Moroz The Common Extremalities in Biology and Physics

Maximum Energy Dissipation Principle in Chemistry, Biology, Physics and Evolution
2. Auflage 2011
ISBN: 978-0-12-385188-8
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 394 Seiten

The Common Extremalities in Biology and Physics is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. - The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective - Discusses emerging fields and analysis - Provides examples

Autoren/Hrsg.

Moroz, Adam

Inhaltsverzeichnis

1;Front Cover;1
2;The Common Extremalities in Biology and Physics;4
3;Copyright Page;5
4;Contents;6
5;Preface;12
6;1 Extreme Energy Dissipation;16
6.1;1.1 Hierarchy of the Energy Transformation;16
6.1.1;1.1.1 Thermodynamics—A Science That Connects Physics and Biology;16
6.1.2;1.1.2 Hierarchy of the Processes and Parameters in Thermodynamics;17
6.1.3;1.1.3 Macroparameters: Energy and the Forms of Its Exchange;18
6.1.4;1.1.4 Macroparameters: Heat as a Nonmechanical Method to Change the Macrostate of Thermodynamic Systems;19
6.1.5;1.1.5 Macroparameters: Physical Work as a Pure Mechanical Way to Change Macroparameters;19
6.1.6;1.1.6 Macroparameters: The Energy Conservation Law;20
6.1.7;1.1.7 Macroparameters: Free Energy—Macroscopic Measure of Nonequilibrium;20
6.1.8;1.1.8 Macroparameters: Universal Fatality of the Processes—The Second Law of Thermodynamics and the Hierarchy of Energy;21
6.1.9;1.1.9 Macroparameters: Helmholtz Free Energy;22
6.1.10;1.1.10 Macroparameters: Enthalpy;22
6.1.11;1.1.11 Link from Macro- to Microparameters: Physical Entropy;23
6.1.12;1.1.12 Microparameters: Statistical Interpretation of Free Energy and Entropy;25
6.1.13;1.1.13 The Removal of Energetical Nonequilibrium and the Entropy Production;26
6.1.14;1.1.14 Dissipation in Chemical Transformations;27
6.1.15;1.1.15 Dissipation of Nonequilibrium in Open Systems;28
6.1.16;1.1.16 Energy Dissipation or Entropy Production—The Energy Picture Can Play a Role;29
6.1.17;1.1.17 Biological Hierarchy and Its Complexity;30
6.1.18;1.1.18 Some Conclusions;32
6.2;1.2 Extreme Properties of Energy Dissipation;33
6.2.1;1.2.1 Comparing Extreme Approaches;33
6.2.2;1.2.2 How Is the Elementary Variational Problem Solved?;38
6.2.3;1.2.3 Other Necessary Conditions for Local Minimum;39
6.2.4;1.2.4 Canonical Equations or Hamiltonian Formulation;40
6.2.5;1.2.5 Conclusions;41
6.3;1.3 Optimal-Control-Based Framework for Dissipative Chemical Kinetics;42
6.3.1;1.3.1 Optimal Control and Mechanics;42
6.3.2;1.3.2 Dynamic Optimal Control Formulation;44
6.3.3;1.3.3 More General Case;48
6.3.4;1.3.4 Optimal Control Interpretations;50
6.3.5;1.3.5 Pure Physical Example—Relaxation in an Ideal Resistor-Capacitor Circuit;53
6.4;1.4 Conclusions;54
6.5;References;55
7;2 Some General Optimal Control Problems Useful for Biokinetics;58
7.1;2.1 Extreme Dissipation, Optimal Control, and the Least Action Principle;58
7.1.1;2.1.1 Conservative Mechanics: Variational Formulation;58
7.1.2;2.1.2 On Optimal Control Formulation of Mechanics;61
7.1.3;2.1.3 Dissipation in Classical Mechanics;62
