Natural Computing

, Volume 16, Issue 1, pp 151–163 | Cite as

Membrane automata for modeling biomolecular processes

Article

Abstract

Bioinspired computation models and mechanisms are widely used in various applications, both in theoretical and practical level. Membrane Computing, a branch of Natural Computing, is constantly producing interesting results the last 15 years. In this work we attempt to describe a mitochondrial fusion process based on membrane automata in a novel way. We combine these computation machines with notions from brane calculus and we depict the procedure of the production of specific proteins that are essential for a successful fusion. We also discuss possible extensions of our methodology stating direction for future works and thoughts.

Keywords

Membrane automata Membrane systems Mitochondrial fusion 

References

  1. Alberts B, Bray D, Hopkin K, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2013) Essential cell biology. Garland Science, New YorkGoogle Scholar
  2. Alexiou AT, Psiha MM, Rekkas JA, Vlamos PM (2011) A stochastic approach of mitochondrial dynamics. World Acad Sci Eng Technol 55:77–80Google Scholar
  3. Alexiou A, Vlamos P (2012) A cultural algorithm for the representation of mitochondrial population. Adv Artif Intell 2012:1CrossRefGoogle Scholar
  4. Aman B, Ciobanu G (2011) Mobility in process calculi and natural computing. Springer, BerlinCrossRefMATHGoogle Scholar
  5. Amos M (2004) Cellular computing (genomics and bioinformatics). Oxford University Press, OxfordGoogle Scholar
  6. Barbuti R, Maggiolo-Schettini A, Milazzo P, Pardini G, Tesei L (2011) Spatial P systems. Nat Comput 10(1):3–16MathSciNetCrossRefMATHGoogle Scholar
  7. Bianco L, Fontana F, Franco G, Manca V (2006) P systems for biological dynamics. Applications of membrane computing. Springer, New York, pp 83–128Google Scholar
  8. Bodei C, Gori R, Levi F (2013) An analysis for causal properties of membrane interactions. Electron Notes Theor Comput Sci 299:15–31CrossRefMATHGoogle Scholar
  9. Broderick G, Ru’aini M, Chan E, Ellison MJ (2005) A life-like virtual cell membrane using discrete automata. In silico Biol 5(2):163–178Google Scholar
  10. Cardelli L (2005) Brane calculi. Computational methods in systems biology. Springer, New York, pp 257–278CrossRefGoogle Scholar
  11. Cardelli L, Păun G (2006) An universality result for a (mem) brane calculus based on mate/drip operations. Int J Found Comput Sci 17(01):49–68MathSciNetCrossRefMATHGoogle Scholar
  12. Cavaliere M, Leupold P (2004) Evolution and observation: a new way to look at membrane systems. Membrane computing. Springer, New York, pp 70–87CrossRefGoogle Scholar
  13. Chan DC (2006) Mitochondrial fusion and fission in mammals. Annu Rev Cell Dev Biol 22:79–99CrossRefGoogle Scholar
  14. Chen H, Ionescu M, Ishdorj TO, Păun A, Păun G, Pérez-Jiménez MJ (2008) Spiking neural P systems with extended rules: universality and languages. Nat Comput 7(2):147–166MathSciNetCrossRefMATHGoogle Scholar
  15. Chen H, Chan DC (2009) Mitochondrial dynamics-fusion, fission, movement, and mitophagy-in neurodegenerative diseases. Hum Mol Genet 18(R2):R169–R176CrossRefGoogle Scholar
  16. Cienciala L, Ciencialová L (2004) Membrane automata with priorities. J Comput Sci Technol 19(1):89–97MathSciNetCrossRefGoogle Scholar
  17. Ciobanu G, Aman B (2008) On the relationship between membranes and ambients. Biosystems 91(3):515–530CrossRefGoogle Scholar
  18. Ciocchetta F, Hillston J (2009) Bio-pepa: a framework for the modelling and analysis of biological systems. Theor Comput Sci 410(33):3065–3084MathSciNetCrossRefMATHGoogle Scholar
