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All issues Volume 4 / No 1 (December 2016) EPJ Nonlinear Biomed Phys, 4 1 (2016) 4 References
The Physics Behind Systems Biology
Open Access
Open Access
Issue
EPJ Nonlinear Biomed Phys
Volume 4, Number 1, December 2016
The Physics Behind Systems Biology
Article Number 4
Number of page(s) 21
DOI https://doi.org/10.1140/epjnbp/s40366-016-0032-x
Published online 04 June 2016
  1. Alder BJ, Wainwright TE. Studies in molecular dynamics. i. general method. J Chem Phys. 1959; 31(2):459. [Google Scholar]
  2. Plimpton SJ. Computational limits of classical molecular-dynamics simulations. Comput Mater Sci. 1995; 4:361–4. [Google Scholar]
  3. Brini E, Algaer EA, Ganguly P, Li C, Rodríguez-Ropero F, van der Vegt NFA. Systematic coarse-graining methods for soft matter simulations - a review. Soft Matter. 2013; 7:2108–119. [Google Scholar]
  4. Saunders MG, Voth GA. Coarse-graining methods for computational biology. Annu Rev Biophys. 2013; 42(2):73–93. [Google Scholar]
  5. Zheng J, Vankataramanan L, Sigwortha FJ. Hidden markov model analysis of intermediate gating steps associated with the pore gate of shaker potassium channels. J Gen Physiol. 2001; 118(5):547–64. [Google Scholar]
  6. Nguyen V, Mathias R, Smith GD. A stochastic automata network descriptor for markov chain models of instantaneously-coupled intracellular Ca2+ channels. Bull Math Biol. 2005; 67(3):393–432. [Google Scholar]
  7. Clapham DE. Calcium signaling. Cell. 1995; 80(2):259–68. [Google Scholar]
  8. Berridge MJ. Elementary and global aspects of calcium signalling. J Physiol (Lond). 1997; 499(Pt 2):291–306. [Google Scholar]
  9. Cheng H, Lederer MR, Lederer WJ, Cannell MB. Ca+ sparks and [Ca2+]i waves in cardiac myocytes. Am J Physiol. 1996; 270(1 Pt 1):148–59. [Google Scholar]
  10. Yao Y, Choi J, Parker I. Quantal puffs of intracellular Ca2+ evoked by inositol trisphosphate in Xenopus oocytes. J Physiol. 1995; 482(Pt 3):533–3. [Google Scholar]
  11. Endo M. Calcium release from the sarcoplasmic reticulum. Phys Rev. 1977; 57(1):71–108. [Google Scholar]
  12. Cheng H, Lederer WJ, Cannell MB. Calcium sparks: elementary events underlying excitation-contraction coupling in heart muscle. Science. 1993; 262(5134):740–4. [Google Scholar]
  13. Parker I, Choi J, Yao Y. Elementary events of IP3-induced Ca2+ liberation in Xenopus oocytes: hot spots, puffs and blips. Cell Calcium. 1996; 20(2):105–21. [Google Scholar]
  14. Shuai JW, Jung P. Optimal ion channel clustering for intracellular calcium signaling. Proc Natl Acad Sci USA. 2003; 100(2):506–10. [Google Scholar]
  15. Cannell MB, Cheng H, Lederer WJ. Spatial non-uniformities in [Ca2+]i during excitation-contraction coupling in cardiac myocytes. Biophys J. 1994; 67(5):1942–56. [Google Scholar]
  16. Colquhoun D, Hawkes A. A Q-matrix cookbook: how to write only one program to calculate the sigle-channel and macroscopic predictions for any kinetic mechanism In: Sakmann B, Neher E, editors. Single-Channel Recording. New York: Plenum Press: 1995. p. 589–633. [Google Scholar]
  17. Smith GD. Modeling the stochastic gating of ion channels In: Fall C, Marland E, Wagner J, Tyson J, editors. Computational Cell Biology. New York: Springer: 2002. p. 291–325. [Google Scholar]
  18. DeRemigio H, Smith GD. Calcium release site ultrastructure and the dynamics of puffs and sparks. Math Med Biol. 2008; 25(1):65–85. [Google Scholar]
  19. Williams GSB, Huertas MA, Sobie EA, Jafri MS, Smith GD. A probability density approach to modeling local control of Ca2+-induced Ca2+ release in cardiac myocytes. Biophys J. 2007; 92(7):2311–28. [Google Scholar]
  20. Williams GSB, Huertas MA, Sobie EA, Jafri MS, Smith GD. Moment closure for local control models of Ca2+-induced Ca2+ release in cardiac myocytes. Biophys J. 2008; 95(4):1689–703. [Google Scholar]
  21. Hao Y, Kemper P, Smith GD. Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation. Chaos. 2009; 5(19):037107. [Google Scholar]
  22. Feldmann AE. Fast balanced partitioning is hard even on grids and trees In: Rovan B, Sassone V, Widmayer P, editors. Mathematical Foundations of Computer Science 2012. Berlin Heidelberg: Springer: 2012. p. 372–82. [Google Scholar]
  23. Holland JH. Adaptation in Natural and Artificial Systems. Ann Arbor: The U. of Michigan Press; 1975. [Google Scholar]
