First steps on asynchronous lattice-gas models with an application to a swarming rule

International audienceLattice-gas cellular automata are often considered as a particular case of cellular automata in which additional constraints apply, such as conservation of particles or spatial exclusion. But what about their updating? How to deal with non-perfect synchrony? Novel definitions of asynchronism are proposed that respect the specific hypotheses of lattice-gas models. These definitions are then applied to a swarming rule in order to explore the robustness of the global emergent behaviour. In particular, we compare the synchronous and asynchronous case, and remark that anti-alignment of particles is no longer observed when a small critical amount of asynchronism is added

Exploring the spatio-temporal dynamics of lipid rafts and their role in Signal transduction: a modeling and simulation approach

The aim of this thesis is to elucidate the biological as well as methodological implications that arise from modeling the spatio-temporal dynamics of lipid rafts. Therefore the effect of raft-dependent receptors dynamics on both, individual signaling events as well as the canonical Wnt signaling pathway, is thoroughly analyzed. To explore the effect of lipid rafts on individual signaling events, a Cellular-Automata based membrane model is developed. The specific involvement of lipid rafts in Wnt/β-catenin signaling is explored by means of an integrated in silico and in vitro approach

Common metrics for cellular automata models of complex systems

The creation and use of models is critical not only to the scientific process, but also to life in general. Selected features of a system are abstracted into a model that can then be used to gain knowledge of the workings of the observed system and even anticipate its future behaviour. A key feature of the modelling process is the identification of commonality. This allows previous experience of one model to be used in a new or unfamiliar situation. This recognition of commonality between models allows standards to be formed, especially in areas such as measurement. How everyday physical objects are measured is built on an ingrained acceptance of their underlying commonality. Complex systems, often with their layers of interwoven interactions, are harder to model and, therefore, to measure and predict. Indeed, the inability to compute and model a complex system, except at a localised and temporal level, can be seen as one of its defining attributes. The establishing of commonality between complex systems provides the opportunity to find common metrics. This work looks at two dimensional cellular automata, which are widely used as a simple modelling tool for a variety of systems. This has led to a very diverse range of systems using a common modelling environment based on a lattice of cells. This provides a possible common link between systems using cellular automata that could be exploited to find a common metric that provided information on a diverse range of systems. An enhancement of a categorisation of cellular automata model types used for biological studies is proposed and expanded to include other disciplines. The thesis outlines a new metric, the C-Value, created by the author. This metric, based on the connectedness of the active elements on the cellular automata grid, is then tested with three models built to represent three of the four categories of cellular automata model types. The results show that the new C-Value provides a good indicator of the gathering of active cells on a grid into a single, compact cluster and of indicating, when correlated with the mean density of active cells on the lattice, that their distribution is random. This provides a range to define the disordered and ordered state of a grid. The use of the C-Value in a localised context shows potential for identifying patterns of clusters on the grid

Introduction to the Modeling and Analysis of Complex Systems

Keep up to date on Introduction to Modeling and Analysis of Complex Systems at http://bingweb.binghamton.edu/~sayama/textbook/! Introduction to the Modeling and Analysis of Complex Systems introduces students to mathematical/computational modeling and analysis developed in the emerging interdisciplinary field of Complex Systems Science. Complex systems are systems made of a large number of microscopic components interacting with each other in nontrivial ways. Many real-world systems can be understood as complex systems, where critically important information resides in the relationships between the parts and not necessarily within the parts themselves. This textbook offers an accessible yet technically-oriented introduction to the modeling and analysis of complex systems. The topics covered include: fundamentals of modeling, basics of dynamical systems, discrete-time models, continuous-time models, bifurcations, chaos, cellular automata, continuous field models, static networks, dynamic networks, and agent-based models. Most of these topics are discussed in two chapters, one focusing on computational modeling and the other on mathematical analysis. This unique approach provides a comprehensive view of related concepts and techniques, and allows readers and instructors to flexibly choose relevant materials based on their objectives and needs. Python sample codes are provided for each modeling example. This textbook is available for purchase in both grayscale and color via Amazon.com and CreateSpace.com.https://knightscholar.geneseo.edu/oer-ost/1013/thumbnail.jp

Topology Optimisation in Crashworthiness Design via Hybrid Cellular Automata for Thin Walled Structures.

