Nonlinear Excitations in Biomolecules

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.