Journal article

ČEŠKA Milan, DANNENBERG Frits, KWIATKOWSKA Marta, PAOLETTI Nicola and BRIM Luboš. Precise parameter synthesis for stochastic biochemical systems. Acta Informatica. 2016, vol. 2016, no. 1, pp. 1-35. ISSN 0001-5903. Available from:
Publication language:english
Original title:Precise parameter synthesis for stochastic biochemical systems
Title (cs):Přesná syntéza parametrů pro stochastické biochemické systémy
Journal:Acta Informatica, Vol. 2016, No. 1, DE
parameter synthesis, stochastic biochemical models, continuous-time Markov Chains, continuous stochastic logic 
We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised or minimised. Our method is based on extending CSL model checking and standard uniformisation to parametric models, in order to compute safe bounds on the satisfaction probability of the property. We develop synthesis algorithms that yield answers that are precise to within an arbitrarily small tolerance value. The algorithms combine the computation of probability bounds with the refinement and sampling of the parameter space. Our methods are precise and efficient, and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for three biologically motivated case studies: infection control for a SIR epidemic model; reliability analysis of molecular computation by a DNA walker; and bistability in the gene regulation of the mammalian cell cycle.
   author = {Milan {\v{C}}e{\v{s}}ka and Frits Dannenberg and
	Marta Kwiatkowska and Nicola Paoletti and
	Lubo{\v{s}} Brim},
   title = {Precise parameter synthesis for stochastic
	biochemical systems},
   pages = {1--35},
   journal = {Acta Informatica},
   volume = {2016},
   number = {1},
   year = {2016},
   ISSN = {0001-5903},
   doi = {10.1007/s00236-016-0265-2},
   language = {english},
   url = {}

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