Bergethon P.R. The physical basis of biochemistry: the foundations of molecular biophysics (New York, 2010). - ОГЛАВЛЕНИЕ / CONTENTS
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ОбложкаBergethon P.R. The physical basis of biochemistry: the foundations of molecular biophysics. - 2nd ed. - New York: Springer, 2010. - xxix, 949 p.: ill. (some col.). - Bibliogr. at the end of the chapters. - Ind.: p.923-942. - ISBN 978-1-4419-6323-9
 

Оглавление / Contents
 
Part I  Principles of Biophysical Inquiry

1  Introduction: To the Student - First Edition ................. 3
2  Philosophy and Practice of Biophysical Study ................. 5
   2.1  What Is Biophysical Chemistry and Why Study It? ......... 5
   2.2  Science Is Not Content but a Unique Method of
        Discovery ............................................... 6
   2.3  The Progression of Inquiry Guides the Scientific
        Modeling Process ........................................ 8
   2.4  A Brief History of Human Methods of Inquiry Reveals
        Important Aspects of the Scientific Method .............. 9
   2.5  The Gedanken Experiment Is a Thought Experiment ........ 12
   2.6  The Beginnings of Modern Science- Kepler and Galileo ... 14
   2.7  Modern Biophysical Studies Still Follow the Paradigm
        of Kepler and Galileo .................................. 16
   Further Reading ............................................. 20
   Problem Sets ................................................ 22
3  Overview of the Biological System Under Study ............... 23
   3.1  Hierarchies of Abstraction Are Essential in the Study
        of Biophysical Chemistry ............................... 24
   3.2  An Overview of the Cell: The Essential Building
        Block of Life .......................................... 25
   3.3  Control Mechanisms Are Essential Process Elements
        of the Biological State Space .......................... 33
   3.4  Biological Energy Transduction Is an Essential
        Process that Provides Energy to Ensure the High
        Degree of Organization Necessary for Life .............. 34
   3.5  The Cell Is a Building Block of Chemical and
        Biological Organization and Also a Key to the Study
        of Biological Complexity ............................... 44
   3.6  A Brief History of Life ................................ 45
   3.7  Evolution Can Be Modeled as a Dynamic Process with
        Many Bifurcations in the State Space of Life ........... 46
   Further Reading ............................................. 54
   Problem Sets ................................................ 55
4  Physical Thoughts, Biological Systems - The Application
   of Modeling Principles to Understanding Biological
   Systems ..................................................... 57
   4.1  The Interaction Between Formal Models and Natural
        Systems Is the Essence of Physical and Biophysical
        Science ................................................ 57
   4.2  Observables Are the Link Between Observer and
        Reality ................................................ 58
   4.3  Systems Science Guides the Linkage of Natural and
        Formal Models .......................................... 60
   4.4  Abstraction and Approximation May Be Useful but Are
        Not Always Correct ..................................... 61
   4.5  The Choices Made in Observables and Measurement
        Influence What Can Be Known About a System ............. 62
   4.6  The Simplifying Concept of Abstraction Is Central to
        Both Scientific Understanding and Misconception ........ 64
   4.7  Equations of State Capture the System Behavior or
        "Systemness" ........................................... 65
   4.8  Equivalent Descriptions Contain the Same Information ... 67
   4.9  Symmetry and Symmetry Operations Allow Molecules to
        Be Placed in Groups .................................... 69
   4.10 The Goodness of the Model Depends on Where You Look
        with Bifurcation Leading to New Discovery .............. 71
   4.11 Bifurcations in State Space Characterize Complex
        Systems ................................................ 72
   4.12 Catastrophes and Chaos Are Examples of Formal
        Mathematical Systems That May Capture Important
        Behaviors of Natural Systems ........................... 74
   Further Reading ............................................. 78
   Problem Sets ................................................ 80
5  Probability and Statistics .................................. 81
   5.1  An Overview of Probability and Statistics .............. 82
   5.2  Discrete Probability Counts the Number of Ways Things
        Can Happen ............................................. 82
   5.3  Specific Techniques Are Needed for Discrete Counting ... 84
   5.4  Counting Conditional and Independent Events That
        Occur in Multistage Experiments Require Special
        Considerations ......................................... 87
   5.5  Discrete Distributions Come from Counting Up the
        Outcomes of Repeated Experiments ....................... 89
   5.6  Continuous Probability Is Represented as a Density
        of Likelihood Rather Than by Counting Events ........... 94
   Further Reading ............................................ 105
   Problem Sets ............................................... 105

