Intermediates, Catalysts, Persistence, and Boundary Steady States

For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We describe two graphical procedures for simplifying reaction networks without breaking known necessary or sufficient conditions for persistence, by iteratively removing so-called intermediates and catalysts from the network. The procedures are easy to apply and, in many cases, lead to highly simplified network structures, such as monomolecular networks. For specific classes of reaction networks, we show that these conditions for persistence are equivalent to one another. Furthermore, they can also be characterized by easily checkable strong connectivity properties of a related graph. In particular, this is the case for (conservative) monomolecular networks, as well as cascades of a large class of post-translational modification systems (of which the MAPK cascade and the $n$-site futile cycle are prominent examples). Since one of the aforementioned sufficient conditions for persistence precludes the existence of boundary steady states, our method also provides a graphical tool to check for that.Comment: The main result was made more general through a slightly different approach. Accepted for publication in the Journal of Mathematical Biolog

Performance Bounds for Synchronized Queueing Networks

Las redes de Petri estocásticas constituyen un modelo unificado de las diferentes extensiones de redes de colas con sincronizaciones existentes en la literatura, válido para el diseño y análisis de prestaciones de sistemas informáticos distribuidos. En este trabajo se proponen técnicas de cálculo de cotas superiores e inferiores de las prestaciones de redes de Petri estocásticas en estado estacionario. Las cotas obtenidas son calculables en tiempo polinómico en el tamaño del modelo, por medio de la resolución de ciertos problemas de programación lineal definidos a partir de la matriz de incidencia de la red (en este sentido, las técnicas desarrolladas pueden considerarse estructurales). Las cotas calculadas dependen sólamente de los valores medios de las variables aleatorias que describen la temporización del sistema, y son independientes de los momentos de mayor orden. Esta independencia de la forma de las distribuciones de probabilidad asociadas puede considerarse como una útil generalización de otros resultados existentes para distribuciones particulares, puesto que los momentos de orden superior son, habitualmente, desconocidos en la realidad y difíciles de estimar. Finalmente, las técnicas desarrolladas se aplican al análisis de diferentes ejemplos tomados de la literatura sobre sistemas informáticos distribuidos y sistemas de fabricación. ******* Product form queueing networks have long been used for the performance evaluation of computer systems. Their success has been due to their capability of naturally expressing sharing of resources and queueing, that are typical situations of traditional computer systems, as well as to their efficient solution algorithms, of polynomial complexity on the size of the model. Unfortunately, the introduction of synchronization constraints usually destroys the product form solution, so that general concurrent and distributed systems are not easily studied with this class of models. Petri nets have been proved specially adequate to model parallel and distributed systems. Moreover, they have a well-founded theory of analysis that allows to investigate a great number of qualitative properties of the system. In the original definition, Petri nets did not include the notion of time, and tried to model only the logical behaviour of systems by describing the causal relations existing among events. This approach showed its power in the specification and analysis of concurrent systems in a way independent of the concept of time. Nevertheless the introduction of a timing specification is essential if we want to use this class of models for the performance evaluation of distributed systems. One of the main problems in the actual use of timed and stochastic Petri net models for the quantitative evaluation of large systems is the explosion of the computational complexity of the analysis algorithms. In general, exact performance results are obtained from the numerical solution of a continuous time Markov chain, whose dimension is given by the size of the state space of the model. Structural computation of exact performance measures has been possible for some subclasses of nets such as those with state machine topology. These nets, under certain assumptions on the stochastic interpretation are isomorphic to Gordon and Newell's networks, in queueing theory terminology. In the general case, efficient methods for the derivation of performance measures are still needed. Two complementary approaches to the derivation of exact measures for the analysis of distributed systems are the utilization of approximation techniques and the computation of bounds. Approximate values for the performance parameters are in general more efficiently derived than the exact ones. On the other hand, "exactness" only exists in theory! In other words, numerical algorithms must be applied in practice for the computation of exact values, therefore making errors is inevitable. Performance bounds are useful in the preliminary phases of the design of a system, in which many parameters are not known accurately. Several alternatives for those parameters should be quickly evaluated, and rejected those that are clearly bad. Exact (and even approximate) solutions would be computationally very expensive. Bounds become useful in these instances since they usually require much less computation effort. The computation of upper and lower bounds for the steady-state performance of timed and stochastic Petri nets is considered in this work. In particular, we study the throughput of transitions, defined as the average number of firings per time unit. For this measure we try to compute upper and lower bounds in polynomial time on the size of the net model, by means of proper linear programming problems defined from the incidence matrix of the net (in this sense, we develop structural techniques). These bounds depend only on the mean values and not on the higher moments of the probability distribution functions of the random variables that describe the timing of the system. The independence of the probability distributions can be viewed as a useful generalization of the performance results, since higher moments of the delays are usually unknown for real cases, and difficult to estimate and assess. From a different perspective, the obtained results can be applied to the analysis of queueing networks extended with some synchronization schemes. Monoclass queueing networks can be mapped on stochastic Petri nets. On the other hand, stochastic Petri nets can be interpreted as monoclass queueing networks augmented with synchronization primitives. Concerning the presentation of this manuscript, it should be mentioned that chapter 1 has been written with the object of giving the reader an outline of the stochastic Petri net model: its definition, terminology, basic properties, and related concepts, together with its deep relation with other classic stochastic network models. Chapter 2 is devoted to the presentation of the net subclasses considered in the rest of the work. The classification presented here is quite different from the one which is usual in the framework of Petri nets. The reason lies on the fact that our classification criterion, the computability of visit ratios for transitions, is introduced for the first time in the field of stochastic Petri nets in this work. The significance of that criterion is based on the important role that the visit ratios play in the computation of upper and lower bounds for the performance of the models. Nevertheless, classical important net subclasses are identified here in terms of the computability of their visit ratios from different parameters of the model. Chapter 3 is concerned with the computation of reachable upper and lower bounds for the most restrictive subclass of those presented in chapter 2: marked graphs. The explanation of this fact is easy to understand. The more simple is the model the more accessible will be the techniques an ideas for the development of good results. Chapter 4 provides a generalization for live and bounded free choice nets of the results presented in the previous chapter. Quality of obtained bounds is similar to that for strongly connected marked graphs: throughput lower bounds are reachable for bounded nets while upper bounds are reachable for 1-bounded nets. Chapter 5 considers the extension to other net subclasses, like mono-T-semiflow nets, FRT-nets, totally open deterministic systems of sequential processes, and persistent nets. The results are of diverse colours. For mono-T-semiflow nets and, therefore, for general FRT-nets, it is not possible (so far) to obtain reachable throughput bounds. On the other hand, for bounded ordinary persistent nets, tight throughput upper bounds are derived. Moreover, in the case of totally open deterministic systems of sequential processes the exact steady-state performance measures can be computed in polynomial time on the net size. In chapter 6 bounds for other interesting performance measures are derived from throughput bounds and from classical queueing theory laws. After that, we explore the introduction of more information from the probability distribution functions of service times in order to improve the bounds. In particular, for Coxian service delay of transitions it is possible to improve the throughput upper bounds of previous chapters which held for more general forms of distribution functions. This improvement shows to be specially fruitful for live and bounded free choice nets. Chapter 7 is devoted to case studies. Several examples taken from literature in the fields of distributed computing systems and manufacturing systems are modelled by means of stochastic Petri nets and evaluated using the techniques developed in previous chapters. Finally, some concluding remarks and considerations on possible extensions of the work are presented

