Preface |
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ix | |
Ways to use this book |
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xiii | |
Acknowledgments |
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xvii | |
Review of Volume I |
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xxi | |
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13 Higher-dimensional differential equations |
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1 | (86) |
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13.1 Eigenvalues in higher dimensions |
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1 | (6) |
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7 | (10) |
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13.3 Michaelis-Menten kinetics |
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17 | (5) |
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13.4 Virus dynamics basics |
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22 | (15) |
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13.5 Immune response dynamics |
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37 | (8) |
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13.6 The Hodgkin-Huxley equations |
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45 | (9) |
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13.7 Chaos in predator-prey systems |
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54 | (9) |
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13.8 The Duffing equation and final state sensitivity |
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63 | (10) |
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73 | (14) |
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87 | (48) |
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88 | (17) |
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14.2 The Perron-Frobenius theorem |
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105 | (9) |
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14.3 Structured populations |
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114 | (9) |
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14.4 Reproductive value and sensitivity analysis |
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123 | (12) |
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15 A tiny bit of genetics |
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135 | (44) |
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15.1 The Hardy-Weinberg law and selection equations |
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136 | (10) |
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15.2 Price's equation and multilevel selection |
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146 | (4) |
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150 | (8) |
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15.4 The quasispecies equation |
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158 | (5) |
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163 | (4) |
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167 | (12) |
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16 Markov chains in biology |
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179 | (46) |
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180 | (10) |
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16.2 Matrix differential equations |
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190 | (7) |
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16.3 Ion channel dynamics |
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197 | (9) |
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16.4 The Clancy-Rudy cardiac arrhythmia model |
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206 | (9) |
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16.5 Tumor suppressor genes |
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215 | (10) |
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225 | (79) |
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226 | (5) |
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231 | (12) |
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243 | (7) |
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250 | (6) |
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17.5 Interesting geometries |
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256 | (7) |
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17.6 Bendixson's criterion |
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263 | (3) |
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17.7 The index of a fixed point |
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266 | (11) |
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277 | (8) |
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285 | (7) |
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292 | (4) |
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296 | (5) |
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301 | (3) |
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18 A glimpse of systems biology |
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304 | (25) |
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18.1 Genetic toggle switch |
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307 | (5) |
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18.2 Transcription networks |
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312 | (11) |
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323 | (5) |
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18.4 Why should this work? |
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328 | (1) |
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329 | (24) |
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19.1 Evolutionary medicine |
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329 | (7) |
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19.2 Translational bioinformatics |
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336 | (5) |
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341 | (10) |
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19.4 No, really, what's next? |
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351 | (2) |
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Appendix A Technical Notes |
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353 | (63) |
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A.12 Some more linear algebra |
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353 | (9) |
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A.13 Some Markov chain properties |
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362 | (8) |
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A.14 Cell membrane channels |
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370 | (3) |
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A.15 Viruses and the immune system |
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373 | (16) |
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A.16 The normal density function |
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389 | (1) |
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A.17 A sketch of the Perron-Frobenius proof |
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390 | (3) |
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A.18 The Leslie matrix characteristic equation |
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393 | (2) |
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395 | (3) |
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A.20 Stochastic resonance and the Duffing equation |
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398 | (4) |
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A.21 Proof of Lienard's theorem |
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402 | (4) |
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A.22 A bit of molecular genetics |
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406 | (10) |
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Appendix B Some Mathematica code |
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416 | (13) |
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B.11 Eigenvalues in higher dimensions |
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416 | (1) |
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417 | (1) |
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B.13 Michaelis-Menten calculations |
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417 | (1) |
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417 | (1) |
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B.15 Immune system dynamics |
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418 | (1) |
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B.16 The Hodgkin-Huxley equations |
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419 | (2) |
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B.17 Chaos in predator-prey models |
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421 | (1) |
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B.18 The Duffing equation |
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421 | (1) |
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422 | (2) |
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B.20 Sensitivity analysis |
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424 | (1) |
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B.21 The Clancy-Rudy model |
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424 | (1) |
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B.22 A genetic toggle switch |
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425 | (1) |
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B.23 Transcription networks |
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426 | (1) |
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426 | (3) |
Appendix C Some useful integrals and hints |
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429 | (4) |
References |
|
433 | (20) |
Index |
|
453 | |