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Physical Approach to Biology
Tetsuya Watanabe
Published Date:
September, 2016
Science Publishing Group
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Table of Contents
The Whole Book
Front Matter
Since September 8, 2016
Chapter 1 Boltzmann Probability Distribution and Entropy
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1.1 Introduction
1.2 Finding the Boltzmann Probability Distribution
1.3 Interacting System
1.4 Partition Functions and Degeneracy
1.5 Translational Distribution of Gasses
1.6 Changes in Energy and Enthalpy in Relation to Changes in States of the System
1.6.1 Internal Energy as a State Function
1.6.2 Joule Free Expansion of Gasses
1.6.3 Enthalpy as a State Function
1.7 Changes in Entropy and Gibbs Free Energy
1.7.1 Entropy as a State Function
1.7.2 Spontaneous Changes
1.8 Definition of Entropy
1.9 Entropy Expressed by Partition Function
1.10 Entropy as the Function of Microstates and Probability of Finding a Particular Microstate of a Molecule
1.11 Separation of Partition Functions
1.12 Application to Monatomic Gas with Translational Energy
1.13 Calculation of Entropy Change Microscopically
1.13.1 Free Expansion of a Gas
1.13.2 Ideal Gas Mixture
1.13.3 Ideal Liquid Mixture
1.14 Double-stranded Polymer Model
1.15 Activation Energy
Chapter 2 Beginning of Quantum Mechanics
2.1 The Classical Wave Equation
2.2 Standing Waves
2.3 Travelling Wave
2.4 The Standing Wave as the Result of a Superposition of Two Traveling Waves
2.5 Superposition of Two Travelling Waves of Slightly Different Wave Length
2.6 Light as a Wave
2.7 Discovery of Electron
2.8 Blackbody Radiation
2.9 Photoelectric Effect Suggesting Light as a Particle
2.10 Light as a Particle Supported by Compton Effect
2.11 Figuring a Model of an Atom
2.12 Discovery of X-ray and Application for Structural Analysis of Solids
2.12.1 X-ray Spectra
2.12.2 X-ray Diffraction and Structural Analysis of Cubic Crystal Systems
2.13 Packing Density of Cubic Crystals
2.14 Wavelike Properties of Electrons
Chapter 3 Quantum Mechanics of Electrons and Diatomic Molecules
3.1 Wavelike Property of Particles
3.2 Derivation of Time Independent Schrodinger Equation
3.3 Classical Mechanical Quantities Represented by Linear Operators
3.4 Translational Motion of a Particle in a One-dimensional Box
3.5 Probability Amplitude and Probability Density
3.6 The Expected Value of Momentum of a Particle in a Box
3.7 Heisenberg Uncertainty Principle
3.8 Three-dimensional Systems
3.9 Particle in a Three-Dimensional Box
3.10 A Harmonic Oscillator as the Model of a Diatomic Molecule
3.11 Approximation of a Diatomic Molecule as a Harmonic Oscillator About Its Minimum of the Internuclear Potential
3.12 Solution of the Quantum Mechanical Harmonic Oscillator
3.13 Quantum Mechanical Operators
3.14 The Commutators of Two Operators
3.15 Operator Method Solution of a Harmonic Oscillator
3.16 Spectroscopic Predictions of a Diatomic Molecule
3.17 Vibrational Heat Capacity of a Diatomic Molecule
3.18 The Rigid Rotator as a Model of Rotating Diatomic Molecule
3.19 Angular Momentum Operator
3.20 Determination of the Eigenvalues of L2 and Lz
3.21 Vector Analysis
3.21.1 Product Rules
3.21.2 Spherical Polar Coordinates
3.21.3 Displacement by Extension and Rotation
3.22 Solving Schrodinger Equation of a Rigid Rotator
3.23 Spectroscopic Determination of a Diatomic Molecule
Chapter 4 Hydrogen Atom
4.1 The Schrodinger Equation for a Hydrogen Atom
4.2 Solution of the Radial Equation
4.3 Wave Functions of the Hydrogen Atom
4.4 Energy Level Diagram for Hydrogen Atom
4.5 Photon Emission
4.6 Radial Distribution Function of Hydrogen Atom
4.7 Probability Distribution Accompanied by Angular Momentum
4.8 Magnetic Field Effect
4.9 Otto Stern and Walther Gerlach Experiment
4.10 Intrinsic Spin Angular Momentum of an Electron
4.11 Pauli Exclusion Principle
Chapter 5 Multi-electron Atoms and Chemical Bonding
5.1 Characteristic Properties of Multi-electron Atoms
5.2 Shielding and Effective Atomic Number of He Atom
5.3 Comparison of Orbital Energy, E2s, E2p, E3s, E3p or E3d
5.4 Electron Configurations and Valence Electrons
5.5 Photoelectron Spectroscopy
5.6 Periodic Table of Elements
5.7 Chemical Bonding
5.7.1 Ionic Bond
5.7.2 Covalent Bond
5.7.3 Partial Ionic Character of Covalent Bond
5.7.4 Hydrogen Bond
5.7.5 London Dispersion Forces
5.7.6 Van der Waals Forces
5.8 Shapes of Molecules
5.8.1 Bonding Electrons and Lone-pair Electrons
5.8.2 Valence Shell Electron Pair Repulsion(VSEPR) Theory
5.9 Free Radicals in Life, Oxygen Radicals and Nitric Oxide