Approximation methods for stochastic petri nets

Stochastic Marked Graphs are a concurrent decision free formalism provided with a powerful synchronization mechanism generalizing conventional Fork Join Queueing Networks. In some particular cases the analysis of the throughput can be done analytically. Otherwise the analysis suffers from the classical state explosion problem. Embedded in the divide and conquer paradigm, approximation techniques are introduced for the analysis of stochastic marked graphs and Macroplace/Macrotransition-nets (MPMT-nets), a new subclass introduced herein. MPMT-nets are a subclass of Petri nets that allow limited choice, concurrency and sharing of resources. The modeling power of MPMT is much larger than that of marked graphs, e.g., MPMT-nets can model manufacturing flow lines with unreliable machines and dataflow graphs where choice and synchronization occur. The basic idea leads to the notion of a cut to split the original net system into two subnets. The cuts lead to two aggregated net systems where one of the subnets is reduced to a single transition. A further reduction leads to a basic skeleton. The generalization of the idea leads to multiple cuts, where single cuts can be applied recursively leading to a hierarchical decomposition. Based on the decomposition, a response time approximation technique for the performance analysis is introduced. Also, delay equivalence, which has previously been introduced in the context of marked graphs by Woodside et al., Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's is slower, but the accuracy is generally better. Delay equivalence often fails to converge, while flow equivalent aggregation can lead to potentially bad results if a strong dependence of the mean completion time on the interarrival process exists

