13th International Conference on Membrane Computing - MTA Sztaki

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B. Aman, G. Ciobanu to reiterate the entire process. Applying CPN Tools on this extended system, we obtain the following output file: Home Markings: All Dead Markings: None; Dead Transition Instances: None Live Transition Instances: All Fairness Properties: All, meaning that from any reachable configuration M i we can always reach any configuration M j (home marking), the computation never stops (dead marking), and so there are infinite occurrence sequences. 7 Conclusion In this paper we continue the research line started in [4], and present a new connection between the systems of mobile membranes and colored Petri nets. The novelty of this formal translation, with respect to the one presented in [4], is that the number of membranes in the system could change during evolution. The systems of mobile membranes with objects on surface used in this translation are bounded to a given number of membranes. The structure of the parallel computations of the mobile membranes is faithfully reflected by the parallel semantics of the corresponding colored Petri nets. In mobile membranes, the parallel way of using the rules means that in each step we apply a maximal set of rules, namely a set of rules such that no further rule can be added to this set. Since we deal with mobility, each object and each membrane can be used only once in the rules applied in a step. We have considered the low-density lipoprotein degradation pathway, and described this biological process by using the mobile membranes with objects on membranes. The translation of mobile membranes into colored Petri nets allows to obtain a description of the biological process into colored Petri net, and then use a software called CPN Tools in analyzing several behavioral properties: reachability, boundedness, liveness, fairness. By encoding biological systems in this way, many interesting biological questions can get precise answers. Using CPN Tools, several (potentially infinite) behaviors can be investigated, a fact that is interesting from a biological point of view. Finally, we have provided a new link between biology, membrane systems and Petri nets which is, hopefully, useful for all these areas. Acknowledgements The work was supported by a grant of the Romanian National Authority for Scientific Research CNCS-UEFISCDI, project number PN-II-ID-PCE-2011-3-0919. The work of Bogdan Aman was also supported by POSDRU/89/1.5/S/49944. References 1. B. Aman, G. Ciobanu. Mobility in Process Calculi and Natural Computing. Springer, 2011. 140
Mobile membranes with objects on surface as colored Petri nets 2. B. Aman, G. Ciobanu. Mutual Mobile Membranes with Objects on Surface. Natural Computing, vol.10, 777–793, 2011. 3. B. Aman, G. Ciobanu. Simple, Enhanced and Mutual Mobile Membranes. Transactions on Computational Systems Biology XI, LNBI vol.5750, 26–44, 2009. 4. B. Aman, G. Ciobanu. Properties of Enhanced Mobile Membranes via Coloured Petri Nets. Information Processing Letters, vol.112, 243–248, 2012. 5. M. Cavaliere, S. Sedwards. Decision Problems in Membrane Systems with Peripheral Proteins, Transport and Evolution. Theoretical Computer Science, vol.404, 40–51, 2008. 6. S. Dal Zilio, E. Formenti. On the Dynamics of PB Systems: A Petri Net View. Lecture Notes in Computer Science, vol.2933, 153–167, 2004. 7. J. Esparza, M. Nielsen. Decibility Issues for Petri Nets - A Survey. Journal of Informatik Processing and Cybernetics, vol.30, 143–160, 1994. 8. C.A. Janeway, P. Travers, M. Walport, M.J. Shlomchik. Immunobiology - The Immune System in Health and Disease. 5th edition, Garland Publishing, 2001. 9. K. Jensen. Colored Petri Nets; Basic Concepts, Analysis Methods and Practical Use. Vol. 1,2 and 3. Monographs in Theoretical Computer Science. Springer, 1992, 1994 and 1997. 10. J. Kleijn, M. Koutny. Petri Nets and Membrane Computing. Oxford Handbook of Membrane Computing, 389–412, 2010. 11. S.N. Krishna. Universality Results for P Systems Based on Brane Calculi Operations. Theoretical Computer Science, vol.371, 83–105, 2007. 12. R. Levins. The Strategy of Model Building in Population Biology. American Scientist, vol.54, 421–431, 1966. 13. H. Lodish, A. Berk, P. Matsudaira, C. Kaiser, M. Krieger, M. Scott, L. Zipursky, J. Darnell. Molecular Cell Biology, 5th edition, W.H. Freeman, 2003. 14. Gh. Păun. Membrane Computing. An Introduction. Springer, 2002. 15. H. Pilegaard, F. Nielson, H.R. Nielson. Static Analysis of a Model of the LDL Degradation Pathway. Proceedings Computational Methods in System Biology, 14– 26, 2005. 16. Z. Qi, J. You, H. Mao. P Systems and Petri Nets. Lecture Notes in Computer Science, vol.2933, 286–303, 2004. 141
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Erzsébet Csuhaj-Varjú Marian Gheo
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Editors Erzsébet Csuhaj-Varjú Dep
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Preface In addition to the texts or
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Contents M.A. Martínez-del-Amor, I
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(Tissue) P systems with decaying ob
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Turing’s three pioneering initiat
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Turing’s three pioneering initiat
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MP systems for systems biology tere
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Yu. Rogozhin this obstacle and to g
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Yu. Rogozhin 10. J. Cocke, M. Minsk
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M. Stannett The question arises, wh
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Regular Contributions
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T. Ahmed, G. DeLancy, A. Paun almos
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A formal framework for P systems wi
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A new approach for solving SAT by P
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Maintenance of chronobiological inf
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4 3.5 3 2.5 2 1.5 1 0.5 0 0 50 100
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Using a kernel P system to solve th
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L.F. Macías-Ramos, M.J. Pérez-Jim
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Membranes with local environments A
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Membranes with local environments T
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Membranes with local environments -
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Membranes with local environments I
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On efficient algorithms for SAT dis
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On efficient algorithms for SAT 2.4
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P. Sosík [9, 10], several research
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P. Sosík The rules of a system lik
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S. Verlan, J. Quiros more relevance
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S. Verlan, J. Quiros digital FPGA c
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Simplifying Event-B models of P sys
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Author Index Adorna H., 143 Agrigor
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