Abstract
As a natural evolution of developments in membrane computing and self-assembly, the time appears ripe to hybridize their principles to explore models capable of exhibiting further properties exhibited by living organisms, while preserving the primary advantages of models in physics, chemistry and computer science, e.g. arising from local interactions of their components and implementable in silico and/or in vitro. We introduce an abstract model named M system, capable of self-assembly and a developmental process, that strikes a balance between these conflicting goals, namely biological realism, physical-chemical realism and computational realism. We demonstrate that such systems are capable of being assembled from scratch from some atomic components, undergo a process of morphogenesis by the unfolding of the self-assembly rules defined by their local interactions, exhibit crucial properties of living cells as the self-healing property or mitosis (cell division), and eventually enter a stable equilibrium of adulthood in which they will continue to function as long as certain conditions in their environment remain. We present some theoretical results on the model, as well as preliminary simulations and experimental results of an M system simulator we have developed to explore this kind of model.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G.: Spatial calculus of looping sequences. Theor. Comput. Sci. 412(43), 5976–6001 (2011)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Pardini, G., Tesei, L.: Spatial P systems. Nat. Comput. 10(1), 3–16 (2011)
Bernardini, F., Brijder, R., Cavaliere, M., Franco, G., Hoogeboom, H.J., Rozenberg, G.: On aggregation in multiset-based self-assembly of graphs. Nat. Comput. 10(1), 17–38 (2011)
Blount, P., Sukharev, S.I., Moe, P.C., Schroeder, M.J., Guy, H., Kung, C.: Membrane topology and multimeric structure of a mechanosensitive channel protein of escherichia coli. EMBO J. 15(18), 4798–4805 (1996)
Bourgine, P., Lesne, A.: Morphogenesis: Origins of Patterns and Shapes. Springer Complexity. Springer, Heidelberg (2010)
Cardelli, L., Gardner, P.: Processes in space. In: Ferreira, F., Löwe, B., Mayordomo, E., Mendes Gomes, L. (eds.) CiE 2010. LNCS, vol. 6158, pp. 78–87. Springer, Heidelberg (2010). doi:10.1007/978-3-642-13962-8_9
Cavaliere, M., Mardare, R., Sedwards, S.: A multiset-based model of synchronizing agents: computability and robustness. Theoret. Comput. Sci. 391(3), 216–238 (2008)
Freund, R., Kari, L., Oswald, M., Sosík, P.: Computationally universal P systems without priorities: two catalysts are sufficient. Theoret. Comput. Sci. 330, 251–266 (2005)
Krasnogor, N., Gustafson, S., Pelta, D., Verdegay, J.: Systems Self-Assembly: Multidisciplinary Snapshots. Studies in Multidisciplinarity. Elsevier Science, Amsterdam (2011)
Manca, V., Pardini, G.: Morphogenesis through moving membranes. Nat. Comput. 13(3), 403–419 (2014)
Moore, T., Garzon, M., Deaton, R.: Probabilistic analysis of pattern formation in monotonic self-assembly. PLoS One 10(9), 1–23 (2015). doi:10.1371/journal.pone.0137982
von Neumann, J.: Probabilistic logics and the synthesis of reliable organisms from unreliable components. Ann. Math. Studies 34, 43–98 (1956)
Păun, A., Popa, B.: P systems with proteins on membranes. Fundamenta Informaticae 72(4), 467–483 (2006)
Păun, A., Popa, B.: P Systems with proteins on membranes and membrane division. In: Ibarra, O.H., Dang, Z. (eds.) DLT 2006. LNCS, vol. 4036, pp. 292–303. Springer, Heidelberg (2006). doi:10.1007/11779148_27
Păun, A., Păun, G.: The power of communication: P systems with symport/antiport. New Gener. Comput. 20(3), 295–305 (2002)
Păun, G.: Computing with membranes. J. Comput. System Sci. 61, 108–143 (2000)
Păun, G.: Membrane Computing - An Introduction. Springer, Berlin (2002)
Păun, G., Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing. Oxford University Press, Oxford (2010)
Păun, G.: P systems with active membranes: attacking NP-complete problems. J. Automata Lang. Comb. 6(1), 75–90 (2001)
Robinson, K., Messerli, M.: Left/right, up/down: the role of endogenous electrical fields as directional signals in development, repair and invasion. BioEssays 25, 759–766 (2003)
Schrödinger, E.: What Is Life? The Physical Aspect of the Living Cell. Trinity College, Dublin (1944)
Tangirala, K., Caragea, D.: Generating features using burrows wheeler transformation for biological sequence classification. In: Pastor, O., et al. (ed.) Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, pp. 196–203. SciTePress (2014)
Tomita, M.: Whole-cell simulation: a grand challenge of the 21st century. Trends Biotechnol. 19(6), 205–210 (2001)
Turing, A.: The chemical basis of morphogenesis. Philos. Trans. R. Soc. Lond. B 237, 7–72 (1950)
Watson, J., Crick, F.: A structure for deoxyribose nucleic acid. Nature 171, 737–738 (1953)
Winfree, E.: Models of experimental self-assembly. Ph.D. thesis, Caltech (1998)
Maxwell-Boltzmann distribution, Wikipedia (cit 2017-1-29). https://en.wikipedia.org/wiki/Maxwell-Boltzmann_distribution
Ziegler, G.: Lectures on Polytopes. Graduate Texts in Mathematics. Springer, New York (1995)
Acknowledgements
This work was supported by the Ministry of Education, Youth and Sports Of the Czech Republic from the National Programme of Sustainability (NPU II) project IT4Innovations Excellence in Science - LQ1602, and by the Silesian University in Opava under the Student Funding Scheme, project SGS/13/2016. We are grateful to anonymous reviewers whose valuable comments helped to improve the paper.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
1 Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Sosík, P., Smolka, V., Drastík, J., Moore, T., Garzon, M. (2017). Morphogenetic and Homeostatic Self-assembled Systems. In: Patitz, M., Stannett, M. (eds) Unconventional Computation and Natural Computation. UCNC 2017. Lecture Notes in Computer Science(), vol 10240. Springer, Cham. https://doi.org/10.1007/978-3-319-58187-3_11
Download citation
DOI: https://doi.org/10.1007/978-3-319-58187-3_11
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-58186-6
Online ISBN: 978-3-319-58187-3
eBook Packages: Computer ScienceComputer Science (R0)