Forecasting a language shift based on cellular automata

Language extinction as a consequence of language shifts is a widespread social phenomenon that affects several million people all over the world today. An important task for social sciences research should therefore be to gain an understanding of language shifts, especially as a way of forecasting the extinction or survival of threatened languages, i.e., determining whether or not the subordinate language will survive in communities with a dominant and a subordinate language. In general, modeling is usually a very difficult task in the social sciences, particularly when it comes to forecasting the values of variables. However, the cellular automata theory can help us overcome this traditional difficulty. The purpose of this article is to investigate language shifts in the speech behavior of individuals using the methodology of the cellular automata theory. The findings on the dynamics of social impacts in the field of social psychology and the empirical data from language surveys on the use of Catalan in Valencia allowed us to define a cellular automaton and carry out a set of simulations using that automaton. The simulation results highlighted the key factors in the progression or reversal of a language shift and the use of these factors allowed us to forecast the future of a threatened language in a bilingual community.

The MIRELA framework: modeling and analyzing mixed reality applications using timed automata

Mixed Reality (MR) aims to link virtual entities with the real world and has many applications such as military and medical domains [JBL+00, NFB07]. In many MR systems and more precisely in augmented scenes, one needs the application to render the virtual part accurately at the right time. To achieve this, such systems acquire data related to the real world from a set of sensors before rendering virtual entities. A suitable system architecture should minimize the delays to keep the overall system delay (also called end-to-end latency) within the requirements for real-time performance. In this context, we propose a compositional modeling framework for MR software architectures in order to specify, simulate and validate formally the time constraints of such systems. Our approach is first based on a functional decomposition of such systems into generic components. The obtained elements as well as their typical interactions give rise to generic representations in terms of timed automata. A whole system is then obtained as a composition of such defined components. To write specifications, a textual language named MIRELA (MIxed REality LAnguage) is proposed along with the corresponding compilation tools. The generated output contains timed automata in UPPAAL format for simulation and verification of time constraints. These automata may also be used to generate source code skeletons for an implementation on a MR platform. The approach is illustrated first on a small example. A realistic case study is also developed. It is modeled by several timed automata synchronizing through channels and including a large number of time constraints. Both systems have been simulated in UPPAAL and checked against the required behavioral properties.

LATTICE BOLTZMANN METHOD AND CELLULAR AUTOMATA SIMULATION OF PARTICLE MOTION AND DEPOSITION IN 2-D CASE

This technical report discusses the application of the Lattice Boltzmann Method (LBM) and Cellular Automata (CA) simulation in fluid flow and particle deposition. The current work focuses on incompressible flow simulation passing cylinders, in which we incorporate the LBM D2Q9 and CA techniques to simulate the fluid flow and particle loading respectively. For the LBM part, the theories of boundary conditions are studied and verified using the Poiseuille flow test. For the CA part, several models regarding simulation of particles are explained. And a new Digital Differential Analyzer (DDA) algorithm is introduced to simulate particle motion in the Boolean model. The numerical results are compared with a previous probability velocity model by Masselot [Masselot 2000], which shows a satisfactory result.

An atomistic simulation of solid state sintering using Monte Carlo methods

This paper presents results on the simulation of the solid state sintering of copper wires using Monte Carlo techniques based on elements of lattice theory and cellular automata. The initial structure is superimposed onto a triangular, two-dimensional lattice, where each lattice site corresponds to either an atom or vacancy. The number of vacancies varies with the simulation temperature, while a cluster of vacancies is a pore. To simulate sintering, lattice sites are picked at random and reoriented in terms of an atomistic model governing mass transport. The probability that an atom has sufficient energy to jump to a vacant lattice site is related to the jump frequency, and hence the diffusion coefficient, while the probability that an atomic jump will be accepted is related to the change in energy of the system as a result of the jump, as determined by the change in the number of nearest neighbours. The jump frequency is also used to relate model time, measured in Monte Carlo Steps, to the actual sintering time. The model incorporates bulk, grain boundary and surface diffusion terms and includes vacancy annihilation on the grain boundaries. The predictions of the model were found to be consistent with experimental data, both in terms of the microstructural evolution and in terms of the sintering time. (C) 2002 Elsevier Science B.V. All rights reserved.