Part II Foundations

6  Energy and Force - The Prime Observables ................... 109
   6.1  Experimental Models Are a Careful Abstraction of
        Either Descriptive or Explanatory Models .............. 109
   6.2  Potential Energy Surfaces Are Tools that Help Find
        Structure Through the Measurement of Energy ........... 110
   6.3  Conservative Systems Find Maximal Choice by
        Balancing Kinetic and Potential Energies Over Time .... 113
   6.4  Forces in Biological Systems Do the Work That
        Influences Structure and Function ..................... 115
   Further Reading ............................................ 122
   Problem Sets ............................................... 123
7  Biophysical Forces in Molecular Systems .................... 125
   7.1  Form and Function in Biomolecular Systems Are
        Governed by a Limited Number of Forces ................ 126
   7.2  Mechanical Motions Can Describe the Behavior of
        Gases and the Migration of Cells ...................... 127
   7.3  The Kinetic Theory of Gases Explains the Properties
        of Gases Based on Mechanical Interactions
        of Molecules .......................................... 129
   7.4  The Electric Force Is the Essential Interaction that
        Leads to the Chemical Nature of the Universe .......... 144
   7.5  Wave Motion Is Important in Electromagnetic and
        Mechanical Interactions in Biological Systems ......... 162
   7.6  Harmonic Waves Are the Result of a Sinusoidal
        Oscillation ........................................... 167
   7.7  Energy and Intensity of Waves ......................... 174
   7.8  Standing Waves ........................................ 176
   7.9  Superposition and Interference - Waves of Different
        Frequencies ........................................... 179
   7.10 Complex Waveforms ..................................... 181
   7.11 Wave Packets .......................................... 182
   7.12 Dispersion ............................................ 184
   7.13 The Wave Equation ..................................... 185
   7.14 Waves in Two and Three Dimensions ..................... 186
   Further Reading ............................................ 189
   Problem Sets ............................................... 189
8  Physical Principles: Quantum Mechanics ..................... 191
   8.1  The Story of the Discovery of Quantum Mechanics
        Is an Instructive History of How Scientific Ideas
        Are Modified .......................................... 192
   8.2  From the Standpoint of the Philosophy of
        Epistemological Science, the Quantum Revolution
        Ended an Age of Certainty ............................. 192
   8.3  The Ultraviolet Catastrophe Is a Term That Refers
        to a Historical Failure of Classical Theory ........... 194
   8.4  The Concept of Heat Capacity Was Modified by Quantum
        Mechanical Considerations ............................. 202
   8.5  The Photoelectric Effect and the Photon-Particle
        Properties of Radiation Could Be Understood Using
        Planck's Quanta ....................................... 203
   8.6  Electromagnetic Radiation Has a Dual Nature ........... 205
   8.7  de Broglie's Postulate Defines the Wavelike
        Properties of Particles ............................... 206
   8.8  The Electron Microscope Employs Particles as Waves
        to Form Images ........................................ 207
   8.9  The Uncertainty Principle Is an Essential Conclusion
        of the Quantum Viewpoint .............................. 209
   8.10 An Historical Approach to Understanding Atomic
        Structure and the Atom ................................ 210
   8.11 Quantum Mechanics Requires the Classical Trajectory
        Across a Potential Energy Surface to be Replaced by
        the Wavefunction ...................................... 218
   8.12 Solutions to the Time-Independent Schrцdinger
        Theory ................................................ 224
   8.13 Building the Atomic Model - One-Electron Atoms ........ 235
   8.14 Building the Atomic Model - Multi-electron Atoms ...... 238
   Further Reading ............................................ 240
   Problem Sets ............................................... 241
9  Chemical Principles ........................................ 243
   9.1  Knowing the Distribution of Electrons in Molecules
        Is Essential for Understanding Chemical Structure
        and Behavior .......................................... 243
   9.2  The Nature of Chemical Interactions ................... 244
   9.3  Electrostatic Forces Describe the Interactions from
        Salt Crystals to van der Waals Attraction ............. 244
   9.4  Covalent Bonds Involve a True Sharing of Electrons
        Between Atoms ......................................... 249
