Biological Cybernetics and the Optimization Problem of Transport of Substances in Cells

The methods of biological cybernetics are used to observe living systems. The models of transport of substances through the biomembrane are discussed. Compartmental models of living systems in control theory are considered. The problem of the “minimal cell” is discussed. The place and role of models of the transport of substances in synthetic and systems biology are discussed. The “one ion—a transport system” algorithm and the game approach, which were previously proposed by the authors to model the transport of ions in cells, are described.

[1]  D. Gadsby,et al.  Voltage Dependence of the Apparent Affinity for External Na+ of the Backward-Running Sodium Pump , 2001, The Journal of general physiology.

[2]  S. Theander,et al.  The K-Cl cotransporter in the lobster stretch receptor neurone--a kinetic analysis. , 2002, Journal of theoretical biology.

[3]  A. Essig,et al.  Bioenergetics and Linear Nonequilibrium Thermodynamics: The Steady State , 1983 .

[4]  Jim Haseloff,et al.  Synthetic biology: history, challenges and prospects , 2009, Journal of The Royal Society Interface.

[5]  M. Bedau.  An Aristotelian account of minimal chemical life. , 2010, Astrobiology.

[6]  V. D. Seleznev,et al.  Model of active transport of ions in biomembranes based on ATP-dependent change of height of diffusion barriers to ions. , 2006, Journal of theoretical biology.

[7]  A. Hodgkin,et al.  The influence of potassium and chloride ions on the membrane potential of single muscle fibres , 1959, The Journal of physiology.

[8]  David Angeli,et al.  Graphs and the Dynamics of Biochemical Networks , 2009 .

[9]  John L. Casti,et al.  Connectivity, Complexity, and Catastrophe in Large-Scale Systems , 1980 .

[10]  A. Melkikh,et al.  Model of active transport of ions in cardiac cell. , 2008, Journal of theoretical biology.

[11]  Mun'delanji C. Vestergaard,et al.  Cascaded Games , 2007, AB.

[12]  Norbert Wiener,et al.  Cybernetics, or control and communication in the animal and the machine, 2nd ed. , 1961 .

[13]  R. Rakowski,et al.  Access channel model for the voltage dependence of the forward-running Na+/K+ pump , 1994, The Journal of general physiology.

[14]  V. D. Seleznev,et al.  Models of active transport of ions in biomembranes of various types of cells. , 2005, Journal of theoretical biology.

[15]  Javier Macía,et al.  Synthetic protocell biology: from reproduction to computation , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  G. Oster,et al.  The physics of molecular motors. , 2001, Accounts of chemical research.

[17]  Question 7: Construction of a Semi-Synthetic Minimal Cell: A Model for Early Living Cells , 2007, Origins of Life and Evolution of Biospheres.

[18]  W. Ashby.  Design for a Brain , 1954 .

[19]  V. D. Seleznev,et al.  Mechanisms and models of the active transport of ions and the transformation of energy in intracellular compartments. , 2012, Progress in biophysics and molecular biology.

[20]  Leslie M Loew,et al.  Computational cell biology: spatiotemporal simulation of cellular events. , 2002, Annual review of biophysics and biomolecular structure.

[21]  B. Palsson,et al.  Systems biology of the human red blood cell. , 2006, Blood cells, molecules & diseases.

[22]  Y Rudy,et al.  Action potential and contractility changes in [Na(+)](i) overloaded cardiac myocytes: a simulation study. , 2000, Biophysical journal.

[23]  Thomas H Segall-Shapiro,et al.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.

[24]  U. Hopfer.  A Maxwell's Demon type of membrane transport: possibility for active transport by ABC-type transporters? , 2002, Journal of theoretical biology.

[25]  N. Sperelakis.  Origin of Resting Membrane Potentials , 2001 .

[26]  D. Bedeaux,et al.  Active transport: a kinetic description based on thermodynamic grounds. , 2004, Journal of theoretical biology.

[27]  Hiroaki Kitano,et al.  Biological robustness , 2008, Nature Reviews Genetics.

