Abstract
In a biological cell, cellular functions and the genetic regula- tory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control genes that produce other regulators, which in turn control other genes. Further, the feed- back pathways appear to incorporate switches that result in changes in the dynamic behavior of the cell. This paper describes a hybrid systems approach to modeling the intra-cellular network using continuous differ- ential equations to model the feedback mechanisms and mode-switching to describe the changes in the underlying dynamics. We use two case studies to illustrate a modular approach to modeling such networks and describe the architectural and behavioral hierarchy in the underlying models. We describe these models using Charon [2], a language that allows formal description of hybrid systems. We provide preliminary sim- ulation results that demonstrate how our approach can help biologists in their analysis of noisy genetic circuits. Finally we describe our agenda for future work that includes the development of models and simulation for stochastic hybrid systems.1
This research was supported in part by DARPA/ITO Mobies project (grant number F33615-00-C-1707) and NSF grant CDS-97-03220.
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Alur, R. et al. (2001). Hybrid Modeling and Simulation of Biomolecular Networks. In: Di Benedetto, M.D., Sangiovanni-Vincentelli, A. (eds) Hybrid Systems: Computation and Control. HSCC 2001. Lecture Notes in Computer Science, vol 2034. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45351-2_6
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DOI: https://doi.org/10.1007/3-540-45351-2_6
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