Models of life: dynamics and regulation in biological systems
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge
Cambridge Univ. Press
2014
|
| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | X, 342 S. Ill., graph. Darst. |
| ISBN: | 9781107061903 1107061903 |
Internformat
MARC
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Datensatz im Suchindex
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|---|---|
| adam_text | Models of Life
Dynamics and Regulation
in Biological Systems
KIM SNEPPEN
Niels Bohr Institute and Center for Models of Life,
Copenhagen University, Denmark
CAMBRIDGE
UNIVERSITY PRESS
Contents
Preface Page ix
1 Life from a physics perspective 1
1 1 Life copies from itself and from other life 1
1 2 Biology is the result of a very long historical process 2
1 3 Self-assembly and the genetic code 3
1 4 Biological molecules have long backbones 6
1 5 Computation 6
1 6 Information gathering and communication 7
1 7 Feedback 7
1 8 Push-pull 8
1 9a Life is modular 9
1 9b Life is not modular 9
1 10 Stochastic processes play an important role in life 9
1 11 Life harvests energy and converts it to cyclic motion 10
1 12 Biological physics is keT physics 13
2 E coli as a model system 17
2 1 DNA, RNA and proteins 17
2 2 The E coli cell 22
2 3 Transcription and translation numbers 24
24E coli content varies with its growth rate 32
2 5 Summary 35
3 Dynamics of regulatory links 36
3 1 Regulating a piece of DNA 36
3 2 Transcription regulation 41
3 3 Post-transcriptional regulation 44
3 4 Summary 48
4 Statistical mechanics of phage A 49
4 1 Lifecycle of A phage 49
4 2 Bacterial growth and counting 56
v
vi Contents
4 3 Chemical binding and counting 59 ]
4 4 Chemistry and co-operativity as statistical mechanics 62 I
4 5 Distant DNA in gene regulation 68 j
4 6 Summary 78 j
5 Diffusion and randomness in transcription 79
5 1 Random walks and diffusion 79 j
5 2 Timescales for target location in a cell 83
5 3 Traffic on DNA 89
5 4 Bursty transcription initiation 94 !
5 5 Economy of operons: noise minimization 100 j
5 6 Summary 102
i
6 Stochastic genes and persistent decisions 104 j
j
6 1 Stochastic simulations 104 j
6 2 Maintenance of lysogeny in the X system 109 j
6 3 The phage X circuit beyond CI and Cro 117 J
6 4 Summary 122
7 c/s-Acting gene regulation and epigenetics 123
7 1 Nucleosomes and their enzymes 123
7 2 Nucleosome-mediated epigenetics 127
73A regulated two-state model 135
7 4 Coupled epigenetics in olfactoric differentiation 142 :
7 5 Other models for cis-mediated gene regulation 146 ;
7 6 Summary 149
8 Feedback circuits 150
8 1 Small regulatory subnetworks 150
8 2 Negative feedback 151
8 3 Positive feedback 159
8 4 Combining feedback in small-molecule regulation 161
8 5 Combined feedback loops and spatial organization 167
8 6 Summary 176 ;
9 Networks 177
9 1 Convergent computation 177
9 2 Connectedness 178
|93 Large-scale molecular networks 190
P ,9 4 Analysis of network topologies 193
/95 Models for scale-free molecular networks 198
*96 Summary 204
Contents vii
10 Signaling and metabolic networks 205
10 1 Signaling across networks 205
10 2 Enzyme kinetics and phosphorylation 212
10 3 Adaptation 216
10 4 Metabolic fluxes 219
10 5 Summary 225
11 Agent-based models of signaling and selection 226
11 1 Excitable agents as cells in a tissue 226
11 2 Information spreading on social scales 227
11 3 Tragedy of the commons 235
11 4 Summary 241
12 Competition and diversity 242
12 1 Phage worlds 242
12 2 Phage-bacteria ecology 252
12 3 Phage games: lysogeny or lysis 265
12 4 Speciation and biodiversity of sessile species 272
12 5 Summary 277
13 Evolution and extinction 279
13 1 History 279
13 2 Fitness landscapes 282
13 3 Punctuated equilibrium and co-evolution 286
13 4 Summary 295
Appendix 296
Langevin versus Fokker-Planck equation 296
Kramers equation 297
First passage for random walks 299
References
Index
|
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| language | English |
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| spelling | Sneppen, Kim Verfasser aut Models of life dynamics and regulation in biological systems Kim Sneppen 1. publ. Cambridge Cambridge Univ. Press 2014 X, 342 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biowissenschaften Mathematisches Modell Life sciences / Mathematical models Biology / Mathematical models Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Biologisches System (DE-588)4122930-7 gnd rswk-swf Biologisches System (DE-588)4122930-7 s Mathematisches Modell (DE-588)4114528-8 s DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027818108&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sneppen, Kim Models of life dynamics and regulation in biological systems Biowissenschaften Mathematisches Modell Life sciences / Mathematical models Biology / Mathematical models Mathematisches Modell (DE-588)4114528-8 gnd Biologisches System (DE-588)4122930-7 gnd |
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| title | Models of life dynamics and regulation in biological systems |
| title_auth | Models of life dynamics and regulation in biological systems |
| title_exact_search | Models of life dynamics and regulation in biological systems |
| title_full | Models of life dynamics and regulation in biological systems Kim Sneppen |
| title_fullStr | Models of life dynamics and regulation in biological systems Kim Sneppen |
| title_full_unstemmed | Models of life dynamics and regulation in biological systems Kim Sneppen |
| title_short | Models of life |
| title_sort | models of life dynamics and regulation in biological systems |
| title_sub | dynamics and regulation in biological systems |
| topic | Biowissenschaften Mathematisches Modell Life sciences / Mathematical models Biology / Mathematical models Mathematisches Modell (DE-588)4114528-8 gnd Biologisches System (DE-588)4122930-7 gnd |
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