An integrated model for simulation of construction phasing of arch concrete dams

Dissertação de mestrado integrado em Civil Engineering

Adaptive numerical simulation of reaction - diffusion systems

Fluidized beds, granulation, heat and mass transfer, calcium dynamics, stochastic process, finite element methods, Rosenbrock methods, multigrid methods, parallelization

Analysis of c-Myc function in mouse epidermis

Abstract The c-myc gene is one of the most frequently mutated oncogenes found in human tumors. c-Myc has been implicated in the regulation of various biological processes including cell cycle progression, cellular growth, differentiation, angiogenesis, immortalization and apoptosis. To assess the normal role of c-Myc in epithelial cell types in vitro and in vivo we have deleted the c-myc gene in keratinocytes and in the adult skin epidermis by conditional Cre/loxP mediated recombination. Similar to what we have previously shown in mouse embryonic fibroblasts acute elimination of c-Myc activity in cultured keratinocytes causes cells to cease proliferation and adapt a flat cell morphology. Mutant cells accumulate in a diploid Ki67neg stage, indicative of a quiescent Go stage. This demonstrates that c-Myc activity is essential to maintain keratinocytes in a productive cell cycle. In addition, mutant keratinocytes showed a defect in Ca2+ induced induction of the differentiation marker Keratin 1 suggesting a role for c-Myc during differentiation. To assess the in vivo role of c-Myc we used a tamoxifen inducible K5::CreERT transgene to delete the c-myc gene in the adult skin epidermis. Unexpectedly, despite strong c-Myc expression in the basal compartment it is not required for maintenance of the skin epidermis in the adult mouse. The epidermis appeared normal with respect to both proliferation and differentiation. In addition, no selection against c-Myc deficient epidermal cells occurred over many months, further confirming that c-Myc is dispensable for normal skin homeostasis. Even more surprising, TPA induced hyperproliferation also occurred in a c-Myc independent manner. Treatment of the skin with the mutagen DMBA prior to TPA is a classical way to induce papillomas by selecting for mutations that lead to dominant activation of the oncogene Ha-Ras. Most interestingly tumor formation was severely inhibited suggesting that tumor progression requires endogenous c-Myc. Further studies are required to address whether the role of c-Myc in the activation of telomerase or the Werner protein, or its role to induce angiogenesis is required for skin tumor progression, In conclusion, this work shows that while c-Myc is not required for maintenance or hyperplasia of mouse epidermis, it is essential for skin tumor progression in collaboration with Ras. Résumé Le gène c-myc est un des oncogènes les plus fréquemment mutés dans les tumeurs humaines. c-Myc est impliqué dans la régulation de processus biologiques variés, comme la progression du cycle cellulaire, la croissance cellulaire, la différenciation, l'angiogenèse, l'immortalisation et l'apoptose. Pour caractériser le rôle physiologique de c-Myc dans les cellules de type épithélial in vitro et in vivo, le gène c-myc a été délété dans des kératinocytes primaires et dans l'épiderme de peau de souris adultes par des recombinaisons conditionnelles (système Cre/loxP). De la même façon que dans les fibroblastes d'embryon de souris, l'élimination aiguë de l'activité de c-Myc dans les kératinocytes en culture primaire provoque l'arrêt de la prolifération des cellules et leur applatissement morphologique. Les cellules mutantes restent dans un stade diploïde Ki67neg, indiquant un stade quiescent Go. Cela démontre que l'activité de c-Myc est essentielle pour maintenir les kératinocytes dans le cycle cellulaire. De plus, les kératinocytes mutants montrent une déficience pour le marqueur de différenciation Kératine 1 au cours de la différenciation induite par le calcium, suggérant un rôle de c-Myc dans la différenciation cellulaire. Pour comprendre le rôle de c-Myc in vivo, le transgène K5::CreERT inductible par le tamoxifen a été utilisé pour déléter le gène c-inyc dans l'épiderme de souris adultes. Etonnemment, malgré une forte expression de c-Myc dans le compartiment basal de l'épiderme, ce gène n'est pas nécessaire pour la maintenance de l'épiderme de la peau chez la souris adulte. L'épiderme apparait normal avec une prolifération et une différenciation physiologique des cellules. De plus, il n'y a pas de sélection contre les cellules épidennales c-Myc déficientes après plusieurs mois, ce qui confirme que c-Myc n'est pas nécessaire pour l'homéostasie normale de la peau. Encore plus surprenant, une hyperprolifération est également induite par du TPA chez les souris mutantes, impliquant une voie de prolifération indépendante de c-Myc. Le traitement de la peau par le mutagène DMBA avant le traitement au TPA est une voie classique d'induction de papillomes, par sélection de mutations conduisant à l'activation de l'oncogène Ha-Ras. La formation des tumeurs est fortement inhibée chez les souris mutantes, suggérant que la progression des tumeurs nécessite la présence endogène de c-Myc. De nouvelles études sont nécessaires pour savoir si c-Myc a un rôle dans l'activation de la télomérase ou de la protéine de Werner, ou encore dans l'angiogénèse, qui sont nécessaires pour la progression tumorale. En conclusion, ce travail montre que même si c-Myc n'est pas nécessaire pour la maintenance ou l'hyperplasie de la peau de souris, il est essentiel pour la progression des tumeurs de la peau en collaboration avec Ras.