7.1.4;2.1.4 On an Alternative Way to Describe Biological and Chemical Dissipation;64
7.1.5;2.1.5 Comparing Closely the Linear Dissipative and Conservative Models;69
7.1.6;2.1.6 A More Biological Approximation of Penalty Potential;71
7.1.7;2.1.7 Simple Biological/Biochemical Example in Terms of Logarithmic Penalty;72
7.1.8;2.1.8 Penalty and Dissipative and Conservative Motion;75
7.2;2.2 Some One-Dimensional Examples of Biokinetics and Optimal Control;77
7.2.1;2.2.1 General One-Dimensional Optimal Control Model;77
7.2.2;2.2.2 “Additive” Control—Relevant to the Control by the Rate;79
7.2.3;2.2.3 “Multiplicative” Control—Relevant to the Control by the Rate Constant;85
7.2.4;2.2.4 General Case of the Cooperative Model;88
7.2.5;2.2.5 General Case of Cooperative Model: Partial Case h(x)=0, Variational Formulation;90
7.2.6;2.2.6 Multiplicative Control Model;91
7.2.7;2.2.7 Logistical Cooperative Model—Pure Variational Formulation;93
7.2.8;2.2.8 Some Other Cooperative Functions;96
7.2.9;2.2.9 On the Introduction of Control into the Logistic Model;100
7.2.10;2.2.10 On Dynamic Optimal Control Interpretations;104
7.3;2.3 General Multidimensional Examples of the Introduction of Optimal Control into Biokinetics;106
7.3.1;2.3.1 “Additive” Control;106
7.3.2;2.3.2 On Vector Formulation of Additive Control;112
7.3.3;2.3.3 Variational Formulation of Additive Control;114
7.3.4;2.3.4 “Multiplicative” Control;115
7.3.5;2.3.5 General Linear “Multiplicative” Control Case;117
7.3.6;2.3.6 An Interesting Two-Dimensional Case: “Cross-Penalty”;119
7.4;2.4 Conclusions;124
7.5;References;124
8;3 Variational and the Optimal Control Models in Biokinetics;126
8.1;3.1 Optimal Control Model of Binding Cooperativity;126
8.1.1;3.1.1 Importance of Low Molecular Binding and Its Cooperativity;126
8.1.2;3.1.2 Binding Kinetics, Cooperativity, and Its Representation;128
8.1.3;3.1.3 Dynamical Optimal Control Outline;131
8.1.4;3.1.4 Optimal Control Lagrange Method;135
8.1.5;3.1.5 Pure Variational Formulation;135
8.1.6;3.1.6 Some Conclusions;137
8.2;3.2 Enzyme Kinetics and Optimal Control;138
8.2.1;3.2.1 The Michaelis–Menten Model;138
8.2.2;3.2.2 General Optimal Control Approach to Michaelis–Menten Kinetics;140
8.2.3;3.2.3 Control by Means of Maximal Reaction Velocity Vmax;142
8.2.3.1;3.2.3.1 Optimal Control Outline;142
8.2.3.2;3.2.3.2 Pure Variational Formulation;143
8.2.4;3.2.4 Hamiltonian Formulation;145
8.2.4.1;3.2.4.1 Back to the Optimal Control Formulation in Terms of State and Control Variables;147
8.2.5;3.2.5 Control by the Michaelis Constant KM;153
8.2.5.1;3.2.5.1 Pure Variational Outline;155
8.2.5.2;3.2.5.2 Hamiltonian Framework;157
8.2.5.3;3.2.5.3 Optimal Control Outline;159
8.2.6;3.2.6 Simultaneous Optimal Control by the Vmax and the Michaelis Constant KM;164
8.2.7;3.2.7 The Link to Biochemical Mechanisms;166
8.3;3.3 Optimal Control, Variational Methods, and Multienzymatic Kinetics;170
8.3.1;3.3.1 Optimal Control Method in Modeling of Multienzymatic Chains;170
8.3.2;3.3.2 Optimal Control Introduction into the Bier-Teusink- Kholodenko- Westerhoff–Volkenstain Model of Glycolysis;171
