Exploring Life Phenomena with Statistical Mechanics of Molecular Liquids

Exploring Life Phenomena

Fumio Hirata

• Publisher: CRC Press
• Year: 2020
• ISBN:
  9781351201414
• Edition: 1
• Topic: History
• Subtopic: World History
• Index: History

In a living body, a variety of molecules are working in a concerted manner to maintain its life, and to carry forward the genetic information from generation to generation. A key word to understand such processes is "water, " which plays an essential role in life phenomena. This book sheds light on life phenomena, which are woven by biomolecules as warp and water as weft, by means of statistical mechanics of molecular liquids, the RISM and 3D-RISM theories, both in equilibrium and non-equilibrium. A considerable number of pages are devoted to basics of mathematics and physics, so that students who have not majored in physics may be able to study the book by themselves. The book will also be helpful to those scientists seeking better tools for the computer-aided-drug-discovery.

• Explains basics of the statistical mechanics of molecular liquids, or RISM and 3D-RISM theories, and its application to water.
• Provides outline of the generalized Langevin theory and the linear response theory, and its application to dynamics of water.
• Applies the theories to functions of biomolecular systems.
• Applies the theories to the computer aided drug design.
• Provides a perspective for future development of the method.

CHAPTER II

Statistical Mechanics of Liquid and Solutions

As was emphasized in the introduction of the book, water is essential for living bodies on the earth. It is because all the biomolecules, including protein and DNA, in our body can maintain their structure, and perform their functions only in aqueous environment. It was also emphasized that microscopic structure of water plays crucial role in the two aspects of biomolecular activity, the self-organization and the molecular recognition. Then, what is the structure of liquids including water, and how it can be characterized? This is the main theme of this chapter.

II-1 Structure of Liquid and Ornstein-Zernike Equation

II-1.1 What is the Structure of Liquid?

It is not difficult to define structure of a molecule. For example, the structure of a water molecule may be characterized by a triangle made of an oxygen atom and two hydrogen atoms, giving the three lengths among O-O, O-H, H-H atoms, or the two O-H-H angles and the H-H length, or the two O-H length and the H-O-H and angle (Fig. II-1.1a). The situation is more or less similar for the case of a solid crystal. Crystal structure can be characterized by giving lattice constant of a unit lattice (Fig. II-1.1b).

However, the liquid structure may not be characterized by the language of geometry, such as bond le...

Table of contents

• Cover
• Title Page
• Copyright Page
• Preface
• Table of Contents
• General Introduction
• I. Fundamentals: Basic Concepts Related to Statistical Mechanics
• II. Statistical Mechanics of Liquid and Solutions
• III. Dynamics of Liquids and Solutions
• IV. Theory of Biomolecular Solvation and Molecular Recognition
• V. Structural Fluctuation and Dynamics of Protein in Aqueous Solutions
• VI. Applications of the Theories to In-silico Drug Discovery
• References
• Index
• Epilogue
• Color Plate Section