Algorithms for optimization of the transport system in living and artificial cells

Systems and Synthetic Biology

Volumn 5, Issue 1, 2011, Pages 87-96

  Melkikh, A V ^a   Sutormina, M I ^a  

^a URAL FEDERAL UNIVERSITY   (Russian Federation)

Author keywords

Efficiency; Game theory; Robustness; Synthetic biology; Systems biology; Transport of ions

Indexed keywords

EID: 80052031531     PISSN: 18725325     EISSN: 18725333     Source Type: Journal    
DOI: 10.1007/s11693-011-9083-6     Document Type: Article

References (29)

1. Alvarez-Leefmans FJ (2001) Intracellular chloride regulation. In: Sperelakis N (ed) Cell physiology sourcebook, 3rd edn. Academic Press, San Diego, pp 301-318.
2. Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3/4): 281-297.
3. El-Shamad D, Goff JP, Khammash M (2002) Calcium homeostasis and parturient hypocalcemiya: an internal feedback perspective. J Theor Biol 214: 17-29.
4. Forster AC, Church GM (2006) Towards synthesis of a minimal cell. Mol Syst Biol 2: 1-10.
5. Fossat B, Porthé-Nibelle J, Pedersen S, Lahlou B (1997) Na+/H+ exchange and osmotic shrinkage in isolated trout hepatocytes. J Exp Biol 200: 2369-2376.
6. Haussinger D (1996) The role of cellular hydration in the regulation of cell function. Biochem J 313: 697-710.
7. Hillier FS, Lieberman GJ (2005) Introduction to operations research, 8th edn. McGraw-Hill Companies, Inc, New York.
8. Jamshidi N, Palsson BO (2006) Systems biology of the human red blood cell. Blood Cells Mol Dis 36(2): 239-247.
9. Kitano H (2004) Biological robustness. Nature 5: 826-837.
10. Kitano H (2007) Towards a theory of biological robustness. Mol Syst Biol 3(137): 1-7.
11. Maguire ME (2006) Magnesium transporters: properties, regulation and structure. Front Biosci 11: 3149-3163.
12. Melkikh AV, Seleznev VD (2005) Models of active transport of ions in biomembranes of various types of cells. J Theor Biol 324(3): 403-412.
13. Melkikh AV, Seleznev VD (2006a) Requirements on models and models of active transport of ions in biomembranes. Bull Math Biol 68: 385-399.
14. Melkikh AV, Seleznev VD (2006b) Model of active transport of ions in biomembranes based on ATP-dependent change of height of diffusion barriers to ions. J Theor Biol 242(3): 617-626.
15. Melkikh AV, Seleznev VD (2007a) Models of active transport of neurotransmitters in synaptic vesicles. J Theor Biol 248(2): 350-353.
16. Melkikh AV, Seleznev VD (2007b) Nonequilibrium statistical model of active transport of ions and ATP production in mitochondria. J Biol Phys 33(2): 161-170.
17. Melkikh AV, Seleznev VD (2008) Early stages of the evolution of life: a cybernetic approach. Orig Life Evol Biospheres 38: 343-353.
18. Melkikh AV, Sutormina MI (2008) Models of active transport of ions in cardiac cell. J Theor Biol 252: 247-254.
19. Munteanu A, Sole RV (2006) Phenotypic diversity and chaos in a minimal cell model. J Theor Biol 240: 434-442.
20. Murtas G (2007) Question 7: construction of a semi-synthetic minimal cell: a model for early living cells. Orig Life Evol Biospheres 37(4-5): 419-422.
21. Nemhauser G, Wolsey L (1988) Integer and combinatorial optimization. John Wiley and Sons, New York.
22. Nicholls JG, Martin AR, Wallace BG, Fuchs PA (2003) From neuron to brain, 4th edn. Sinauer Associates, Sunderland, MA.
23. Oster GF, Perelson AS, Katchalsky A (1973) A network thermodynamics: dynamic modelling of biophysical systems. Q Rev Biophys 6: 1-134.
24. Payne JA, Xu J-C, Haas M, Lytle CY, Ward D, Forbush B III (1995) Primary structure, functional expression, and chromosomal localization of the bumetanide-sensitive Na-K-Cl cotransporter in human colon. J Biol Chem 270: 17977-17985.
25. Rodrigues-Navarro S (1987) Na-atphases and Na+/H+ antiporters in fungi. Biochim Biophis Acta 5: 203-205.
26. Rodriguez-Navarro A, Quintero FJ, Garciadeblas B (1994) Na-ATPases and Na+/H+ antiporters in fungi. Biochim Biophys Acta 1187(2): 203-205.
27. Silva-Graca M, Lucas C (2003) Physiological studies on long-term adaptation to salt stress in the extremely halotolerant yeast Candida versatilis CBS 4019 (syn C. halophila). FEMS Yeast Res 3: 247-260.
28. Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J (2004) Robustness of cellular functions. Cell 118: 675-685.
29. Yilmaz FB, Oktem H, Weber GW (2004) Mathematical modeling and approximation of gene expression patterns and gene networks. In: Fleuren F, den Hertog D, Kort P (eds) Operations research proceedings. International Conference on Operations Research, Tilburg, The Netherlands, pp 280-287.