Behavioural queueing : cellular automata and a laboratory experiment

Dans cette thèse, nous étudions les aspects comportementaux d'agents qui interagissent dans des systèmes de files d'attente à l'aide de modèles de simulation et de méthodologies expérimentales. Chaque période les clients doivent choisir un prestataire de servivce. L'objectif est d'analyser l'impact des décisions des clients et des prestataires sur la formation des files d'attente. Dans un premier cas nous considérons des clients ayant un certain degré d'aversion au risque. Sur la base de leur perception de l'attente moyenne et de la variabilité de cette attente, ils forment une estimation de la limite supérieure de l'attente chez chacun des prestataires. Chaque période, ils choisissent le prestataire pour lequel cette estimation est la plus basse. Nos résultats indiquent qu'il n'y a pas de relation monotone entre le degré d'aversion au risque et la performance globale. En effet, une population de clients ayant un degré d'aversion au risque intermédiaire encoure généralement une attente moyenne plus élevée qu'une population d'agents indifférents au risque ou très averses au risque. Ensuite, nous incorporons les décisions des prestataires en leur permettant d'ajuster leur capacité de service sur la base de leur perception de la fréquence moyenne d'arrivées. Les résultats montrent que le comportement des clients et les décisions des prestataires présentent une forte "dépendance au sentier". En outre, nous montrons que les décisions des prestataires font converger l'attente moyenne pondérée vers l'attente de référence du marché. Finalement, une expérience de laboratoire dans laquelle des sujets jouent le rôle de prestataire de service nous a permis de conclure que les délais d'installation et de démantèlement de capacité affectent de manière significative la performance et les décisions des sujets. En particulier, les décisions du prestataire, sont influencées par ses commandes en carnet, sa capacité de service actuellement disponible et les décisions d'ajustement de capacité qu'il a prises, mais pas encore implémentées. - Queuing is a fact of life that we witness daily. We all have had the experience of waiting in line for some reason and we also know that it is an annoying situation. As the adage says "time is money"; this is perhaps the best way of stating what queuing problems mean for customers. Human beings are not very tolerant, but they are even less so when having to wait in line for service. Banks, roads, post offices and restaurants are just some examples where people must wait for service. Studies of queuing phenomena have typically addressed the optimisation of performance measures (e.g. average waiting time, queue length and server utilisation rates) and the analysis of equilibrium solutions. The individual behaviour of the agents involved in queueing systems and their decision making process have received little attention. Although this work has been useful to improve the efficiency of many queueing systems, or to design new processes in social and physical systems, it has only provided us with a limited ability to explain the behaviour observed in many real queues. In this dissertation we differ from this traditional research by analysing how the agents involved in the system make decisions instead of focusing on optimising performance measures or analysing an equilibrium solution. This dissertation builds on and extends the framework proposed by van Ackere and Larsen (2004) and van Ackere et al. (2010). We focus on studying behavioural aspects in queueing systems and incorporate this still underdeveloped framework into the operations management field. In the first chapter of this thesis we provide a general introduction to the area, as well as an overview of the results. In Chapters 2 and 3, we use Cellular Automata (CA) to model service systems where captive interacting customers must decide each period which facility to join for service. They base this decision on their expectations of sojourn times. Each period, customers use new information (their most recent experience and that of their best performing neighbour) to form expectations of sojourn time at the different facilities. Customers update their expectations using an adaptive expectations process to combine their memory and their new information. We label "conservative" those customers who give more weight to their memory than to the xiv Summary new information. In contrast, when they give more weight to new information, we call them "reactive". In Chapter 2, we consider customers with different degree of risk-aversion who take into account uncertainty. They choose which facility to join based on an estimated upper-bound of the sojourn time which they compute using their perceptions of the average sojourn time and the level of uncertainty. We assume the same exogenous service capacity for all facilities, which remains constant throughout. We first analyse the collective behaviour generated by the customers' decisions. We show that the system achieves low weighted average sojourn times when the collective behaviour results in neighbourhoods of customers loyal to a facility and the customers are approximately equally split among all facilities. The lowest weighted average sojourn time is achieved when exactly the same number of customers patronises each facility, implying that they do not wish to switch facility. In this case, the system has achieved the Nash equilibrium. We show that there is a non-monotonic relationship between