Property-preserving subnet reductions for designing manufacturing systems with shared resources

AbstractThis paper handles two problems in manufacturing system design: resource sharing and system abstraction. In a manufacturing system, resources such as robots, machines, etc. are shared by several processes. When the resources are switched from one process to another, they may need some modifications such as cleaning oil, adding equipments and so on. Previous designing methods assume that the resources have no intermediate modifications. Hence, they need to be extended to handle such kinds of resource-sharing problems. As for abstraction, modeling operations with single places in manufacturing system design is very popular. From the viewpoint of verification, the objective is to verify whether the reduced model has the same desirable properties as the original one. This paper presents three kinds of property-preserving subnet reduction methods. For each reduction method, conditions are presented for ensuring that the properties liveness, boundedness and reversibility are preserved. Applications of these reduction methods to handling the above resource sharing and system abstraction problems are illustrated with an example from the manufacturing system

Investigating photoexcitation-induced mitochondrial damage by chemotherapeutic corroles using multimode optical imaging

We recently reported that a targeted, brightly fluorescent gallium corrole (HerGa) is highly effective for breast tumor detection and treatment. Unlike structurally similar porphryins, HerGa exhibits tumor-targeted toxicity without the need for photoexcitation. We have now examined whether photoexcitation further modulates HerGa toxicity, using multimode optical imaging of live cells, including two-photon excited fluorescence, differential interference contrast (DIC), spectral, and lifetime imaging. Using two-photon excited fluorescence imaging, we observed that light at specific wavelengths augments the HerGa-mediated mitochondrial membrane potential disruption of breast cancer cells in situ. In addition, DIC, spectral, and fluorescence lifetime imaging enabled us to both validate cell damage by HerGa photoexcitation and investigate HerGa internalization, thus allowing optimization of light dose and timing. Our demonstration of HerGa phototoxicity opens the way for development of new methods of cancer intervention using tumor-targeted corroles

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

Synthesis of asynchronous controllers using integer linear programming

A novel strategy for the logic synthesis of asynchronous control circuits is presented. It is based on the structural theory of Petri nets and integer linear programming. Techniques that are capable of checking implementability conditions, such as complete state coding, and deriving a gate netlist to implement the specified behavior are presented. These techniques can handle Petri net specifications consisting of several thousands of transitions and provide a significant speed-up compared with techniques that have previously been proposed.Peer ReviewedPostprint (published version

A role in pH homeostasis regulation by genes related to Neurodevelopmental Disorders: TBC1D24 and ATP6V1A.

TBC1D24 is a gene mutated in a spectrum of neurodevelopmental disorders, from mild epilepsy to severe epileptic encephalopathy. TBC1D24 is involved in brain development, synaptic vesicle trafficking and synaptic function; yet the molecular mechanisms mediating these roles and their relationship to brain dysfunction are largely unknown. TBC1D24 is unique in containing conserved TBC and TLDc domains; importantly, TLDc proteins have been recently described as interactors of the essential complex of V-ATPase. V-ATPase is a multisubunit proton pump that acidifies intracellular organelles through the hydrolysis of ATP. In this thesis, we aimed to explore the interaction between Tbc1d24 and V-ATPase and its physio-pathological role in neuronal cells. We found that Tbc1d24 interacts with the V-ATPase V1 cytosolic domain subunits ATP6V1A and ATP6V1B2 in the brain. By employing a mouse model of chronic loss of Tbc1d24, we demonstrated that loss of Tbc1d24 led to a cytosolic shift of ATP6V1A and ATP6V1B2 subunits, suggesting an unproper assembly state of the complex. This phenotype was accompanied by the alteration of intracellular organelles acidification with increased pH and impairment of autophagic flux. Given the localization of Tbc1d24 at synaptic sites and the relevance of V-ATPase proton pumping activity in synaptic vesicles, we evaluated synaptic ultrastructure and synaptic vesicles acidification. In lack of Tbc1d24, presynaptic compartments showed fewer synaptic vesicles and the accumulation of aberrant endosomal-like structures that engulfed the pre-synapse. Moreover, we found an increased luminal pH of synaptic vesicles. Concurrently, in collaboration with the group of Professor Guerrini (Meyer Hospital, Florence) we identified de novo mutations in ATP6V1A in patients affected by epileptic encephalopathy with different severity. We characterized patients’ fibroblasts finding that pathogenic mutations can alter protein stability and the overall functionality of V-ATPase complex, leading to alterations in the endo-lysosomal pH. Ultrastructural analysis of patients’ fibroblasts and patients-derived iNeurons revealed the presence of aberrant lysosomes engulfed with different non-degraded materials, a typical hallmark of lysosomal diseases. All together these findings uncover a novel function for Tbc1d24 as regulator of V-ATPase activity and suggest pH dysregulation as key cellular mechanism that possibly underpin the pathogenesis in TBC1D24- and ATP6V1A-associated disorders

