Photosynthesis in silico: understanding complexity from molecules to ecosystems
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Dordrecht
Springer
2009
|
| Schriftenreihe: | Advances in photosynthesis and respiration
29 |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXI, 503 S., 6 Taf. graph. Darst. |
| ISBN: | 9781402092367 |
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Datensatz im Suchindex
| _version_ | 1804142726402277376 |
|---|---|
| adam_text | Titel: Photosynthesis in silico
Autor: Laisk, Agu
Jahr: 2009
Contents
From the Series Editor v
Preface xv
The Editors xvii
Author Index xxi
Color Plates CP1
Part I: General Problems of Biological Modeling
1 Trends and Tools for Modeling in Modern Biology 3-15
Michael Hucka and James Schaff
Summary 3
I. Introduction 4
II. Representing Model Structure and Mathematics 4
III. Augmenting Models with Semantic Annotations 6
IV. Connecting Models to Results 9
V. Future Directions for Systems Biology Markup Language (SBML) 13
VI. Conclusions 13
References 14
Scaling and Integration of Kinetic Models of Photosynthesis:
Towards Comprehensive E-Photosynthesis 17-29
Ladislav Nedbal, Jan Cervenyand Henning Schmidt
Summary 17
I. Introduction 18
II. Mapping Partial Photosynthesis Models into the Comprehensive
Model Space (CMS): The Principles and Strategies 19
III. Mapping of Photosystem II Models into the Comprehensive
Model Space (CMS) 21
IV. Concluding Remarks 27
Acknowledgments 28
References 28
Vll
Part II: Modeling of Light Harvesting and Primary
Charge Separation
3 Modeling Light Harvesting and Primary Charge Separation
in Photosystem I and Photosystem II 33-53
Rienk van Grondelle, Vladimir I. Novoderezhkin and Jan P. Dekker
Summary 34
I. Introduction 34
II. Physical Models of Energy Transfer 35
III. Exciton Spectra and Energy Transfer in Photosystem I (PS I) Core 40
IV. Excitation Dynamics in Major Light Harvesting Complex II (LHCII) 41
V. Energy Transfers and Primary Charge Separation in Photosystem II
Reaction Center 44
VI. Concluding Remarks 50
Acknowledgments 50
References 50
4 Unraveling the Hidden Nature of Antenna Excitations 55-82
Arvi Freiberg and Gediminas Trinkunas
Summary 55
I. Introduction 56
II. Disordered Frenkel Exciton Model for Absorbing States
of Circular Antenna Aggregates 59
III. Shortcomings of the Disordered Frenkel Exciton Model 63
IV. Excitonic Polaron Model of the Antenna Fluorescing States 64
V. Evaluation of the Model Parameters from the Experimental Spectra 70
VI. Conclusions and Outlook 76
Acknowledgments 77
References 77
Part HI: Modeling Electron Transport and Chlorophyll Fluorescence
5 Models of Chlorophyll a Fluorescence Transients 85-123
Dusan Lazar and Gert Schansker
Summary 86
I. Fluorescence Induction 86
II. Approaches and Assumptions in the Modeling of the Fluorescence Rise 91
III. Particular Models for the Fluorescence Rise 100
IV. Modeling the Whole Fluorescence Induction 111
V. Conclusions and Future Perspectives 115
Acknowledgments 115
References 115
VUl
6 Modeling of Chlorophyll a Fluorescence Kinetics in Plant Cells:
Derivation of a Descriptive Algorithm 125-149
Wim Vredenberg and Ondrej Prasil
Summary 126
I. Introduction 126
II. Variable (Chlorophyll) Fluorescence - Some Basics 128
III. Application of Single, Twin and Multiple Turnover Flashes 132
IV. Distinguishable Phases of Fluorescence Response
upon Multiturnover Excitation 135
V. Fluorescence Induction Algorithm for Experimental Curves 137
VI. Concluding Remarks 144
Acknowledgments 146
References 146