[28]  A. Hodgkin,et al.  The effect of sodium ions on the electrical activity of the giant axon of the squid , 1949, The Journal of physiology.

[29]  D. E. Goldman.  POTENTIAL, IMPEDANCE, AND RECTIFICATION IN MEMBRANES , 1943, The Journal of general physiology.

[30]  Francis J. Doyle,et al.  Robustness and Sensitivity Analyses in Cellular Networks , 2009 .

[31]  M. Khammash,et al.  Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. , 2002, Journal of theoretical biology.

[32]  A. Katchalsky,et al.  Thermodynamic analysis of the permeability of biological membranes to non-electrolytes. , 1958, Biochimica et biophysica acta.

[33]  J. Stelling,et al.  Robustness of Cellular Functions , 2004, Cell.

[34]  W. Murdoch.  POPULATION REGULATION AND POPULATION INERTIA , 1970 .

[35]  Pablo A. Iglesias,et al.  Control Theory and Systems Biology , 2009 .

[36]  H. Kitano.  Towards a theory of biological robustness , 2007, Molecular systems biology.

[37]  J. Freedman.  Biophysical Chemistry of Physiological Solutions , 2001 .

[38]  D. Bernardo,et al.  A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches , 2009, Cell.

[39]  J. Jacquez.  Compartmental analysis in biology and medicine , 1985 .

[40]  Ricard V Solé,et al.  Phenotypic Diversity and Chaos in a Minimal Cell Model , 2005 .

[41]  C. S. Holling.  Resilience and Stability of Ecological Systems , 1973 .

[42]  J. Lopreato,et al.  General system theory : foundations, development, applications , 1970 .

[43]  J. Doyle,et al.  Reverse Engineering of Biological Complexity , 2002, Science.

[44]  G. Murtas,et al.  Artificial assembly of a minimal cell. , 2009, Molecular bioSystems.

[45]  V. D. Seleznev,et al.  Requirements on Models and Models of Active Transport of Ions in Biomembranes , 2006, Bulletin of mathematical biology.

[46]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[47]  Peter F. Stadler,et al.  Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism , 2004, Origins of life and evolution of the biosphere.

[48]  E. Szathmáry,et al.  The principles of life , 2003 .

[49]  T. Tsong,et al.  Ion pump as Brownian motor: theory of electroconformational coupling and proof of ratchet mechanism for Na,K-ATPase action , 2003 .

[50]  Roger Brent,et al.  A partnership between biology and engineering , 2004, Nature Biotechnology.

[51]  近久 芳昭,et al.  N.Rashevsky: "Mathematical Biophysics, Physico-Mathematical Foundations of Biology", Dover Publications, New York, 1960. VoI. I, 488頁, Vol. II, 462頁, 14×20.5cm, 各巻$2.50. , 1961 .

[52]  Pamela A. Silver,et al.  Informing Biological Design by Integration of Systems and Synthetic Biology , 2011, Cell.

[53]  Norbert Wiener,et al.  Cybernetics: Control and Communication in the Animal and the Machine. , 1949 .

[54]  T. Waterman.  Systems Theory and Biology—View of a Biologist , 1968 .

[55]  K. Bellmann,et al.  Jacquez, J. A.: Compartmental analysis. Biology and Medicine. Elsevier Publ. Co., Amsterdam, New York 1972. XIV, 237 S., 93 Abb., 1 Tab., $24.35 , 1974 .

[56]  John Doyle,et al.  Complexity and robustness , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[57]  V. D. Seleznev,et al.  Early Stages of the Evolution of Life: a Cybernetic Approach , 2008, Origins of Life and Evolution of Biospheres.

[58]  Pasquale Stano,et al.  Chemical approaches to synthetic biology. , 2009, Current opinion in biotechnology.

[59]  A. Kabakov.  Activation of KATP channels by Na/K pump in isolated cardiac myocytes and giant membrane patches. , 1998, Biophysical journal.

[60]  W. Zerges.  Does complexity constrain organelle evolution? , 2002, Trends in plant science.

[61]  A. V. Melkikh,et al.  Algorithms for optimization of the transport system in living and artificial cells , 2011, Systems and Synthetic Biology.