Randomly Evolving Idiotypic Networks: Structural Properties and Architecture

We consider a minimalistic dynamic model of the idiotypic network of B-lymphocytes. A network node represents a population of B-lymphocytes of the same specificity (idiotype), which is encoded by a bitstring. The links of the network connect nodes with complementary and nearly complementary bitstrings, allowing for a few mismatches. A node is occupied if a lymphocyte clone of the corresponding idiotype exists, otherwise it is empty. There is a continuous influx of new B-lymphocytes of random idiotype from the bone marrow. B-lymphocytes are stimulated by cross-linking their receptors with complementary structures. If there are too many complementary structures, steric hindrance prevents cross-linking. Stimulated cells proliferate and secrete antibodies of the same idiotype as their receptors, unstimulated lymphocytes die. Depending on few parameters, the autonomous system evolves randomly towards patterns of highly organized architecture, where the nodes can be classified into groups according to their statistical properties. We observe and describe analytically the building principles of these patterns, which allow to calculate number and size of the node groups and the number of links between them. The architecture of all patterns observed so far in simulations can be explained this way. A tool for real-time pattern identification is proposed.Comment: 19 pages, 15 figures, 4 table

Studies on the dynamics of chaotic multi-wavelet reentrant propagation using a hybrid cellular automaton model of excitable tissue

There is a compelling body of evidence implicating continuous propagation (reentry) sustained by multiple meandering wavelets in the pathology of advanced human atrial fibrillation (AF). This forms the basis for many current therapies such as the Cox MAZE procedure and its derivatives, which aim to create non-conducting lesions in order to "transect" these circuits before they form. Nevertheless, our ability to successfully treat persistent and permanent AF using catheter ablation remains inadequate due to current limitations of clinical mapping technology as well as an incomplete understanding of how to place lesions in order to maximize circuit transection and, more importantly, minimize AF burden. Here, we used a hybrid cellular automaton model to study the dynamics of chaotic, multi-wavelet reentry (MWR) in excitable tissue. First, we used reentry as an exemplar to investigate a hysteretic disease mechanism in a multistable nonlinear system. We found that certain interactions with the environment can cause persistent changes to system behavior without altering its structure or properties, thus leading to a disconnect between clinical symptoms and the underlying state of disease. Second, we developed a novel analytical method to characterize the spatiotemporal dynamics of MWR. We identified a heterogeneous spatial distribution of reentrant pathways that correlated with the spatial distribution of cell activation frequencies. Third, we investigated the impact of topological and geometrical substrate alterations on the dynamics of MWR. We demonstrated a multi-phasic relationship between obstacle size and the fate of individual episodes. Notably, for a narrow range of sizes, obstacles appeared to play an active role in rapidly converting MWR to stable structural reentry. Our studies indicate that reentrant-pathway distributions are non-uniform in heterogeneous media (such as the atrial myocardium) and suggest a clinically measurable correlate for identifying regions of high circuit density, supporting the feasibility of patient-specific targeted ablation. Moreover, we have elucidated the key mechanisms of interaction between focal obstacles and MWR, which has implications for the use of spot ablation to treat AF as some recent studies have suggested

GPU Accelerated Approach to Numerical Linear Algebra and Matrix Analysis with CFD Applications

A GPU accelerated approach to numerical linear algebra and matrix analysis with CFD applications is presented. The works objectives are to (1) develop stable and efficient algorithms utilizing multiple NVIDIA GPUs with CUDA to accelerate common matrix computations, (2) optimize these algorithms through CPU/GPU memory allocation, GPU kernel development, CPU/GPU communication, data transfer and bandwidth control to (3) develop parallel CFD applications for Navier Stokes and Lattice Boltzmann analysis methods. Special consideration will be given to performing the linear algebra algorithms under certain matrix types (banded, dense, diagonal, sparse, symmetric and triangular). Benchmarks are performed for all analyses with baseline CPU times being determined to find speed-up factors and measure computational capability of the GPU accelerated algorithms. The GPU implemented algorithms used in this work along with the optimization techniques performed are measured against preexisting work and test matrices available in the NIST Matrix Market. CFD analysis looked to strengthen the assessment of this work by providing a direct engineering application to analysis that would benefit from matrix optimization techniques and accelerated algorithms. Overall, this work desired to develop optimization for selected linear algebra and matrix computations performed with modern GPU architectures and CUDA developer which were applied directly to mathematical and engineering applications through CFD analysis

