Preface Part I Basic models in mathematical biophysics Chapter 1 Growth and catalysis models Unlimited growth. Exponential growth. Self-catalysis (Auto-catalysis) Limited growth. The Verhulst equation Constraints with respect to substrate. Models of Monod and Michaelis-Menten Competition. Selection Jacob and Monod trigger system Classic Lotka and Volterra models Models of species interactions Models of the enzyme catalysis Model of a continuous microorganism culture Age structured populations Leslie matrices Continuous models of age structure Chapter 2 Oscillations, rhythms and chaos in biological systems Oscillations in glycolysis Intracellular calcium oscillations Deterministic Chaos Chaos in the community of three species Periodic supply of substrate in the system of glycolysis Chapter 3 Spatiotemporal self-organization of biological systems Waves of life Autowaves and dissipative structures Basic model "Brusselator" Localized dissipative structures Belousov-Zhabotinsky reaction Chapter 4 Model of the impact of a weak electric field on the nonlinear system of trans-membrane ion transport Transmembrane ion transport model Bistable model Auto -oscillating system Part II Models of complex systems Chapter 5 Oscillations and periodic space structures of pH and electric potential along the cell membrane of algae Chara corallina Kinetic model of the proton ATPase (pump) Equation, describing dynamics of proton concentration in the vicinity of the cell Equation for potential dynamics Oscillations in the local system pH patterns along the cellular membrane Dependence of the processes on light intensity. Hysteresis Scheme of interactions of photosynthesis and ion fluxes leading to the nonlinear dynamics Chapter 6 Models of Morphogenesis Turing instability Morphogenetic field Model of a distributed trigger Animal coat markings Models of amoeba aggregation. The role of chemotaxis Chapter 7 Autowave processes, nerve pulse propagation, and heart activity Experiments and model of Hodgkin and Huxley Reduced FitzHugh-Nagumo Model Excited element of the local system Running pulses Detailed models of cardiomyocytes Axiomatic models of excited medium.
Autowave processes and cardiac arrhythmia Chapter 8 Nonlinear models of DNA dynamics Hierarchy of structural and dynamical models Linear DNA theory Simple linear model of an elastic bar Nonlinear models of DNA mobility. Mechanical analogue Mathematical model, simulating single DNA base''s nonlinear oscillations Physical analogues of real DNA sequences Long-range effects Nonlinear mechanisms of transcription regulation Part III Kinetic models of photosynthetic processes Chapter 9 Models of photosynthetic electron transport. Electron transfer in a multienzyme complex Organization of processes in photosynthetic membrane Kinetic description of redox reactions in solution Modeling electron transfer in a multienzyme complex Electron transfer in a two-component complex Electron transfer in a n-carrier complex Electron transport via mobile carriers Electron transport in an isolated photosynthetic reaction center Chapter 10 Kinetic model of interaction of two photosystems Types of regulation of photosynthetic processes Model of PSI and PSII interaction Subsystem PSII Scheme of PSII states Charge separation Submodel of PSI Description of the mobile carrier redox evolution Relationships between total concentrations of electron carriers Modeling of electron transport chain of wild type and mutant Arabidopsys thaliana Chapter 11 Detailed model of electron transfer in PSIIFluorescence as an indicator of the state of the photosystem Scheme of PSII states Equations describing processes in PSII Dependence of rate constants on thylakoid transmembrane electric potential Energy loss processes Experiment Description of events in PSII electron transport system after a short light flash Chapter 12 Generalized kinetic model of primary photosynthetic processes The structure of the model Photosystem II complex Cytochrome b6f complex Photosystem I complex Mobile carriers in the kinetic model Role of transmembrane electric potential Transmembrane ion transfer and generation Buffer properties of lumen and stroma Parameter values Simulation of fluorescence transients at different light intensities The role of different states of photosystem II in fluorescence induction Simulation of kinetics Part IV Direct multiparticle models of processes in subcellular systems Chapter 13 Method of direct multiparticle simulation of protein interactions Restricted diffusion of mobile electron carriers in photosynthetic membrane Direct model scene Brownian dynamics of mobile carriers Simulation of cyclic electron transport around photosystem I Chapter 14 Modeling of protein complex formation in solution with diffusion and electrostatic interactions Steps of redox protein interactions Model of protein-protein interaction in solution Protein diffusion. Approximation with ellipsoids of revolution Simulation of geometric shape of proteins and their collisions Electrostatic interactions Simulation of complex formation Docking rate constant dependence on ionic strength of solution Comparative analysis of the interaction of Pc with Cyt f and PSI reaction centers in higher plants and cyanobacteria. Role of electrostatics Chapter 15 Modeling of protein interactions in photosynthetic membrane Interaction of Pc with Cyt f in thylakoid lumen Modeling of Pc -PSI interaction considering membrane surface charge and multienzyme complexes embedded in the membrane Modeling of Pc interaction with cyt f and PSI considering membrane surface charge and multienzyme complexes embedded in the membrane Chapter 16 Spaciotemporal evolution of electrochemical potential ΔμH+ in photosynthetic membrane Modeling of proton transfer Model of proton release into lumen Model of lateral diffusion of protons Proton flow through the ATP-synthase and ATP synthesis Computer simulation of proton gradient evolution and ATP creation Conclusion References Index.