Finding weakly reversible realizations of chemical reaction networks using optimization

An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem statement can be traced back at least 30 years ago. The algorithm uses standard linear and mixed integer linear programming, and it is based on elementary graph theory and important former results on the dense realizations of CRNs. The proposed method is also capable of determining if no dynamically equivalent weakly reversible structure exists for a given reaction network with a previously fixed complex set.Comment: 18 pages, 9 figure

CSL model checking of Deterministic and Stochastic Petri Nets

Deterministic and Stochastic Petri Nets (DSPNs) are a widely used high-level formalism for modeling discrete-event systems where events may occur either without consuming time, after a deterministic time, or after an exponentially distributed time. The underlying process dened by DSPNs, under certain restrictions, corresponds to a class of Markov Regenerative Stochastic Processes (MRGP). In this paper, we investigate the use of CSL (Continuous Stochastic Logic) to express probabilistic properties, such a time-bounded until and time-bounded next, at the DSPN level. The verication of such properties requires the solution of the steady-state and transient probabilities of the underlying MRGP. We also address a number of semantic issues regarding the application of CSL on MRGP and provide numerical model checking algorithms for this logic. A prototype model checker, based on SPNica, is also described

A Linear Programming Approach to Weak Reversibility and Linear Conjugacy of Chemical Reaction Networks

15 páginas, 2 figuras.-- The final publication is available at www.springerlink.comA numerically effective procedure for determining weakly reversible chemical reaction networks that are linearly conjugate to a known reaction network is proposed in this paper. The method is based on translating the structural and algebraic characteristics of weak reversibility to logical statements and solving the obtained set of linear (in)equalities in the framework of mixed integer linear programming. The unknowns in the problem are the reaction rate coefficients and the parameters of the linear conjugacy transformation. The efficacy of the approach is shown through numerical examples.Matthew D. Johnston and David Siegel acknowledge the support of D. Siegel’s Natural Sciences and Engineering Research Council of Canada Discovery Grant. Gàbor Szederkényi acknowledges the support of the Hungarian National Research Fund through grant no. OTKA K-83440 as well as the support of project CAFE (Computer Aided Process for Food Engineering) FP7-KBBE-2007-1 (Grant no: 212754).Peer reviewe

On the graph structure of the Web of Data

This article describes how the Web of Data has emerged as the realization of a machine readable web relying on the resource description framework language as a way to provide richer semantics to datasets. While the web of data is based on similar principles as the original web, being interlinked in the principal mechanism to relate information, the differences in the structure of the information is evident. Several studies have analysed the graph structure of the web, yielding important insights that were used in relevant applications. However, those findings cannot be transposed to the Web of Data, due to fundamental differences in the production, link creation and usage. This article reports on a study of the graph structure of the Web of Data using methods and techniques from similar studies for the Web. Results show that the Web of Data also complies with the theory of the bow-tie. Other characteristics are the low distance between nodes or the closeness and degree centrality are low. Regarding the datasets, the biggest one is Open Data Euskadi but the one with more connections to other datasets is Dbpedia.European Commissio

Automatic Evaluation of Multidisciplinary Derivatives Using a Graph-Based Problem Formulation in OpenMDAO

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140432/1/6.2014-2042.pd

Localization, fractality, and ergodicity in a monitored qubit

We study the statistical properties of a single two-level system (qubit) subject to repetitive ancilla-based measurements. This setup is a fundamental minimal model for exploring the intricate interplay between the unitary dynamics of the system and the nonunitary stochasticity introduced by quantum measurements, which is central to the phenomenon of measurement-induced phase transitions. We demonstrate that this "toy model" harbors remarkably rich dynamics, manifesting in the distribution function of the qubit's quantum states in the long-time limit. We uncover a compelling analogy with the phenomenon of Anderson localization, albeit governed by distinct underlying mechanisms. Specifically, the state distribution function of the monitored qubit, parameterized by a single angle on the Bloch sphere, exhibits diverse types of behavior familiar from the theory of Anderson transitions, spanning from complete localization to almost uniform delocalization, with fractality occurring between the two limits. By combining analytical solutions for various special cases with two complementary numerical approaches, we achieve a comprehensive understanding of the structure delineating the "phase diagram" of the model. We categorize and quantify the emergent regimes and identify two distinct phases of the monitored qubit: ergodic and nonergodic. The transition between these two phases is our main finding.Comment: 47 pages, 23 figures. Comments welcom

