1. Introduction 172. Dynamics of many-body systems 192.1 Effective dynamics of reduced
systems 212.2 The constraint of thermodynamic equilibrium 242.3 Mean-field theories 253 …

An understanding of molecular interactions is essential for insight into biological systems at
the molecular scale. Among the various components of molecular interactions, electrostatics …

Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …

We present the three-dimensional molecular theory of solvation (also known as 3D-RISM)
coupled with molecular dynamics (MD) simulation by contracting solvent degrees of …

The first dynamical simulation of a protein based on a detailed atomic model was reported in
1977. Since then, the uses of various theoretical and computational approaches have …

We show that an Ng bridge function modified version of the three-dimensional reference
interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict …

The use of computer simulations in investigations of protein− protein interactions is
discussed. First, crystallographic analyses of known protein− protein complexes are …

We report a simple universal method to systematically improve the accuracy of hydration
free energies calculated using an integral equation theory of molecular liquids, the 3D …

The energetic representation of the molecular configuration in a dilute solution is introduced
to express the solvent distribution around the solute over a one-dimensional coordinate …

Water and other polar liquids exhibit nanoscale structuring near charged interfaces. When a
polar liquid is confined between two charged surfaces, the interfacial solvent layers begin to …