W. Guowei, N. Baker
    Explicit inclusion of induced polarization in atomistic force fields based on the classical Drude oscillator model, A. Savelyev, B. Roux, A. D. Mackerell, Jr.
    Multipolar force fields for atomistic simulations, M. Meuwly, T. Bereau
    Quantum mechanics based polarizable force field for proteins, C. Ji, Y. Mei, J. Zhang
    Status of the Gaussian electrostatic model, a density-based polarizable force field, G. A. Cisneros, J.-P. Piquemal
    Water models: Looking forward by looking backward, T. Ichiye

    Coarse-Grained Models
    A physics-based coarse-grained model with electric multipoles, G. Li
    Coarse-grained membrane force field based on Gay–Berne potential and electric multipoles, D. Lin, A. Grossfield
    Perspectives on the coarse-grained models of DNA, I. Echeverria, G. Papoian
    RNA coarse-grained model theory, D. Bell, P. Ren


    Qiang Cui is professor of chemistry at the University of Wisconsin-Madison, USA. He is interested in developing theoretical/computational methods for the analysis of biomolecular systems, especially concerning chemical reactions in enzymes, energy transduction in biomolecular machines, and, more recently, interaction between biomolecules, lipids, and inorganic materials.

    Markus Meuwly is professor of physical and computational chemistry at the Department of Chemistry of the University of Basel and adjunct research professor at Brown University, USA. He is interested in developing computational/theoretical methods for quantitative atomistic simulations, specifically multipolar force fields and reactive processes in complex systems.

    "This book is a state-of-the-art report on the description of molecular energetics using force fields, which are the most critical element in computer simulations of biomolecular systems. The 16 chapters, written by leaders in the field, provide in-depth reports on all important current issues, including the representation of polarization, quantum mechanics-based force fields, and coarse-grained approaches for RNA, DNA, and membranes. This is an important reference for anyone involved in computational studies in chemistry and biology, especially those who want a deeper understanding of the underlying representations of intra- and intermolecular energetics."
    —Prof. William L. Jorgensen, Yale University, USA