Design domains: their relations and transformations as revealed through the practice of Paul Minifie

This thesis is a reflective account of a series of architectural design projects completed by the author. It seeks to outline the constructive concepts and methodological approaches involved in their production. It begins by positing that architectural design always occurs within a particular design domain – defined by a limited and internally consistent set of elements and operations that can be combined to construct building instances. It is proposed that particular organisational techniques structure a design domain such that the set of architectural instances comprising that domain are quite distinct. For example, geometric ideas such as cellular automata, minimal surfaces or voronoi tessellations possess inherent relationships that can lead to an ordering of building elements quite different from and incommensurable with the kind of arrangements that might derive from working with a more familiar Cartesian gridded space. A specific building instance belonging to a design domain is realised as a traversal across that domain – the performance of a particular sequence of operations within its given rules and structures. Analogous to composition, a traversal yields a particular assemblage of qualities and attributes in a building and enables a project to posses a valency - that is, the ability to form plausible associations and connections outside itself. This mapping between elements and properties of a building instance and some object or phenomena external to it is discussed in the thesis as an injection. An examination of the projects shows a preference for multiple over singular mappings as this opens the possibility to destabilise the context of the thing to which a connection is made. Informed by an examination of the workings of computational geometries, the projects comprise a speculation on how those workings might re-propose architectural themes and transform architectural effects. Put loosely, they propose that operations and methods intrinsic to computation can reformulate, in positive and sometimes unexpected ways, deep-seated patterns of architectural thinking. This kind of investigation, as an architect, into computational methods also reformulates the usual narrow frame of discussion of computation in design. It assumes a vantage point where a computation is no longer directly concerned with instrumental issues of problem solving, optimisation or connectivity. Rather, the methods of achieving these things are selectively picked over and re-purposed to illuminate thematic architectural concerns. The notion of the ‘Techne Trouve’ arises here as an approach employing this re-purposing. The projects ultimately seek to make sense in the broad context of the discipline of architecture. The examination of concepts from mathematics, computing, economics and biology are pursued as a means to understand architectural motivations and intentions

Spatial Interaction of Agricultural Land Uses and their Impacts on Ecosystem Service Provision at the Landscape Scale

The relationship between agricultural land use and it impact on ecosystem services, including nutrient cycling and biodiversity conservation, is extremely complex. This complexity has been augmented by isolated research on the impact of agriculture land uses on the landscape's capacity to provide ecosystem services (ES) particularly in most vulnerable areas of Sub-Saharan Africa. Though a considerable number of studies emphasize the nexus between specific land use types and their impact on N-deposition across agriculture landscapes, a sufficient modeling basis for an empirical consideration of spatial interactions between different agricultural land use types at the landscape scale across rural-urbanizing areas in Sub-Saharan Africa is consistently missing. In view of this, the motivation to understand, assess and address significant roles that size, shape, spatial location, and interactivity of different land use patch types play in assessing land use interactions and their impact on ecosystem service provision and the overall landscape resilience necessitated the core of this PhD thesis. This thesis aimed at finding answers to the question of which assessment framework could be employed to understand the interaction of land use types and their impact on ecosystem services, the present thesis introduces a semi-quantitative assessment framework implemented in the GISCAME suite to provide scientific and practical answers to this question. Ahead of the framework development, a thorough review of land use planning documents from selected countries within the WASCAL project area to uncover the key relevance government places on incorporating the ES concept was undertaken. This was with the view that mentioning the concept in such legal document alone does not suggest its relevance if road maps for their implementation is not sufficiently provided, with laid down institutional provisions, roles, responsibilities, support systems and commitments. The outcome of this objective significantly influenced the subsequent objectives of this thesis. Subsequently, I employed Voronoi tessellation and midpoint displacement algorithms implemented in the Structure Generator (SG4GISCAME) to generate alternative land use mosaics to mimic the patchy agricultural landscape character of the study area. The key objective here was to present the output of this alternative landscape as a partial solution to the data scarcity issue which hinders mapping and hypothetical testing of the landscape structure and their role in landscape resilience. To achieve the objective of identifying core sets of landscape indicators to explore the significant influence of the landscape structure and pattern as an influence on landscape resilience, I employed analytical and statistical multivariate principal component and factor analysis to eliminate the landscape metric redundancy. The outcome helped to propose core set as indicators capable to be used for ecosystem services assessment and land use planning. The result revealed that only 6 landscape metrics had the capacity to explicitly define the configuration and compositional landscape character of the Vea catchment area. This result served a critical input into the development of the assessment framework. In developing a framework to assess the contribution of the landscape spatial structure to the resilience of the socio-ecological system (SES), I mapped the capacity of the landscape structure to provide regulating ecosystem services with the aid of land use maps as proxies. Analytical Hierarchical Processes and Expert stakeholder approaches were used to identify and subsequently map key regulating ES identified from the catchment area. Following, a multi-criteria analysis was employed to link stakeholder mapping and landscape metrics to provide a functional understanding of the interrelationship of both methods and how they provide integrative insights into the landscape resilience and ES trade-off concepts respectively. This assessment was undertaken using a 2012 multi-temporal RapidEye land use classification data and implemented with the aid of the cellular automaton module in GISCAME. In the absence of explicit ecological modeling and spatial data, the result of this methodology provides a comprehensively rich ES assessment approach not only for the research area, but for transferability across West Africa. The result of this assessment is to inform, across governance levels, different planning, and development scenarios with the potential to alter the landscapes structural character and thereby impede ES flow and resilience of the SES. Indirectly, the relevance of the landscape structure to land use planning was significant across the outcomes of the thesis. Further, the approach establishes potential trade-offs and synergies across the agricultural landscapes structure and thereby suggest planning and management supports to optimize agricultural production and improve ecosystem service flows in Sub-Saharan Africa. Overall, the implementation of the multi-criteria evaluation function in GISCAME demonstrated beyond question, the functional relevance of the GISCAME software tool as the only tried and tested ES integration framework implemented within the WASCAL project area

