References 413Decroly, D. and Goldbeter, A., 1982. Biorhythmicity, chaos and other patterns of temporal selforganisationin a multiply regulated biochemical system. Proc. Natl. Acad. Sci. U.S.A., 79,6917–6921.Decroly, D. and Goldbeter, A., 1987. From simple to complex oscillatory behaviour. Analysis ofbursting in a multiply regulated biochemical system. J. Theor. Biol., 124, 219–250.De Gennes, P-G., 1969. Some conformation problems for long macromolecules. Rep. Prog. Phys.,32, 187–206.Degn, H., Holden, A. V., Olsen, A. F., eds., 1987. Chaos in Biological Systems, Plenum, NY.De Groot, S. R. and Mazur, P., 1962. Non-equilibrium Thermodynamics, North-Holland, Amsterdam.Demeriel, Y. and Sandler, S. I., 2002. Thermodynamics and bioenergetics. Biophys. Chem., 97, 87–111.Dennett, D. C., 1991. Consciousness Explained, Little, Brown & Co., New York.Di Giulio, M., 1997. On the origin of the genetic code. J. Theor. Biol., 187, 573–581.Ding, M., Grebogi, C., Ott, E., Sauer, T., and Yorke, J. A., 1993. Plateau onset for correlation dimension:when does it occur? Phys. Rev. Lett., 70, 1993.Ditto, W. L., Rauseo, S. N., and Spano, M. L., 1990. Experimental control of chaos. Phys. Rev. Lett.,65, 3211–3214.Dobson, C. M., 1999. Protein misfolding evolution and disease. Trends Biochem. Sci., 24, 329–332.Dobson, C. M., 2002. Protein misfolding diseases getting out of shape. Nature, 418, 729–730.Donald, M. J., 1990. Quantum theory and the brain. Proc. R. Soc. London, Ser. A, 427, 43–93.Dykman, M. I., Luchinsky, D. G., Manella, R., McClintock, P. V. E., Stein, N. D., and Stocks, N. G.,1995. Stochastic resonance in perspective. II Nuovo Cimento, 17D, 661–685.Dykman, M. I. and McClintock, 1998. What can stochastic resonance do? Nature, 391, 344.Dyson, F., 1985. Origins of Life, Cambridge University Press, Cambridge.Earman, J., 1986. A Primer on Determinism, D. Reidel, Dordrecht, The Netherlands.Eccles, J. C., 1990. A unitary hypothesis of mind-brain interaction in the cerebral cortex. Proc.R. Soc. London, Ser. B, 240, 433–445.Eckmann, J. P. and Ruelle, D., 1985. Ergodic theory of chaos and strange attractors. Rev. Mod. Phys.,57, 617–656.Eckmann, J. P. and Ruelle, D., 1992. Fundamental limitations for estimating dimensions and Lyapunovexponents. Physica D, 56, 185–187.Edelman, G., 1992. Bright Air, Brilliant Fire. On the matter of the mind, Allen Lane, Penguin Press,London.Edholm, O. and Blomberg, C., 1981. Brownian motion description of activation energies from NMRrelaxation times for rotating molecular groups. Chem. Phys., 56, 9–14.Edholm, O. and Blomberg, C., 2000. Stretched exponentials and barrier distribution. Chem. Phys.,252, 221–225.Ehrenberg, M. and Blomberg, C., 1980. Thermodynamic constraints on kinetic proofreading in biosyntheticpathways. Biophys. J., 31, 333–358.Ehrenberg, M. and Blomberg, C., 1981. Thermodynamic constraints on kinetic proofreading inbiosynthetic pathways. Biophys. J., 31, 333–358.Eigen. M., 1971. Self-organization of matter and the evolution of biological macromolecules.Naturwissenschaften, 58, 465–523.Eigen, M., Gardiner, W. G., and Schuster, P., 1980. Hypercycles and compartments. J. Theor. Biol.,85, 407–411.Eigen, M. and Schuster, P., 1979. The Hypercycle: A Principle of Natural Self-Organisation,Springer, Berlin.Essig, A., 1975. Energetics of active transport processes. Biophys. J., 15, 651–661.Farmer, J. D., Ott, E., and Yorke, J. A., 1983. The dimension of chaotic attractors. Physica D, 7, 153–180.Feigenbaum, M. J., 1978. Quantitative universality for a class of nonlinear transformations. J. Stat.Phys., 19, 25–52.Ferris, J. O., 2002. Montmorillonite Catalysis of 30–50 Mer Oligonucleotides: LaboratoryDemonstration of Potential Steps in the Origin of the RNA World. Origins of Life, 323, 283–401.Fersht, A., 1999. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis andProtein Folding, W.H. Freeman, New York.