  24. Gesú VD, Giancarlo R, Bosco GL, Raimondi A, Scaturro D. Genclust: a genetic algorithm for clustering gene expression data. BMC Bioinformatics. 2005; 6:289. [Google Scholar]
  25. To C, Vohradsky J. A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in streptomyces coelicolor. BMC Genomics. 2007; 8:49. [Google Scholar]
  26. Hill T, Lundgren A, Fredriksson R, Schioth H. Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins. Biochim Biophys Acta. 2005; 1725(1):19–29. [Google Scholar]
  27. Groenendaal W, Ortega FA, Kherlopian AR, Zygmunt AC, Krogh-Madsen T, Christini DJ. Cell-specific cardiac electrophysiology models. PLoS Comput Biol. 2015; 11(4):1004242. [Google Scholar]
  28. Hartman JA, Sobie EA, Smith GD. Calcium sparks and homeostasis in a minimal model of local and global calcium responses in quiescent ventricular myocytes. AJP: Heart Circ Physiol. 2010. doi:10.1152/ajpheart.00293.2010. [Google Scholar]
  29. Hinch R, Greenstein JL, Tanskanen AJ, Xu L, Winslow RL. A simplified local control model of calcium-induced calcium release in cardiac ventricular myocytes. Biophys J. 2004; 87(6):3723–6. [Google Scholar]
  30. Hinch R, Greenstein JL, Winslow RL. Multi-scale models of local control of calcium induced calcium release. Prog Biophys Mol Biol. 2006; 90(1-3):136–50. [Google Scholar]
  31. Greenstein JL, Hinch R, Winslow RL. Mechanisms of excitation-contraction coupling in an integrative model of the cardiac ventricular myocyte. Biophys J. 2006; 90(1):77–91. [Google Scholar]
  32. Mazzag B, Tignanelli C, Smith GD. The effect of residual Ca2+ on the stochastic gating of Ca2+-regulated Ca2+ channels. J Theor Biol. 2005; 235(1):121–50. [Google Scholar]
  33. Huertas MA, Smith GD. The dynamics of luminal depletion and the stochastic gating of Ca2+-activated Ca2+ channels and release sites. J Theor Biol. 2007; 246(2):332–54. [Google Scholar]
  34. Davis L. Handbook Of Genetic Algorithms. New York: Van Nostrand Reingold; 1991. [Google Scholar]
  35. Michalewicz Z. Genetic Algorithms + Data Structures = Evolution Programs. New York: Springer; 1994. [Google Scholar]
  36. Nicola V. Lumping in markov reward processes. Technical report, RC14719, IBM Thomas Watson Research Centre, PO Box 704, Yorktown Heights, NY 10598;1998. [Google Scholar]
  37. Shannon TR, Wang F, Puglisi J, Weber C, Bers DM. A mathematical treatment of integrated Ca2+ dynamics within the ventricular myocyte. Biophys J. 2004; 87(5):3351–71. [Google Scholar]
  38. Stevens SC, Terentyev D, Kalyanasundaram A, Periasamy M, Györke S. Intra-sarcoplasmic reticulum Ca2+ oscillations are driven by dynamic regulation of ryanodine receptor function by luminal Ca2+ in cardiomyocytes. J Physiol (Lond). 2009; 587(20):4863–72. published in October 2009. [Google Scholar]
  39. Groff JR, Smith GD. Calcium-dependent inactivation and the dynamics of calcium puffs and sparks. J Theor Biol. 2008; 253(3):483–99. [Google Scholar]
  40. Györke I, Györke S. Regulation of the cardiac ryanodine receptor channel by luminal Ca2+ involves luminal Ca2+ sensing sites. Biophys J. 1998; 75(6):2801–10. [Google Scholar]
  41. Keizer J, Levine L. Ryanodine receptor adaptation and Ca2+(-)induced Ca2+ release-dependent Ca2+ oscillations. Biophys J. 1996; 71(6):3477–487. [Google Scholar]
  42. Rückl M, Parker I, Marchant JS, Nagaiah C, Johenning FW, Rüdiger S. Modulation of elementary calcium release mediates a transition from puffs to waves in an IP3R cluster model. PLoS Comput Biol. 2015; 11(1):1003965. [Google Scholar]
  43. Rüdiger S, Shuai JW, Huisinga W, Nagaiah C, Warnecke G, Parker I, Falcke M. Hybrid stochastic and deterministic simulations of calcium blips. Biophys J. 2007; 93:1847–57. [Google Scholar]
  44. Karafotias G, Hoogendoorn M, Eiben AE. Parameter control in evolutionary algorithms: Trends and challenges. IEEE Trans Evol. 2015; 19(2):167–87. [Google Scholar]
  45. Cao P, Tan X, Donovan G, Sanderson MJ, Sneyd J. A deterministic model predicts the properties of stochastic calcium oscillations in airway smooth muscle cells. PLoS Comput Biol. 2014; 10(8):1003783. [Google Scholar]
  46. Cao P, Donovan G, Falcke M, Sneyd J. A stochastic model of calcium puffs based on single-channel data. Biophys J. 2013; 105:1133–42. [Google Scholar]