Proceedings of JAC 2010. Journées Automates Cellulaires

The second Symposium on Cellular Automata “Journ´ees Automates Cellulaires” (JAC 2010) took place in Turku, Finland, on December 15-17, 2010. The first two conference days were held in the Educarium building of the University of Turku, while the talks of the third day were given onboard passenger ferry boats in the beautiful Turku archipelago, along the route Turku–Mariehamn–Turku. The conference was organized by FUNDIM, the Fundamentals of Computing and Discrete Mathematics research center at the mathematics department of the University of Turku. The program of the conference included 17 submitted papers that were selected by the international program committee, based on three peer reviews of each paper. These papers form the core of these proceedings. I want to thank the members of the program committee and the external referees for the excellent work that have done in choosing the papers to be presented in the conference. In addition to the submitted papers, the program of JAC 2010 included four distinguished invited speakers: Michel Coornaert (Universit´e de Strasbourg, France), Bruno Durand (Universit´e de Provence, Marseille, France), Dora Giammarresi (Universit` a di Roma Tor Vergata, Italy) and Martin Kutrib (Universit¨at Gie_en, Germany). I sincerely thank the invited speakers for accepting our invitation to come and give a plenary talk in the conference. The invited talk by Bruno Durand was eventually given by his co-author Alexander Shen, and I thank him for accepting to make the presentation with a short notice. Abstracts or extended abstracts of the invited presentations appear in the first part of this volume. The program also included several informal presentations describing very recent developments and ongoing research projects. I wish to thank all the speakers for their contribution to the success of the symposium. I also would like to thank the sponsors and our collaborators: the Finnish Academy of Science and Letters, the French National Research Agency project EMC (ANR-09-BLAN-0164), Turku Centre for Computer Science, the University of Turku, and Centro Hotel. Finally, I sincerely thank the members of the local organizing committee for making the conference possible. These proceedings are published both in an electronic format and in print. The electronic proceedings are available on the electronic repository HAL, managed by several French research agencies. The printed version is published in the general publications series of TUCS, Turku Centre for Computer Science. We thank both HAL and TUCS for accepting to publish the proceedings.Siirretty Doriast

