From theory to modelling : urban systems as complex systems

The question of complexity and its increasing application to social sciences is challenging the modelling of spatial systems. New concepts and new methods have been proposed and invite to reformulate classical modelling frames. This approach is demanding to open a better informed dialogue between the disciplines which supply models and tools and those where the existing knowledge is reformulated inside this new frame. Actually, creating an « artificial geography » is not straightforward. It is rather easy to translate urban theories within the paradigm of complex systems, but their modelling, for instance by using multi-agents systems, still raises many conceptual and practical difficulties. We underline here some problems in defining significant urban entities and exploring the evolution of their spatial relationships over time. We briefly present which options have been selected for developing the SIMPOP2 model which is conceived for simulating the evolution of systems of cities over long periods of time.La modélisation des systèmes spatiaux se confronte aux théories de la complexité et à leurs applications en sciences sociales. De nouveaux concepts et de nouvelles méthodes sont proposés, qui invitent à reformuler les modèles classiques. Cette démarche suppose d'ouvrir un dialogue mieux informé entre les disciplines qui offrent les modèles et les outils et celles qui tentent de reformuler leurs connaissances dans ce nouveau cadre. En effet, la création d'une « géographie artificielle » ne va pas de soi. S'il est relativement aisé de traduire les théories urbaines en termes de systèmes complexes, leur modélisation, par exemple au moyen de systèmes multi-agents, soulève encore de nombreuses difficultés conceptuelles et pratiques. Nous insistons notamment sur la définition des entités urbaines et sur les variations de leurs relations dans l'espace au cours du temps. Nous présentons enfin rapidement les principales options retenues pour le modèle SIMPOP2 conçu pour simuler le devenir des systèmes de villes dans la longue durée

East-West Paths to Unconventional Computing

Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured. This article includes idiosyncratic accounts of ‘unconventional computing’ scientists reflecting on their personal experiences, what attracted them to the field, their inspirations and discoveries.info:eu-repo/semantics/publishedVersio

Unraveling the Reaction Mechanism of Industrial Processes in Zeolite Catalysis: a Quantum Chemical Approach