Energy-aware routing techniques for software-defined networks

Achieving energy efficiency has recently become a key topic of networking research due to the ever-increasing power consumption and CO2 emissions generated by large data networks. This problem is becoming even more concerning and challenging given the drastic traffic increase expected over the next few years. However, the use of efficient energy-aware strategies could overturn this situation reducing the electricity consumption of Internet data transmission networks, as well as contributing to mitigate the environmental impact of other sectors. The existence of redundant network elements with high capacities is a common design practice in current network infrastructures in order to face suddenly failures or peak traffic flows. However, these additional resources remain either unused or barely used most of the time leading to an undesired energy waste. Therefore, putting into sleep mode (i.e. a low-power state) unused elements is an effective and widely-accepted strategy to decrease the consumption of data networks. In this context, SDN can be seen as an attractive solution to achieve the long-awaited energy efficiency in current communications systems, since they allow a flexible programmability suitable for this problem. This doctoral thesis tackles the problem of optimizing the power consumption in SDN through the design of energy-aware routing techniques that minimize the number of network elements required to satisfy an incoming traffic load. Different from existing related works, we focus on optimizing energy consumption in SDN with in-band control traffic in order to close this important gap in the literature and provide solutions compatible with operational backbone networks. Complementing the general aim of improving the energy efficiency in SDN, this research is also intended to cover important related features such as network performance, QoS requirements and real-time operation. Accordingly, this study gives a general perspective about the use of energy efficient routing techniques, which cover integrated routing considerations for the data and control plane traffic in SDN. By using realistic input data, significant values of switched-off links and nodes are reached, which demonstrates the great opportunity for saving energy given by our proposals. The obtained results have also validated the intrinsic trade-off between environmental and performance concerns, considering several performance indicators. These findings confirm that energy-aware routing schemes should be designed considering specific traffic requirements and performance metric bounds. Moreover, it is shown that jointly considering QoS requirements and energy awareness is an effective approach to improve, not only the power consumption, but the performance on critical parameters such as control traffic delay and blocking rate. Similarly, the proposed dynamic traffic allocation with congestion-aware rerouting is able to handle demanding traffic arrival without degrading the performance of higher priority traffic. In general, our proposals are fine-grained, easy to implement and quite balanced and effective in their results looking for a suitable and readily deployment in real-world SDN scenarios. Therefore, the conducted research and contributions reported through this document not only add to what is known about the potential of energy-aware routing techniques, but also stand as a valuable solution on the road to a sustainable networking.L'assoliment de l'eficiència energètica s'ha convertit recentment en un tema clau de recerca de xarxes a causa dels creixents nivells de consum d'energia i emissions de CO2 generats per les xarxes de dades. Aquest problema es torna cada vegada més preocupant i desafiant, donat el dràstic augment del trànsit esperat en els propers anys. No obstant això, l'ús d'estratègies energètiques eficients podria invertir aquesta situació, reduint el consum d'electricitat de les xarxes de dades d'Internet i contribuint a mitigar l'impacte ambiental d'altres sectors. L'existència d'elements de xarxa redundants i amb grans capacitats és una pràctica de disseny habitual en les infraestructures de xarxes actuals per afrontar fallades sobtades o fluxos de trànsit més elevats. Tanmateix, aquests recursos addicionals romanen poc o gens utilitzats la major part del temps, generant un desaprofitament d'energia no desitjat. Per tant, posar en mode de repòs (és a dir, un estat de baixa potència) elements no utilitzats és una estratègia efectiva i àmpliament acceptada per disminuir el consum en xarxes de dades. En aquest context, les xarxes definides per programari (SDN) es poden considerar una solució atractiva per aconseguir l'esperada eficiència energètica en els sistemes de comunicacions actuals, ja que permeten una flexible programabilitat idònia per a aquest problema. Aquesta tesi doctoral aborda el problema d'optimitzar el consum d'energia en SDN a través del disseny de tècniques d'encaminament conscients de l'energia que minimitzen la quantitat d'elements de xarxa necessaris per satisfer una càrrega de trànsit entrant. Diferent dels treballs existents, aquesta tesi es centra a optimitzar el consum d'energia en SDN amb el control de tràfic dins de banda per tancar aquesta important bretxa en la literatura i proporcionar solucions compatibles amb xarxes troncals operatives. Complementant l'objectiu general de millorar l'eficiència energètica en SDN, aquesta recerca també pretén cobrir altres importants paràmetres relacionats, com ara el rendiment de la xarxa, els requisits de qualitat de servei (QoS) i el funcionament en temps real. En conseqüència, aquest estudi ofereix una perspectiva general sobre l'ús de tècniques d'encaminament eficients energèticament, que contempla consideracions integrades per al tràfic de dades i del pla de control en SDN. Prenent dades d'entrada realistes, es van aconseguir desconnectar significatives quantitats d'enllaços i nodes, la qual cosa demostra la gran oportunitat d'estalvi d'energia que ofereixen les nostres propostes. Els resultats obtinguts també validen el estret compromís entre les preocupacions ambientals i les qüestions de rendiment de la xarxa, considerant diversos indicadors de rendiment. Aquests resultats confirmen que els esquemes d'encaminament conscients de l'energia s'han de dissenyar tenint en compte els requisits de tràfic específics i els límits desitjats de les mètriques de rendiment. A més, es demostra que, considerant conjuntament els requisits de QoS i de l'energia necessària, és un enfocament eficaç per millorar, no només el consum d'energia, sinó també el rendiment en paràmetres crítics, com la latència del tràfic de control i la probabilitat de bloqueig. De manera semblant, l'assignació dinàmica de tràfic proposta, amb re-encaminament conscient de la congestió, permet gestionar grans volums de trànsit sense degradar el rendiment de les demandes de major prioritat. En general, les nostres propostes són precises, fàcils d'implementar i bastant equilibrades i efectives en els seus resultats, buscant un desplegament adequat i fàcil en escenaris pràctics de SDN. Per tant, la recerca realitzada i les contribucions contingudes en aquest document no només afegeixen el que es coneix sobre el potencial de les tècniques d'encaminament conscients de l'energia, sinó que també representen una valuosa solució en el camí cap a una xarxa sostenibl