Chapter 6 Molecular Orbital Theory and Its Application to Biochemistry
6.1 Molecular Orbital Formed by Linear Combination of s-Orbitals
6.2 Molecular Orbitals Originating from p-Orbitals
6.3 Molecular Orbital Diagram and Electron Configuration
6.4 Paramagnetism and Diamagnetism
6.5 Hybridization of Atomic Orbitals
6.5.1 sp3 Hybridization
6.5.2 sp2 hybridization
6.5.3 sp Hybridization
6.6 Resonance Structures
6.7 Proteins
6.7.1 Secondary Structure of Proteins
6.7.2 Tertiary Structure of Proteins
6.7.3 Quaternary Structure of Proteins
6.8 Lipids
6.8.1 Fats and Oils
6.8.2 Phospholipids
6.8.3 Steroids
Chapter 7 Equilibrium of Chemical Reaction and Phase Change
7.1 Introduction
7.2 Heat of Formation
7.3 Entropy for Reactions
7.4 Free Energy of Formation and for Reactions
7.5 Entropy and Gibbs Free Energy in Dilution
7.6 Kinetics and Chemical Equilibrium
7.7 Changes in Gibbs Free Energy for Reactions at Constant Temperature
7.8 Changes in Gibbs Free Energy in Relation to Reaction Quotient over Equilibrium Constant
7.9 Variation of Chemical Equilibrium Constant with Temperature
7.10 Variation of Vapor Pressure with Temperature
7.11 Non-expansive Reversible Work at Constant Temperature and Pressure
7.12 Cell Potential and Gibbs Free Energy
7.13 Nernst Equation
Chapter 8 Rate of Reaction and Population Growth
8.1 Nuclear Reaction
8.2 Introduction to Chemical Kinetics
8.3 First Order Chemical Reactions
8.4 Second Order Chemical Reactions
8.5 Determining Orders of Reactions from Experimental Data
8.5.1 Reactions with One Reactant ( A →Product)
8.5.2 Reactions with More Than One Reactant ( A+B+C →Products)
8.6 Complex Reactions and Mechanisms
8.6.1 Parallel First Order Reactions
8.6.2 Consecutive First Order Reactions
8.6.3 Reversible First Order Reactions
8.6.4 Series Reversible First Order Reactions
8.7 Enzymes as Catalyst of Life
8.7.1 Introduction
8.7.2 Enzyme Kinetics
8.7.3 Inhibition of Enzyme Activity
8.8 Population Model of Bacterial Growth
8.9 Pharmacokinetics
Chapter 9 Application to Physiology and Pharmacology
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9.1 The Cell Membrane
9.2 Shape of protein in Aqueous Solution
9.3 Transmembrane Proteins
9.4 Discovery of Aquaporins
9.5 Osmotic Pressure
9.6 Primary Active Transport
9.7 Resting Membrane Potential
9.8 Goldman Equation
9.9 Action Potential
9.10 Graded Potential
9.11 Tissues with Voltage Gated Channels
9.11.1 Nerve Cell
9.11.2 Muscle Fibers and Receptors
9.12 Intracellular Messenger, Cyclic AMP
9.13 Inhibition of Acetylcholinesterase
9.14 Role of Adenosine Triphosphate (ATP) in Cell Metabolism
9.15 Nucleic Acids (DNA and RNA)
9.16 Semiconservative Replication of DNA
9.17 Protein Synthesis in the Living Cells
9.17.1 Transcription
9.17.2 Translation
9.18 Transfection of Foreign DNA into Host Cells and Restriction Enzymes
9.19 Plasmids as Vectors
9.20 Polymerase Chain Reaction
9.21 DNA Sequencing Reaction
9.22 Reverse Transcription Polymerase Chain Reaction
9.23 Mutations
Back Matter
Since September 8, 2016
Dr. Tetsuya Watanabe, the author of this book, is a President of Watanabe Institute of Mathematical Biology, Hamamatsu, Japan. He graduated from Kanagawa Dental College, Japan and holds a DDS degree in dental medicine. He received Postgraduate Training and Fellowship Appointments and successively Faculty Appointments of Instructor and Associate at Dept. of Pharmacology, University of Pennsylvania, Philadelphia, USA. He was an Assistant Professor, Dept. of Pharmacology, Medical School, University of Pennsylvania from 1977 to 1980.
Chemical process proceeds toward the state of lowered Gibbs energy usually accompanied by increasing randomness. If outer most electrons of atoms interact, they will form bonding only when their molecular orbitals become in lower energy state. The quantum theory is applied to chemistry to explain chemical bonding and reactions. Experimental approach to biology has demonstrated that functions of living cells are regulated by charged or polar signaling small molecules called ligands. On the other hand physical approach explains the selective permeability of membrane which causes osmosis and the membrane potential. In the nucleus of the cell there are chromosomes made by DNA. The genetic code on DNA is carried out by m-RNA which provides the basic instructions for production of proteins in the cytoplasm. Because enzymes are proteins, their activity might be changed if the code marked on DNA is changed by mutation that could cause diseases.
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