Even though acidic zeolites form a crucial catalyst for many petrochemical processes, much of their fundamental reactive behavior is only superficially understood. Most often, catalysts are proposed on an 'ad hoc' basis, without a detailed understanding of their functioning on an atomic scale. It can indeed be difficult to identify the elementary steps of complex reaction networks from a purely experimental basis. For these issues, quantum chemical molecular modeling techniques provide an excellent complementary tool to laboratory data. This relatively new field of research has seen an enormous surge in popularity, mainly because of the rapid increase in computer power and the development of sufficiently accurate theoretical methods, which together make it possible now to model complex industrial processes. In this thesis, we use these modeling techniques for a detailed study on elementary reaction steps in zeolite catalysis.This summary gives only a very short overview of the work, and the interested reader is referred to the more elaborate full text or, for even more detail, to the research articles on which it is based, which are also included at the end of each relevant chapter. In a preparatory chapter, several general terms and methods used throughout the thesis are introduced. First, two fundamental characteristics of zeolites that are vital in industrial catalysis - the topologically induced shape selectivity and the isomorphic substitution leading to a Bronsted acid site - are briefly explained. Then, the practical aspects of quantum chemical modeling of zeolites are discussed, with special attention given to the model space approximations that are necessary for such extended systems. Chemical reactions need to be modeled by computationally very demanding quantum chemical methods if we are to describe the changes in electronic binding pattern appropriately. Different approximations are possible, with an increase in accuracy usually accompanied by an increase in computational cost. Since zeolites are extended materials with a large number of atoms, a complete and accurate quantum chemical description of the entire system is not only extraordinarily demanding but also, at the moment at least, simply not feasible. This issue has, however, led to the development recently of some advanced techniques that do allow an accurate description of at least the chemically active part of the system. Finally, since in this thesis the most important conclusions are based on rate coefficients, the basics of chemical kinetics are also introduced, describing the molecular-scale calculation of macroscopic quantities using transition state theory. Subsequently one of the most intriguing substantive problems in heterogeneous catalysis is tackled: the reaction mechanism of the methanol-to-olefin process (MTO). First, a whole class of reaction mechanisms, the so-called direct mechanisms, are investigated, for which initial C-C coupling is taken to occur from C1 species only. Earlier theoretical studies tended to be fragmentary, typically investigating only a single reaction step rather than a complete pathway. Nevertheless, the existence of these individual reaction steps was often considered theoretical evidence for the direct proposal, even though no one had succeeded in defining a complete low-energy pathway. To resolve this complex issue, an extensive reaction scheme is presented in this thesis, including all the possible pathways and their constituent elementary reaction steps on a consistent basis. By combining the individual steps, it is demonstrated that the direct mechanism concept cannot explain the initial C-C coupling. Three bottlenecks are identified: - the instability of ylide and carbene intermediates, - the extremely slow conversion of a methane/formaldehyde mixture to ethanol, and - the excessively high energy barriers for concerted C-C coupling steps. Any alternative proposal, like the up-and-coming 'hydrocarbon pool' hypothesis, needs to provide C-C coupling steps that circumvent these bottlenecks. The hydrocarbon pool model states that organic species trapped in the zeolite pores serve as building platforms, to which C1 species can attach methyl groups. The methylated species subsequently undergoes specific rearrangements and/or additional methylation steps, to finally split off light olefins. The original molecule is then regenerated by additional methylation steps. This way, the highly activated steps of the direct mechanisms could be bypassed. In this thesis, the initiating methylation (and at the same time C-C coupling) step is investigated. The results shed new light on the role of the zeolite framework in this process, and also in how the organic species and the inorganic zeolite cooperate as a supramolecular catalyst. The supramolecular picture is extended here by the explicit inclusion of previously omitted aspects like transition state shape selectivity and electronic stabilization of vital cationic intermediates by the zeolite framework. We should definitely look beyond pure geometrical aspects since electronic embedding plays an equally important role. Additional insight into the hydrocarbon pool hypothesis is, however, required for a guided optimization of the catalyst. A first step to catalyst improvement has already been made by investigating the effect that small organic groups built into the catalyst might have on the elementary reaction steps. Two such modifications - methylene and amine moieties that are iso-electronic with oxygen - are theoretically investigated here. The methylene moiety is one of the simplest organic groups that fits perfectly as a bridge between two silicon atoms to form the functional Si-CH2-Si group. Even though such mesoporous organosilicate materials have been successfully synthesized before, only recently has a research team been able to synthesize methylene-substituted alumino-silicate zeolites. They failed to explain the observed framework defects, though, like the presence of end-standing Si-CH3 groups. In this thesis the influence of the methylene moiety on fundamental adsorption properties is discussed for both neutral probe molecules and charge compensating cations. Additionally, we demonstrate how the combination of aluminum atoms (plus a Bronsted acid proton) with a methylene moiety will inevitably lead to protonation of the organic group and subsequent cleavage of the framework. For similar amine-functionalized zeolites, this thesis also shows that protonation of the amine group will not necessarily lead to cleavage of the zeolite structure. Furthermore, Si-NH-Si moieties will provide additional basic sites, comparable to traditional Al-O-Si sites but not constrained to the aluminum tetrahedron. This enables more proton locations as well as the possibility of more favorable transition state geometries. This can result in a drastic reduction in energy barrier for those reactions which would otherwise have a highly strained transition state. Summarizing, we demonstrate how small organic modifications to the zeolite framework can have a considerable effect on the fundamental catalytic properties and MTO-related reactivity. However, neither methylene nor amine groups can be located on the aluminum tetrahedron without being automatically protonated, which in the case of methylene-modified zeolites even results in cleavage of the framework. This thesis shows very clearly how theoretical modeling is capable of providing new insights into zeolite catalysis. The applications presented here are already located near the limits of what is currently feasible, considering computer power, method development and the current lack of insights into the possible supramolecular character of the system. The rapid evolution in this field of research, even within the timescale of this thesis, makes it as good as certain that further significant advances will soon be within reach, and the thesis closes with the identification of our high-priority research goals for the immediate future. Especially in identification of elementary reaction steps and optimization of the catalyst, there are still quite some challenges ahead

