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. A modified divide-and-conquer linear-scaling quantum force field
with multipolar charge densities. Explicit polarization theory. Effective
fragment potential method. Quantum mechanical methods for quantifying and
analyzing non-covalent interactions and for force-field development. Force
field development with density-based energy decomposition analysis. Atomistic
Models. Differential geometry-based solvation and electrolyte transport
models for biomolecular modeling: a review. Explicit inclusion of induced
polarization in atomistic force fields based on the classical Drude
oscillator model. Multipolar force fields for atomistic simulations. Quantum
mechanics based polarizable force field for proteins. Status of the Gaussian
electrostatic model, a density-based polarizable force field. Water models:
Looking forward by looking backward. Coarse-Grained Models. A physics-based
coarse-grained model with electric multipoles. Coarse-grained membrane force
field based on GayBerne potential and electric multipoles. Perspectives on
the coarse-grained models of DNA. RNA coarse-grained model theory.
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.
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