PhDCrashworthiness design is one of the most critical areas of automotive design. It is really demanding for the structure and can therefore have a large in uence on the nal design. It is also di cult to model accurately and costly to simulate which has an important impact on the design process. Most car companies have now stopped addressing crashworthiness design with trial and error approaches, in favour of more advanced automated structural optimisation methods. While most relevant applications so far use size or shape optimisation, the ultimate way to achieve signi cant mass reduction is to use topology optimisation. However, topology optimisation methods for crashworthiness design are still a work in progress. Due to the high non-linearity of crash simulations, well-established classic topology optimisation methods cannot be applied directly to crashworthiness design. Alternative methods have been and keep being developed such as the Equivalent Static Loads method, the Ground Structure Approach or the Hybrid Cellular Automata (HCA). This thesis introduces an adapted version of Hybrid Cellular Automata using thinwalled ground structures. It combines the advantages of computing a real crash simulation while producing as an output a thin walled based topology needing minimal post-processing e ort to be translated into a realistic design. In this method, the topology optimisation domain is lled up with a ground structure of thin walls which constitutes the elementary cells of the HCA method. These macro-elements replace the solid mesh elements used in the classic HCA approach. The details and implementation of the method are presented and discussed. Di erent application examples are detailed, including de ning reinforcement patterns within extruded beams. Enriched space llings patterns are studied and industrial application examples are presented. Eventually, recommendations for further studies and applications of the method are given.School of Engineering and Materials Science and SFE GmbH for funding this researc

Lattice-Boltzmann simulations of cerebral blood flow

Computational haemodynamics play a central role in the understanding of blood behaviour in the cerebral vasculature, increasing our knowledge in the onset of vascular diseases and their progression, improving diagnosis and ultimately providing better patient prognosis. Computer simulations hold the potential of accurately characterising motion of blood and its interaction with the vessel wall, providing the capability to assess surgical treatments with no danger to the patient. These aspects considerably contribute to better understand of blood circulation processes as well as to augment pre-treatment planning. Existing software environments for treatment planning consist of several stages, each requiring significant user interaction and processing time, significantly limiting their use in clinical scenarios. The aim of this PhD is to provide clinicians and researchers with a tool to aid in the understanding of human cerebral haemodynamics. This tool employs a high performance fluid solver based on the lattice-Boltzmann method (coined HemeLB), high performance distributed computing and grid computing, and various advanced software applications useful to efficiently set up and run patient-specific simulations. A graphical tool is used to segment the vasculature from patient-specific CT or MR data and configure boundary conditions with ease, creating models of the vasculature in real time. Blood flow visualisation is done in real time using in situ rendering techniques implemented within the parallel fluid solver and aided by steering capabilities; these programming strategies allows the clinician to interactively display the simulation results on a local workstation. A separate software application is used to numerically compare simulation results carried out at different spatial resolutions, providing a strategy to approach numerical validation. This developed software and supporting computational infrastructure was used to study various patient-specific intracranial aneurysms with the collaborating interventionalists at the National Hospital for Neurology and Neuroscience (London), using three-dimensional rotational angiography data to define the patient-specific vasculature. Blood flow motion was depicted in detail by the visualisation capabilities, clearly showing vortex fluid ow features and stress distribution at the inner surface of the aneurysms and their surrounding vasculature. These investigations permitted the clinicians to rapidly assess the risk associated with the growth and rupture of each aneurysm. The ultimate goal of this work is to aid clinical practice with an efficient easy-to-use toolkit for real-time decision support

Efficient algorithms for the realistic simulation of fluids

Nowadays there is great demand for realistic simulations in the computer graphics field. Physically-based animations are commonly used, and one of the more complex problems in this field is fluid simulation, more so if real-time applications are the goal. Videogames, in particular, resort to different techniques that, in order to represent fluids, just simulate the consequence and not the cause, using procedural or parametric methods and often discriminating the physical solution. This need motivates the present thesis, the interactive simulation of free-surface flows, usually liquids, which are the feature of interest in most common applications. Due to the complexity of fluid simulation, in order to achieve real-time framerates, we have resorted to use the high parallelism provided by actual consumer-level GPUs. The simulation algorithm, the Lattice Boltzmann Method, has been chosen accordingly due to its efficiency and the direct mapping to the hardware architecture because of its local operations. We have created two free-surface simulations in the GPU: one fully in 3D and another restricted only to the upper surface of a big bulk of fluid, limiting the simulation domain to 2D. We have extended the latter to track dry regions and is also coupled with obstacles in a geometry-independent fashion. As it is restricted to 2D, the simulation loses some features due to the impossibility of simulating vertical separation of the fluid. To account for this we have coupled the surface simulation to a generic particle system with breaking wave conditions; the simulations are totally independent and only the coupling binds the LBM with the chosen particle system. Furthermore, the visualization of both systems is also done in a realistic way within the interactive framerates; raycasting techniques are used to provide the expected light-related effects as refractions, reflections and caustics. Other techniques that improve the overall detail are also applied as low-level detail ripples and surface foam