Adamatzky, A.,Computing in Nonlinear Media and Automata Collectives, IOP Publishing Ltd, Philadelphia, PA, 2001.
Aslanidi, O. V., & Mornev, O. A. (1999). Soliton-like regimes and excitation pulse reflection (echo) in homogeneous cardiac Purkinje Fibers: Results of numerical simulations. Journal of Biological Physics, 25, 149-164.
Aslanidi O.V., Mornev O.A. Soliton-like regime in the Hodgkin-Huxley equations. International Conference Mathematical Models of Nonlinear Excitation Processes, Tver, Russia, July 2-5, 1996.
Aslanidi O.V., Gapeyev A.B., Kazachenko V.N., Mornev O.A., Chemeris N.K. Stochastic resonance in the Hodgkin-Huxley nerve fibre model. International Symposium Electrical Activity of The Brain: Mathematical Models & Analytical Methods, Pushchino, Russia, May 25-28, 1997.
Brown, J. H., Enquist, B. J., & West, G. B. (1999). The fourth dimension of life: Fractal geometry and allometric scaling of organisms. Science, 284:1677-1678.
Brown, J. H., Enquist, B. J. & West, G. B. (1997). A general model for the origin of allometric scaling laws in biology. Science, 276:122-126.
Caspi, S. and Ben-Jacob, E Toy model studies of soliton mediated protein folding and conformational changes. Europhys. Lett. 47, 522-527, 1999.
Changeux, J-P., & DeHaene, S. (1993) Neuronal models of cognitive functions. In M. Johnson (Ed.). Brain Development and Cognition. Blackwell, Cambridge, MA. pp. 363-402.
Davydov, A.S., Biology and Quantum Mechanics. Pergamon Press, Oxford, (1982) .
Dewey, G.D, Fractals in Molecular Biophysics, Oxford University Press, Inc, New York (1997) pp. 120-166
Englander S. W, Kallenbach, N. R, Heeger, A. J, Krumhansl, J. A, and Litwin A., 1980 Nature of the open state in long poly-nucleotide double helices: possibility of soliton excitations. Proceedings of the Natl. Acad. Sci. USA, 77, 7222-7226.
Gibson, J. J. (1979) The Ecological Approach to Visual Perception. Houghton Mifflin Co., Boston., 2, 10-29.
Grendel, B. T, BJ»RNSTAD, O. N, & KAPPEY, J, Travelling waves and spatial hierarchies in measles epidemics, Nature 414, 716đ723 (2001).
Gueron, S and Liron, N. 1989, A model of herd grazing as a travelling wave, chemotaxis and stability, Journal of Mathematical Biolology, 27: 595-608.
Hermon, Z., Caspi, S. & Ben-Jacob, E., (1998) Prediction of charge and dipole solitons in DNA molecules based on the behaviour of phosphate bridges as tunnel elements, Europhysics Letters, 44 (4), 482-487.
Jinguji, M., M. Ishihara, T. Nakazawa and H. Nagashima., Formation and propagation of rectangular chemical waves in the Belousov--Zhabotinskii reaction, PHYSICA D (Nonlinear Phenomena) Volume 84, 246-252
Lashley, K. S. (1942). The problem of cerebral organization in vision. In H. Kluver (Ed.), Biological Symposia, VII (pp. 301-322). Lancaster, PA: Jacques Cattell Press.
Maturana, H. R., and Varela F. , Autopoiesis and Cognition: The Realization of the Living, Boston Studies in the Philosophy of Science [Robert S Cohen and Marx W. Wartofsky (Eds.) ], Vol. 42, Dordecht (Holland): D. Reidel Publishing Co., 1980.
Odell, G. M. 1980, Biological waves, In L.A Segal (ed.), Mathematical Models in Molecular and Cellular Biology, Chapt. 6, 7, pp 523-567, Cambridge University Press.
Petoukhov, S. (1999) Biosolitons - One Secret of Living Matter-The Bases of Solitonic Biology. Mechanical Engineering Research Institute, Russian Academy of Sciences, Malii Haritonievskii pereulok, Moscow, Centre, 101830, Russia.
Ratliff, F. (1983). Acceptance speech on receiving the Pisart Vision Award. Quoted in R. Shepard (1984).
Rodgers C., Shadwick W., Backlund Transformations and their Applications, In Mathematics in Science and Engineering, V.161, Academic, New York, 1982.
Sataric, M.V., Ivic, Z., Tuszynski, J. A., & Zakula, R. (1991) Influence of a solitonic mechanism on the process of chemical catalysis, Journal of Molecular Electronics, 7, 39-46.
Sataric, M.V, Zakula, R.B, and Tuszynski, J.A, A model of the energy transfer mechanism in microtubules involving a single soliton, Nanobiology 1, 445-456 (1992).
Schrodinger, E. (1979). What is Life & What is Mind, Cambridge University press, New York, Based on lectures delivered under the auspices of the Dublin Institute for advanced Studies at Trinity College Dublin, in February 1943.
Scott, A. (1999) Nonlinear Science: Emergence and Dynamics of Coherent Structures. Oxford University Press, Oxford.
Shepard, R. N. (1984). Ecological constraints on internal representation: Resonant kinematics of perceiving, imaging, thinking, and dreaming. Psychological Review, 91, 417-447.
Yakushevich, L.V. (2001). Is DNA a nonlinear dynamical system where solitary conformational waves are possible? Journal of Bioscience, 26, 101-109.
Schneider, E.D., & Kay, J.J. (1994). Complexity and Thermodynamics - Towards a new Ecology. Futures, Butterworth - Heimann. 26(6) 626-647.
Swenson, R. & Turvey, M.T., Thermodynamic Reasons for Perception-Action Cycles, Ecological Psychology, 2(4), 317-348 (1991).
1. I would like to gratefully acknowledge my friend and mentor, Paul Gray, whose help, inspiration and guidance in developing these ideas has been constant along an uncertain path. I would also like to thank my advisor and friend Professor Patricia Carpenter whose invaluable experience and insight has helped to transform a loose collection of ideas into a coherent theory. I would also like to thank Carnegie Mellon University and the funding from the National Institute for Neurological Diseases and Stroke (Grant # P01NS35949 to P. Carpenter) for giving me the opportunity to research these ideas.