  19. Claros MG, Vincens P (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur J Biochem 241(3):779–786CrossRefGoogle Scholar
  20. Colombini M (2004) VDAC: the channel at the interface between mitochondria and the cytosol. Mol Cell Biochem 256(1–2):107–115CrossRefGoogle Scholar
  21. Csuhaj-Varjú E, Martin-Vide C, Mitrana V (2001) Multiset automata. Multiset processing. Springer, New York, pp 69–83CrossRefGoogle Scholar
  22. Csuhaj-Varjú E (2005) P automata. Membrane computing. Springer, New York, pp 19–35CrossRefGoogle Scholar
  23. Csuhaj-Varjú E, Ibarra OH, Vaszil G (2005) On the computational complexity of P automata. DNA computing. Springer, New York, pp 76–89CrossRefGoogle Scholar
  24. Csuhaj-Varjú E, Ibarra OH, Vaszil G (2006) On the computational complexity of P automata. Nat Comput 5(2):109–126MathSciNetCrossRefMATHGoogle Scholar
  25. Csuhaj-Varjú E (2010) P automata: concepts, results, and new aspects. Membrane computing. Springer, New York, pp 1–15CrossRefGoogle Scholar
  26. Csuhaj-Varjú E (2012) P and dp automata: unconventional versus classical automata. Developments in language theory. Springer, New York, pp 7–22CrossRefGoogle Scholar
  27. Csuhaj-Varjú E, Vaszil G (2003) P automata or purely communicating accepting P systems. Membrane computing. Springer, New York, pp 219–233CrossRefGoogle Scholar
  28. Csuhaj-Varjú E, Vaszil G (2008) (Mem)brane automata. Theor Comput Sci 404(1):52–60MathSciNetCrossRefMATHGoogle Scholar
  29. Csuhaj-Varjú E, Vaszil G (2013) On the power of P automata. Unconventional computation and natural computation. Springer, New York, pp 55–66CrossRefGoogle Scholar
  30. Detmer SA, Chan DC (2007) Functions and dysfunctions of mitochondrial dynamics. Nat Rev Mol Cell Biol 8(11):870–879CrossRefGoogle Scholar
  31. Freund R, Kari L, Oswald M, Sosík P (2005) Computationally universal P systems without priorities: two catalysts are sufficient. Theor Comput Sci 330(2):251–266MathSciNetCrossRefMATHGoogle Scholar
  32. Freund R, Oswald M (2002) A short note on analysing P systems with antiport rules. Bull EATCS 78:231–236MathSciNetMATHGoogle Scholar
  33. Freund R, Oswald M (2008) Regular \(\omega \)-languages defined by finite extended spiking neural P systems. Fundam Inform 83(1):65–73MathSciNetMATHGoogle Scholar
  34. Frisco P (2005) About P systems with symport/antiport. Soft Comput 9(9):664–672CrossRefMATHGoogle Scholar
  35. Gheorghe M, Manca V, Romero-Campero FJ (2010) Deterministic and stochastic P systems for modelling cellular processes. Nat Comput 9(2):457–473MathSciNetCrossRefMATHGoogle Scholar
  36. Giannakis K, Andronikos T (2015) Mitochondrial fusion through membrane automata. GeNeDis 2014. Springer, New York, pp 163–172Google Scholar
  37. Gramatovici R, Enguix GB (2006) Parsing with P automata. Applications of membrane computing. Springer, New York, pp 389–410Google Scholar
  38. Ibarra OH, Dang Z, Egecioglu O (2004) Catalytic P systems, semilinear sets, and vector addition systems. Theor Comput Sci 312(2):379–399MathSciNetCrossRefMATHGoogle Scholar
  39. Ibarra OH, Pérez-Jiménez MJ, Yokomori T (2010) On spiking neural P systems. Nat Comput 9(2):475–491MathSciNetCrossRefMATHGoogle Scholar
  40. Koski T (2001) Hidden Markov models for bioinformatics, vol 2. Springer, New YorkMATHGoogle Scholar
  41. Krishna SN (2006) On pure catalytic p systems. Unconventional computation. Springer, New York, pp 152–165CrossRefGoogle Scholar
  42. Krishna SN, Păun G (2005) P systems with mobile membranes. Nat Comput 4(3):255–274MathSciNetCrossRefMATHGoogle Scholar
