Measurements, Models, Systems and Design

531 s.

Industrial Applications: New Solutions for the New Era

This book reprints articles from the Special Issue "Industrial Applications: New Solutions for the New Age" published online in the open-access journal Machines (ISSN 2075-1702). This book consists of twelve published articles. This special edition belongs to the "Mechatronic and Intelligent Machines" section

Computing multi-scale organizations built through assembly

The ability to generate and control assembling structures built over many orders of magnitude is an unsolved challenge of engineering and science. Many of the presumed transformational benefits of nanotechnology and robotics are based directly on this capability. There are still significant theoretical difficulties associated with building such systems, though technology is rapidly ensuring that the tools needed are becoming available in chemical, electronic, and robotic domains. In this thesis a simulated, general-purpose computational prototype is developed which is capable of unlimited assembly and controlled by external input, as well as an additional prototype which, in structures, can emulate any other computing device. These devices are entirely finite-state and distributed in operation. Because of these properties and the unique ability to form unlimited size structures of unlimited computational power, the prototypes represent a novel and useful blueprint on which to base scalable assembly in other domains. A new assembling model of Computational Organization and Regulation over Assembly Levels (CORAL) is also introduced, providing the necessary framework for this investigation. The strict constraints of the CORAL model allow only an assembling unit of a single type, distributed control, and ensure that units cannot be reprogrammed - all reprogramming is done via assembly. Multiple units are instead structured into aggregate computational devices using a procedural or developmental approach. Well-defined comparison of computational power between levels of organization is ensured by the structure of the model. By eliminating ambiguity, the CORAL model provides a pragmatic answer to open questions regarding a framework for hierarchical organization. Finally, a comparison between the designed prototypes and units evolved using evolutionary algorithms is presented as a platform for further research into novel scalable assembly. Evolved units are capable of recursive pairing ability under the control of a signal, a primitive form of unlimited assembly, and do so via symmetry-breaking operations at each step. Heuristic evidence for a required minimal threshold of complexity is provided by the results, and challenges and limitations of the approach are identified for future evolutionary studies

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Dynamics and Effective Connectivity in Bi- and Three–dimensional Neuronal Cultures: from Self–organization to Engineering