   9.5  Hydrogen Bonds Are a Unique Hybrid of Interactions
        and Play a Fundamental Role in the Behavior of
        Biological Systems .................................... 262
   9.6  Biological Systems Are Made from a Limited Number of
        Elements .............................................. 264
   Further Reading ............................................ 266
   Problem Sets ............................................... 267
10 Measuring the Energy of a System: Energetics and the
   First Law of Thermodynamics ................................ 269
   10.1 Historically Heat Was Thought to Be a Fluid or "the
        Caloric" .............................................. 269
   10.2 The Thermodynamic Modeling Space Is a Systemic
        Approach to Describing the World ...................... 271
   10.3 The First Law States that "The Energy of the
        Universe Is Conserved" ................................ 276
   10.4 The Heat Capacity Is a Property that Can Reflect the
        Internal Energy of a System ........................... 283
   10.5 Enthalpy Is Defined When a System Is Held at Constant
        Pressure .............................................. 285
   Thought Questions .......................................... 289
   Further Reading ............................................ 289
   Problem Sets ............................................... 290
11 Entropy and the Second Law of Thermodynamics ............... 293
   11.1 The Arrow of Time and Impossible Existence of
        Perpetual Motion Machines Are Both Manifestations of
        the Second Law of Thermodynamics ...................... 294
        11.1.1 The Movement of a System Toward Equilibrium
               Is the Natural Direction ....................... 295
   11.2 The Design of a Perfect Heat Engine Is an Important
        Thought Experiment .................................... 295
   11.3 A Mechanical/Kinetic Approach to Entropy .............. 307
   11.4 Statistical Thermodynamics Yields the Same
        Conclusions as Classical Treatment of
        Thermodynamics ........................................ 310
   11.5 Entropy Can Be Described and Understood on
        a Statistical Basis ................................... 321
   11.6 The Third Law of Thermodynamics Defines an Absolute
        Measure of Entropy .................................... 324
   Further Reading ............................................ 324
   Problem Sets ............................................... 325
12 Which Way Is That System Going? The Gibbs Free Energy ...... 327
   12.1 The Gibbs Free Energy Is a State Function that
        Indicates the Direction and Position of a System's
        Equilibrium ........................................... 327
   12.2 The Gibbs Free Energy Has Specific Properties ......... 329
   12.3 The Free Energy Per Mole, μ, Is an Important
        Thermodynamic Quantity ................................ 333
   12.4 The Concept of Activity Relates an Ideal System to
        a Real System ......................................... 333
   12.5 The Application of Free Energy Considerations to
        Multiple-Component Systems ............................ 334
   12.6 The Chemical Potential Is an Important Driving
        Force in Biochemical Systems .......................... 335
   12.7 Entropy and Enthalpy Contribute to Calculations
        of the Free Energy of Mixing .......................... 337
   12.8 Finding the Chemical Equilibrium of a System Is
        Possible by Making Free Energy Calculations ........... 340
   12.9 The Thermodynamics of Galvanic Cells Is Directly
        Related to the Gibbs Free Energy ...................... 345
   12.10 Free Energy Changes Relate the Equilibrium Position
        of Biochemical Reactions .............................. 348
   Further Reading ............................................ 348
   Problem Sets ............................................... 349
13 The Thermodynamics of Phase Equilibria ..................... 351
   13.1 The Concept of Phase Equilibrium Is Important
        in Biochemical Systems ................................ 351
   13.2 Thermodynamics of Transfer Between Phases ............. 353
   13.3 The Phase Rule Relates the Number of Variables of
        State to the Number of Components and Phases at
        Equilibrium ........................................... 353
   13.4 The Equilibrium Between Different Phases Is Given
        by the Clapeyron Equation ............................. 355
   13.5 Surface Phenomena Are an Important Example of Phase
        Interaction ........................................... 362
   13.6 Binding Equilibria Relate Small Molecule Binding
        to Larger Arrays ...................................... 364
   Further Reading ............................................ 383
   Problem Sets ............................................... 383

