Nonlinear Excitations in Biomolecules

In the last few years, hopes have emerged that simple concepts could perhaps explain the extremely complicated biomolecular processes which are known to a greater and greater accuracy thanks to the extraordinary progress of biology. In parallel, powerful methods in physics, especially nonlinearity and cooperative effects, have been developed. They apply especially to biological phenomena and can explain coherent excitations with remarkable properties. This book provides a pedagogical introduction to the theory of nonlinear excitations and solitons in a biological environment, and also to the structure and function of biomolecules as well as energy and charge transport in biophysics.

The aim of the book is to emphasize the link between physics and biology and to provide the reader with a powerful tool for attacking the extreme complexity of nature. The book addresses researchers in biophysics, biochemistry and molecular biology.

Lecture 1 The intersection of nonlinear science, molecular biology, and condensed matter physics. Viewpoints.- Lecture 2 Introduction to solitons and their applications in physics and biology.- I DNA, structure and function.- Lecture 3 Selected topics in molecular biology, in need of "hard" science.- Lecture 4 Modelling the DNA double helix: techniques and results.- Lecture 5 Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems.- Lecture 6 Inelastic neutron scattering studies of oriented DNA.- Lecture 7 Model simulations of base pair motion in B-DNA.- Lecture 8 A nonlinear model for DNA melting.- Lecture 9 Dynamics of conformational excitations in the DNA macromolecule.- Lecture 10 Nonlinear dynamics of plasmid pBR322 promoters.- Lecture 11 Helical geometry and DNA models.- Lecture 12 Nonlinear localized excitations and the dynamics of H-bonds in DNA.- II Proteins, conformation and dynamics.- Lecture 13 Proteins and the physics of complexity.- Lecture 14 Multi-basin dynamics of a protein in aqueous solution.- Lecture 15 Nonlinear excitations in molecular crystals with chains of peptide bonds.- Lecture 16 Low temperature Raman spectra of acetanilide and its deuterated derivatives: comparison with normal mode analysis.- Lecture 17 Conformational dynamics of proteins: beyond the nanosecond time scale.- Lecture 18 Motions and correlations of the transmembrane domain of a protein receptor studied by molecular dynamics simulation.- III Energy and charge transport.- Lecture 19 Solitary waves in biology.- Lecture 20 Exact two-quantum states of the semiclassical Davydov model and their thermal stability.- Lecture 21 Post-soliton quantum mechanics.- Lecture 22 Dynamic form factor for the Yomosa model for the energytransport in proteins.- Lecture 23 Energy and charge transfer in photosynthesis.- Lecture 24 The role of nonlinearity in modelling energy transfer in Scheibe aggregates.- Lecture 25 Protons in hydrated protein powders.- Lecture 26 Nonlinear models of collective proton transport in hydrogen-bonded systems.- Lecture 27 Proton-solitons bridge physics with biology.- Lecture 28 Neutron scattering studies of biopolymer-water systems: solvent mobility and collective excitations.- IV Beyond biological molecules.- Lecture 29 The cell's microtubules: self-organization and information processing properties.- Lecture 30 Translation optimization in bacteria: statistical models.- Lecture 31 Dynamics of vibrational dissociation of a pseudo-cluster.- Lecture 32 The step-potential model for ?-electrons in hydrocarbon-systems.- Conclusion.