Theoretical molecular biophysics:
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Heidelberg [u.a.]
Springer
2010
|
| Series: | Biological and medical physics, biomedical engineering
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIII, 371 S. graph. Darst. |
| ISBN: | 9783540856092 |
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| 245 | 1 | 0 | |a Theoretical molecular biophysics |c P. O. J. Scherer ; Sighart F. Fischer |
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Record in the Search Index
| _version_ | 1804142697725820928 |
|---|---|
| adam_text | Titel: Theoretical molecular biophysics
Autor: Scherer, Philipp Otto Julius
Jahr: 2010
Contents
Part I Statistical Mechanics of Biopolymers
1 Random Walk Models for the Conformation............... 3
1.1 The Freely Jointed Chain................................. 3
1.1.1 Entropic Elasticity ................................ 4
1.1.2 Force-Extension Relation........................... 6
1.2 Two-Component Model .................................. 9
1.2.1 Force-Extension Relation........................... 9
1.2.2 Two-Component Model with Interactions............. 11
Problems ................................................... 16
2 Flory?Huggins Theory for Biopolymer Solutions........... 19
2.1 Monomeric Solution ..................................... 19
2.2 Polymeric Solution ...................................... 22
2.3 Phase Transitions ....................................... 26
2.3.1 Stability Criterion................................. 26
2.3.2 Critical Coupling.................................. 28
2.3.3 Phase Diagram.................................... 30
Problems ................................................... 33
Part II Protein Electrostatics and Solvation
3 Implicit Continuum Solvent Models ....................... 37
3.1 Potential of Mean Force.................................. 37
3.2 Dielectric Continuum Model.............................. 38
3.3 Born Model............................................. 39
3.4 Charges in a Protein..................................... 40
3.5 Generalized Born Models................................. 43
VIII Contents
4 Debye-Hiickel Theory..................................... 45
4.1 Electrostatic Shielding by Mobile Charges.................. 45
4.2 1-1 Electrolytes......................................... 46
4.3 Charged Sphere......................................... 47
4.4 Charged Cylinder ....................................... 49
4.5 Charged Membrane (Gouy-Chapman Double Layer)......... 52
4.6 Stern Modification of the Double Layer..................... 57
Problems ................................................... 58
5 Protonation Equilibria..................................... 61
5.1 Protonation Equilibria in Solution......................... 61
5.2 Protonation Equilibria in Proteins......................... 64
5.2.1 Apparent pi a Values.............................. 65
5.2.2 Protonation Enthalpy.............................. 66
5.2.3 Protonation Enthalpy Relative to the Uncharged State . 68
5.2.4 Statistical Mechanics of Protonation................. 69
5.3 Abnormal Titration Curves of Coupled Residues ............ 70
Problems ................................................... 71
Part III Reaction Kinetics
6 Formal Kinetics ........................................... 75
6.1 Elementary Chemical Reactions........................... 75
6.2 Reaction Variable and Reaction Rate ...................... 75
6.3 Reaction Order.......................................... 76
6.3.1 Zero-Order Reactions.............................. 77
6.3.2 First-Order Reactions.............................. 77
6.3.3 Second-Order Reactions............................ 77
6.4 Dynamical Equilibrium................................... 78
6.5 Competing Reactions.................................... 79
6.6 Consecutive Reactions ................................... 79
6.7 Enzymatic Catalysis..................................... 80
6.8 Reactions in Solutions.................................... 82
6.8.1 Diffusion-Controlled Limit.......................... 83
6.8.2 Reaction-Controlled Limit.......................... 84
Problems ................................................... 84
7 Kinetic Theory: Fokker?Planck Equation.................. 87
7.1 Stochastic Differential Equation for Brownian Motion........ 87
7.2 Probability Distribution.................................. 89
7.3 Diffusion............................................... 90
7.3.1 Sharp Initial Distribution........................... 91
7.3.2 Absorbing Boundary............................... 92
7.4 Fokker-Planck Equation for Brownian Motion............... 93
Contents IX
7.5 Stationary Solution to the Focker-Planck Equation.......... 94
7.6 Diffusion in an External Potential......................... 96
7.7 Large Friction Limit: Smoluchowski Equation............... 98
7.8 Master Equation........................................ 98
Problems ................................................... 98
8 Kramers Theory..........................................101
8.1 Kramers Model.........................................101
8.2 Kramers Calculation of the Reaction Rate .................102
9 Dispersive Kinetics........................................107
9.1 Dichotomous Model......................................107
9.1.1 Fast Solvent Fluctuations ..........................110
9.1.2 Slow Solvent Fluctuations..........................Ill
9.1.3 Numerical Example (Fig. 9.3).......................112
9.2 Continuous Time Random Walk Processes..................112
9.2.1 Formulation of the Model ..........................112
9.2.2 Exponential Waiting Time Distribution..............114