Contributions to the deadlock problem in multithreaded software applications observed as Resource Allocation Systems

Desde el punto de vista de la competencia por recursos compartidos sucesivamente reutilizables, se dice que un sistema concurrente compuesto por procesos secuenciales está en situación de bloqueo si existe en él un conjunto de procesos que están indefinidamente esperando la liberación de ciertos recursos retenidos por miembros del mismo conjunto de procesos. En sistemas razonablemente complejos o distribuidos, establecer una política de asignación de recursos que sea libre de bloqueos puede ser un problema muy difícil de resolver de forma eficiente. En este sentido, los modelos formales, y particularmente las redes de Petri, se han ido afianzando como herramientas fructíferas que permiten abstraer el problema de asignación de recursos en este tipo de sistemas, con el fin de abordarlo analíticamente y proveer métodos eficientes para la correcta construcción o corrección de estos sistemas. En particular, la teoría estructural de redes de Petri se postula como un potente aliado para lidiar con el problema de la explosión de estados inherente a aquéllos. En este fértil contexto han florecido una serie de trabajos que defienden una propuesta metodológica de diseño orientada al estudio estructural y la correspondiente corrección física del problema de asignación de recursos en familias de sistemas muy significativas en determinados contextos de aplicación, como el de los Sistemas de Fabricación Flexible. Las clases de modelos de redes de Petri resultantes asumen ciertas restricciones, con significado físico en el contexto de aplicación para el que están destinadas, que alivian en buena medida la complejidad del problema. En la presente tesis, se intenta acercar ese tipo de aproximación metodológica al diseño de aplicaciones software multihilo libres de bloqueos. A tal efecto, se pone de manifiesto cómo aquellas restricciones procedentes del mundo de los Sistemas de Fabricación Flexible se muestran demasiado severas para aprehender la versatilidad inherente a los sistemas software en lo que respecta a la interacción de los procesos con los recursos compartidos. En particular, se han de resaltar dos necesidades de modelado fundamentales que obstaculizan la mera adopción de antiguas aproximaciones surgidas bajo el prisma de otros dominios: (1) la necesidad de soportar el anidamiento de bucles no desplegables en el interior de los procesos, y (2) la posible compartición de recursos no disponibles en el arranque del sistema pero que son creados o declarados por un proceso en ejecución. A resultas, se identifica una serie de requerimientos básicos para la definición de un tipo de modelos orientado al estudio de sistemas software multihilo y se presenta una clase de redes de Petri, llamada PC2R, que cumple dicha lista de requerimientos, manteniéndose a su vez respetuosa con la filosofía de diseño de anteriores subclases enfocadas a otros contextos de aplicación. Junto con la revisión e integración de anteriores resultados en el nuevo marco conceptual, se aborda el estudio de propiedades inherentes a los sistemas resultantes y su relación profunda con otros tipos de modelos, la confección de resultados y algoritmos eficientes para el análisis estructural de vivacidad en la nueva clase, así como la revisión y propuesta de métodos de resolución de los problemas de bloqueo adaptadas a las particularidades físicas del dominio de aplicación. Asimismo, se estudia la complejidad computacional de ciertas vertientes relacionadas con el problema de asignación de recursos en el nuevo contexto, así como la traslación de los resultados anteriormente mencionados sobre el dominio de la ingeniería de software multihilo, donde la nueva clase de redes permite afrontar problemas inabordables considerando el marco teórico y las herramientas suministradas para subclases anteriormente explotadas

Dynamic Protocol Reverse Engineering a Grammatical Inference Approach

Round trip engineering of software from source code and reverse engineering of software from binary files have both been extensively studied and the state-of-practice have documented tools and techniques. Forward engineering of protocols has also been extensively studied and there are firmly established techniques for generating correct protocols. While observation of protocol behavior for performance testing has been studied and techniques established, reverse engineering of protocol control flow from observations of protocol behavior has not received the same level of attention. State-of-practice in reverse engineering the control flow of computer network protocols is comprised of mostly ad hoc approaches. We examine state-of-practice tools and techniques used in three open source projects: Pidgin, Samba, and rdesktop . We examine techniques proposed by computational learning researchers for grammatical inference. We propose to extend the state-of-art by inferring protocol control flow using grammatical inference inspired techniques to reverse engineer automata representations from captured data flows. We present evidence that grammatical inference is applicable to the problem domain under consideration