Community and Identity in Contemporary Technosciences

This open access edited book provides new thinking on scientific identity formation. It thoroughly interrogates the concepts of community and identity, including both historical and contemporaneous analyses of several scientific fields. Chapters examine whether, and how, today’s scientific identities and communities are subject to fundamental changes, reacting to tangible shifts in research funding as well as more intangible transformations in our society’s understanding and expectations of technoscience. Authors: Karen Kastenhofer, Susan Molyneux-Hodgson, Clemens Blümel, Bettina Bock von Wülfingen, Béatrice Cointe, Carlos Cuevas-Garcia, Sarah R Davies, Alexander Degelsegger-Márquez, Juliane Jarke, Pierre-Benoît Joly, Marianne Noël, Benjamin Raimbault, Andrea Schikowitz, Sarah M. Schönbauer, Inga Ulnicane-Ozolina, Caitlin D. WylieDer vorgelegte Open Access Band befasst sich mit Identität und Gemeinschaft in den TechnoWissenschaften. Er widmet sich wesentlichen soziologischen Konzepten und präsentiert sowohl historische, als auch aktuelle Fallbeispiele, darunter Supramolekulare Chemie, Synthetische Biologie, Nanotechnologie und Nachhaltigkeitsforschung. AutorInnen: Karen Kastenhofer, Susan Molyneux-Hodgson, Clemens Blümel, Bettina Bock von Wülfingen, Béatrice Cointe, Carlos Cuevas-Garcia, Sarah R Davies, Alexander Degelsegger-Márquez, Juliane Jarke, Pierre-Benoît Joly, Marianne Noël, Benjamin Raimbault, Andrea Schikowitz, Sarah M. Schönbauer, Inga Ulnicane-Ozolina, Caitlin D. Wyli

A MODELING PERSPECTIVE ON DEVELOPING NATURALISTIC NEUROPROSTHETICS USING ELECTRICAL STIMULATION

Direct electrical stimulation of neurons has been an important tool for understanding the brain and neurons, since the field of neuroscience began. Electrical stimulation was used to first understand sensation, the mapping of the brain, and more recently function, and, as our understanding of neurological disorders has advanced, it has become an increasingly important tool for interacting with neurons to design and carry out treatments. The hardware for electrical stimulation has greatly improved during the last century, allowing smaller scale, implantable treatments for a variety of disorders, from loss of sensations (hearing, vision, balance) to Parkinson’s disease and depression. Due to the clinical success of these treatments for a variety of impairments today, there are millions of neural implant users around the globe, and interest in medical implants and implants for human-enhancement are only growing. However, present neural implant treatments restore only limited function compared to natural systems. A limiting factor in the advancement of electrical stimulation-based treatments has been the restriction of using charge-balanced and typically short sub-millisecond pulses in order to safely interact with the brain, due to a reliance on durable, metal electrodes. Material science developments have led to more flexible electrodes that are capable of delivering more charge safely, but a focus has been on density of electrodes implanted over changing the waveform of electrical stimulation delivery. Recently, the Fridman lab at Johns Hopkins University developed the Freeform Stimulation (FS)– an implantable device that uses a microfluidic H-bridge architecture to safely deliver current for prolonged periods of time and that is not restricted to charge-balanced waveforms. In this work, we refer to these non-restricted waveforms as galvanic stimulation, which is used as an umbrella term that encompasses direct current, sinusoidal current, or alternative forms of non-charge-balanced current. The invention of the FS has opened the door to usage of galvanic stimulation in neural implants, begging an exploration of the effects of local galvanic stimulation on neural function. Galvanic stimulation has been used in the field of neuroscience, prior to concerns about safe long-term interaction with neurons. Unlike many systems, it had been historically used in the vestibular system internally and in the form of transcutaneous stimulation to this day. Historic and recent studies confirm that galvanic stimulation of the vestibular system has more naturalistic effects on neural spike timing and on induced behavior (eye velocities) than pulsatile stimulation, the standard in neural implants now. Recent vestibular stimulation studies with pulses also show evidence of suboptimal responses of neurons to pulsatile stimulation in which suprathreshold pulses only induce about half as many action potentials as pulses. This combination of results prompted an investigation of differences between galvanic and pulsatile electrical stimulation in the vestibular system. The research in this dissertation uses detailed biophysical modeling of single vestibular neurons to investigate the differences in the biophysical mechanism of galvanic and pulsatile stimulation. In Chapter 2, a more accurate model of a vestibular afferent is constructed from an existing model, and it is used to provide a theory for how galvanic stimulation produces a number of known effects on vestibular afferents. In Chapter 3, the same model is used to explain why pulsatile stimulation produces fewer action potentials than expected, and the results show that pulse amplitude, pulse rate, and the spontaneous activity of neurons at the axon have a number of interactions that lead to several non-monotonic relationships between pulse parameters and induced firing rate. Equations are created to correct for these non-monotonic relationships and produce intended firing rates. Chapter 4 focuses on how to create a neural implant that induces more naturalistic firing using the scientific understanding from Chapters 2 and 3 and machine learning. The work concludes by describing the implications of these findings for interacting with neurons and population and network scales and how this may make electrical stimulation increasingly more suited for treating complex network-level and psychiatric disorders