9.2.3 Coupled Equations................................115
9.3 Power Time Law Kinetics ................................119
Problems ...................................................121
Part IV Transport Processes
10 Nonequilibrium Thermodynamics..........................125
10.1 Continuity Equation for the Mass Density..................125
10.2 Energy Conservation.....................................127
10.3 Entropy Production .....................................128
10.4 Phenomenological Relations ..............................130
10.5 Stationary States........................................130
Problems ...................................................132
11 Simple Transport Processes................................133
11.1 Heat Transport .........................................133
11.2 Diffusion in an External Electric Field .....................134
Problems ...................................................136
12 Ion Transport Through a Membrane.......................139
12.1 Diffusive Transport......................................139
12.2 Goldman-Hodgkin-Katz Model...........................141
12.3 Hodgkin-Huxley Model..................................144
X Contents
13 Reaction-Diffusion Systems................................147
13.1 Derivation..............................................147
13.2 Linearization............................................148
13.3 Fitzhugh-Nagumo Model.................................149
Part V Reaction Rate Theory
14 Equilibrium Reactions.....................................155
14.1 Arrhenius Law..........................................155
14.2 Statistical Interpretation of the Equilibrium Constant........157
15 Calculation of Reaction Rates .............................159
15.1 Collision Theory ........................................159
15.2 Transition State Theory..................................162
15.3 Comparison Between Collision Theory and Transition State
Theory.................................................164
15.4 Thermodynamical Formulation of TST.....................165
15.5 Kinetic Isotope Effects...................................166
15.6 General Rate Expressions ................................168
15.6.1 The Flux Operator................................168
Problems ...................................................170
16 Marcus Theory of Electron Transfer.......................173
16.1 Phenomenological Description of ET.......................173
16.2 Simple Explanation of Marcus Theory......................175
16.3 Free Energy Contribution of the Nonequilibrium
Polarization ............................................177
16.4 Activation Energy.......................................180
16.5 Simple Model Systems...................................184
16.5.1 Charge Separation.................................186
16.5.2 Charge Shift......................................186
16.6 The Energy Gap as the Reaction Coordinate................187
16.7 Inner-Shell Reorganization................................189
16.8 The Transmission Coefficient for Nonadiabatic
Electron Transfer........................................189
Problems ...................................................190
Part VI Elementary Photophysics
17 Molecular States...........................................195
17.1 Born-Oppenheimer Separation............................195
17.2 Nonadiabatic Interaction.................................197
Contents XI
18 Optical Transitions........................................201
18.1 Dipole Transitions in the Condon Approximation............201
18.2 Time Correlation Function Formalism......................202
Problems ...................................................203
19 The Displaced Harmonic Oscillator Model.................205
19.1 The Time Correlation Function in the Displaced Harmonic
Oscillator Approximation.................................205
19.2 High-Frequency Modes...................................206
19.3 The Short-Time Approximation...........................207
20 Spectral Diffusion .........................................209
20.1 Dephasing..............................................209
20.2 Gaussian Fluctuations ...................................211
20.2.1 Long Correlation Time.............................212
20.2.2 Short Correlation Time............................213
20.3 Markovian Modulation...................................214
Problems ...................................................217
21 Crossing of Two Electronic States .........................219
21.1 Adiabatic and Diabatic States.............................219
21.2 Semiclassical Treatment..................................223
21.3 Application to Diabatic ET...............................224
21.4 Crossing in More Dimensions .............................225
Problems ...................................................227
22 Dynamics of an Excited State .............................229
22.1 Green s Formalism.......................................230
22.2 Ladder Model...........................................233
22.3 A More General Ladder Model............................237
22.4 Application to the Displaced Oscillator Model...............240
Problems ...................................................242
Part VII Elementary Photoinduced Processes
23 Photophysics of Chlorophylls and Carotenoids.............247
23.1 MO Model for the Electronic States........................248
23.2 The Free Electron Model for Polyenes......................249
23.3 The LCAO Approximation ...............................250
23.4 Hiickel Approximation...................................251
23.5 Simplified CI Model for Polyenes..........................253
23.6 Cyclic Polyene as a Model for Porphyrins...................253
