Computer simulations of self-organization in biological systems:
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
London [u. a.]
Croom Helm
1988
|
| Series: | Computers in biology series
|
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XI, 353 S. Ill. |
| ISBN: | 0709938675 |
Staff View
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| 245 | 1 | 0 | |a Computer simulations of self-organization in biological systems |c Narendra S. Goel and Richard L. Thompson |
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Record in the Search Index
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|---|---|
| adam_text | Computer
Simulations of
Self-Organization in
Biological Systems
NARENDRA S GOEL,
Department of Systems Science,cState University of New York at
Binghamton
and
RICHARD L THOMPSON,
La Jolla Institute, La Jolla, California
CROOM HELM
London amp; Sydney
Contents
Preface ix
1 Introduction 1
Part I: Principles and Techniques of Biological Modeling
2 Models and their Roles in Biology 11
A What Is a Model? 11
B Why Develop a Model? 12
C How Does One Develop a Model? 12
D Classification of Models IS
References 18
3 Some Tools for Computer Simulation 20
A Computer Programming Languages 21
A I Factors to consider in choosing a computer language 22
B Computer Graphics Display 25
B I Display hardware 26
B 2 Display modes 27
B 3 Transformations • 28
B 4 Three-dimensional display0 29
B S Graphic display implementation 30
References 32
4 Basic Principles of Biological Organization 33
A The Principle of Subassembly 33
B The Principle of Optimization 35
C The Principle of Evolutionary Optimization 37
D Conformational Programming 39
References 42
5 General Classes of Models for Self-organization in Biological
Systems 44
A Physically Realistic Models 44
B Models Based on Reaction-Diffusion Equations 45
C Cellular Automaton Models 46
D Movable Finite Automata (MFA) Models 47
References 50
Part II: Specific Models of Biological Self-organization and Evolution
6 Folding of Globular Proteins 55
A Biophysical Background 56
B General Geometrical Models 57
CONTENTS /
B I Specific model and results 59
C MFA Models and Results 76
C 1 Definition of a polypeptide chain 78
C 2 Approximation of a continuous system using discrete steps 80
C 3 Chain folding through nonlinear optimization 81
C 4 Generating beta-sheets 82
C 5 Generating an alpha-helix 84
D Comments and Future Work 92
References 93
Appendix A: A General Optimization Algorithm 96
7 Formation of Protein Quaternary Structures 98
A Biophysical Background 98
B MFA Model and Results 99
B 1 Specificity and hydrophobic interactions 103
B11 Calculation of Nfree 107
B12 Calculation of probability distribution of d 109
B13 Results for specificity 110
B 2 Effects of hydrogen bonding on specificity 114
C Comments and Future Work 116
References 117
8 Bacteriophage Assembly and Function 119
A Conformational Switching in Protein Complexes 119
B Biophysical Background of Bacteriophage Assembly and
Operation 122
B I Head assembly 122
B 2 Tail and tail fiber assembly 124
B21 Tail assembly 124
B22 Tail fiber assembly 126
B 3 Thejjrocess of infection — adsorption and penetration 128
C MFA Models for the Bacteriophage and Results 130
C I Description of the subunits 131
~---C 1 1 Cell wall molecules 132
CI2 Phage subunits 133
C13 Subunit interactions 135
C 2 Simulation dynamics 136
C 3 Phage designs 141
C 4 Simulation case histories: the two-dimensional phages 151
C 5 Simulation case history: the three-dimensional phage 158
D Comments and Future Work
t 163
D I Other systems involving protein assembly 166
DII Networks of contractile or structural fibers in cells 166
DI2 The swimming apparatus of a bacterium 166
DI3 The cell membrane 167
References 168
vi
CONTENTS
9 Aggregation of Cells into Tissues and Embryonic Development 170
A Self-sorting of Cells 171
A I Biophysical background 172
A 2 The cellular automaton model and results 174
A21 Equilibrium configurations for isotropic cells 177
A22 Equilibrium configurations for anisotropic cells 178
A23 Cellular movement and dynamics 180
B Cellular Compaction and Internalization in Mammalian
Embryo Development 185
B I Biophysical background 186
B 2 Basic model 189
B 3 Two-dimensional cells and results 190
B31 Dynamics of compaction and internalization 195
B 4 Three-dimensional cells 198
B41 Special models for three-dimensional cells and
results 199
C Comments and Future Work 207
References 214
Appendix B: Compaction vs Internalization for Three-dimensional
Cells 217
10 Protein Biosynthesis: Elongation of the Polypeptide Chain 221
A Biophysical Background Q
O 223
A I Codon-Anticodon recognition and binding 228
A 2 The EF-TU enzyme 229
A 3 Transpeptidation 231
A 4 The EF-G enzyme 231
A 5 Translocation 232
B An MFA Model of Protein Biosynthesis and Results 232
B I Bonding rules 233
B 2 Random thermal fluctuations and state transitions 234
B 3 Description of models for the key structures 238
B31 The ribosome and the mRNA molecule 239
B32 tRNA molecules and amino acid residues 241
B33 The EFT complex 244
B34 The EFG complex 244
B 4 The dynamics of the model 246
B 5 Simulation case history - 250
B 6 Details of the operation of the model 259
B61 The proofreading mechanism and its energetics 259
B62 Implementation of proofreading 262
B63 Translocation 268
C Comments and Future Work 271
References 273
vn
CONTENTS /
Appendix C: Justification of the Approximation Defined by
Equations (10 9) 273
•11 The Evolution of the Trilobite Eye 275
A Biophysical Background 276
B Basic Model and Results 277
C Comments and Future Work 286
References 289
12 Computer Models and Evolution of Macromolecular Machinery 291
A Bacteriophage Evolution 291
A I Evolutionary context 292
A 2 Phage subunits and their genes 293
A21 Mutation rules 294
A22 Evolutionary transformations 295
B Comments and Future Work 307
B I The origin of life 310
References 313
Part III: Final Comments and Perspectives
13 Information Theory and Self-organization 317
A Some Concepts of Information Theory 317
B Self-organization as the Transformation of Information 320
C Explanation and Information Compression 321
D Shared Information and Modeling 323
E Ultimate Limitations on Explanation in Biology 326
F Algorithmic Self-organization 332
References 334
14 Afterword 335
Author Index 342
Subject Index 346
vm
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| spelling | Goel, Narendra S. 1941- Verfasser (DE-588)136917321 aut Computer simulations of self-organization in biological systems Narendra S. Goel and Richard L. Thompson London [u. a.] Croom Helm 1988 XI, 353 S. Ill. txt rdacontent n rdamedia nc rdacarrier Computers in biology series Thompson, Richard L. 1947-2008 Verfasser (DE-588)1049230051 aut HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=019794184&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Goel, Narendra S. 1941- Thompson, Richard L. 1947-2008 Computer simulations of self-organization in biological systems |
| title | Computer simulations of self-organization in biological systems |
| title_auth | Computer simulations of self-organization in biological systems |
| title_exact_search | Computer simulations of self-organization in biological systems |
| title_full | Computer simulations of self-organization in biological systems Narendra S. Goel and Richard L. Thompson |
| title_fullStr | Computer simulations of self-organization in biological systems Narendra S. Goel and Richard L. Thompson |
| title_full_unstemmed | Computer simulations of self-organization in biological systems Narendra S. Goel and Richard L. Thompson |
| title_short | Computer simulations of self-organization in biological systems |
| title_sort | computer simulations of self organization in biological systems |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=019794184&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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