Community and Identity in Contemporary Technosciences

This open access edited book provides new thinking on scientific identity formation. It thoroughly interrogates the concepts of community and identity, including both historical and contemporaneous analyses of several scientific fields. Chapters examine whether, and how, today’s scientific identities and communities are subject to fundamental changes, reacting to tangible shifts in research funding as well as more intangible transformations in our society’s understanding and expectations of technoscience. In so doing, this book reinvigorates the concept of scientific community. Readers will discover empirical analyses of newly emerging fields such as synthetic biology, systems biology and nanotechnology, and accounts of the evolution of theoretical conceptions of scientific identity and community. With inspiring examples of technoscientific identity work and community constellations, along with thought-provoking hypotheses and discussion, the work has a broad appeal. Those involved in science governance will benefit particularly from this book, and it has much to offer those in scholarly fields including sociology of science, science studies, philosophy of science and history of science, as well as teachers of science and scientists themselves. ; Reinvigorates the concept of scientific community Delineates ongoing changes across a range of epistemic cultures Elaborates on social, cultural and political aspects of contemporary technoscience Traces historical influences on technoscience, including in the European context Provides new thinking on scientific identity formatio

Collaborating with the Behaving Machine: simple adaptive dynamical systems for generative and interactive music

Situated at the intersection of interactive computer music and generative art, this thesis is inspired by research in Artificial Life and Autonomous Robotics and applies some of the principles and methods of these fields in a practical music context. As such the project points toward a paradigm for computer music research and performance which comple- ments current mainstream approaches and develops upon existing creative applications of Artificial Life research. Many artists have adopted engineering techniques from the field of Artificial Life research as they seem to support a richer interactive experience with computers than is often achieved in digital interactive art. Moreover, the low level aspects of life which the research programme aims to model are often evident in these artistic appropriations in the form of bizarre and abstract but curiously familiar digital forms that somehow, despite their silicon make-up, appear to accord with biological convention. The initial aesthetic motivation for this project was very personal and stemmed from interests in adaptive systems and improvisation and a desire to unite the two. In sim- ple terms, I wanted to invite these synthetic critters up on stage and play with them. There has been some similar research in the musical domain, but this has focused on a very small selection of specific models and techniques which have been predominantly applied as compositional tools rather than for use in live generative music. This thesis considers the advantages of the Alife approach for contemporary computer musicians and offers specific examples of simple adaptive systems as components for both compo- sitional and performance tools. These models have been implemented in a range of generative and interactive works which are described here. These include generative sound installations, interactive instal- lations and a performance system for collaborative man-machine improvisation. Public response at exhibitions and concerts suggests that the approach taken here holds much promise

Identifying the molecular components that matter: a statistical modelling approach to linking functional genomics data to cell physiology

Functional genomics technologies, in which thousands of mRNAs, proteins, or metabolites can be measured in single experiments, have contributed to reshape biological investigations. One of the most important issues in the analysis of the generated large datasets is the selection of relatively small sub-sets of variables that are predictive of the physiological state of a cell or tissue. In this thesis, a truly multivariate variable selection framework using diverse functional genomics data has been developed, characterized, and tested. This framework has also been used to prove that it is possible to predict the physiological state of the tumour from the molecular state of adjacent normal cells. This allows us to identify novel genes involved in cell to cell communication. Then, using a network inference technique networks representing cell-cell communication in prostate cancer have been inferred. The analysis of these networks has revealed interesting properties that suggests a crucial role of directional signals in controlling the interplay between normal and tumour cell to cell communication. Experimental verification performed in our laboratory has provided evidence that one of the identified genes could be a novel tumour suppressor gene. In conclusion, the findings and methods reported in this thesis have contributed to further understanding of cell to cell interaction and multivariate variable selection not only by applying and extending previous work, but also by proposing novel approaches that can be applied to any functional genomics data