the degree of risk-aversion and system performance. Customers with an intermediate degree of riskaversion typically achieve higher sojourn times; in particular they rarely achieve the Nash equilibrium. Risk-neutral customers have the highest probability of achieving the Nash Equilibrium. Chapter 3 considers a service system similar to the previous one but with risk-neutral customers, and relaxes the assumption of exogenous service rates. In this sense, we model a queueing system with endogenous service rates by enabling managers to adjust the service capacity of the facilities. We assume that managers do so based on their perceptions of the arrival rates and use the same principle of adaptive expectations to model these perceptions. We consider service systems in which the managers' decisions take time to be implemented. Managers are characterised by a profile which is determined by the speed at which they update their perceptions, the speed at which they take decisions, and how coherent they are when accounting for their previous decisions still to be implemented when taking their next decision. We find that the managers' decisions exhibit a strong path-dependence: owing to the initial conditions of the model, the facilities of managers with identical profiles can evolve completely differently. In some cases the system becomes "locked-in" into a monopoly or duopoly situation. The competition between managers causes the weighted average sojourn time of the system to converge to the exogenous benchmark value which they use to estimate their desired capacity. Concerning the managers' profile, we found that the more conservative Summary xv a manager is regarding new information, the larger the market share his facility achieves. Additionally, the faster he takes decisions, the higher the probability that he achieves a monopoly position. In Chapter 4 we consider a one-server queueing system with non-captive customers. We carry out an experiment aimed at analysing the way human subjects, taking on the role of the manager, take decisions in a laboratory regarding the capacity of a service facility. We adapt the model proposed by van Ackere et al (2010). This model relaxes the assumption of a captive market and allows current customers to decide whether or not to use the facility. Additionally the facility also has potential customers who currently do not patronise it, but might consider doing so in the future. We identify three groups of subjects whose decisions cause similar behavioural patterns. These groups are labelled: gradual investors, lumpy investors, and random investor. Using an autocorrelation analysis of the subjects' decisions, we illustrate that these decisions are positively correlated to the decisions taken one period early. Subsequently we formulate a heuristic to model the decision rule considered by subjects in the laboratory. We found that this decision rule fits very well for those subjects who gradually adjust capacity, but it does not capture the behaviour of the subjects of the other two groups. In Chapter 5 we summarise the results and provide suggestions for further work. Our main contribution is the use of simulation and experimental methodologies to explain the collective behaviour generated by customers' and managers' decisions in queueing systems as well as the analysis of the individual behaviour of these agents. In this way, we differ from the typical literature related to queueing systems which focuses on optimising performance measures and the analysis of equilibrium solutions. Our work can be seen as a first step towards understanding the interaction between customer behaviour and the capacity adjustment process in queueing systems. This framework is still in its early stages and accordingly there is a large potential for further work that spans several research topics. Interesting extensions to this work include incorporating other characteristics of queueing systems which affect the customers' experience (e.g. balking, reneging and jockeying); providing customers and managers with additional information to take their decisions (e.g. service price, quality, customers' profile); analysing different decision rules and studying other characteristics which determine the profile of customers and managers.

Transfer entropy reconstruction and labeling of neuronal connections from simulated calcium imaging

Neuronal dynamics are fundamentally constrained by the underlying structural network architecture, yet much of the details of this synaptic connectivity are still unknown even in neuronal cultures in vitro. Here we extend a previous approach based on information theory, the Generalized Transfer Entropy, to the reconstruction of connectivity of simulated neuronal networks of both excitatory and inhibitory neurons. We show that, due to the model-free nature of the developed measure, both kinds of connections can be reliably inferred if the average firing rate between synchronous burst events exceeds a small minimum frequency. Furthermore, we suggest, based on systematic simulations, that even lower spontaneous inter-burst rates could be raised to meet the requirements of our reconstruction algorithm by applying a weak spatially homogeneous stimulation to the entire network. By combining multiple recordings of the same in silico network before and after pharmacologically blocking inhibitory synaptic transmission, we show then how it becomes possible to infer with high confidence the excitatory or inhibitory nature of each individual neuron.

