A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics

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A multi-scaled approach to artificial life simulation with P systems and dissipative particle dynamics

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Genetic And Evolutionary Computation Conference archive
Proceedings of the 10th annual conference on Genetic and evolutionary computation table of contents

Atlanta, GA, USA

SESSION: Artificial life, evolutionary robotics, adaptive behavior, evolvable hardware papers table of contents

Pages 249-256

Year of Publication: 2008

ISBN:978-1-60558-130-9

Authors

James Smaldon	University of Nottingham, Nottingham, United Kingdom
Jonathan Blakes	University of Nottingham, Nottingham, United Kingdom
Natalio Krasnogor	University of Nottingham, Nottingham, United Kingdom
Doron Lancet	Weizmann Institute of Science, Rehovot, Israel

Sponsors

ACM: Association for Computing Machinery
SIGEVO: ACM Special Interest Group on Genetic and Evolutionary Computation

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ACM New York, NY, USA

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ABSTRACT

Compartmentalisation is thought to have been a crucial step in the origin of life. To help us bridge the gap between self-assembly processes behind the formation of bio-compartments and metabolic and information bearing processes we refer to DPD and P Systems Simulations. In this paper we outline a new software platform linking a high level abstract computational formalism (P Systems) with a molecular scale model (Dissipative Particle Dynamics) by linking the membranes which delimit the cellular regions within P Systems to self-assembled phospholipid based vesicles in DPD. We test the platform by modelling a passive transport process involving vesicles containing membrane inclusions similar to pore complexes such as ±-hemolysin. In doing so, we illustrate the usefulness of the modelling approach and derive a more realistic parameter set for the P system through the dissipative particle dynamics simulation.

REFERENCES

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	1	Francesco Bernardini , Marian Gheorghe , Natalio Krasnogor, Quorum sensing P systems, Theoretical Computer Science, v.371 n.1-2, p.20-33, February, 2007 [doi>10.1016/j.tcs.2006.10.012]
	2	L. Bianco, D. Pescini, P. Siepman, N. Krasnogor, F. Romero-Campero, and M. Gheorghe. Towards a P systems pseudomonas quorum sensing model. Lecture Notes in Computer Science, Volume 4361/2006, pages 197--214. Springer, 2006.
	3	A. G. Cairns-Smith. The origin of life and the nature of the primitive gene. Journal of Theoretical Biology, 10(1):53--88, Jan. 1966.
	4	L. Cronin, N. Krasnogor, B. G. Davis, C. Alexander, N. Robertson, J. H. G. Steinke, S. L. M. Schroeder, A. N. Khlobystov, G. Cooper, P. M. Gardner, P. Siepmann, B. J. Whitaker, and D. Marsh. The imitation game -- a computational chemical approach to recognizing life. Nat Biotech, 24(10):1203--1206, Oct. 2006.
	5	P. Eggenberger. Evolving morphologies of simulated 3d organisms based on differential gene expression, 1997.
	6	P. Espanol and P. Warren. Statistical-mechanics of dissipative particle dynamics. Europhys. Lett., 30:191--196, 1995.
	7	Nicholas Geard , Janet Wiles, A Gene Network Model for Developing Cell Lineages, Artificial Life, v.11 n.3, p.249-268, September 2005 [doi>10.1162/1064546054407202]
	8	D. T. Gillespie. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem., 58:35--55, 2007.
	9	A. Grafmuller, J. Shillcock, and R. Lipowsky. Pathway of membrane fusion with two tension-dependent energy barriers. Phys. Rev. Lett., 98(21):218101, 2007.
	10	R. D. Groot and K. L. Rabone. Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. Biophys. Journal, 81:725--736, 2001.
	11	R. D. Groot and P. Warren. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys., 107:4423--4435, Sept. 1997.
	12	D. Harel. A turing-like test for biological modeling. Nat Biotech, 23(4):495--496, Apr. 2005.
	13	P. Hoogerbrugge and J. Koelman. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhysics Letters, 19:155, June 1992.
	14	M. Kranenburg, M. Venturoli, and B. Smit. Phase behavior and induced interdigitation in bilayers studied with dissipative particle dynamics. J. Phys. Chem. B, 107(41):11491--11501, 2003.
	15	C. Lattaud and S. Bornhofen. Advances in artificial life: A brief history of evolutionary individual based models. In 7th International Conference on Artificial Evolution, pages 226--237. Springer, 2005.
	16	H. Lodish, A. Berk, C. Kaiser, M. Krieger, M. Scott, A. Bretscher, H. Ploegh, and P. Matsudaira. Molecular Cell Biology. W.H.Freeman & Co Ltd, 2007.
	17	P. L. Luisi. Self-reproduction of micelles and vesicles: Models for the mechanisms of life from the perspective of compartmented chemistry. In S. A. R. I. Prigogine, editor, Advances in Chemical Physics, pages 425--438. John Wiley & Sons, Inc, 1996.
	18	John Von Neumann , Arthur W. Burks, Theory of Self-Reproducing Automata, University of Illinois Press, Champaign, IL, 1966
	19	A. Oparin. Origin Of Life On Earth. Elsevier, 1959.
	20	V. Ortiz, S. Nielsen, D. Discher, M. Klein, R. Lipowsky, and J. Shillcock. Dissipative particle dynamics simulations of polymersomes. Journal of Physical Chemistry B, 109(37):17708--17714, 2005.
	21	Gheorghe Paun, Membrane Computing: An Introduction, Springer-Verlag New York, Inc., Secaucus, NJ, 2002
	22	A. Pohorille and D. Deamer. Artificial cells: prospects for biotechnology. Trends in Biotechnology, 20(3):123--128, Mar. 2002.
	23	Steen Rasmussen , Liaohai Chen , Martin Nilsson , Shigeaki Abe, Bridging nonliving and living matter, Artificial Life, v.9 n.3, p.269-316, Summer 2003 [doi>10.1162/106454603322392479]
	24	Craig W. Reynolds, Flocks, herds and schools: A distributed behavioral model, ACM SIGGRAPH Computer Graphics, v.21 n.4, p.25-34, July 1987
	25	D. Segre, D. Ben-Eli, D. W. Deamer, and D. Lancet. The lipid world. Origins of Life and Evolution of Biospheres, 31(1):119--145, Feb. 2001.
	26	J. Shillcock and R. Lipowsky. Tension-induced fusion of bilayer membranes and vesicles. Nature Materials, 4:225--228, 2005.
	27	C. Tanford. The Hydrophobic Effect. New York: Wiley, 1973.
	28	D. Segre, D. Ben-Eli and D. Lancet. Compositional genomes: prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA (2000), 97(8), 4112--4117.
	29	B. Shenhav, D. Segre and D. Lancet. Mesobiotic emergance: Molecular and ensemble complexity in early evolution Advances in Complex Systems (2003), 6(1), 15--35.
	30	B. Shenhav, A. Solomon, D. Lancet and R. Kafri. Early Systems Biology and Prebiotic Networks C. Transactions on Computational Systems Biology , LNCS 3380, p. 14--17, 2005.
	31	A. Hunding, F. Kepes, D. Lancet, A. Minsky, V. Norris, D. Raine, K. Sriram, R. Root-Bernstein Compositional Complementarity and Prebiotic Ecology in the Origin of Life. Bioessays. 2006 Apr;28(4):399--412