Developing Synthetic Transport Systems, 2013

?Understanding the general laws of an effective system for the transport of substances in cells is an important goal of systems and synthetic biology and will help us to answer why the transport subsystem of a cell is arranged as it is. In addition, the construction of models for optimizing transport systems is of considerable importance in the early stages in the development of a functioning protocell. The aim of this book is to describe the latest techniques for the calculation of the optimal parameters of the transport subsystem of a cell at its maximum efficiency. The book will describe linear and nonlinear programming, dynamic programming, game theory for models of ion transport in different types of cells (e.g. mammalian cells, bacteria, plants and fungi). ?

Introduction.- Chapter 1 Biological Cybernetics and the optimization problem of transport of substances in the cells.- 1.1 Methods of optimization and living systems.- 1.1.1 Control theory and biosystems.- 1.1.2 Optimality and living systems.- 1.1.3 Compartmental models of living systems in biological cybernetics.- 1.1.4 Biological cybernetics, synthetic biology and the “minimal cell”.- 1.2 Transport of ions through cell membranes – models and methods of optimization.- 1.2.1 Active and passive transport of ions. Resting potential.- 1.2.2 Osmotic pressure of solutions inside and outside the cell.- 1.2.3 Classification of models of ion transport. Two-level model. Algorithm “one ion – one transport system”.- 1.2.4 Methods of optimizations and transport of substances.- 1.2.5 Two transport systems for one substance.- 1.2.6 An optimization of the transport system of a cell as a game problem.- References.- Chapter 2 Models of ion transport in mammalian cells.- 2.1Cardiac cells.- 2.1.1 Model of transport systems.- 2.1.2 Regulation of ion transport.- 2.2 Neurons.- 2.2.1 Model of transport systems.- 2.2.2 Model of ion transport with a restriction of deviation from the experimental data.- 2.2.3 Regulation of ion transport.- 2.3 Erythrocytes.- 2.3.1 Model of ion transport.- 2.3.2 The model of regulation of ion transport: efficiency or robustness?- 2.4 Hepatocytes.- 2.4.1 Model for ion transport.- 2.4.2 Regulation of ion transport.- 2.5 Regulation of ion transport in compartments of a mammalian cell.- 2.5.1 Mitochondria.- 2.5.2 Sarcoplasmic and endoplasmic reticulum.- 2.5.3 Synaptic vesicles.- Conclusions.- References.- Chapter 3 Models of ion transport and regulation in plant cells and unicellular organisms.- 3.1 Archaea.- 3.2 Diatomei.- 3.3 E. coli.- 3.3.1 Transport model of basic ions.- 3.3.2 Calculation of the osmotic pressure difference in bacteria.- 3.4 Regulation of ion transport in select microorganisms.- 3.5 Possible regulatory strategies for bacterial transport of heavy metals.- 3.6 Plant cells.- 3.7 Vacuoles.- 3.8 Thylakoids.-  Conclusions.- References.- Chapter  4 Optimization of the transport of substances in cells.- 4.1 Optimization methods used for models of transport subsystems of living and artificial cells.- 4.1.1.- Effectiveness of the energy conversion in the transport of substances through biomembranes.- 4.1.2 Synthesis of the transport system of an artificial cell based on the method of dynamic programming.- 4.1.3 Ideal transport system: simultaneous optimization of robustness and effectiveness.- 4.1.4 Method of the critical point.- 4.1.5 Controllability and paradox of ions transport.- 4.1.6 Cascades and networks of the transport molecular machines.- 4.1.7 Regulation of the pressure in generalized cells. Cells in fresh and distilled water. Transport of water.- 4.1.8 Transport of ions with a lack of energy and diffusion of ATP.- 4.2 Protocells at the early stages of evolution.- 4.2.1 Early stages of evolution and origin of the first cells.- 4.2.2 A model of the simplest transport system in a minimal cell.- 4.2.3 A model of the simplest system for the control of transport processes in a cell.- 4.2.4 Physico-chemical models of cellular movement.- 4.2.5 Sunlight as a possible source of energy for movement.- 4.2.6 The energy balance in protocells.- 4.2.7 The problem of control and reception of information: strategies used by protocells for directed motion. 4.3. The transport of large molecules in living and artificial cells.- Conclusion.- Appendix 1 Methods of optimization.- A1.1 Conditional extremum and nonlinear programming.- A1.2 Linear programming.- A1.3 Integer programming.- A1.4 The packing problem (backpack).- A1.5 Dynamic programming.- A1.6 Matrix games.- Appendix 2 Controllability of linear control systems.- References. Index.