Regulation of epidermal tight junctions by calcium ATPases and p38

The epidermis is the upper layer of the skin and keratinocytes are its most abundant cells. Tight junctions are cell junctions located in the granular layer of the epidermis. They maintain the polarity of the cells and regulate the movement of water-soluble molecules. Epidermal tight junctions may lose their integrity when there are defects in intercellular calcium regulation. Hailey-Hailey and Darier´s disease are dominantly inherited, blistering skin diseases. Hailey-Hailey disease is caused by mutations in the ATP2C1 gene encoding a calcium/manganese ATPase SPCA1 of the Golgi apparatus. Darier´s disease is caused by mutations in the ATP2A2 gene encoding a calcium ATPase SERCA2 of the endoplasmic reticulum. p38 regulates the differentiation of keratinocytes. The overall regulation of epidermal tight junctions is not well understood. The present study examined the regulation of tight junctions in the human epidermis with a focus on calcium ATPases and p38. Skin from Hailey-Hailey and Darier´s disease patients was studied by using immunofluorescence labeling which targeted intercellular junction proteins. Transepidermal water loss was also measured. ATP2C1 gene expression was silenced in cultured keratinocytes, by siRNA, which modeled Hailey-Hailey disease. Expression of intercellular junction proteins was studied at the mRNA and protein levels. Squamous cell carcinoma and normal human keratinocytes were used as a model for impaired and normal keratinocyte differentiation, and the role of p38 isoforms alpha and delta in the regulation of intercellular junction proteins was studied. Both p38 isoforms were silenced by adenovirus cell transduction, chemical inhibitors or siRNA and keratinocyte differentiation was assessed. The results of this thesis revealed that: i.) intercellular junction proteins are expressed normally in acantholytic skin areas of patients with Hailey-Hailey or Darier´s disease but the localization of ZO-1 expanded to the stratum spinosum; ii.) tight junction proteins, claudin-1 and -4, are regulated by ATP2C1 in non-differentiating keratinocytes; and iii.) p38 delta regulates the expression of tight junction protein ZO-1 in proliferating keratinocytes and in squamous cell carcinoma derived cells. ZO-1 silencing, however, did not affect the expression of other tight junction proteins, suggesting that they are differently regulated. This thesis introduces new mechanisms involved in the regulation of tight junctions revealing new interactions. It provides novel evidence linking intracellular calcium regulation and tight junctions.

Model based analysis of the post-combustion calcium looping process for carbon dioxide capture

This thesis presents a one-dimensional, semi-empirical dynamic model for the simulation and analysis of a calcium looping process for post-combustion CO2 capture. Reduction of greenhouse emissions from fossil fuel power production requires rapid actions including the development of efficient carbon capture and sequestration technologies. The development of new carbon capture technologies can be expedited by using modelling tools. Techno-economical evaluation of new capture processes can be done quickly and cost-effectively with computational models before building expensive pilot plants. Post-combustion calcium looping is a developing carbon capture process which utilizes fluidized bed technology with lime as a sorbent. The main objective of this work was to analyse the technological feasibility of the calcium looping process at different scales with a computational model. A one-dimensional dynamic model was applied to the calcium looping process, simulating the behaviour of the interconnected circulating fluidized bed reactors. The model incorporates fundamental mass and energy balance solvers to semi-empirical models describing solid behaviour in a circulating fluidized bed and chemical reactions occurring in the calcium loop. In addition, fluidized bed combustion, heat transfer and core-wall layer effects were modelled. The calcium looping model framework was successfully applied to a 30 kWth laboratory scale and a pilot scale unit 1.7 MWth and used to design a conceptual 250 MWth industrial scale unit. Valuable information was gathered from the behaviour of a small scale laboratory device. In addition, the interconnected behaviour of pilot plant reactors and the effect of solid fluidization on the thermal and carbon dioxide balances of the system were analysed. The scale-up study provided practical information on the thermal design of an industrial sized unit, selection of particle size and operability in different load scenarios.

Développement d’une méthode de simulation multi-échelle pour l’étude des grandes transformations dans les protéines

Les films de simulations qui accompagnent le document ont été réalisés avec Pymol.