A case study in model-driven synthetic biology

We report on a case study in synthetic biology, demonstrating the modeldriven design of a self-powering electrochemical biosensor. An essential result of the design process is a general template of a biosensor, which can be instantiated to be adapted to specific pollutants. This template represents a gene expression network extended by metabolic activity. We illustrate the model-based analysis of this template using qualitative, stochastic and continuous Petri nets and related analysis techniques, contributing to a reliable and robust design

Solving myopia in real-time decision-making using Petri nets models’ knowledge for service-oriented manufacturing systems

This paper introduces a novel approach to the real-time decision-making in service-oriented manufacturing systems, addressing the myopia problem usually presented in such systems. The proposed decision method considers the knowledge extracted from the Petri nets models used to describe the services process behavior, mainly the T-invariants, combined with a multi-criteria function customized according to the system’s particularities and strategies. An experimental laboratorial case study was used to demonstrate the applicability of the proposed real-time decision-making approach in service-oriented manufacturing systems, considering some productivity and energy efficiency criteria

Timed event-graph and performance evaluation of systems

Bibliography: p. 16.Suppport provided by the Joint Director's Laboratories under contract no. N00014-85-K-0782 Support provided by the Office of Naval Research under contract no. N00014-84-K-0519by Herve P. Hillion, Alexander H. Levis

On the design of distributed organizational structures

"July 1986."Includes bibliographical references.Supported by the U.S. Office of Naval Research. N00014-84-K-0519 Supported by the Joint Directors of Laboratories through the Office of Naval Research. ONR/N00014-85-K-0782by Pascal A. Remy, Alexander H. Levis, Victoria Y.-Y. Jin

Analysis of structural properties of Petri nets based on product incidence matrix

summary:This paper presents some structural properties of a generalized Petri net (PN) with an algorithm to determine the (partial) conservativeness and (partial) consistency of the net. A product incidence matrix $A=CC^T$ or $\tilde{A}=C^TC$ is defined and used to further improve the relations among PNs, linear inequalities and matrix analysis. Thus, based on Cramer's Rule, a new approach for the study of the solution of a linear system is given in terms of certain sub-determinants of the coefficient matrix and an efficient algorithm is proposed to compute these sub-determinants. The paper extends the common necessary and/or sufficient conditions for conservativeness and consistency in previous papers and some examples are designed to explain the conclusions finally

Performance evaluation of decisionmaking organizations

Caption title.Bibliography: p. 7-8.Supported, in part, by a contract from the Office of Naval Research. N00014-85-K-0519 Supported, in part, by a contract from the Joint Directors of Laboraties through the Office of Naval Research. N00014-85-K-0782by Herve P. Hillion, Alexander H. Levis

Energy aware knowledge extraction from Petri nets supporting decision-making in service-oriented automation

This paper introduces an approach to decision support systems in service-oriented automation control systems, which considers the knowledge extracted from the Petri nets models used to describe and execute the process behavior. Such solution optimizes the decision-making taking into account multi-criteria, namely productive parameters and also energy parameters. In fact, being manufacturing processes typically energy-intensive, this allows contributing for a clean and saving environment (i.e. a better and efficient use of energy). The preliminary experimental results, using a real laboratorial case study, demonstrate the applicability of the knowledge extracted from the Petri nets models to support real-time decision-making systems in service-oriented automation systems, considering some energy efficiency criteria

A Petri Net Approach to Verify and Debug Simulation Models

Verification and Simulation share many issues, one is that simulation models require validation and verification. In the context of simulation, verification is understood as the task to ensure that an executable simulation model matches its conceptual counterpart while validation is the task to ensure that a simulation model represents the system under study well enough with respect to the goals of the simulation study. Both, validation and verification, are treated in the literature at a rather high level and seem to be more an art than engineering. This paper considers discrete event simulation of stochastic models that are formulated in a process-oriented language. The ProC/B paradigm is used as a particular example of a class of simulation languages which follow the common process interaction approach and show common concepts used in performance modeling, namely a) layered systems of virtual machines that contain resources and provide services and b) concurrent processes that interact by message passing and shared memory. We describe how Petri net analysis techniques help to verify and debug a large and detailed simulation model of airport logistics. We automatically derive a Petri net that models the control flow of a Proc/B model and we make use of invariant analysis and modelchecking to shed light on the allocation of resources, constraints among entities and causes for deadlocks

Tools for efficient analysis of concurrent software systems

The ever increasing use of distributed computing as a method of providing added computing power and reliability has sparked interest in methods to model and analyze concurrent hardware/ software systems. Efficient automated analysis tools are needed to aid designers of such systems. The Distributed Systems Project at UCI has been developing a suite of tools (dubbed the P-NUT system) which supports efficient analysis of models of concurrent software. This paper presents the principles which guide the development of P-NUT tools and discusses the development of one of the tools: the Reachability Graph Builder (RGB). The P-NUT approach to tool development has resulted in the production of a highly efficient tool for constructing reachability graphs. The careful design of data structures and associated algorithms has significantly enlarged the class of models which can be analyzed

The Reachability Problem for Petri Nets is Not Elementary

Petri nets, also known as vector addition systems, are a long established model of concurrency with extensive applications in modelling and analysis of hardware, software and database systems, as well as chemical, biological and business processes. The central algorithmic problem for Petri nets is reachability: whether from the given initial configuration there exists a sequence of valid execution steps that reaches the given final configuration. The complexity of the problem has remained unsettled since the 1960s, and it is one of the most prominent open questions in the theory of verification. Decidability was proved by Mayr in his seminal STOC 1981 work, and the currently best published upper bound is non-primitive recursive Ackermannian of Leroux and Schmitz from LICS 2019. We establish a non-elementary lower bound, i.e. that the reachability problem needs a tower of exponentials of time and space. Until this work, the best lower bound has been exponential space, due to Lipton in 1976. The new lower bound is a major breakthrough for several reasons. Firstly, it shows that the reachability problem is much harder than the coverability (i.e., state reachability) problem, which is also ubiquitous but has been known to be complete for exponential space since the late 1970s. Secondly, it implies that a plethora of problems from formal languages, logic, concurrent systems, process calculi and other areas, that are known to admit reductions from the Petri nets reachability problem, are also not elementary. Thirdly, it makes obsolete the currently best lower bounds for the reachability problems for two key extensions of Petri nets: with branching and with a pushdown stack.Comment: Final version of STOC'1