414 ReferencesFersht, A. R. and Daggett, V., 2002. Protein folding and unfolding at atomic resolution. Cell, 108,573–582.Feynman, R. P., Leighton, R. B., and Sands, M., 1963. The Feynman Lecture on Physics, Vol. 1,Chapter 46, Addison-Wesley, Reading, MA.FitzHugh, R., 1969. Mathematical models for excitation and propagation in nerve. In: BiologicalEngineering (ed. H. P. Schewan), McGraw Hill, New York.FitzHugh, R., 1961. Impulses and physiological states in models of nerve membranes. Biophys. J., 1,445–466.Fontana, W., Schnabl, W., and Schuster, P., 1989. Physical aspects of evolutionary optimization. Phys.Rev. A., 40, 3301–3321.Fox, R. F., 1998. Rectified Brownian movement in molecular and cell biology. Phys. Rev., E57,2177–2203.Fox, S. and Dose, K., 1977. Evolution and the Origin of Life, Marcell Dekker, New York.Frank, F. C., 1953. On spontaneous asymmetric synthesis. Biochim. Biophys. Acta, 11, 459–463.Frauenfelder, H., McMahon, B. H., Austin, R. H., Chu, K. and Groves, J. T., 2001. The role of structure,energy landscape, dynamics and allostery in the enzymatic function of myoglobin. Proc. Acad.Sci. USA, 98, 2370–2374.Freeman, W. J., 1992. Tutorial on neurobiology: from single neurons to brain chaos. Int. J. Bifurcat.Chaos, 2, 451.Freeman, W. J., Chang, H. J., Burke, B. C., Rose, P. A., and Badler, J., 1998. Taming chaos: stabilizationof aperiodic attractors by noise. IEEE Trans. Circuits System, 49, 989.Fröhlich, H., 1948. Trans. Faraday Soc., 44, 258.Fröhlich, H., 1958. Dielectric Constant and Dielectric Loss, 2nd edn., Oxford University Press, Oxford.Fröhlich, H., 1968. Long-range coherence and energy storage in biological systems. Int. J. QuantumChem., 2, 641–649.Fuchs, A., Friedrich, R., Haken, H., and Lehman, D., 1987. Spatio-temporal analysis of a multichannela-EEG map series. In: Computational Systems — Natural and Artificial (ed. H. Haken),Springer, Berlin.Garfinkel, A., Spano, M. L., Ditto, W. L., and Weiss, J. N., 1992. Controlling cardiac chaos. Science, 257,1230–1235.Gaspard, P. and Wang, X. J., 1993. Noise, Chaos, and (, t)-entropy per unit time. Phys. Rep., 235,291–345.Gilbert, W., 1986. The RNA world. Nature, 319, 618.Gillespie, D. T., 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem.,812, 2340.Go, N., 1983. Protein folding as a stochastic process. J. Stat. Phys., 30, 413–423.Goldbeter, A., 1996. Biochemical Oscillations and Cellular Rhythms. The Molecular Basis of Periodicand Chaotic Behaviour, Cambridge University Press, Cambridge.Goldbeter, A., 2002. Computational approaches to cellular rhythms. Nature, 420, 238.Goldbeter, A. and Decroly, D., 1983. Temporal self-organisation in biochemical systems: periodicbehaviour versus chaos. Am. J. Physiol., 245, R478–R485.Goldstein, R. F. and Bialek, W., 1986. Protein dynamics and reaction rates: are simple models useful.Comments. Mol. Cell. Biophys., 3, 407–438.Gorini, L., 1974. Streptomycin and misreading of the genetic code. In: Ribosomes (eds. M. Normura,A. Tissiers, and O. Lengyel), Cold Spring Harbor laboratory, Cold Spring Harbor, NY, p. 791.Greenberg, J. M., Kouchi, A., Biessen, W., Irth, H., van Paradijs, J., de Groot, H., and Hermsen, W.,1995. Interstellar dust, chirality, comets and the origin of life. Life from dead stars. J. Biol. Phys.,20, 61–70.Haken, H., 1983. Synergetics: An Introduction, Springer, Berlin.Haken, H., 1987. Advanced Synergetics, Springer, Berlin.Haken, H., 1996. Principles of Brain Functioning. A Synergetic Approach to Brain Activity andCognition, Springer, Berlin.Halliwell, J. J., Pérez-Mercader, and Zurek, W. H., eds., 1994. Physical Origins of Time Symmetry,Cambridge University Press, Cambridge.
