A projective brane calculus with activate, bud and mate as primitive actions

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5750 LNBI, Issue , 2009, Pages 164-186

  David, Maria Pamela C ^a   Bantang, Johnrob Y ^a,b,c   Mendoza, Eduardo R ^a,d  

^a UNIVERSITY OF MUNICH   (Germany)

^b MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

^c University of the Philippines ^*  (Philippines)

^d UNIVERSITY OF THE PHILIPPINES   (Philippines)

Author keywords

[No Author keywords available]

Indexed keywords

BETA BINDERS; BIOLOGICAL CHARACTERISTIC; BRANE CALCULI; CARDELLI'S BRANE CALCULUS; MULTIPLE-ASSOCIATION; PRIMITIVE ACTIONS; REACTION PROBABILITY; RECEPTOR LIGANDS;

BIOINFORMATICS; BIOLOGY;

CALCULATIONS;

EID: 70450238020     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04186-0_8     Document Type: Conference Paper

References (32)

1. Pǎun, G.: Introduction to membrane computing. In: Applications of Membrane Computing, pp. 1-42 (2006)
2. Regev, A., Shapiro, E.: The π-calculus as an abstraction for biomolecular systems. In: Modelling in Molecular Biology (2004)
3. Cardelli, L.: Brane calculi: interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257-278. Springer, Heidelberg (2005)
4. Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 20-33. Springer, Heidelberg (2005)
5. Danos, V., Pradalier, S.: Projective brane calculus. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 134-148. Springer, Heidelberg (2005)
6. Guerriero, M.L., Priami, C., Romanel, A.: Modeling Static Biological Compartments with Beta-binders. In: Anai, H., Horimoto, K., Kutsia, T. (eds.) Ab 2007. LNCS, vol. 4545, pp. 247-261. Springer, Heidelberg (2007)
7. Phillips, A., Cardelli, L.: Efficient, correct simulation of biological processes in the stochastic pi-calculus. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 184-199. Springer, Heidelberg (2007)
8. Busi, N., Zandron, C.: Modelling and analysis of biological processes by (mem)brane calculi and systems. In: Proceedings of the 2006 Winter Simulation Conference, pp. 1646-1655 (2006)
9. Guglielmo, G.D., Drake, P., Baass, P., Authier, F., Posner, B., Bergeron, J.: Insulin receptor internalization and signalling. Mol. Cell. Biochem. 182, 59-63 (1998)
10. Hsu, S., Bonvin, A.: Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120. Proteins: structure, function and bioinformatics 3, 582-593 (2004)
11. Keskin, O.: Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies. BMC Structural Biology 7, 31 (2007)
12. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., Watson, J.: Molecular Biology of the Cell, New York (2002)
13. David, M., Asprer, J., Ibana, J., Concepcion, G., Padlan, E.: A study of the structural correlates of affinity maturation: antibody affinity as a function of chemical interactions, structural plasticity and stability. Mol. Immunol. 44, 1342-1351 (2006)
14. Dimitrov, D.: Virus entry: molecular mechanisms and biomedical applications. Nature Reviews Microbiology 2, 109-122 (2004)
15. Kim, W., Hudson, B., Moser, B., Guo, J., Rong, L., Yu, L., Qu, W., Lalla, E., Lerner, S., Chen, Y., Yan, S.D., D'Agati, V., Naka, Y., Ramasamy, R., Herold, K., Yan, S., Schmidt, A.: Receptor for advanced glycation end products and its ligands: A journey from the complications of diabetes to its pathogenesis. Annals of the New York Academy of Sciences 1043, 553-561 (2006)
16. Thulke, S., Radonic, A., Nitsche, A., Siegert, W.: Quantitative expression analysis of HHV-6 cell receptor CD46 on cells of human cord blood, peripheral blood and G-CSF mobilised leukapheresis cells. Virology Journal 3, 77-81 (2006)
17. Simons, K., Vaz, W.L.C.: Model Systems, Lipid Rafts, and Cell Membranes. Annual Review of Biophysics and Biomolecular Structure 33(1) (June 2004)
18. Sutton, R.B., Fasshauer, D., Jahn, R., Brunger, A.T.: Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 Å resolution. Nature 395 (6700), 347-353 (1998)
19. Chiu, D., Wilson, C., Karlsson, A., Danielsson, A., Lunqvist, A., Stroemberg, A., Ryttsen, F., Davidson, M., Nordholm, S., Orwar, O., Zare, R.: Manipulating the biochemical nanoenvironment around single molecules contained within vesicles. Chem. Phys. 247, 133-139 (1999)
20. Jahn, R., Grubmüller, H.: Membrane fusion. Current Opinion in Cell Biology 14, 488-495 (2002)
21. Phillips, A., Cardelli, L.: A Correct Abstract Machine for the Stochastic Pi-calculus. In: Concurrent Models in Molecular Biology (2004)
22. Poland, G.A., Tosh, P., Jacobson, R.M.: Requiring influenza vaccination for health care workers: seven truths we must accept. Vaccine 23(17-18), 2251-2255 (2005); Vaccines and Immunisation. Based on the Fourth World Congress on Vaccines and Immunisation
23. Baccam, P., Beauchemin, C., Macken, C.A., Hayden, F.G., Perelson, A.S.: Kinetics of Influenza A Virus Infection in Humans. J. Virol. 80(15), 7590-7599 (2006)
24. Sidorenko, Y., Reichl, U.: Structured model of influenza virus replication in mdck cells. Biotechnology and bioengineering 88, 1-14 (2004)
25. Bardiya, N., Bae, J.: Influenza vaccines: recent advances in production technologies. Applied Microbiology and Biotechnology 67(3), 299-305 (2005)
26. Genzel, Y., Schulze-Horsel, J., Möhler, L., Sidorenko, Y., Reichl, U.: Influenza vaccines-challenges in mammalian cell culture technology. Cell Technology for Cell Products, 503-508 (2007)
27. Nayak, D.P., Hui, E.K.-W., Barman, S.: Assembly and budding of influenza virus. Virus Research 106, 147-165 (2004)
28. de Ronde, J.J., Ndjehan, C.P.: Modelling Networks and Pathways in Systems Biology. Technical report, CA545 Practicum, School of Computing, Dublin City University (2005/2006)
29. David, M.P.C.: BCD: Design and implementation of a stochastic brane machine. Master's thesis, Department of Computer Science, University of the Philippines, Diliman, Quezon City (2008)
30. Segata, N., Blanzieri, E., Priami, C.: Stochastic π-calculus modelling of multisite phosphorylation based signaling: in silico analysis of the Pho4 transcription factor and the PHO pathway in Saccharomyces cerevisiae. Technical report, Center for Computational and Systems Biology, The Microsoft Research - University of Trento (2007)
31. Yap, J.M.: A Pi-Calculus Model of the CD95 Receptor Medicated Pathway of Apoptosis. Philippine Information Techonology Journal 1(1) (2008)
32. Zhang, B.T., Hikawa, N., Horie, H., Takenaka, T.: Mitogen induced proliferation of isolated adult mouse Schwann cells. J. Neurosci. Res., 648-654 (1995)