  43. Kubli DA, Gustafsson ÅB (2012) Mitochondria and mitophagy the yin and yang of cell death control. Circ Res 111(9):1208–1221CrossRefGoogle Scholar
  44. Long H, Fu Y (2007) A general approach for building combinational P automata. Int J Comput Math 84(12):1715–1730MathSciNetCrossRefMATHGoogle Scholar
  45. Longo DL, Archer SL (2013) Mitochondrial dynamics-mitochondrial fission and fusion in human diseases. N Engl J Med 369(23):2236–2251CrossRefGoogle Scholar
  46. Madhu M, Krithivasan K (2003) On a class of P automata. Int J Comput Math 80(9):1111–1120MathSciNetCrossRefMATHGoogle Scholar
  47. Margenstern M, Martin-Vide C, Păun G (2002) Computing with membranes: variants with an enhanced membrane handling. DNA computing. Springer, New York, pp 340–349CrossRefGoogle Scholar
  48. Martin-Vide C, Pazos J, Păun G, Rodríguez-Patón A (2002) A new class of symbolic abstract neural nets: tissue P systems. Computing and combinatorics. Springer, New York, pp 290–299CrossRefGoogle Scholar
  49. Martın-Vide C, Păun G, Pazos J, Rodrıguez-Patón A (2003) Tissue P systems. Theor Comput Sci 296(2):295–326MathSciNetCrossRefMATHGoogle Scholar
  50. Meeusen S, DeVay R, Block J, Cassidy-Stone A, Wayson S, McCaffery JM, Nunnari J (2006) Mitochondrial inner-membrane fusion and crista maintenance requires the dynamin-related gtpase mgm1. Cell 127(2):383–395CrossRefGoogle Scholar
  51. Milner R, Parrow J, Walker D (1992) A calculus of mobile processes, i. Inf Comput 100(1):1–40MathSciNetCrossRefMATHGoogle Scholar
  52. Păun G (2000) Computing with membranes. J Comput Syst Sci 61(1):108–143MathSciNetCrossRefMATHGoogle Scholar
  53. Păun A (2001a) On P systems with active membranes. Unconventional models of computation, UMC2K. Springer, New York, pp 187–201CrossRefGoogle Scholar
  54. Păun G (2001b) Computing with membranes: attacking NP-complete problems. Unconventional models of computation, UMC2K. Springer, New York, pp 94–115CrossRefGoogle Scholar
  55. Păun G, Rozenberg G, Salomaa A (2010) The Oxford handbook of membrane computing. Oxford University Press, Inc, OxfordCrossRefMATHGoogle Scholar
  56. Păun G, Pérez-Jiménez MJ et al (2012) Languages and P systems: recent developments. Comput Sci 20(2):59MathSciNetMATHGoogle Scholar
  57. Pescini D, Besozzi D, Mauri G, Zandron C (2006) Dynamical probabilistic P systems. Int J Found Comput Sci 17(01):183–204MathSciNetCrossRefMATHGoogle Scholar
  58. Phillips A (2009) An abstract machine for the stochastic bioambient calculus. Electron Notes Theor Comput Sci 227:143–159CrossRefMATHGoogle Scholar
  59. Rabin MO, Scott D (1959) Finite automata and their decision problems. IBM J Res Dev 3(2):114–125MathSciNetCrossRefMATHGoogle Scholar
  60. Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E (2004) Bioambients: an abstraction for biological compartments. Theor Comput Sci 325(1):141–167MathSciNetCrossRefMATHGoogle Scholar
  61. Sipser M (2006) Introduction to the theory of computation, 2nd edn. Thomson Course Technology, StamfordMATHGoogle Scholar
  62. Song Z, Ghochani M, McCaffery JM, Frey TG, Chan DC (2009) Mitofusins and OPA1 mediate sequential steps in mitochondrial membrane fusion. Mol Biol Cell 20(15):3525–3532CrossRefGoogle Scholar
  63. van der Bliek AM, Shen Q, Kawajiri S (2013) Mechanisms of mitochondrial fission and fusion. Cold Spring Harb Perspect Biol 5(6):a011072Google Scholar
  64. Ye X, Tai W, Zhang D (2012) The early events of alzheimer’s disease pathology: from mitochondrial dysfunction to bdnf axonal transport deficits. Neurobiol Aging 33(6):1122-e1CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Department of InformaticsIonian UniversityCorfuGreece

Personalised recommendations