This book provides theoretical foundation for processes such as molecular recognition, which play essential roles in life phenomena. A key word to understand such processes is “water," which playsan essential role in life phenomena both in equilibrium and non-equilibrium processes. The book starts from explaining the RISM and 3D-RISM theories, the statistical mechanics of water and aqueous solutions, both in equilibrium and non-equilibrium, to cover wide spectrum of life phenomena including enzymatic reactions and ion channels. The book will be also beneficial to those scientists seeking better tools for the computer-aided drug-discovery.
Introduction. Boltzmann distribution and statistical ensembles. Central limiting theorem and Gaussian fluctuation. Fluctuation of thermodynamic variables (Fluctuation theory of Landau). Molecular Theory of Solvation (RISM and 3D-RISM). Liquid state theory and aqueous solutions. Biomolecular solvation. Molecular recognition in biomolecules. Molecular recognition and biological functions. Enzymatic reactions, molecular channels, etc. Theoretical treatment of molecular recognitions. Dynamics of Liquids and Solutions. Generalized Langevin theory. Generalized Langevin theory combined with the RISM theory. Dynamics of liquid and solutions. Structural Dynamics and Fluctuation of Biomolecules in Solution. A Generalized Langevin equation of a biomolecule in solution. Coarse-grained dynamics of biomolecules in solution. Molecular theory of Gaussian fluctuation. Structural fluctuation of a biomolecule induced by thermodynamic perturbation. Structural dynamics of biomolecules induced by a perturbation. Possible Application of Theories to In-silico Drug-discovery. In-silico mutation of protein. Binding affinity of a drug-molecule at an active-site of protein. Fragment-based drug design. Local thermodynamics of solutions at active-sites of protein (SolutionMap)