Part III Building a Model of Biomolecular Structure

14 Water: A Unique Solvent and Vital Component of Life ........ 389
   14.1 An Introduction to the Most Familiar of All Liquids ... 389
   14.2 The Physical Properties of Water Are Consistent with
        a High Degree of Intermolecular Interaction ........... 391
   14.3 Considering the Properties of Water as a Liquid ....... 392
   14.4 The Structure of Monomolecular Water Can Be
        Described Using a Variety of Models ................... 394
   14.5 The Capacity of Water to Form Hydrogen Bonds
        Underlies Its Unusual Properties ...................... 398
   14.6 The Structure and Dynamics of Liquid Water Results
        in "Ordered Diversity" That Is Probably Distinct
        from Ice .............................................. 402
   14.7 Hydrophobic Forces Reference Interactions Between
        Water and Other Molecules ............................. 405
   Further Reading ............................................ 407
   Problem Sets ............................................... 408
15 Ion-Solvent Interactions ................................... 409
   15.1 The Nature of Ion-Solvent Interactions Can Be
        Discovered Through the Progression of Inquiry ......... 409
   15.2 The Born Model Is a Thermodynamic Cycle That Treats
        the Interaction Energy Between a Simplified Ion and
        a Structureless Solvent ............................... 410
   15.3 Adding Water Structure to the Solvent Continuum ....... 418
   15.4 Extending the Ion-Solvent Model Beyond the Born
        Model ................................................. 429
   15.5 Solutions of Inorganic Ions ........................... 435
   15.6 Ion-Solvent Interactions in Biological Systems ........ 437
   Further Reading ............................................ 438
   Problem Sets ............................................... 438
16 Ion-Ion Interactions ....................................... 441
   16.1 Ion-Ion Interactions Can Be Modeled and These Models
        Can Be Experimentally Validated and Refined ........... 441
   16.2 The Debye-Hückel Model Is a Continuum Model That
        Relates a Distribution of Nearby Ions to a Central
        Reference Ion ......................................... 444
   16.3 The Predictions Generated by the Debye-Hückel Model
        Can Be Experimentally Evaluated ....................... 453
   16.4 More Rigorous Treatment of Assumptions Leads to an
        Improved Performance of the Debye-Hückel Model ....... 455
   16.5 Consideration of Other Interactions Is Necessary to
        Account for the Limits of the Debye-Hückel Model ..... 457
        16.5.1 Bjerrum Suggested That Ion Pairing Could
               Affect the Calculation of Ion-Ion
               Interactions ................................... 457
   Further Reading ............................................ 458
   Problem Sets ............................................... 459
17 Lipids in Aqueous Solution ................................. 461
   17.1 Biological Membranes Form at the Interface Between
        Aqueous and Lipid Phases .............................. 461
   17.2 Aqueous Solutions Can Be Formed with Small Nonpolar
        Molecules ............................................. 462
   17.3 Aqueous Solutions of Organic Ions Are an Amalgam of
        Ion-Solvent and Nonpolar Solute Interaction ........... 465
   17.4 Lipids Can Be Placed into Several Major Classes ....... 468
