Self-assembly Models of Variable Resolution

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• 作者：Andrzej Mizera (22)
  Eugen Czeizler (23)
  Ion Petre (22)
  
• 刊名：Lecture Notes in Computer Science
• 出版年：2012
• 出版时间：2012
• 年：2012
• 卷：7625
• 期：1
• 页码：204-232
• 全文大小：377KB
• 参考文献：1. Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Essential Cell Biology, 2nd edn. Garland Science, New York (2004)
  2. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular Biology of the Cell, 4th edn. Garland Science, New York (2002)
  3. Back, R.-J., von Wright, J.: Refinement Calculus. Springer (1998)
  4. Bruggeman, F.J., Westerhoff, H.V.: The nature of systems biology. Trends in Microbiology?15(1), 45-0 (2007) CrossRef
  5. Chen, W.W., Schoeberl, B., Jasper, P.J., Niepel, M., Nielsen, U.B., Lauffenburger, D.A., Sorger, P.K.: Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Molecular Systems Biology?5(239) (2009)
  6. Czeizler, E., Mizera, A., Czeizler, E., Back, R.-J., Eriksson, J.E., Petre, I.: Quantitative analysis of the self-assembly strategies of intermediate filaments from tetrameric vimentin (2010) (manuscipt)
  7. Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-Based Modelling, Symmetries, Refinements. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol.?5054, pp. 103-22. Springer, Heidelberg (2008) CrossRef
  8. Vries, G.d., Hillen, T., Lewis, M., Müller, J., Sch?nfisch, B.: A Course in Mathematical Biology: Quantitative Modelling with Mathematical and Computational Methods. Monographs on Mathematical Modeling and Computation. SIAM (2006)
  9. Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics?22, 403-34 (1976) CrossRef
  10. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry?81(25), 2340-361 (1977) CrossRef
  11. Henrikson, R.C., Kaye, G.I., Mazurkiewicz, J.E.: NMS Histology. National Medical Series for Independent Study. Lippincott Williams & Wilkins (1997)
  12. Herrmann, H., H?ner, M., Brettel, M., Ku, N.-O., Aebi, U.: Characterization of distinct early assembly units of different intermediate filament proteins. Journal of Molecular Biology?286(5), 1403-420 (1999) CrossRef
  13. Herrmann, H., H?ner, M., Brettel, M., Müller, S.A., Goldie, K.N., Fedtke, B., Lustig, A., Franke, W.W., Aebi, U.: Structure and assembly properties of the intermediate filament protein vimentin: the role of its head, rod and tail domains. Journal of Molecular Biology?264(5), 933-53 (1996) CrossRef
  14. Iverson, K.E.: A Programming Language, 4th edn. Wiley, New York (1962)
  15. Kirmse, R., Portet, S., Mücke, N., Aebi, U., Herrmann, H., Langowski, J.: A quantitative kinetic model for the in vitro assembly of intermediate filaments from tetrameric vimentin. Journal of Biological Chemistry?282(52), 18563-8572 (2007) CrossRef
  16. Kitano, H.: Systems biology: A brief overview. Science?295(5560), 1662-664 (2002) CrossRef
  17. Klipp, E., Herwig, R., Kowald, A., Wierling, C., Lehrach, H.: Systems Biology in Practice. Wiley-VCH (2006)
  18. Knuth, D.: Two notes on notation. American Mathematical Monthly?99(5), 403-22 (1992) CrossRef
  19. Lander, A.D.: The edges of understanding. BMC Biology?8, 40 (2010) CrossRef
  20. Lok, L., Brent, R.: Automatic generation of cellular reaction networks with moleculizer 1.0. Nat. Biotechnol.?23, 131-36 (2005) CrossRef
  21. Murphy, E., Danos, V., Feret, J., Krivine, J., Harmer, R.: Rule-based modeling and model refinement. In: Lodhi, H.M., Muggleton, S.H. (eds.) Elements of Computational Systems Biology. John Wiley & Sons, Inc., Hoboken (2010)
  22. Raman, K., Chandra, N.: Systems biology. Resonance?15(2), 131-53 (2010) CrossRef
  23. Scherlis, W.L., Scott, D.S.: First steps towards inferential programming. In: Mason, R.E.A. (ed.) Information Processing 83: Proceedings of the IFIP 9th World Computer Congress (1983)
  24. Wirth, N.: Program development by stepwise refinement. Communications of the ACM?14(4), 221-27 (1971) CrossRef
  
• 作者单位：Andrzej Mizera (22)
  Eugen Czeizler (23)
  Ion Petre (22)
  
  22. Department of Information Technologies, ?bo Akademi University, Finland
  23. Department of Information and Computer Science, Aalto University, Finland
  
• ISSN：1611-3349

文摘

Model refinement is an?important aspect of the model-building process. It can be described as a?procedure which, starting from an?abstract model of a?system, performs a?number of refinement steps in result of which a?more detailed model is obtained. At the same time, in order to be correct, the refinement mechanism has to be capable of preserving already proven systemic quantitative properties of the original model, e.g.?model fit, stochastic semantics, etc. In this study we concentrate on the refinement in the case of self-assembly models. Self-assembly is a?process in which a?disordered ensemble of basic components forms an?organized structure as a?result of specific, local interactions among these components, without external guidance. We develop a?generic formal model for this process and introduce a?notion of model resolution capturing the maximum size up to which objects can be distinguished individually in the model. All bigger objects are treated homogenously in the model. We show how this self-assembly model can be systematically refined in such a?way that its resolution can be increased and decreased while preserving the original model fit to experimental data, without the need for tedious, computationally expensive process of parameter refitting. We demonstrate how the introduced methodology can be applied to a?previously published model: we consider the case-study of in vitro self-assembly of intermediate filaments.