8.3.3;3.3.3 Direct Optimal Control Outline;172
8.3.4;3.3.4 Variational Formulation;176
8.3.5;3.3.5 Statistical Method to Study the Robustness;179
8.3.5.1;3.3.5.1 Optimal Control by KM in the BTKW Model of Glycolysis;181
8.3.6;3.3.6 Optimal Control and Multienzyme Kinetics;185
8.4;3.4 Optimal Control in Hierarchical Biological Systems: Organism and Metabolic Hierarchy;188
8.5;References;193
9;4 Extreme Character of Evolution in Trophic Pyramid of Biological Systems and the Maximum Energy Dissipation/Least Action Principle;202
9.1;4.1 Acceleration of Dissipation in Molecular Processes is the Cause of Emergence of Trophic Pyramid of Biological Systems;202
9.1.1;4.1.1 Autocatalysis and Self-Reproduction;203
9.1.2;4.1.2 Competition: Result of Relationships Between Various Types of Autocatalysis in the System of Chemical Reactions;205
9.1.3;4.1.3 Molecular Symbiosis;207
9.1.4;4.1.4 Advanced Symbiosis: Autocatalytic Hypercycles;208
9.1.5;4.1.5 Effect of Feedback Extent;210
9.1.6;4.1.6 Role of Information Mapping: Hypercycles with the Translation;213
9.1.7;4.1.7 Phase Separation;218
9.1.8;4.1.8 Some Conclusions;219
9.2;4.2 Maximum Energy Dissipation Principle and Evolution of Biological Systems;222
9.2.1;4.2.1 Role of Energetical Perspective of Biological Evolution;222
9.2.2;4.2.2 General Characteristic of the Energy Dissipation in the Global Biological Trophic Pyramid;225
9.2.3;4.2.3 Biological Evolution and the Maximum Energy Dissipation Principle;228
9.2.4;4.2.4 Cooperations of Macromolecules—From Molecular Hypercycles to Protobiocells;228
9.2.5;4.2.5 Bacterial Social Behavior;233
9.2.6;4.2.6 Eukaryotic Cells and Collective/Social Behavior;234
9.2.7;4.2.7 Organismic Level—From Acellular to Multicellular Biosystems;234
9.2.8;4.2.8 Symbiosis Is Fundamental for Developing Essentially New Dissipative Manners of Metabolism, Which Use Qualitatively New Free Energy Resources;236
9.2.9;4.2.9 Organizational Levels of the Global Biological Dissipative Pyramid;237
9.2.10;4.2.10 Limitations in the Scale of Free Energy Dissipation at Every Level of Bioorganization;241
9.2.11;4.2.11 Limitation in the Informational Mapping/Cognition;243
9.2.11.1;4.2.11.1 Informational Processing at the Level of Biosocial Species;247
9.2.11.2;4.2.11.2 Communication Languages in Social Multicellular Organisms: Dance Communications;247
9.2.12;4.2.12 Conclusions;253
9.3;4.3 The Pinnacle of Trophic Pyramid of Biological Systems—Symbiosis of Biological and Nonbiological Accelerating Loops: Technological Accelerating Loop;255
9.3.1;4.3.1 General Approach;255
9.3.2;4.3.2 Biological Component: Data on the Population Growth;258
9.3.3;4.3.3 Self-Reproductive-Like Growth of the Industrial (Nonbiological) Component;258
9.3.4;4.3.4 Symbiotic Accelerative Cycle of Biological and Nonbiological Things;263
9.3.5;4.3.5 More “Economic” Model: Four-Level Scheme of Level Interaction;267
9.3.6;4.3.6 Economic Interpretation of Optimal Control and the Biological Analogies;275
9.3.7;4.3.7 On the Interpretation of Static Optimization;276
