Simulating FAS-induced apoptosis by using P systems

Pre-Proceedings of the International Conference on Bio-Inspired Computing - Theory and Applications: Membrane Computing Section, BIC-TA 2006

Volumn , Issue , 2006, Pages 71-81

  Cheruku, Smitha ^a   Paun, Andrei ^a   Romero Campero, Francisco J ^b   Perez Jimenez, Mario J ^b   Ibarra, Oscar H ^c  

^a Louisiana Tech University   (United States)

^b UNIVERSITY OF SEVILLE   (Spain)

^c University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PHENOMENA; CELL SURFACES; CURRENT SIMULATION; GILLESPIE ALGORITHM; KEY FEATURE; STRUCTURAL ORGANIZATION; SYSTEMS BIOLOGY; UNCONVENTIONAL MODEL OF COMPUTATION;

ALGORITHMS; BIOINFORMATICS; CELL MEMBRANES; CELL SIGNALING; DIFFERENTIAL EQUATIONS;

COMPUTATION THEORY;

EID: 38149021582     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (23)

1. G. Ciobanu, Gh. Pa̧un, M.J. Pérez-.Jiménez, eds.: Applications of Membrane Computing. Springer-Verlag, Berlin, '2006.
2. E.H Cheng, M.C. Wei, S. Weiler, R.A. Flavell, T.W. Mak, T. Lindsten, S.J. Korsmeyer: BCL-2, BCL- XL sequester BH3 domain-only molecules preventing BAX- And BAK-mediated mitochondrial apoptosis. Molecular Cell, 8 (2001), 705-711.
3. D.T. Gillespie: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics, 22 (1976), 403-434,.
4. D.T. Gillespie: Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81 (1997), 2340-2361.
5. D.T. Gillespie: Approximate accelerated stochastic simulation of chemically reacting systems. Journal of Chemical Physics, 115 (2001), 1716-1733.
6. D.T. Gillespie: Improved leap-size selection for accelerated stochastic simulation. Journal of Chemical Physics, 119 (2003), 8229-8234.
7. F. Hua, M. Cornejo, M. Cardone, C. Stokes, D. Lauffenburger: Effects of Bcl-2 levels on FAS signaling- induced Caspase-3 activation: Molecular genetic tests of computational model predictions. The Journal of Immunology, 175 (2005), 985-995, and correction 175 (2005), 6235-6237.
8. O.H. Ibarra, A. Pa̧un; Counting time in computing with cells. Proceedings of DNA Bused Computing, DNAU, London, Ontario, 2005, 25-36.
9. P.H. Krammer: CD95's deadly mission in the immune system. Nature, 407 (2000), 789-795.
10. V. Manca, L. Bianco, F. Fontana: Evolution and oscillation in P systems: Applications to biological phenomena, Lecture Notes in Computer Science, 3365 (2005), 63-84.
11. T.C'. Meng, S. Somani, P. Dhar; Modelling and simulation of biological systems -with stochasticity. In Sxhco Biology, 4 (2004), 293-309.
12. Z.N. Oltavi, C.L. Milliman, S.J. Korsmeyer: Bcl-2 heterodimerizes in vivo with a conserved homolog, Bax, that accelerates programmed cell death. Cell, 74 (1993), 509-619.
13. Gh. Pa̧un: Membrane Computing, An Introduction. Springer-Verlag, Berlin, 2002.
14. A. Philips, L. Cardelli: A correct abstract machine for the stochastic Pi-calculus. Electronical Notes in Theoretical Computer Science, to appear.
15. C. Priami, A. Regev, E. Shapiro, W. Silverman: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80 (2001), 25-31.
16. M.J. Pérez-Jiménez, F.J. Romero-Campero: A study of the robustness of the EGFR signalling cascade using continuous membrane systems. Lecture Notes in Computer Science, 3561 (2005), 268-278.
17. M.J. Pérez-Jiménez, F.J. Romero-Campero: P systems, a new computational modeling tool for systems biology, Transactions on Computational Systems Biology, to appear.
18. C. Scaffidi, S. Fulda. A. Srinivasan, C. Friesen, F. Li, K.J. Tomaselli, K.M. Debatin, P.H. Krammer, M.E. Peter: Two CD95 (APO-l/Fas) signaling pathways. The Ernbo Journal, 17 (1998), 1675-1687.
19. A.B. Stundzia, C.J. Lumsden: Stochastic simulation of coupled reaction-diffusion processes. Journal of Computational Physics, 127 (1996), 196-207,.
20. The Stochastic Pi-Machine: http://www.doc.ic.ac.uk/~anp/spim/.
21. N.G. VanKampen: Stochastic Processes in Physics and Chemistry. Elsevier Science B. V., Amsterdam, 1992.
22. K. Wang, X.M. Yin, D.T. Cltao, C.L. Milliman, S.L Korsmeyer: BID: A novel BH3 domain-only death agonist. Genes & Development, 10 (1996), 2859-2869.
23. The P Systems Website: http://psystems.disco.unimib.it.