Modelling non-Markovian dynamics in biochemical reactions

Biochemical reactions are often modelled as discrete-state continuous-time stochastic processes evolving as memoryless Markov processes. However, in some cases, biochemical systems exhibit non-Markovian dynamics. We propose here a methodology for building stochastic simulation algorithms which model more precisely non-Markovian processes in some specific situations. Our methodology is based on Constraint Programming and is implemented by using Gecode, a state-of-the-art framework for constraint solving

Hybrid Behaviour of Markov Population Models

We investigate the behaviour of population models written in Stochastic Concurrent Constraint Programming (sCCP), a stochastic extension of Concurrent Constraint Programming. In particular, we focus on models from which we can define a semantics of sCCP both in terms of Continuous Time Markov Chains (CTMC) and in terms of Stochastic Hybrid Systems, in which some populations are approximated continuously, while others are kept discrete. We will prove the correctness of the hybrid semantics from the point of view of the limiting behaviour of a sequence of models for increasing population size. More specifically, we prove that, under suitable regularity conditions, the sequence of CTMC constructed from sCCP programs for increasing population size converges to the hybrid system constructed by means of the hybrid semantics. We investigate in particular what happens for sCCP models in which some transitions are guarded by boolean predicates or in the presence of instantaneous transitions

Portable parallel stochastic optimization for the design of aeropropulsion components

This report presents the results of Phase 1 research to develop a methodology for performing large-scale Multi-disciplinary Stochastic Optimization (MSO) for the design of aerospace systems ranging from aeropropulsion components to complete aircraft configurations. The current research recognizes that such design optimization problems are computationally expensive, and require the use of either massively parallel or multiple-processor computers. The methodology also recognizes that many operational and performance parameters are uncertain, and that uncertainty must be considered explicitly to achieve optimum performance and cost. The objective of this Phase 1 research was to initialize the development of an MSO methodology that is portable to a wide variety of hardware platforms, while achieving efficient, large-scale parallelism when multiple processors are available. The first effort in the project was a literature review of available computer hardware, as well as review of portable, parallel programming environments. The first effort was to implement the MSO methodology for a problem using the portable parallel programming language, Parallel Virtual Machine (PVM). The third and final effort was to demonstrate the example on a variety of computers, including a distributed-memory multiprocessor, a distributed-memory network of workstations, and a single-processor workstation. Results indicate the MSO methodology can be well-applied towards large-scale aerospace design problems. Nearly perfect linear speedup was demonstrated for computation of optimization sensitivity coefficients on both a 128-node distributed-memory multiprocessor (the Intel iPSC/860) and a network of workstations (speedups of almost 19 times achieved for 20 workstations). Very high parallel efficiencies (75 percent for 31 processors and 60 percent for 50 processors) were also achieved for computation of aerodynamic influence coefficients on the Intel. Finally, the multi-level parallelization strategy that will be needed for large-scale MSO problems was demonstrated to be highly efficient. The same parallel code instructions were used on both platforms, demonstrating portability. There are many applications for which MSO can be applied, including NASA's High-Speed-Civil Transport, and advanced propulsion systems. The use of MSO will reduce design and development time and testing costs dramatically

Transient Reward Approximation for Continuous-Time Markov Chains

We are interested in the analysis of very large continuous-time Markov chains (CTMCs) with many distinct rates. Such models arise naturally in the context of reliability analysis, e.g., of computer network performability analysis, of power grids, of computer virus vulnerability, and in the study of crowd dynamics. We use abstraction techniques together with novel algorithms for the computation of bounds on the expected final and accumulated rewards in continuous-time Markov decision processes (CTMDPs). These ingredients are combined in a partly symbolic and partly explicit (symblicit) analysis approach. In particular, we circumvent the use of multi-terminal decision diagrams, because the latter do not work well if facing a large number of different rates. We demonstrate the practical applicability and efficiency of the approach on two case studies.Comment: Accepted for publication in IEEE Transactions on Reliabilit

Diseño para operabilidad: Una revisión de enfoques y estrategias de solución

In the last decades the chemical engineering scientific research community has largely addressed the design-foroperability problem. Such an interest responds to the fact that the operability quality of a process is determined by design, becoming evident the convenience of considering operability issues in early design stages rather than later when the impact of modifications is less effective and more expensive. The necessity of integrating design and operability is dictated by the increasing complexity of the processes as result of progressively stringent economic, quality, safety and environmental constraints. Although the design-for-operability problem concerns to practically every technical discipline, it has achieved a particular identity within the chemical engineering field due to the economic magnitude of the involved processes. The work on design and analysis for operability in chemical engineering is really vast and a complete review in terms of papers is beyond the scope of this contribution. Instead, two major approaches will be addressed and those papers that in our belief had the most significance to the development of the field will be described in some detail.En las últimas décadas, la comunidad científica de ingeniería química ha abordado intensamente el problema de diseño-para-operabilidad. Tal interés responde al hecho de que la calidad operativa de un proceso esta determinada por diseño, resultando evidente la conveniencia de considerar aspectos operativos en las etapas tempranas del diseño y no luego, cuando el impacto de las modificaciones es menos efectivo y más costoso. La necesidad de integrar diseño y operabilidad esta dictada por la creciente complejidad de los procesos como resultado de las cada vez mayores restricciones económicas, de calidad de seguridad y medioambientales. Aunque el problema de diseño para operabilidad concierne a prácticamente toda disciplina, ha adquirido una identidad particular dentro de la ingeniería química debido a la magnitud económica de los procesos involucrados. El trabajo sobre diseño y análisis para operabilidad es realmente vasto y una revisión completa en términos de artículos supera los alcances de este trabajo. En su lugar, se discutirán los dos enfoques principales y aquellos artículos que en nuestra opinión han tenido mayor impacto para el desarrollo de la disciplina serán descriptos con cierto detalle.Fil: Blanco, Anibal Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; ArgentinaFil: Bandoni, Jose Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Planta Piloto de Ingeniería Química. Universidad Nacional del Sur. Planta Piloto de Ingeniería Química; Argentin

A fluid analysis framework for a Markovian process algebra

Markovian process algebras, such as PEPA and stochastic π-calculus, bring a powerful compositional approach to the performance modelling of complex systems. However, the models generated by process algebras, as with other interleaving formalisms, are susceptible to the state space explosion problem. Models with only a modest number of process algebra terms can easily generate so many states that they are all but intractable to traditional solution techniques. Previous work aimed at addressing this problem has presented a fluid-flow approximation allowing the analysis of systems which would otherwise be inaccessible. To achieve this, systems of ordinary differential equations describing the fluid flow of the stochastic process algebra model are generated informally. In this paper, we show formally that for a large class of models, this fluid-flow analysis can be directly derived from the stochastic process algebra model as an approximation to the mean number of component types within the model. The nature of the fluid approximation is derived and characterised by direct comparison with the Chapman–Kolmogorov equations underlying the Markov model. Furthermore, we compare the fluid approximation with the exact solution using stochastic simulation and we are able to demonstrate that it is a very accurate approximation in many cases. For the first time, we also show how to extend these techniques naturally to generate systems of differential equations approximating higher order moments of model component counts. These are important performance characteristics for estimating, for instance, the variance of the component counts. This is very necessary if we are to understand how precise the fluid-flow calculation is, in a given modelling situation