biophysics - gbv · 2.5 secondary bonds 21 exercises 22 further reading 22 3 energies, forces and...
TRANSCRIPT
BiophysicsAn Introduction
Rodney M. J. Cotterill
Preface
x i
1 Introduction
1Exercises
6Further reading
6
2 Chemical Binding
72 .1 Quantum Mechanics
72 .2 Pauli Exclusion Principle
92 .3 Ionization Energy, Electron Affinity and Chemical Binding
1 02 .4 Electronegativity and Strong Bonds
1 52 .5 Secondary Bonds
2 1Exercises
22Further reading
22
3 Energies, Forces and Bonds
233 .1 Interatomic Potentials for Strong Bonds
2 33 .2 Interatomic Potentials for Weak Bonds
2 93 .3 Non-central Forces
3 23 .4 Bond Energies
3 33 .5 Spring Constants
3 9Exercises
4 0Further reading
4 1
4 Rates of Reaction
434.1 Free Energy
4 34.2 Internal Energy
4 54 .3 Thermodynamics and Statistical Mechanics
4 64 .4 Reaction Kinetics
5 54 .5 Water, Acids, Bases and Aqueous Reactions
5 94 .6 Radiation Energy
6 5Exercises
6 7Further reading
68
5 Transport Processes
695 .1 Diffusion
6 9
5 .2 Viscosity
7 6
5 .3 Thermal Conduction
8 0
Exercises
8 1
Further reading
8 1
6 Some Techniques and Methods
836 .1 X-Ray Diffraction and Molecular Structure
8 3
6 .2 Nuclear Magnetic Resonance
9 3
6.3 Scanning Tunnelling Microscopy
9 8
6.4 Atomic Force Microscopy
102
6 .5 Optical Tweezers
10 3
6 .6 Patch Clamping
108
6 .7 Molecular Dynamics
11 2
6 .8 Potential Energy Contour Tracing
11 5
Exercises
11 8
Further reading
11 9
7 Biological Polymers
1237 .1 Nucleic Acids
124
7 .2 Nucleic Acid Conformation : DNA
129
7 .3 Nucleic Acid Conformation : RNA
132
7 .4 Proteins
134
7 .5 Protein Folding
15 1
Exercises
15 7
Further reading
15 8
8 Biological Membranes
1618 .1 Historical Background
16 1
8 .2 Membrane Chemistry and Structure
16 6
8 .3 Membrane Physics
17 4
Exercises
18 4
Further reading
18 5
9 Biological Energy
1879 .1 Energy Consumption
18 7
9 .2 Respiration
18 8
9 .3 Photosynthesis
19 0
9 .4 ATP Synthesis
19 9
Exercises
20 6
Further reading
20 7
10 Movement of Organisms
20910 .1 Bacterial Motion
209
10 .2 Chemical Memory in Primitive Organisms
218
10 .3 Muscular Movement
220
10 .4 Human Performance
23 3Exercises
23 5Further reading
235
11 Excitable Membranes
23711 .1 Diffusion and Mobility of Ions
23711 .2 Resting Potential
240
Exercises
246
Further reading
246
12 Nerve Signals
24912 .1 Passive Response
249
12 .2 Nerve Impulses (Action Potentials)
25 6
12 .3 The Nervous System
26 8
Exercises
27 5
Further reading
27 5
13 Memory
27713 .1 Hebbian Learning
27 7
13 .2 Neural Networks
28 1
13 .3 Auto-association
28 8
Exercises
29 3
Further reading
29 4
14 Control of Movement
29714 .1 The Primacy of Movement
29 7
14 .2 Ballistic Control in a Simplified Visual System
29 9
14 .3 More Sophisticated Modes of Control
30 4
14 .4 The Heterogeneous Structure of Muscle Fibres
30 5
14 .5 Central Pattern Generators
30 7
14 .6 Conditioned Reflexes
31 1
14 .7 Volition and Free Will
31 4
14 .8 What Purpose Does Consciousness Serve?
32 0
14 .9 Passive versus Active in Mental Processing
32 5
14 .10 The Relevant Anatomy and Physiology
32 8
14 .11 Intelligence and Creativity
33 5
14 .12 A Final Word
33 8Exercises
33 9Further reading
33 9
Appendix A: Elements of Quantum Mechanics
343A.1 Quantization of Energy
343A.2 Atomic Structure
345A.3 The Wave Equation
347A.4 Quantum Mechanical Tunnelling
350
Exercises
35 2Further reading
35 2
Appendix B: The Hydrogen Atom
353B.1 The Hamiltonian
35 3B.2 The Hydrogen Atom
35 3B.3 Solution of the di Equation
35 6B.4 Solution of the O Equation
35 7B.5 Solution of the R Equation
35 8B.6 Quantum Numbers and Energy Levels
360B.7 Wave Functions
360Exercises
364Further reading
364
Appendix C: Thermal Motion
365C.1 Ideal Gases
365C.2 Liquids
369Exercises
37 1Further reading
37 1
Appendix D : Probability Distributions
373D.1 Bernoulli Trials and the Binomial Distribution
37 3D.2 The Poisson Approximation
37 3D.3 The Normal, or Gaussian, Distribution
37 5Further reading
37 6
Appendix E : Differential Equations
377Further reading
37 9
Name Index
38 1Subject Index
385