7 Modeling of the Primary Processes in a Photosynthetic Membrane 151-176
Andrew Rubin and Galina Riznichenko
Summary 151
I. Introduction 152
II. Fluorescence as an Indicator of the Photosystem State 153
III. General Kinetic Model of the Processes in Photosynthetic
Thylakoid Membrane 154
IV. Multiparticle Modeling of the Processes in the Photosynthetic Membrane 166
V. Concluding Remarks and Future Perspectives 171
Acknowledgments 171
References 171
8 Clustering of Electron Transfer Components:
Kinetic and Thermodynamic Consequences 177-205
Jerome Lavergne
Summary 177
I. Introduction 178
II. Thermodynamic Performance of Integrated and Diffusive
Photosynthetic Models 179
III. I ntegrated Versus Diffusive Electron Transfer Chain 183
IV. The Small Apparent Equilibrium Constant in the Donor Chain
of Rhodobacter sphaeroides 189
V. Quinone Domains 195
VI. Statistical and Non Statistical Heterogeneities 198
VII. Pool Function Test at Steady State 199
VIII. Kinetic Analysis: Playing with Inhibitors, Redox Potential and Flash Intensity 201
IX. Concluding Remarks 203
Acknowledgments 203
References 203
IX
Part IV: Integrated Modeling of Light and Dark Reactions
of Photosynthesis
9 Biochemical Model of C3 Photosynthesis 209-230
Susanne von Caemmerer, Graham Farquhar and Joseph Berry
Summary 210
I. Introduction 210
II. The Rate Equations of CO2 Assimilation 211
III. Parameters and their Temperature Dependencies 215
IV. The Role of Rubisco Activation State 218
V. Estimating Chloroplast pCO2 219
VI. Predicting Photosynthesis from Chloroplast Biochemistry 220
VII. Predicting Chloroplast Biochemistry from Leaf Gas Exchange 223
VIII. Concluding Remarks 224
References 225
10 Modeling the Temperature Dependence of C3 Photosynthesis 231-246
Carl J. Bemacchi, David M. Rosenthal, Carlos Pimentel,
Stephen P. Long and Graham D. Farquhar
Summary 232
I. Introduction 232
II. Processes Limiting to C3 Photosynthesis 233
III. Modeling Photosynthesis and the Supply of CO2 240
IV. Concluding Remarks 242
Acknowledgments 243
References 243
11 A Model of the Generalized Stoichiometry of Electron Transport
Limited C3 Photosynthesis: Development and Applications 247-273
Xinyou Yin, Jeremy Harbinson and Paul C. Struik
Summary 247
I. Introduction 248
II. Model Development 250
III. Model Applications 255
IV. Concluding Remarks 269
Acknowledgments 269
References 270
12 Modeling the Kinetics of Activation and Reaction of Rubisco
from Gas Exchange 275-294
Hadi Farazdaghi
Summary 275
I. Introduction 276
II. Fundamental Photosynthesis Models 276
III. Rubisco and Its Sequentially Ordered Reaction 279
IV. Rubisco in Steady State: Biochemical Models 281
V. Experimental Evaluation of the Models 287
VI. Concluding Remarks 290
Acknowledgments 291
References 291
13 Leaf C3 Photosynthesis in silico:
Integrated Carbon/Nitrogen Metabolism 295-322
Agu Laisk, Hillar Eichelmann and Velio Oja
Summary 295
I. Introduction 296
II. The Structure of the Model 297
III. Mathematics 302
IV. Simulations 312
V. Concluding Remarks 317
Acknowledgments 319
References 319
14 Leaf C4 Photosynthesis in silico:
The CO2 Concentrating Mechanism 323-348
Agu Laisk and Gerald Edwards
Summary 324
324
325
329
334
338
345
345
15 Flux Control Analysis of the Rate of Photosynthetic
CO2 Assimilation 349-360
Ian E. Woodrow
Summary 349
I. Introduction 350
II. Flux Control Coefficients: Theory and Challenges 352
III. Reversible Reactions Can Be Flux Limiting 352
IV. Small Control Coefficients Are Hard to Detect 354
V. Enzymes with Higher Control Coefficients 356