9.3.8;4.3.8 Economic Interpretation of Dynamic Optimization;280
9.3.9;4.3.9 The Limitations in Purely Biological and Biosocial Parts of the Global Trophic Pyramid;283
9.3.10;4.3.10 Limitation in the Sociobiological Form of Information Mapping;288
9.3.11;4.3.11 Possible Postsocial Stage of Development of Dissipative Systems;292
9.3.12;4.3.12 Conclusions;293
9.4;References;295
10;5 Phenomenological Cost and Penalty Interpretation of the Lagrange Formalism in Physics;302
10.1;5.1 Fusing Mechanics and Optimal Control;302
10.1.1;5.1.1 Introduction;302
10.1.2;5.1.2 Mechanical Degrees of Freedom;302
10.1.3;5.1.3 Measurement Differences;303
10.1.4;5.1.4 The Penalty Example for a One-Dimensional Harmonic Oscillator;314
10.1.5;5.1.5 Dissipative, More Biological Analogue;315
10.1.6;5.1.6 Conclusions;317
10.2;5.2 Finiteness of the Propagation Velocity of Physical Interactions and Physical Penalty;318
10.3;5.3 Phenomenology of the Nonmechanical Penalty for Free Fields;324
10.3.1;5.3.1 Scalar Field;327
10.3.2;5.3.2 Complex Scalar Field: Charged Scalar Particles;328
10.3.3;5.3.3 Vector Field;330
10.3.4;5.3.4 Electromagnetic Field;331
10.3.5;5.3.5 Spinor Field;332
10.3.6;5.3.6 Massless Spinor Field;335
10.3.7;5.3.7 Penalty and Gravity;337
10.3.8;5.3.8 Einstein Equations;339
10.3.9;5.3.9 Some Final Remarks;340
10.4;5.4 Internal Symmetry of the Physical Penalty;342
10.4.1;5.4.1 Symmetry Breaking;349
10.4.2;5.4.2 Standard Model Illustrating the Physical Penalty;355
10.4.3;5.4.3 Grand Symmetry of the Physical Penalty;357
10.4.4;5.4.4 Supersymmetry of the Physical Penalty;358
10.4.5;5.4.5 Noncompensation of the Internal Penalty;359
10.5;5.5 Physical Interactions and Penalty;361
10.6;5.6 Physical Evolution in Light of Maximum Energy Dissipation Principle;369
10.6.1;5.6.1 Before the Epoch of Space-Time and Substance–Energy Separation;372
10.6.2;5.6.2 First Epoch: Epoch of the Barions Origin, 10-15GeV–2000GeV;372
10.6.3;5.6.3 Second Epoch: Epoch of Intermediate Vector Bosons, Temperature Drops from 2000 down to 50GeV;373
10.6.4;5.6.4 Third Epoch: Hadron Epoch;373
10.6.5;5.6.5 Fourth Epoch: Photon–Lepton Epoch;373
10.7;5.7 Conclusion: Physical Phenomena from the Point of View of Biological Ones;376
10.8;References;378
11;6 Conceptual Aspects of the Common Extrema in Biology and Physics;380
11.1;6.1 Self-Sufficiency of Extreme Transformations;380
11.1.1;6.1.1 Nonequilibrium/Instability;380
11.1.2;6.1.2 Motion Is a Striving Toward Stability;381
11.1.3;6.1.3 Extremeness;381
11.1.4;6.1.4 Ordered Way/Regularity;381
11.1.5;6.1.5 New Instability—The Result of the Ordered, Structured Process of the Elimination of Extreme Instability;382
11.2;6.2 Intensive and Extensive Property of Displaying of Material Instability;383
11.2.1;6.2.1 Energy in the Penalty Sense;385
11.2.2;6.2.2 Time in the Penalty Sense;385
11.3;6.3 Natural and Biotic Things—Lethal Gap or Irrational Compromise;387
11.3.1;6.3.1 “Continuous” Model—The Irrational Compromise;387
11.3.2;6.3.2 “Alternative” Model;389
12;Main Conclusions and Remaining Questions;392