Cellular automata and dynamical systems

In this thesis we investigate the theoretical nature of the mathematical structures termed cellular automata. Chapter 1: Reviews the origin and history of cellular automata in order to place the current work into context. Chapter 2: Develops a cellular automata framework which contains the main aspects of cellular automata structure which have appeared in the literature. We present a scheme for specifying the cellular automata rules for this general model and present six examples of cellular automata within the model. Chapter 3: Here we develop a statistical mechanical model of cellular automata behaviour. We consider the relationship between variations within the model and their relationship to dynamical systems. We obtain results on the variance of the state changes, scaling of the cellular automata lattice, the equivalence of noise, spatial mixing of the lattice states and entropy, synchronous and asynchronous cellular automata and the equivalence of the rule probability and the time step of a discrete approximation to a dynamical system. Chapter 4: This contains an empirical comparison of cellular automata within our general framework and the statistical mechanical model. We obtain results on the transition from limit cycle to limit point behaviour as the rule probabilities are decreased. We also discuss failures of the statistical mechanical model due to failure of the assumptions behind it. Chapter 5: Here a practical application of the preceding work to population genetics is presented. We study this in the context of some established population models and show it may be most useful in the field of epidemiology. Further generalisations of the statistical mechanical and cellular automata models allow the modelling of more complex population models and mobile populations of organisms. Chapter 6: Reviews the results obtained in the context of the open questions introduced in Chapter 1. We also consider further questions this work raises and make some general comments on how these may apply to related fields

Material-based design computation

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Architecture, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 306-328).The institutionalized separation between form, structure and material, deeply embedded in modernist design theory, paralleled by a methodological partitioning between modeling, analysis and fabrication, resulted in geometric-driven form generation. Such prioritization of form over material was carried into the development and design logic of CAD. Today, under the imperatives and growing recognition of the failures and environmental liabilities of this approach, modern design culture is experiencing a shift to material aware design. Inspired by Nature's strategies where form generation is driven by maximal performance with minimal resources through local material property variation, the research reviews, proposes and develops models and processes for a material-based approach in computationally enabled form-generation. Material-based Design Computation is developed and proposed as a set of computational strategies supporting the integration of form, material and structure by incorporating physical form-finding strategies with digital analysis and fabrication. In this approach, material precedes shape, and it is the structuring of material properties as a function of structural and environmental performance that generates design form. The thesis proposes a unique approach to computationally-enabled form-finding procedures, and experimentally investigates how such processes contribute to novel ways of creating, distributing and depositing material forms. Variable Property Design is investigated as a theoretical and technical framework by which to model, analyze and fabricate objects with graduated properties designed to correspond to multiple and continuously varied functional constraints. The following methods were developed as the enabling mechanisms of Material Computation: Tiling Behavior & Digital Anisotropy, Finite Element Synthesis, and Material Pixels. In order to implement this approach as a fabrication process, a novel fabrication technology, termed Variable Property Rapid Prototyping has been developed, designed and patented. Among the potential contributions is the achievement of a high degree of customization through material heterogeneity as compared to conventional design of components and assemblies. Experimental designs employing suggested theoretical and technical frameworks, methods and techniques are presented, discussed and demonstrated. They support product customization, rapid augmentation and variable property fabrication. Developed as approximations of natural formation processes, these design experiments demonstrate the contribution and the potential future of a new design and research field.by Neri Oxman.Ph.D

Raum-zeitliche Dynamik von primären Lymphoiden-Follikeln während der Organogenese und Lymphneogenese