[eng] This thesis was part of the European consortium MESOBRAIN, a team of 5 organizations that joined efforts in nanofabrication, cell culturing, imaging and data analysis to build tailored human 3D networks. The thesis timing was limited to 3 years, and several of the resources needed for its development were built from scratch. The main objective of this Ph.D. thesis was to explore complex characteristics of cortical neuronal cultures in terms of effective connectivity and exhaustive network analyses. This objective comprised four research lines: (i) The evaluation of neuronal network resilience and emerging plasticity mechanisms, (ii) the characterization of functional development to underline crucial timepoints in healthy neuronal networks, (iii) the study of 3D network interactions of neurons embedded inside an ECM--like environment, and (iv) the design, construction and viability inspection of neurons seeded on tiny 3D nanoprinted solid scaffold structures as a first step towards recreating cortical columns in vitro. For these multiple lines, we used either primary rat cultures (i,iii,iv) or human--derived neurons (ii). The former group corresponds to cultures with long established protocols that have been thoroughly studied in the field. The latter group corresponds to human neurons derived from iPSCs, a relatively novel model with promising and thrilling applications in regenerative medicine. Despite the increasing use of stem cells in neuroscience, complex systems and medicine, they still lack a thorough exploration in terms of neuronal and circuit formation as well as the properties of the emergent activity patterns. With either primary or stem cells, we explored the formation of neuronal circuits in 2D and 3D, characterized the effective connectivity and rendered a number of network traits. This Thesis combines experiments of highly difficult implementation with detailed data analysis. It was necessary to develop brand new protocols for culturing 3D neuronal networks and for human-derived neurons, the use of different microscopy setups the programming of object detection and tracking software and advance the analysis toolbox of calcium fluorescence data. First, resilience experiments on primary clustered neuronal cultures consisted on progressive perturbations through chemical receptor antagonists. This study represents an inspiring numerical--experimental model to comprehend the impact of plasticity mechanisms in the spontaneous activity of neuronal circuits. The results showed that, upon progressive connectivity blockade through chemical receptors' antagonists, only--excitatory neuronal networks displayed a surprising hyper--efficiency (HE) state for early--onset doses. As plasticity mechanisms influence the response of effective connectivity in the presence of perturbations, these compensatory mechanisms, usually disregarded, must be included in biological modeling as accurately as possible. Otherwise, episodes of functional rewiring and synaptic strengthening could mask important phenomena during experiments that alter channel communication. A simple algorithm that hypothesized an effective synaptic scaling was able to capture the hyper--efficiency state seen in experimental data, while percolation models wrongly predicted a progressive decay. The second research line was a sum of engineering efforts within the MESOBRAIN consortium, the European adventure to build 3D neuronal cultures embedded in hydrogels and with the presence of scaffolds. After several months of biomaterials testing, the candidate D--Clear resulted suitable for the construction of scaffolds, both with primary rat cells and hiPSCs, due to its good optical properties, manageability and biocompatibility. To our knowledge, D--Clear was never used before outside the orthodontic field and could provide a new catalogue of interesting designs for support and guidance of neuronal assemblies. Using this material, we developed a series of designs to offer support and guidance to cortical neurons in a 3D platform. The third research line focused on the study of neuronal development and cell-to-cell interactions in a semi-synthetic hydrogel that resembles the extracellular matrix of the brain. These hydrogel cultures keep the advantages of in vitro models while achieving an effective connectivity and architecture closer to in vivo. Finally, the fourth line of research applied cortical neurons from human-derived pluripotent stem cells to study key developmental stages and characterize the healthy maturation of these cells in vitro. As this technology has tremendous potential for regenerative medicine and to model neuronal diseases, it is urgent to consolidate the capacity of these human neuronal networks to reproduce efficient activity patterns of healthy patients, and explore the differences against the results obtained with animal models.[spa] La presente tesis doctoral se enmarca en el contexto de la Física de la Materia Condensada, la Biofísica y la Neurociencia. Principalmente, se centra en el estudio de la conectividad funcional en cultivos neuronales bidimensionales (2D) y tridimensionales (3D). El trabajo se ha desarrollado en el Laboratorio del director de tesis Dr. Jordi Soriano, en la Facultad de Física de la Universitat de Barcelona, junto con el codirector Dr. Daniel Tornero, en el Hospital Clínic de Barcelona. Esta tesis forma parte del proyecto europeo MESO-BRAIN, del programa Future and Emergent Technologies (FET) de la Comisión Europea, Horizon2020. El trabajo de investigación combina experimentos con cultivos neuronales (de rata embrionaria o células humanas pluripotentes) y un análisis detallado en el contexto de teoría de redes y sistemas complejos. Los principales núcleos del trabajo realizado son los siguientes: (i) Actividad funcional en cultivos de redes neuronales y los mecanismos homeostáticos que emergen en presencia de perturbaciones; (ii) el desarrollo de herramientas de neuroingeniería para preparar cultivos ad hoc con conectividad dirigida mediante scaffolds; (iii) el análisis exhaustivo de los procesos de formación y madurez de redes funcionales humanas obtenidas de células madre pluripotentes inducidas, una nueva tecnología que promete revolucionar el campo de la medicina regenerativa; y (iv) la caracterización de cultivos neuronales 3D en estructuras que imitan la matriz extracelular natural de su entorno. Entre las diversas técnicas para la realización de cultivos tridimensionales, destacan los hidrogeles semi-sintéticos, constituidos en base a polímeros altamente hidratados con alta biocompatibilidad y cuyas propiedades mecánicas pueden ser manipuladas para obtener la estructura óptima según el tipo de tejido. En conjunto, los resultados de la presente tesis muestran la gran versatilidad de los cultivos neuronales y aportan avances relevantes en el estudio de plasticidad en redes neuronales, madurez y desarrollo tanto en 2D como en 3D, con sus correspondientes diferencias, incluyendo el uso de neuronas humanas derivadas de células madre inducidas. En el futuro, estos estudios nos permitirán incrementar nuestro conocimiento sobre el funcionamiento global del cerebro y avanzar en la investigación de diferentes enfermedades neurodegenerativas

Model based test suite minimization using metaheuristics

Software testing is one of the most widely used methods for quality assurance and fault detection purposes. However, it is one of the most expensive, tedious and time consuming activities in software development life cycle. Code-based and specification-based testing has been going on for almost four decades. Model-based testing (MBT) is a relatively new approach to software testing where the software models as opposed to other artifacts (i.e. source code) are used as primary source of test cases. Models are simplified representation of a software system and are cheaper to execute than the original or deployed system. The main objective of the research presented in this thesis is the development of a framework for improving the efficiency and effectiveness of test suites generated from UML models. It focuses on three activities: transformation of Activity Diagram (AD) model into Colored Petri Net (CPN) model, generation and evaluation of AD based test suite and optimization of AD based test suite. Unified Modeling Language (UML) is a de facto standard for software system analysis and design. UML models can be categorized into structural and behavioral models. AD is a behavioral type of UML model and since major revision in UML version 2.x it has a new Petri Nets like semantics. It has wide application scope including embedded, workflow and web-service systems. For this reason this thesis concentrates on AD models. Informal semantics of UML generally and AD specially is a major challenge in the development of UML based verification and validation tools. One solution to this challenge is transforming a UML model into an executable formal model. In the thesis, a three step transformation methodology is proposed for resolving ambiguities in an AD model and then transforming it into a CPN representation which is a well known formal language with extensive tool support. Test case generation is one of the most critical and labor intensive activities in testing processes. The flow oriented semantic of AD suits modeling both sequential and concurrent systems. The thesis presented a novel technique to generate test cases from AD using a stochastic algorithm. In order to determine if the generated test suite is adequate, two test suite adequacy analysis techniques based on structural coverage and mutation have been proposed. In terms of structural coverage, two separate coverage criteria are also proposed to evaluate the adequacy of the test suite from both perspectives, sequential and concurrent. Mutation analysis is a fault-based technique to determine if the test suite is adequate for detecting particular types of faults. Four categories of mutation operators are defined to seed specific faults into the mutant model. Another focus of thesis is to improve the test suite efficiency without compromising its effectiveness. One way of achieving this is identifying and removing the redundant test cases. It has been shown that the test suite minimization by removing redundant test cases is a combinatorial optimization problem. An evolutionary computation based test suite minimization technique is developed to address the test suite minimization problem and its performance is empirically compared with other well known heuristic algorithms. Additionally, statistical analysis is performed to characterize the fitness landscape of test suite minimization problems. The proposed test suite minimization solution is extended to include multi-objective minimization. As the redundancy is contextual, different criteria and their combination can significantly change the solution test suite. Therefore, the last part of the thesis describes an investigation into multi-objective test suite minimization and optimization algorithms. The proposed framework is demonstrated and evaluated using prototype tools and case study models. Empirical results have shown that the techniques developed within the framework are effective in model based test suite generation and optimizatio

