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2017 | OriginalPaper | Buchkapitel

Analysis of Timed Properties Using the Jump-Diffusion Approximation

verfasst von : Paolo Ballarini, Marco Beccuti, Enrico Bibbona, Andras Horvath, Roberta Sirovich, Jeremy Sproston

Erschienen in: Computer Performance Engineering

Verlag: Springer International Publishing

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Abstract

Density dependent Markov chains (DDMCs) describe the interaction of groups of identical objects. In case of large numbers of objects a DDMC can be approximated efficiently by means of either a set of ordinary differential equations (ODEs) or by a set of stochastic differential equations (SDEs). While with the ODE approximation the chain stochasticity is not maintained, the SDE approximation, also known as the diffusion approximation, can capture specific stochastic phenomena (e.g., bi-modality) and has also better convergence characteristics. In this paper we introduce a method for assessing temporal properties, specified in terms of a timed automaton, of a DDMC through a jump diffusion approximation. The added value is in terms of runtime: the costly simulation of a very large DDMC model can be replaced through much faster simulation of the corresponding jump diffusion model. We show the efficacy of the framework through the analysis of a biological oscillator.

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Fußnoten
1
I.e., for \(N=1\) we assumed the discrete initial populations and reaction intensities being equal to the continuous ones as given in [15], note that this is in agreement with a cell volume \(V=10^9/n_A\) where \(n_A\) is the Avogadro number given that species concentrations and kinetic rate constants of the ODE model are expressed in nM.
 
2
Notice that zero-order and second-order reactions’ rates are dependent on N because for these conversion from continuous to discrete rates depends on cell’s volume.
 
3
\(\mathbf {L}\) and \(\mathbf {H}\), where \(\mathbf {L}\!<\!\mathbf {H}\), are two thresholds chosen so that the minimal, resp. maximal, peaks of oscillation are most likely to fall below \(\mathbf {L}\), resp. above \(\mathbf {H}\).
 
4
I.e., we use the DTA in Fig. 3 but without the \(T_ min \le x \le T_ max \) conjunct on the edge from low \(_3\)-mid \(_{\text {end}}\), which allows us to obtain the value of the clock x at the moment of reaching the final location of this modified DTA: this value gives the length of the first non-spurious oscillation period.
 
5
Observe that the dimension of integration step is dynamically computed through a heuristic function which provides a good trade-off between speed-up and precision of the solution.
 
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Metadaten
Titel
Analysis of Timed Properties Using the Jump-Diffusion Approximation
verfasst von
Paolo Ballarini
Marco Beccuti
Enrico Bibbona
Andras Horvath
Roberta Sirovich
Jeremy Sproston
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-66583-2_5

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