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PHYSICS OF LIFEThe Physicist’s Ro
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PHYSICS OF LIFEThe Physicist’s Ro
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ContentsPrefaceixPart I General int
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Contentsvii20E Birth-death process
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PrefaceFor me, the journey to the p
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Part IGeneral introduction§ 1 INTR
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Chapter 1. Introduction: the aim an
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Chapter 2. The physics of life: phy
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Chapter 2. The physics of life: phy
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Chapter 2. The physics of life: phy
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Part IIThe physics basis§ 3 CONCEP
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Chapter 4. Basics of classical (New
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Chapter 4. Basics of classical (New
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Chapter 5. Electricity: the core of
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Chapter 6. Quantum mechanics 45(I h
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Chapter 6. Quantum mechanics 47The
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Chapter 6. Quantum mechanics 49prin
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Chapter 6. Quantum mechanics 51that
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Chapter 6. Quantum mechanics 53“v
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Chapter 6. Quantum mechanics 57If w
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Chapter 6. Quantum mechanics 59On t
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Chapter 6. Quantum mechanics 61than
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Chapter 7. Basic thermodynamics: in
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Part IIIThe general trends and obje
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Chapter 9. Some trends in 20th cent
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Chapter 10. From the simple equilib
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Chapter 10. From the simple equilib
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Chapter 10. From the simple equilib
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Chapter 11. Theoretical physics mod
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Chapter 11. Theoretical physics mod
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 12. The biological molecule
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Chapter 13. What is life? 113Figure
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Chapter 13. What is life? 115after
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Part IVGoing further with thermodyn
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 14. Thermodynamics formalis
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Chapter 15. Examples of entropy and
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Chapter 15. Examples of entropy and
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Chapter 15. Examples of entropy and
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Chapter 15. Examples of entropy and
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Chapter 16. Statistical thermodynam
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Part VStochastic dynamics§ 17 PROB
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Chapter 17. Probability concepts 17
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Chapter 17. Probability concepts 17
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Chapter 18. Stochastic processes 17
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Chapter 18. Stochastic processes 18
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Chapter 19. Random walk 183The tota
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Chapter 19. Random walk 185r in the
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Chapter 19. Random walk 187boundary
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Chapter 19. Random walk 189The sum
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 20. Step processes: master
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Chapter 21. Brownian motion: first
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Chapter 21. Brownian motion: first
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 22. Diffusion and continuou
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Chapter 23. Brownian motion and con
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Part VIMacromolecular applications
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Chapter 24. Protein folding and str
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Chapter 24. Protein folding and str
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Chapter 25. Enzyme kinetics 2550log
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Chapter 25. Enzyme kinetics 257and
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Chapter 25. Enzyme kinetics 259long
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Chapter 25. Enzyme kinetics 261the
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Chapter 25. Enzyme kinetics 263nota
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Chapter 25. Enzyme kinetics 265As f
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Part VIINon-linearity§ 26 WHAT DOE
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Chapter 26. What does non-linearity
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Chapter 26. What does non-linearity
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 27. Oscillations and space
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Chapter 28. Deterministic chaos 289
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Chapter 28. Deterministic chaos 291
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Chapter 28. Deterministic chaos 293
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Chapter 28. Deterministic chaos 295
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Chapter 28. Deterministic chaos 297
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Chapter 28. Deterministic chaos 299
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Chapter 28. Deterministic chaos 301
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Chapter 28. Deterministic chaos 303
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Chapter 28. Deterministic chaos 305
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Chapter 28. Deterministic chaos 307
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Chapter 28. Deterministic chaos 309
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Chapter 29. Noise and non-linear ph
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Chapter 29. Noise and non-linear ph
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Chapter 29. Noise and non-linear ph
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Chapter 29. Noise and non-linear ph
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Chapter 29. Noise and non-linear ph
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Part VIIIApplications§ 30 RECOGNIT
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 30. Recognition and selecti
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Chapter 31. Brownian ratchet: unidi
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Chapter 32. The neural system 343Fi
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Chapter 32. The neural system 345ev
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Chapter 32. The neural system 347Th
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Chapter 32. The neural system 34932
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Chapter 33. Origin of life 351once
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Chapter 33. Origin of life 353It is
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Chapter 33. Origin of life 355as am
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Chapter 33. Origin of life 357What
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Chapter 33. Origin of life 359world
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Chapter 33. Origin of life 361This
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- Page 426 and 427: References 415Hammerhoff, S. R., 19
- Page 428 and 429: References 417Mosekilde, E., 1996.
- Page 430 and 431: References 419Tsong, T. Y. and Chan
- Page 432 and 433: Indexa-helix, 99s-bond, 50-51, 99d-
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