   17.5 The Organization of Lipids into Membranes Occurs
        When Aqueous and Lipid Phases Come in Contact ......... 474
   17.6 The Physical Properties of Lipid Membranes ............ 478
   17.7 Biological Membranes: A More Complete Picture ......... 482
   Further Reading ............................................ 483
18 Macromolecules in Solution ................................. 485
   18.1 The Physical Interactions of Polymers in Solution
        Are Not Unique but Modeling the Interactions Will
        Require Different Considerations Than Those of
        Smaller Molecules ..................................... 486
   18.2 Thermodynamics of Solutions of Polymers ............... 487
   18.3 The Conformation of Simple Polymers Can Be Modeled
        by a Random Walk and a Markov Process ................. 505
   18.4 The Major Classes of Biochemical Species Form
        Macromolecular Structures ............................. 506
   18.5 Nonpolar Polypeptides in Solution ..................... 523
   18.6 Polar Polypeptides in Solution ........................ 527
   18.7 Transitions of State .................................. 531
   18.8 The Protein Folding Problem ........................... 538
   18.9 Pathological Protein Folding .......................... 542
   Further Reading ............................................ 549
   Problem Sets ............................................... 551
19 Molecular Modeling - Mapping Biochemical State Space ....... 553
   19.1 The Prediction of Macromolecular Structure and
        Function Is a Goal of Molecular Modeling .............. 553
   19.2 Molecular Modeling Is Built on Familiar Principles .... 554
   19.3 Empirical Methods Use Carefully Constructed Physical
        Models ................................................ 555
   19.4 Computational Methods Are the Ultimate Gedanken
        Experiments ........................................... 569
   19.5 Molecular Mechanics Is a Newtonian or Classical
        Mechanical Modeling Approach .......................... 571
   19.6 Quantum Mechanical Methods Are Computational
        Difficult but Theoretically "Pure" .................... 579
   Further Reading ............................................ 581
   Problem Sets ............................................... 582
20 The Electrified Interphase ................................. 583
   20.1 The Interphase Is Formed When Phases Meet ............. 583
   20.2 A Detailed Structural Description of the Interphase
        Is a Task for Physical Study .......................... 587
   20.3 The Simplest Picture of the Interphase Is the
        Helmholtz-Perrin Model ................................ 589
   20.4 The Balance Between Thermal and Electrical Forces Is
        Seen as Competition Between Diffuse-Layer Versus
        Double-Layer Interphase Structures .................... 590
   20.5 The Stern Model Is a Combination of the Capacitor
        and Diffuse Layer Models .............................. 591
   20.6 A More Complete Picture of the Double-Layer Forms
        with Added Detail ..................................... 593
   20.7 Colloidal Systems and the Electrified Interface Give
        Rise to the Lyophilic Series .......................... 595
   20.8 Salting Out Can Be Understood in Terms of
        Electrified Interphase Behavior ....................... 599
   Further Reading ............................................ 600
   Problem Sets ............................................... 600

