Many-Body Effects and Electrostatics in Biomolecules

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

Biography

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