Event structures for Petri nets with persistence

Event structures are a well-accepted model of concurrency. In a seminal paper by Nielsen, Plotkin and Winskel, they are used to establish a bridge between the theory of domains and the approach to concurrency proposed by Petri. A basic role is played by an unfolding construction that maps (safe) Petri nets into a subclass of event structures, called prime event structures, where each event has a uniquely determined set of causes. Prime event structures, in turn, can be identified with their domain of configurations. At a categorical level, this is nicely formalised by Winskel as a chain of coreflections. Contrary to prime event structures, general event structures allow for the presence of disjunctive causes, i.e., events can be enabled by distinct minimal sets of events. In this paper, we extend the connection between Petri nets and event structures in order to include disjunctive causes. In particular, we show that, at the level of nets, disjunctive causes are well accounted for by persistent places. These are places where tokens, once generated, can be used several times without being consumed and where multiple tokens are interpreted collectively, i.e., their histories are inessential. Generalising the work on ordinary nets, Petri nets with persistence are related to a new subclass of general event structures, called locally connected, by means of a chain of coreflections relying on an unfolding construction

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Towards a Notion of Distributed Time for Petri Nets

We set the ground for research on a timed extension of Petri nets where time parameters are associated with tokens and arcs carry constraints that qualify the age of tokens required for enabling. The novelty is that, rather than a single global clock, we use a set of unrelated clocks --- possibly one per place --- allowing a local timing as well as distributed time synchronisation. We give a formal definition of the model and investigate properties of local versus global timing, including decidability issues and notions of processes of the respective models

Process algebra for performance evaluation

This paper surveys the theoretical developments in the field of stochastic process algebras, process algebras where action occurrences may be subject to a delay that is determined by a random variable. A huge class of resource-sharing systems – like large-scale computers, client–server architectures, networks – can accurately be described using such stochastic specification formalisms. The main emphasis of this paper is the treatment of operational semantics, notions of equivalence, and (sound and complete) axiomatisations of these equivalences for different types of Markovian process algebras, where delays are governed by exponential distributions. Starting from a simple actionless algebra for describing time-homogeneous continuous-time Markov chains, we consider the integration of actions and random delays both as a single entity (like in known Markovian process algebras like TIPP, PEPA and EMPA) and as separate entities (like in the timed process algebras timed CSP and TCCS). In total we consider four related calculi and investigate their relationship to existing Markovian process algebras. We also briefly indicate how one can profit from the separation of time and actions when incorporating more general, non-Markovian distributions

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

Distributed Markovian Bisimulation Reduction aimed at CSL Model Checking

The verification of quantitative aspects like performance and dependability by means of model checking has become an important and vivid area of research over the past decade.\ud \ud An important result of that research is the logic CSL (continuous stochastic logic) and its corresponding model checking algorithms. The evaluation of properties expressed in CSL makes it necessary to solve large systems of linear (differential) equations, usually by means of numerical analysis. Both the inherent time and space complexity of the numerical algorithms make it practically infeasible to model check systems with more than 100 million states, whereas realistic system models may have billions of states.\ud \ud To overcome this severe restriction, it is important to be able to replace the original state space with a probabilistically equivalent, but smaller one. The most prominent equivalence relation is bisimulation, for which also a stochastic variant exists (Markovian bisimulation). In many cases, this bisimulation allows for a substantial reduction of the state space size. But, these savings in space come at the cost of an increased time complexity. Therefore in this paper a new distributed signature-based algorithm for the computation of the bisimulation quotient of a given state space is introduced.\ud \ud To demonstrate the feasibility of our approach in both a sequential, and more important, in a distributed setting, we have performed a number of case studies

Properties of Distributed Time Arc Petri Nets

In recent work we started a research on a distributed-timed extension of Petri nets where time parameters are associated with tokens and arcs carry constraints that qualify the age of tokens required for enabling. This formalism enables to model e.g. hardware architectures like GALS. We give a formal definition of process semantics for our model and investigate several properties of local versus global timing: expressiveness, reachability and coverability

SPDL Model Checking via Property-Driven State Space Generation

In this report we describe how both, memory and time requirements for stochastic model checking of SPDL (stochastic propositional dynamic logic) formulae can significantly be reduced. SPDL is the stochastic extension of the multi-modal program logic PDL.\ud SPDL provides means to specify path-based properties with or without timing restrictions. Paths can be characterised by so-called programs, essentially regular expressions, where the executability can be made dependent on the validity of test formulae. For model-checking SPDL path formulae it is necessary to build a product transition system (PTS)\ud between the system model and the program automaton belonging to the path formula that is to be verified.\ud In many cases, this PTS can be drastically reduced during the model checking procedure, as the program restricts the number of potentially satisfying paths. Therefore, we propose an approach that directly generates the reduced PTS from a given SPA specification and an SPDL path formula.\ud The feasibility of this approach is shown through a selection of case studies, which show enormous state space reductions, at no increase in generation time.\u

Generalized Communicating P Systems Working in Fair Sequential Model

In this article we consider a new derivation mode for generalized communicating P systems (GCPS) corresponding to the functioning of population protocols (PP) and based on the sequential derivation mode and a fairness condition. We show that PP can be seen as a particular variant of GCPS. We also consider a particular stochastic evolution satisfying the fairness condition and obtain that it corresponds to the run of a Gillespie's SSA. This permits to further describe the dynamics of GCPS by a system of ODEs when the population size goes to the infinity.Comment: Presented at MeCBIC 201