VI. Photosynthetic Electron Transport 358
VII. Concluding Remarks 358
Acknowledgments 359
References 359
XI
I. Introduction
II. Principles of NADP-ME Type C4 Photosynthesis
III. The C4 Model
IV. Simulations
V. Knowns and Unknowns in Photosynthesis
Acknowledgments
References
Part V: From Leaves to Canopies to the Globe
16 Packing the Photosynthetic Machinery: From Leaf to Canopy 363-399
Ulo Niinemets and Niels P.R. Anten
Summary 364
I. Introduction 364
II. Inherent Differences in Microenvironment and Photosynthetic Potentials
Within the Canopy 367
III. Scaling Photosynthesis from Leaves to Canopy 379
IV. Concluding Remarks 389
Acknowledgments 389
References 390
17 Can Increase in Rubisco Specificity Increase Carbon Gain
by Whole Canopy? A Modeling Analysis 401-416
Xin-Guang Zhu and Stephen P. Long
Summary 401
I. Introduction 402
II. Theory and Model Description 404
III. The Impact of the Inverse Relationship on Leaf and Canopy
Level Photosynthesis 407
IV. Current Efforts of Engineering Rubisco for Higher Photosynthesis 410
V. Why Has Evolution Failed to Select the Optimal Rubisco? 412
VI. Concluding Remarks 413
Acknowledgments 413
References 413
18 Role of Photosynthetic Induction for Daily and Annual Carbon
Gains of Leaves and Plant Canopies 417-440
Manfred Kuppers and Michael Pfiz
Summary 417
I. Introduction 418
II. Representation of Plant Architecture by Digital Reconstruction 418
III. The Dynamic Light Environment 419
IV. Models of Dynamic Photosynthesis 427
V. Calculation of Crown Carbon Acquisition 429
VI. Annual Carbon Gains from Steady-state and Dynamic
Photosynthesis Simulations 431
VII. Concluding Remarks 436
Acknowledgments 436
References 436
XII
19 Photosynthesis Within Large-Scale Ecosystem Models 441-464
Stephan A. Pietsch and Hubert Hasenauer
Summary 441
I. Introduction 442
II. Biogeochemical Cycles 443
III. Models of Biogeochemical Cycles 446
IV. Model Application 452
V. Examples of Model Application 456
VI. Concluding Remarks 461
Acknowledgments 462
Références 462
20 Photosynthesis in Global-Scale Models 465-497
Andrew D. Friend, Richard J. Geider, Michael J. Behrenfeld
and Christopher J. Still
Summary 466
I. Introduction 467
II. Description of Model Approaches 469
III. Global Simulation 480
IV. Concluding Remarks 486
Acknowledgments 488
Références 488
Index 499
X1J1
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| discipline | Biologie |
| format | Book |
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| spellingShingle | Photosynthesis in silico understanding complexity from molecules to ecosystems Advances in photosynthesis and respiration |
| title | Photosynthesis in silico understanding complexity from molecules to ecosystems |
| title_auth | Photosynthesis in silico understanding complexity from molecules to ecosystems |
| title_exact_search | Photosynthesis in silico understanding complexity from molecules to ecosystems |
| title_full | Photosynthesis in silico understanding complexity from molecules to ecosystems ed. by Agu Laisk ... |
| title_fullStr | Photosynthesis in silico understanding complexity from molecules to ecosystems ed. by Agu Laisk ... |
| title_full_unstemmed | Photosynthesis in silico understanding complexity from molecules to ecosystems ed. by Agu Laisk ... |
| title_short | Photosynthesis in silico |
| title_sort | photosynthesis in silico understanding complexity from molecules to ecosystems |
| title_sub | understanding complexity from molecules to ecosystems |
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