CANCER TREATMENT BY TARGETING HDAC4 TRANSLOCATION INDUCED BY MICROSECOND PULSED ELECTRIC FIELD EXPOSURE: MECHANISTIC INSIGHTS THROUGH KINASES AND PHOSPHATASES

Epigenetic modifications, arising from sub-cellular shifts in histone deacetylase (HDAC) activity and localization, present promising strategies for diverse cancer treatments. HDACs, enzymes responsible for post-translational histone modifications, induce these epigenetic changes by removing acetyl groups from ε-N-acetyl-lysine residues on histones, thereby suppressing gene transcription. Within the HDAC group, class IIa HDACs are notable for their responsiveness to extracellular signals, bridging the gap between external stimuli, plasma membrane, and genome through nuclear-cytoplasmic translocation. This localization offers two significant mechanisms for cancer treatment: nuclear accumulation of HDACs represses oncogenic transcription factors, such as myocyte-specific enhancer factor 2C (MEF2C), triggering various cell death pathways. Conversely, cytoplasmic HDAC accumulation acts similarly to HDAC inhibitors by silencing genes. My dissertation introduces an innovative approach for glioblastoma and breast cancer treatment by investigating the application of microsecond pulsed electric fields. It particularly focuses on HDAC4, a class IIa HDAC overexpressed in these cancers. Beyond demonstrating HDAC4 translocation, my research delves into the intricate roles of kinases and phosphatases, shedding light on the underlying factors governing HDAC4 translocation

Production of gelatin methacrylate printable bioinks for cancer cells studies

In questo elaborato è presentato uno studio volto alla produzione di hydrogels semisintetici, a base di gelatina di origine animale funzionalizzata con gruppi metacrilici, utilizzabili come inchiostri biocompatibili per la stampa con tecnologie di micro estrusione di matrici tridimensionali, ottimizzate nella forma e nelle dimensioni per studi sul comportamento di cellule tumorali di Neuroblastoma

Modeling Autonomous Agents In Military Simulations

Simulation is an important tool for prediction and assessment of the behavior of complex systems and situations. The importance of simulation has increased tremendously during the last few decades, mainly because the rapid pace of development in the field of electronics has turned the computer from a costly and obscure piece of equipment to a cheap ubiquitous tool which is now an integral part of our daily lives. While such technological improvements make it easier to analyze well-understood deterministic systems, increase in speed and storage capacity alone are not enough when simulating situations where human beings and their behavior are an integral part of the system being studied. The problem with simulation of intelligent entities is that intelligence is still not well understood and it seems that the field of Artificial Intelligence (AI) has a long way to go before we get computers to think like humans. Behavior-based agent modeling has been proposed in mid-80\u27s as one of the alternatives to the classical AI approach. While used mainly for the control of specialized robotic vehicles with very specific sensory capabilities and limited intelligence, we believe that a behavior-based approach to modeling generic autonomous agents in complex environments can provide promising results. To this end, we are investigating a behavior-based model for controlling groups of collaborating and competing agents in a geographic terrain. In this thesis, we are focusing on scenarios of military nature, where agents can move within the environment and adversaries can eliminate each other through use of weapons. Different aspects of agent behavior like navigation to a goal or staying in group formation, are implemented by distinct behavior modules and the final observed behavior for each agent is an emergent property of the combination of simple behaviors and their interaction with the environment. Our experiments show that while such an approach is quite efficient in terms of computational power, it has some major drawbacks. One of the problems is that reactive behavior-based navigation algorithms are not well suited for environments with complex mobility constraints where they tend to perform much worse than proper path planning. This problem represents an important research question, especially when it is considered that most of the modern military conflicts and operations occur in urban environments. One of the contributions of this thesis is a novel approach to reactive navigation where goals and terrain information are fused based on the idea of transforming a terrain with obstacles into a virtual obstacle-free terrain. Experimental results show that our approach can successfully combine the low run-time computational complexity of reactive methods with the high success rates of classical path planning. Another interesting research problem is how to deal with the unpredictable nature of emergent behavior. It is not uncommon to have situations where an outcome diverges significantly from the intended behavior of the agents due to highly complex nonlinear interactions with other agents or the environment itself. Chances of devising a formal way to predict and avoid such abnormalities are slim at best, mostly because such complex systems tend to be be chaotic in nature. Instead, we focus on detection of deviations through tracking group behavior which is a key component of the total situation awareness capability required by modern technology-oriented and network-centric warfare. We have designed a simple and efficient clustering algorithm for tracking of groups of agent suitable for both spatial and behavioral domain. We also show how to detect certain events of interest based on a temporal analysis of the evolution of discovered clusters