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Stochastic Semantics of Signaling as a Composition of Agent-view Automata

Koeppl, Heinz ; Petrov, Tatjana (2024)
Stochastic Semantics of Signaling as a Composition of Agent-view Automata.
In: Electronic Notes in Theoretical Computer Science, 2011, 272
doi: 10.26083/tuprints-00026721
Article, Secondary publication, Publisher's Version

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Item Type: Article
Type of entry: Secondary publication
Title: Stochastic Semantics of Signaling as a Composition of Agent-view Automata
Language: English
Date: 30 April 2024
Place of Publication: Darmstadt
Year of primary publication: 4 May 2011
Place of primary publication: Amsterdam
Publisher: Elsevier
Journal or Publication Title: Electronic Notes in Theoretical Computer Science
Volume of the journal: 272
DOI: 10.26083/tuprints-00026721
Corresponding Links:
Origin: Secondary publication service

In this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in a rule-set is finite. We illustrate the framework by an example that is related to cellular signaling events.

Uncontrolled Keywords: Cell signaling, Continuous-time Markov chain, Stochastic automata composition
Status: Publisher's Version
URN: urn:nbn:de:tuda-tuprints-267211
Classification DDC: 500 Science and mathematics > 570 Life sciences, biology
600 Technology, medicine, applied sciences > 621.3 Electrical engineering, electronics
Date Deposited: 30 Apr 2024 09:13
Last Modified: 30 Apr 2024 09:14
URI: https://tuprints.ulb.tu-darmstadt.de/id/eprint/26721
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