23.7 The Four Orbital Model for Porphyrins ....................254
23.8 Energy Transfer Processes................................256
Problems...................................................257
XII Contents
24 Incoherent Energy Transfer................................259
24.1 Excited States ..........................................259
24.2 Interaction Matrix Element...............................260
24.3 Multipole Expansion of the Excitonic Interaction............262
24.4 Energy Transfer Rate....................................263
24.5 Spectral Overlap........................................264
24.6 Energy Transfer in the Triplet State.......................268
25 Coherent Excitations in Photosynthetic Systems...........269
25.1 Coherent Excitations.....................................270
25.1.1 Strongly Coupled Dimers...........................270
25.1.2 Excitonic Structure of the Reaction Center...........273
25.1.3 Circular Molecular Aggregates......................274
25.1.4 Dimerized Systems of LH2..........................280
25.2 Influence of Disorder.....................................285
25.2.1 Symmetry-Breaking Local Perturbation..............285
25.2.2 Periodic Modulation...............................287
25.2.3 Diagonal Disorder.................................290
25.2.4 Off-Diagonal Disorder..............................292
Problems ...................................................293
26 Ultrafast Electron Transfer Processes
in the Photosynthetic Reaction Center ....................297
27 Proton Transfer in Biomolecules...........................301
27.1 The Proton Pump Bacteriorhodopsin......................301
27.2 Born-Oppenheimer Separation............................303
27.3 Nonadiabatic Proton Transfer (Small Coupling).............305
27.4 Strongly Bound Protons..................................306
27.5 Adiabatic Proton Transfer................................308
Part VIII Molecular Motor Models
28 Continuous Ratchet Models ...............................311
28.1 Transport Equations.....................................311
28.2 Chemical Transitions ....................................313
28.3 The Two-State Model....................................314
28.3.1 The Chemical Cycle...............................314
28.3.2 The Fast Reaction Limit ...........................317
28.3.3 The Fast Diffusion Limit...........................317
28.4 Operation Close to Thermal Equilibrium...................319
Problems...................................................320
29 Discrete Ratchet Models ..................................323
29.1 Linear Model with Two Internal States.....................324
Contents XIII
Part IX Appendix
A The Grand Canonical Ensemble ...........................329
A.l Grand Canonical Distribution.............................32!)
A.2 Connection to Thermodynamics...........................331
B Time Correlation Function of the Displaced Harmonic
Oscillator Model...........................................333
B.l Evaluation of the Time Correlation Function................333
B.2 Boson Algebra..........................................334
B.2.1 Derivation of Theorem 1 ...........................334
B.2.2 Derivation of Theorem 2 ...........................335
B.2.3 Derivation of Theorem 3 ...........................335
B.2.4 Derivation of Theorem 4 ...........................336
C The Saddle Point Method .................................339
Solutions......................................................341
References.....................................................305
Index..........................................................369
|
| any_adam_object | 1 |
| author | Scherer, Philipp O. J. Fischer, Sighart |
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| dewey-ones | 572 - Biochemistry |
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| discipline | Physik Biologie |
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| physical | XIII, 371 S. graph. Darst. |
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| spelling | Scherer, Philipp O. J. Verfasser (DE-588)110745108 aut Theoretical molecular biophysics P. O. J. Scherer ; Sighart F. Fischer Heidelberg [u.a.] Springer 2010 XIII, 371 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biological and medical physics, biomedical engineering Molekulare Biophysik (DE-588)4170391-1 gnd rswk-swf Theoretische Biophysik (DE-588)4185096-8 gnd rswk-swf Molekulare Biophysik (DE-588)4170391-1 s Theoretische Biophysik (DE-588)4185096-8 s DE-604 Fischer, Sighart Verfasser aut Erscheint auch als Online-Ausgabe 978-3-540-85610-8 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020129958&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Scherer, Philipp O. J. Fischer, Sighart Theoretical molecular biophysics Molekulare Biophysik (DE-588)4170391-1 gnd Theoretische Biophysik (DE-588)4185096-8 gnd |
| subject_GND | (DE-588)4170391-1 (DE-588)4185096-8 |
| title | Theoretical molecular biophysics |
| title_auth | Theoretical molecular biophysics |
| title_exact_search | Theoretical molecular biophysics |
| title_full | Theoretical molecular biophysics P. O. J. Scherer ; Sighart F. Fischer |
| title_fullStr | Theoretical molecular biophysics P. O. J. Scherer ; Sighart F. Fischer |
| title_full_unstemmed | Theoretical molecular biophysics P. O. J. Scherer ; Sighart F. Fischer |
| title_short | Theoretical molecular biophysics |
| title_sort | theoretical molecular biophysics |
| topic | Molekulare Biophysik (DE-588)4170391-1 gnd Theoretische Biophysik (DE-588)4185096-8 gnd |
| topic_facet | Molekulare Biophysik Theoretische Biophysik |
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