Part IV  Function and Action Biological State Space

21 Transport - A Non-equilibrium Process ...................... 605
   21.1 Transport Is an Irreversible Process and Does Not
        Occur at Equilibrium .................................. 605
   21.2 The Principles of Non-equilibrium Thermodynamics Can
        Be Related to the More Familiar Equilibrium Treatment
        with the Idea of Local Equilibrium .................... 606
   Further Reading ............................................ 610
22 Flow in a Chemical Potential Field: Diffusion .............. 611
   22.1 Transport in Chemical, Electrical, Pressure, and
        Thermal Gradients Are All Treated with the Same
        Mathematics ........................................... 611
   22.2 Diffusion or the Flow of Particles Down
        a Concentration Gradient Can Be Described
        Phenomenologically .................................... 612
   22.3 The Random Walk Forms the Basis for a Molecular
        Picture of Flux ....................................... 616
   Further Reading ............................................ 622
   Problem Sets ............................................... 622
23 Flow in an Electric Field: Conduction ...................... 625
   23.1 Transport of Charge Occurs in an Electric Field ....... 625
   23.2 Describing a System of Ionic Conduction Includes
   Electronic, Electrodic, and Ionic Elements ................. 627
   23.3 The Flow of Ions Down a Electrical Gradient Can Be
        Described Phenomenologically .......................... 631
   23.4 A Molecular View of Ionic Conduction .................. 637
   23.5 Interionic Forces Affect Conductivity ................. 640
   23.6 Proton Conduction Is a Special Case that Has a Mixed
        Mechanism ............................................. 643
   Further Reading ............................................ 646
   Problem Sets ............................................... 647
24 Forces Across Membranes .................................... 649
   24.1 Energetics and Force in Membranes ..................... 649
   24.2 The Donnan Equilibrium Is Determined by a Balance
        Between Chemical and Electrical Potential in a Two-
        Phase System .......................................... 650
   24.3 Electric Fields Across Membranes Are of Substantial
        Magnitude ............................................. 653
   24.4 Electrostatic Profiles of the Membrane Are Potential
        Energy Surfaces Describing Forces in the Vicinity of
        Membranes ............................................. 657
   24.5 The Electrochemical Potential Is a Thermodynamic
        Treatment of the Gradients Across a Cellular
        Membrane .............................................. 661
   24.6 Transport Through the Lipid Bilayer of Different
        Molecules Requires Various Mechanisms ................. 661
   Further Reading ............................................ 666
   Problem Sets ............................................... 667
25 Kinetics - Chemical Kinetics ............................... 669
   25.1 The Equilibrium State Is Found by Chemical
        Thermodynamics but Chemical Kinetics Tells the Story
        of Getting There ...................................... 670
   25.2 A Historical Perspective on the Development of
        Chemical Kinetics ..................................... 671
   25.3 Kinetics Has a Specific and Systemic Language ......... 675
   25.4 Order of a Reaction Relates the Concentration of
        Reactants to the Reaction Velocity .................... 676
   25.5 Expressions of the Rate Laws Are Important
        Properties of a Reaction .............................. 677
   25.6 Elementary Reactions Are the Elements of the
        System That Defines a Chemical Mechanism .............. 681
   25.7 Reaction Mechanisms Are a System of Interacting
        Elements (Molecules) in the Context of a Potential
        Energy Surface ........................................ 682
   25.8 Solution Kinetics Are More Complicated Than the
        Simple Kinetic Behavior of Gases ...................... 699
   25.9 Enzymes Are Macromolecular Catalysts with Enormous
        Efficiency ............................................ 699
   Further Reading ............................................ 710
   Problem Sets ............................................... 710
26 Dynamic Bioelectrochemistry - Charge Transfer in
   Biological Systems ......................................... 713
   26.1 Electrokinetics and Electron Charge Transfer Depend
        on Electrical Current Flow in Biochemical Systems ..... 713
   26.2 Electrokinetic Phenomena Occur When the Elements of
        the Biological Electrical Double Layer Experience
        Either Mechanical or Electrical Transport ............. 714
   26.3 Electron Transfer Is an Essential Form of Biological
        Charge Transfer ....................................... 722
   Further Reading ............................................ 736
   Problem Sets ............................................... 737

