Entropy-Enthalpy Compensation: Finding a Methodological Common Denominator through Probability, Statistics, and Physics

Cover
Half Title
Title Page
Copyright Page
Dedication
Contents
Preface
1. Entropy-Enthalpy Compensation and Exploratory Factor Analysis of Correlations: Are There Common Points?
	1.1 Introduction
	1.2   Results and Discussion
		1.2.1 Macroscopic Thermodynamics Considered from the Standpoint of van der Waals Equation of State
		1.2.2 Correctness of Our Macroscopic-Thermodynamic  Approach
		1.2.3 What Is the Actual Difference between Gibbs and Helmholtz Functions?
		1.2.4 The Actual Physical Sense of the EEC
		1.2.5 Statistical-Mechanical Standpoint
		1.2.6 What Is the Actual Probability Distribution behind the Statistical Mechanics?
		1.2.7 Bayesian Statistical Thermodynamics of Real Gases
		1.2.8 Applicability of Linhart’s Approach to Real Gases
		1.2.9 Is There Some Physical Connection between Boltzmann’s and Gibbs’ Entropy Formulae?
		1.2.10 Can Our Approach Be Really Productive?
		1.2.11 A Methodological Perspective
		1.2.12 What Is the Actual Zest of Our Approach?
	1.3 Conclusions
	1.4 Outlook
	Appendix 1 to Chapter
	Appendix 2 to Chapter 1: Methodological Roots and Significance of Energetics
		A2.1 Introduction
		A2.2 Energetics Is a Generally Applicable Concept
			A2.2.1 Foreword
			A2.2.2 The First Definition of Entropy
			A2.2.3 Introduction and Preliminary Concepts
			A2.2.4 Succinct Presentation of Thermodynamic Principles
				A2.2.4.1 Joule-Mayer principle
				A2.2.4.2 Principle of Carnot-Clausius
			A2.2.5 Energy and the Forms of Sensitivity
			A2.2.6 Third Part
				A2.2.6.1 The muscle system and energetics
				A2.2.6.2 Analogy between the muscle system and the nervous system
				A2.2.6.3 Energetics and the nervous system
				A2.2.6.4 Energetics and the nervous system (Continued)
			A2.2.7 Thermodynamic Design of Some Mental Situations
			A2.2.8 Summary and Conclusions
		A2.3 Our General Conclusion
			A2.3.1 The Balance of Bodies: Types of Body Balance
			A2.3.2 Our Immediate Comment
		A2.4 How to Employ the Ideas of Energetics: A Methodological Reiteration
			A2.4.1 How to Make a Mechanical Theory of Mental Phenomena
			A2.4.2
			A2.4.3
			A2.4.4
		A2.4.5 The Senses: Theory of the Consecutive Images
		A2.4.6 Demential Law by Paul Janet
		A2.4.7 Psychoses
		A2.4.8 Mechanical Representation of Psychic Phenomena
			A2.4.8.1 Mechanism of dementia
			A2.4.8.2 Mechanism of sensations
			A2.4.8.3 Mechanism of psychoses
			A2.4.8.4 Consequences
			A2.4.8.5 Influence of the cerebral inertia coefficient
		A2.4.9 Conclusion
	Appendix 3 to Chapter 1: A Methodological Outlook
2. Polynomial Exploratory Factor Analysis on Molecular Dynamics Trajectory of the Ras-GAP System: A Possible Theoretical Approach to Enzyme Engineering
	2.1 Introduction
	2.2 Results and Discussion
		2.2.1 Linear Exploratory Factor Analysis Results
		2.2.2 Nonlinear Exploratory Factor Analysis Results
	2.3 Detailed Description of the Method
		2.3.1 Difference between Confirmatory and Exploratory Factor Analysis
		2.3.2 Difficulty Factors in Factor Analysis
		2.3.3 Difference between Linear and Nonlinear Factor Analysis
		2.3.4 The System under Study: Choosing the Proper Variables to Analyze the Macromolecular Dynamics
		2.3.5 Technical Details of the MD Simulation and Data Processing
			2.3.5.1 The system setup
			2.3.5.2 MD simulation procedure
			2.3.5.3 Analyses of MD trajectories
	2.4 Conclusion
	Supplementary Material to Chapter 2
Index