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Register a new userModeling of Resilience Properties in Oscillatory Biological Systems using Parametric Time Petri Nets, Supplementary Information
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Added by
Alexander Andreychenko
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the dynamic behavior of biological oscillatory systems. In particular, we focus on the resilience properties of such systems. This notion is crucial to understand the behavior of biological systems (e.g. the mammalian circadian rhythm) that are reactive and adaptive enough to endorse major changes in their environment (e.g. jet-lags, day-night alternating work-time). We formalize these properties through parametric TCTL and demonstrate how changes of the environmental conditions can be tackled to guarantee the resilience of living organisms. In particular, we are able to discuss the influence of various perturbations, e.g. artificial jet-lag or components knock-out, with regard to quantitative delays. This analysis is crucial when it comes to model elicitation for dynamic biological systems. We demonstrate the applicability of this technique using a simplified model of circadian clock.
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We investigate the problem of parameter synthesis for time Petri nets with a cost variable that evolves both continuously with time, and discretely when firing transitions. More precisely, parameters are rational symbolic constants used for time constraints on the firing of transitions and we want to synthesise all their values such that some marking is reachable, with a cost that is either minimal or simply less than a given bound. We first prove that the mere existence of values for the parameters such that the latter property holds is undecidable. We nonetheless provide symbolic semi-algorithms for the two synthesis problems and we prove them both sound and complete when they terminate. We also show how to modify them for the case when parameter values are integers. Finally, we prove that these modifi
We consider approaches for causal semantics of Petri nets, explicitly representing dependencies between transition occurrences. For one-safe nets or condition/event-systems, the notion of process as defined by Carl Adam Petri provides a notion of a run of a system where causal dependencies are reflected in terms of a partial order. A well-known problem is how to generalise this notion for nets where places may carry several tokens. Goltz and Reisig have defined such a generalisation by distinguishing tokens according to their causal history. However, this so-called individual token interpretation is often considered too detailed. A number of approaches have tackled the problem of defining a more abstract notion of process, thereby obtaining a so-called collective token interpretation. Here we give a short overview on these attempts and then identify a subclass of Petri nets, called structural conflict nets, where the interplay between conflict and concurrency due to token multiplicity does not occur. For this subclass, we define abstract processes as equivalence classes of Goltz-Reisig processes. We justify this approach by showing that we obtain exactly one maximal abstract process if and only if the underlying net is conflict-free with respect to a canonical notion of conflict.
Blockchain technology has evolved through many changes and modifications, such as smart-contracts since its inception in 2008. The popularity of a blockchain system is due to the fact that it offers a significant security advantage over other traditional systems. However, there have been many attacks in various blockchain systems, exploiting different vulnerabilities and bugs, which caused a significant financial loss. Therefore, it is essential to understand how these attacks in blockchain occur, which vulnerabilities they exploit, and what threats they expose. Another concerning issue in this domain is the recent advancement in the quantum computing field, which imposes a significant threat to the security aspects of many existing secure systems, including blockchain, as they would invalidate many widely-used cryptographic algorithms. Thus, it is important to examine how quantum computing will affect these or other new attacks in the future. In this paper, we explore different vulnerabilities in current blockchain systems and analyse the threats that various theoretical and practical attacks in the blockchain expose. We then model those attacks using Petri nets concerning current systems and future quantum computers.
In the early two-thousands, Recursive Petri nets have been introduced in order to model distributed planning of multi-agent systems for which counters and recursivity were necessary. Although Recursive Petri nets strictly extend Petri nets and context-free grammars, most of the usual problems (reachability, coverability, finiteness, boundedness and termination) were known to be solvable by using non-primitive recursive algorithms. For almost all other extended Petri nets models containing a stack, the complexity of coverability and termination are unknown or strictly larger than EXPSPACE. In contrast, we establish here that for Recursive Petri nets, the coverability, termination, boundedness and finiteness problems are EXPSPACE-complete as for Petri nets. From an expressiveness point of view, we show that coverability languages of Recursive Petri nets strictly include the union of coverability languages of Petri nets and context-free languages. Thus we get a more powerful model than Petri net for free.
We prove that $omega$-languages of (non-deterministic) Petri nets and $omega$-languages of (non-deterministic) Turing machines have the same topological complexity: the Borel and Wadge hierarchies of the class of $omega$-languages of (non-deterministic) Petri nets are equal to the Borel and Wadge hierarchies of the class of $omega$-languages of (non-deterministic) Turing machines which also form the class of effective analytic sets. In particular, for each non-null recursive ordinal $alpha < omega_1^{{rm CK}} $ there exist some ${bf Sigma}^0_alpha$-complete and some ${bf Pi}^0_alpha$-complete $omega$-languages of Petri nets, and the supremum of the set of Borel ranks of $omega$-languages of Petri nets is the ordinal $gamma_2^1$, which is strictly greater than the first non-recursive ordinal $omega_1^{{rm CK}}$. We also prove that there are some ${bf Sigma}_1^1$-complete, hence non-Borel, $omega$-languages of Petri nets, and that it is consistent with ZFC that there exist some $omega$-languages of Petri nets which are neither Borel nor ${bf Sigma}_1^1$-complete. This answers the question of the topological complexity of $omega$-languages of (non-deterministic) Petri nets which was left open in [DFR14,FS14].
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