Part V  Methods for the Measuring Structure and Function

27 Separation and Characterization of Biomolecules Based
   on Macroscopic Properties .................................. 741
   27.1 Introduction: Mechanical Motion Interacts with Mass,
        Shape, Charge, and Phase to Allow Analysis of
        Macromolecular Structure .............................. 742
   27.2 Buoyant Forces Are the Result of Displacement of the
        Medium by an Object ................................... 742
   27.3 Systems Study in the Biological Science Requires
        Methods of Separation and Identification to Describe
        the "State of a Biological System" .................... 760
   27.4 Electrophoresis Is a Practical Application of
        Molecular Motion in an Electrical Field Based on
        Charge and Modified by Conformation and Size .......... 760
   27.5 Chromatographic Techniques Are Based on the
        Differential Partitioning of Molecules Between Two
        Phases in Relative Motion ............................. 763
   27.6 The Motion Induced by a Magnetic Interaction Is
        Essential for Determination of Molecular Mass in
        Modern Biological Investigations ...................... 767
   Further Reading ............................................ 775
   Problem Sets ............................................... 775
28 Analysis of Molecular Structure with Electronic
   Spectroscopy ............................................... 779
   28.1 The Interaction of Light with Matter Allows
        Investigation of Biochemical Properties ............... 780
   28.2 The Motion of a Dipole Radiator Generates
        Electromagnetic Radiation ............................. 780
   28.3 Optical Interactions Can Be Treated at Varying
        Levels of Abstraction ................................. 780
   28.4 Atomic and Molecular Energy levels Are a Quantum
        Phenomenon That Provide a Window on Molecular
        Structure ............................................. 782
   28.5 Absorption Spectroscopy Has Important Applications
        to Biochemical Analysis ............................... 789
   28.6 Fluorescence and Phosphorescence Occur When Trapped
        Photon Energy Is Re-radiated After a Finite
        Lifetime .............................................. 794
   28.7 Electron Paramagnetic Resonance (EPR) and Nuclear
        Magnetic Resonance (NMR) Depend on Interactions
        Between Photons and Molecules in a Magnetic Field ..... 797
   Further Reading ............................................ 812
   Problem Sets ............................................... 813
29 Molecular Structure from Scattering Phenomena .............. 815
   29.1 The Interference Patterns Generated by the
        Interaction of Waves with Point Sources Is
        a Valuable Tool in the Analysis of Structure .......... 815
   29.2 Diffraction Is the Result of the Repropagation of
        a Wave ................................................ 819
   29.3 X-Ray Diffraction Is a Powerful Fool for Structure
        Determination ......................................... 822
   29.4 Scattering of Light Rather Than Its Absorption Can
        Be Used to Probe Molecular Structure and
        Interaction ........................................... 831
   Further Reading ............................................ 835
30 Analysis of Structure - Microscopy ......................... 837
   30.1 Seeing Is Believing ................................... 837
   30.2 The Light Microscope Allows Visualization of
        Structures on the Dimensional Scale of the
        Wavelength of a Photon ................................ 839
   30.3 Visualization Requires Solving the Problem of
        Contrast .............................................. 843
   30.4 Scanning Probe Microscopy Creates an Image of a
        Structures by Interactions on a Molecular Scale ....... 849
   Further Reading ............................................ 854
   Problem Sets ............................................... 855
31 Epilogue ................................................... 857
   Now Try .................................................... 857
32 Physical Constants ......................................... 859
   Conversions ................................................ 859

Appendix A: Mathematical Methods .............................. 861
   A.l  Units and Measurement ................................. 861
   A.2  Exponents and Logarithms .............................. 862
   A.3  Trigonometric Functions ............................... 865
   A.4  Expansion Series ...................................... 869
   A.5  Differential and Integral Calculus .................... 870
   A.6  Partial Differentiation ............................... 870
   A.7  Vectors ............................................... 872
Appendix B: Quantum Electrodynamics ........................... 875
Appendix C: The Pre-Socratic Roots of Modern Science .......... 877
Appendix D: The Poisson Function .............................. 879
Appendix E: Assumptions of a Theoretical Treatment of the
   Ideal Gas Law .............................................. 881
Appendix F: The Determination of the Field from the
   Potential in Cartesian Coordinates ......................... 883
Appendix G: Geometrical Optics ................................ 885
   G.l  Reflection and Refraction of Light .................... 885
   G.2  Mirrors ............................................... 886
   G.3  Image Formation by Refraction ......................... 889
   G.4  Prisms and Total Internal Reflection .................. 891
Appendix H: The Compton Effect ................................ 893
Appendix I: Hamilton's Principle of Least Action/Fermat's
   Principle of Least Time .................................... 895
Appendix J: Derivation of the Energy of Interaction Between
   Two Ions ................................................... 897
Appendix K: Derivation of the Statement, qrev > qirrev ......... 899
Appendix L: Derivation of the Clausius-Clapeyron Equation ..... 901
Appendix M: Derivation of the van't Hoff Equation for
   Osmotic Pressure ........................................... 903
Appendix N: Fictitious and Pseudoforces - The Centrifugal
   Force ...................................................... 905
Appendix O: Derivation of the Work to Charge and Discharge
   a Rigid Sphere ............................................. 907
Appendix P: Review of Circuits and Electric Current ........... 909
   P.l  Current Density and Flux .............................. 909
   P.2  Circuits .............................................. 911
   P.3  Measuring Instruments ................................. 916
Appendix Q: Fermi's Golden Rule ............................... 919
Appendix R: The Transition from Reactant to Product:
   Adiabatic and Non-adiabatic Transitions .................... 921

Index ......................................................... 923


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