Primary lymphoid follicles are structures which are important for adaptive immune responses in mammals. Within the follicles follicular dendritic cells (FDC) are maintained by constant stimuli provided by B cells. It is thought that the FDC are important for immune response. It is of interest to know how lymphoid follicles are regulated in order to understand their role in various autoimmune diseases in which these follicles are created ectopically. With the help of a tissue simulation relying on an agent-based cell model on top of a regular triangulation various scenarios suggested by the available experimental data have been investigated. In order to cope with the complexity in the simulation of immune tissue the regular triangulation has been implemented for the use on parallel computers. The algorithms for kinetic and dynamic regular triangulation have been created newly. Also the cell model underlying the simulation has been designed newly in many aspects. The simulations allowed to identify common factors that regulate the formation of lymphoid follicles normally during organogenesis in development and lymphneogenesis in the course of diseases. The generation of FDC from local stromal populations under the influence of B cell aggregates is shown to be possible with the given experimental parameters. The sequence of the organogenesis and lymphneogenesis can be described with regard to the morphology of the B and T zone. Tests for the stability of the primary lymphoid follicle system constraints the regulation of the B cell efflux. The required lymphatic vessels around the lymphoid follicle are shown to be negatively correlated with the FDC network. Moreover it is shown that the adjacent T zone consisting of its own stromal population and T cells has similar regulation principles. This easily explains the intermediate ring of B cells found around the T zone during development and certain signaling molecule deficiencies. A major result of this thesis is that the generation of FDC needs negative regulation while a number of other possible mechanisms is incompatible with the available experimental data. Moreover the observed microanatomy was brought into a functional relationship with data on the cellular level finally culminating in the proposal of new experiments that shed light on the dynamics of the primary lymphoid follicle. One conclusion is that the FDC directly or indirectly influence the angiogenesis and lymphangiogenesis processes in secondary lymphoid tissues. The work presented here may help to guide experiments with the help of computers in order to reduce the amount of experiments and design them in a way to maximize the amount of information about biological systems.In Säugetieren spielen primäre lymphoide Follikel eine wichtige Rolle bei der adaptiven Immunantwort. Innerhalb der Follikel werden follikuläre dendritische Zellen (FDZ) durch eine konstante Stimulation durch B-Zellen generiert und erhalten. Diese FDZ-Population is wichtig für bestimmte Immunreaktionen. Die Erzeugung und Regulierung der Follikel is interessant insbesondere im Hinblick auf ihre ektopische Erzeugung im Laufe von Autoimmunreaktionen. Mit Hilfe von Gewebesimulationen ausgehend von einem Individual-basierten Zellmodells, das auf einer Delaunay-Triangulation aufbaut, wurden verschiedene aus Experimenten generierter Szenarien untersucht. Zur Lösung des Komplexitäts-Problems der vielen zu simulierende Zellen des Gewebes wurde größtenteils neue Algorithmen zur parallelen Verarbeitung der Kinetik und Dynamik der Delaunay-Triangulation erstellt. Das darauf aufbauende Zellmodell ist ebenfalls der parallelen Verarbeitung angepaßt. Die Simulationen führten zur Identifizierung gemeinsamer Zusammenhänge der Regulation lymphoider Follikel währen der Organogenese und der krankheitsbedingten Lymphneogenese. Die Erzeugung von FDZ aus lokalen Populationen stromaler Zellen durch Aggregate von B-Lypmozyten ist im Bereich der experimentellen Parameter möglich. Die Sequenz der Musterbildung von B- und T-Zone des Follikels während Organogenese und Lymphneogenese kann simuliert werden. Stabilitätskriterien für das primäre lymphoide Follikel schränken die möglichen Mechanismen der Regulation des B-Lymphozyten-Efflux ein. Die dafür notwendigen lymphatischen Gefäße um das Follikel sind negativ mit den FDZ korreliert, um eine Position um das Follikel herum einzunehmen. Ebenso wird gezeigt, das die spezifischen stromalen Populationen der T-Zone zusammen mit den T-Lymphozyten ähnlichen Organisationsprinzipien gehorchen, wie das benachbarte Follikel. Dies erklärt auf einfache Weise, das Auftreten einer charakteristischen intermediären Morphologie des Follikels als B-Lymphozyten-Ring um die T-Zone sowohl während der normalen Entwicklung als auch als Resultat bestimmter Signalmolekül-Defizite. Ein zentrales Ergebnis dieser Arbeit ist, dass die Erzeugung der FDZ einer negativen Regulation unterliegen muss, während eine Reihe anderer denkbarer Mechanismen nicht mit den verfügbaren experimentellen Daten in Einklang zu bringen ist. Darüber hinaus konnten Morphologie und Funktion mit Daten der zellulären Ebene in Beziehung gesetzt werden. Daraus sind neue Experimente zur Dynamik primärer lymphoider Follikel abgeleitet worden. Ein Beispiel hierfü ist der Einfluss der FDZ auf die Angiogenese und Lymphangiogenese in sekundären lymphoiden Geweben. Die hier aufgeführte Arbeit stellt so einen Beitrag dar, Experimente mit Hilfe von Computer Simulationen zu entwerfen, um sowohl die Zahl der notwendigen Experimente zu reduzieren als auch deren Informationsgewinn über ein biologisches System zu maximieren