Dynamics of embodied dissociated cortical cultures for the control of hybrid biological robots.

The thesis presents a new paradigm for studying the importance of interactions between an organism and its environment using a combination of biology and technology: embodying cultured cortical neurons via robotics. From this platform, explanations of the emergent neural network properties leading to cognition are sought through detailed electrical observation of neural activity. By growing the networks of neurons and glia over multi-electrode arrays (MEA), which can be used to both stimulate and record the activity of multiple neurons in parallel over months, a long-term real-time 2-way communication with the neural network becomes possible. A better understanding of the processes leading to biological cognition can, in turn, facilitate progress in understanding neural pathologies, designing neural prosthetics, and creating fundamentally different types of artificial cognition. Here, methods were first developed to reliably induce and detect neural plasticity using MEAs. This knowledge was then applied to construct sensory-motor mappings and training algorithms that produced adaptive goal-directed behavior. To paraphrase the results, most any stimulation could induce neural plasticity, while the inclusion of temporal and/or spatial information about neural activity was needed to identify plasticity. Interestingly, the plasticity of action potential propagation in axons was observed. This is a notion counter to the dominant theories of neural plasticity that focus on synaptic efficacies and is suggestive of a vast and novel computational mechanism for learning and memory in the brain. Adaptive goal-directed behavior was achieved by using patterned training stimuli, contingent on behavioral performance, to sculpt the network into behaviorally appropriate functional states: network plasticity was not only induced, but could be customized. Clinically, understanding the relationships between electrical stimulation, neural activity, and the functional expression of neural plasticity could assist neuro-rehabilitation and the design of neuroprosthetics. In a broader context, the networks were also embodied with a robotic drawing machine exhibited in galleries throughout the world. This provided a forum to educate the public and critically discuss neuroscience, robotics, neural interfaces, cybernetics, bio-art, and the ethics of biotechnology.Ph.D.Committee Chair: Steve M. Potter; Committee Member: Eric Schumacher; Committee Member: Robert J. Butera; Committee Member: Stephan P. DeWeerth; Committee Member: Thomas D. DeMars

Embedded System Design

A unique feature of this open access textbook is to provide a comprehensive introduction to the fundamental knowledge in embedded systems, with applications in cyber-physical systems and the Internet of things. It starts with an introduction to the field and a survey of specification models and languages for embedded and cyber-physical systems. It provides a brief overview of hardware devices used for such systems and presents the essentials of system software for embedded systems, including real-time operating systems. The author also discusses evaluation and validation techniques for embedded systems and provides an overview of techniques for mapping applications to execution platforms, including multi-core platforms. Embedded systems have to operate under tight constraints and, hence, the book also contains a selected set of optimization techniques, including software optimization techniques. The book closes with a brief survey on testing. This fourth edition has been updated and revised to reflect new trends and technologies, such as the importance of cyber-physical systems (CPS) and the Internet of things (IoT), the evolution of single-core processors to multi-core processors, and the increased importance of energy efficiency and thermal issues

Embedded System Design

A unique feature of this open access textbook is to provide a comprehensive introduction to the fundamental knowledge in embedded systems, with applications in cyber-physical systems and the Internet of things. It starts with an introduction to the field and a survey of specification models and languages for embedded and cyber-physical systems. It provides a brief overview of hardware devices used for such systems and presents the essentials of system software for embedded systems, including real-time operating systems. The author also discusses evaluation and validation techniques for embedded systems and provides an overview of techniques for mapping applications to execution platforms, including multi-core platforms. Embedded systems have to operate under tight constraints and, hence, the book also contains a selected set of optimization techniques, including software optimization techniques. The book closes with a brief survey on testing. This fourth edition has been updated and revised to reflect new trends and technologies, such as the importance of cyber-physical systems (CPS) and the Internet of things (IoT), the evolution of single-core processors to multi-core processors, and the increased importance of energy efficiency and thermal issues