Adaptable processes

We propose the concept of adaptable processes as a way of overcoming the limitations that process calculi have for describing patterns of dynamic process evolution. Such patterns rely on direct ways of controlling the behavior and location of running processes, and so they are at the heart of the adaptation capabilities present in many modern concurrent systems. Adaptable processes have a location and are sensible to actions of dynamic update at runtime; this allows to express a wide range of evolvability patterns for concurrent processes. We introduce a core calculus of adaptable processes and propose two verification problems for them: bounded and eventual adaptation. While the former ensures that the number of consecutive erroneous states that can be traversed during a computation is bound by some given number k, the latter ensures that if the system enters into a state with errors then a state without errors will be eventually reached. We study the (un)decidability of these two problems in several variants of the calculus, which result from considering dynamic and static topologies of adaptable processes as well as different evolvability patterns. Rather than a specification language, our calculus intends to be a basis for investigating the fundamental properties of evolvable processes and for developing richer languages with evolvability capabilities

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

On Minimum-time Control of Continuous Petri nets: Centralized and Decentralized Perspectives

Muchos sistemas artificiales, como los sistemas de manufactura, de logística, de telecomunicaciones o de tráfico, pueden ser vistos "de manera natural" como Sistemas Dinámicos de Eventos Discretos (DEDS). Desafortunadamente, cuando tienen grandes poblaciones, estos sistemas pueden sufrir del clásico problema de la explosión de estados. Con la intención de evitar este problema, se pueden aplicar técnicas de fluidificación, obteniendo una relajación fluida del modelo original discreto. Las redes de Petri continuas (CPNs) son una aproximación fluida de las redes de Petri discretas, un conocido formalismo para los DEDS. Una ventaja clave del empleo de las CPNs es que, a menudo, llevan a una substancial reducción del coste computacional. Esta tesis se centra en el control de Redes de Petri continuas temporizadas (TCPNs), donde las transiciones tienen una interpretación temporal asociada. Se asume que los sistemas siguen una semántica de servidores infinitos (velocidad variable) y que las acciones de control aplicables son la disminución de la velocidad del disparo de las transiciones. Se consideran dos interesantes problemas de control en esta tesis: 1) control del marcado objetivo, donde el objetivo es conducir el sistema (tan rápido como sea posible) desde un estado inicial a un estado final deseado, y es similar al problema de control set-point para cualquier sistema de estado continuo; 2) control del flujo óptimo, donde el objetivo es conducir el sistema a un flujo óptimo sin conocimiento a priori del estado final. En particular, estamos interesados en alcanzar el flujo máximo tan rápido como sea posible, lo cual suele ser deseable en la mayoría de sistemas prácticos. El problema de control del marcado objetivo se considera desde las perspectivas centralizada y descentralizada. Proponemos varios controladores centralizados en tiempo mínimo, y todos ellos están basados en una estrategia ON/OFF. Para algunas subclases, como las redes Choice-Free (CF), se garantiza la evolución en tiempo mínimo; mientras que para redes generales, los controladores propuestos son heurísticos. Respecto del problema de control descentralizado, proponemos en primer lugar un controlador descentralizado en tiempo mínimo para redes CF. Para redes generales, proponemos una aproximación distribuida del método Model Predictive Control (MPC); sin embargo en este método no se considera evolución en tiempo mínimo. El problema de control de flujo óptimo (en nuestro caso, flujo máximo) en tiempo mínimo se considera para redes CF. Proponemos un algoritmo heurístico en el que calculamos los "mejores" firing count vectors que llevan al sistema al flujo máximo, y aplicamos una estrategia de disparo ON/OFF. También demostramos que, debido a que las redes CF son persistentes, podemos reducir el tiempo que tarda en alcanzar el flujo máximo con algunos disparos adicionales. Los métodos de control propuestos se han implementado e integrado en una herramienta para Redes de Petri híbridas basada en Matlab, llamada SimHPN

Measurements, Models, Systems and Design

531 s.

Discrete Event Systems: Models and Applications; Proceedings of an IIASA Conference, Sopron, Hungary, August 3-7, 1987

Work in discrete event systems has just begun. There is a great deal of activity now, and much enthusiasm. There is considerable diversity reflecting differences in the intellectual formation of workers in the field and in the applications that guide their effort. This diversity is manifested in a proliferation of DEM formalisms. Some of the formalisms are essentially different. Some of the "new" formalisms are reinventions of existing formalisms presented in new terms. These "duplications" reveal both the new domains of intended application as well as the difficulty in keeping up with work that is published in journals on computer science, communications, signal processing, automatic control, and mathematical systems theory - to name the main disciplines with active research programs in discrete event systems. The first eight papers deal with models at the logical level, the next four are at the temporal level and the last six are at the stochastic level. Of these eighteen papers, three focus on manufacturing, four on communication networks, one on digital signal processing, the remaining ten papers address methodological issues ranging from simulation to computational complexity of some synthesis problems. The authors have made good efforts to make their contributions self-contained and to provide a representative bibliography. The volume should therefore be both accessible and useful to those who are just getting interested in discrete event systems