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.
  2. Plimpton SJ. Computational limits of classical molecular-dynamics simulations. Comput Mater Sci. 1995; 4:361–4.
  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.
  4. Saunders MG, Voth GA. Coarse-graining methods for computational biology. Annu Rev Biophys. 2013; 42(2):73–93.
  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.
  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.
  7. Clapham DE. Calcium signaling. Cell. 1995; 80(2):259–68.
  8. Berridge MJ. Elementary and global aspects of calcium signalling. J Physiol (Lond). 1997; 499(Pt 2):291–306.
  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.
  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.
  11. Endo M. Calcium release from the sarcoplasmic reticulum. Phys Rev. 1977; 57(1):71–108.
  12. Cheng H, Lederer WJ, Cannell MB. Calcium sparks: elementary events underlying excitation-contraction coupling in heart muscle. Science. 1993; 262(5134):740–4.
  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.
  14. Shuai JW, Jung P. Optimal ion channel clustering for intracellular calcium signaling. Proc Natl Acad Sci USA. 2003; 100(2):506–10.
  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.
  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.
  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.
  18. DeRemigio H, Smith GD. Calcium release site ultrastructure and the dynamics of puffs and sparks. Math Med Biol. 2008; 25(1):65–85.
  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.
  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.
  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.
  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.
  23. Holland JH. Adaptation in Natural and Artificial Systems. Ann Arbor: The U. of Michigan Press; 1975.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  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.
  34. Davis L. Handbook Of Genetic Algorithms. New York: Van Nostrand Reingold; 1991.
  35. Michalewicz Z. Genetic Algorithms + Data Structures = Evolution Programs. New York: Springer; 1994.
  36. Nicola V. Lumping in markov reward processes. Technical report, RC14719, IBM Thomas Watson Research Centre, PO Box 704, Yorktown Heights, NY 10598;1998.
  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.
  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.
  39. Groff JR, Smith GD. Calcium-dependent inactivation and the dynamics of calcium puffs and sparks. J Theor Biol. 2008; 253(3):483–99.
  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.
  41. Keizer J, Levine L. Ryanodine receptor adaptation and Ca2+(-)induced Ca2+ release-dependent Ca2+ oscillations. Biophys J. 1996; 71(6):3477–487.
  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.
  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.
  44. Karafotias G, Hoogendoorn M, Eiben AE. Parameter control in evolutionary algorithms: Trends and challenges. IEEE Trans Evol. 2015; 19(2):167–87.
  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.
  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.

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.