Software Tools For Large Scale Interactive Hydrodynamic Modeling

Running hydrodynamic models interactively allows both visual exploration and change of model state during simulation. One of the main characteristics of an interactive model is that it should provide immediate feedback to the user, for example respond to changes in model state or view settings. For this reason, such features are usually only available for models with a relatively small number of computational cells, which are used mainly for demonstration and educational purposes. It would be useful if interactive modeling would also work for models typically used in consultancy projects involving large scale simulations. This results in a number of technical challenges related to the combination of the model itself and the visualisation tools (scalability, implementation of an appropriate API for control and access to the internal state). While model parallelisation is increasingly addressed by the environmental modeling community, little effort has been spent on developing a high-performance interactive environment. What can we learn from other high-end visualisation domains such as 3D animation, gaming, virtual globes (Autodesk 3ds Max, Second Life, Google Earth) that also focus on efficient interaction with 3D environments? In these domains high efficiency is usually achieved by the use of computer graphics algorithms such as surface simplification depending on current view, distance to objects, and efficient caching of the aggregated representation of object meshes. We investigate how these algorithms can be re-used in the context of interactive hydrodynamic modeling without significant changes to the model code and allowing model operation on both multi-core CPU personal computers and high-performance computer clusters.

Large-scale protein structure modeling of the Saccharomyces cerevisiae genome

The function of a protein generally is determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from the many genome projects. To this end, fold assignment, comparative protein structure modeling, and model evaluation were automated completely. As an illustration, the method was applied to the proteins in the Saccharomyces cerevisiae (baker’s yeast) genome. It resulted in all-atom 3D models for substantial segments of 1,071 (17%) of the yeast proteins, only 40 of which have had their 3D structure determined experimentally. Of the 1,071 modeled yeast proteins, 236 were related clearly to a protein of known structure for the first time; 41 of these previously have not been characterized at all.

A integração do Building Information Modeling (BIM) num projeto de reabilitação

Dissertação de mestrado integrado em Engenharia Civil

Dynamical modeling and analysis of large cellular regulatory networks.

The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

Let's talk: public evaluation of large projects: variational inequialities, bilevel programming and complementarity. a survey

Large projects evaluation rises well known difficulties because -by definition- they modify the current price system; their public evaluation presents additional difficulties because they modify too existing shadow prices without the project. This paper analyzes -first- the basic methodologies applied until late 80s., based on the integration of projects in optimization models or, alternatively, based on iterative procedures with information exchange between two organizational levels. New methodologies applied afterwards are based on variational inequalities, bilevel programming and linear or nonlinear complementarity. Their foundations and different applications related with project evaluation are explored. As a matter of fact, these new tools are closely related among them and can treat more complex cases involving -for example- the reaction of agents to policies or the existence of multiple agents in an environment characterized by common functions representing demands or constraints on polluting emissions.

Influence of structural heterogeneities and of large scale topography on imbricate gravitational rock slope failures: New insights from 3-D physical modeling and geomorphological analysis

Initial topography and inherited structural discontinuities are known to play a dominant role in rock slope stability. Previous 2-D physical modeling results demonstrated that even if few preexisting fractures are activated/propagated during gravitational failure all of those heterogeneities had a great influence on mobilized volume and its kinematics. The question we address in the present study is to determine if such a result is also observed in 3-D. As in 2-D previous models we examine geologically stable model configuration, based upon the well documented landslide at Randa, Switzerland. The 3-D models consisted of a homogeneous material in which several fracture zones were introduced in order to study simplified but realistic configurations of discontinuities (e.g. based on natural example rather than a parametric study). Results showed that the type of gravitational failure (deep-seated landslide or sequential failure) and resulting slope morphology evolution are the result of the interplay of initial topography and inherited preexisting fractures (orientation and density). The three main results are i) the initial topography exerts a strong control on gravitational slope failure. Indeed in each tested configuration (even in the isotropic one without fractures) the model is affected by a rock slide, ii) the number of simulated fracture sets greatly influences the volume mobilized and its kinematics, and iii) the failure zone involved in the 1991 event is smaller than the results produced by the analog modeling. This failure may indicate that the zone mobilized in 1991 is potentially only a part of a larger deep-seated landslide and/or wider deep seated gravitational slope deformation.

Budgeting rockfall and modeling sedimentary delivery in torrent systems

This thesis is a compilation of projects to study sediment processes recharging debris flow channels. These works, conducted during my stay at the University of Lausanne, focus in the geological and morphological implications of torrent catchments to characterize debris supply, a fundamental element to predict debris flows. Other aspects of sediment dynamics are considered, e.g. the coupling headwaters - torrent, as well as the development of a modeling software that simulates sediment transfer in torrent systems. The sediment activity at Manival, an active torrent system of the northern French Alps, was investigated using terrestrial laser scanning and supplemented with geostructural investigations and a survey of sediment transferred in the main torrent. A full year of sediment flux could be observed, which coincided with two debris flows and several bedload transport events. This study revealed that both debris flows generated in the torrent and were preceded in time by recharge of material from the headwaters. Debris production occurred mostly during winter - early spring time and was caused by large slope failures. Sediment transfers were more puzzling, occurring almost exclusively in early spring subordinated to runoffconditions and in autumn during long rainfall. Intense rainstorms in summer did not affect debris storage that seems to rely on the stability of debris deposits. The morpho-geological implication in debris supply was evaluated using DEM and field surveys. A slope angle-based classification of topography could characterize the mode of debris production and transfer. A slope stability analysis derived from the structures in rock mass could assess susceptibility to failure. The modeled rockfall source areas included more than 97% of the recorded events and the sediment budgets appeared to be correlated to the density of potential slope failure. This work showed that the analysis of process-related terrain morphology and of susceptibility to slope failure document the sediment dynamics to quantitatively assess erosion zones leading to debris flow activity. The development of erosional landforms was evaluated by analyzing their geometry with the orientations of potential rock slope failure and with the direction of the maximum joint frequency. Structure in rock mass, but in particular wedge failure and the dominant discontinuities, appear as a first-order control of erosional mechanisms affecting bedrock- dominated catchment. They represent some weaknesses that are exploited primarily by mass wasting processes and erosion, promoting not only the initiation of rock couloirs and gullies, but also their propagation. Incorporating the geological control in geomorphic processes contributes to better understand the landscape evolution of active catchments. A sediment flux algorithm was implemented in a sediment cascade model that discretizes the torrent catchment in channel reaches and individual process-response systems. Each conceptual element includes in simple manner geomorphological and sediment flux information derived from GIS complemented with field mapping. This tool enables to simulate sediment transfers in channels considering evolving debris supply and conveyance, and helps reducing the uncertainty inherent to sediment budget prediction in torrent systems. Cette thèse est un recueil de projets d'études des processus de recharges sédimentaires des chenaux torrentiels. Ces travaux, réalisés lorsque j'étais employé à l'Université de Lausanne, se concentrent sur les implications géologiques et morphologiques des bassins dans l'apport de sédiments, élément fondamental dans la prédiction de laves torrentielles. D'autres aspects de dynamique sédimentaire ont été abordés, p. ex. le couplage torrent - bassin, ainsi qu'un modèle de simulation du transfert sédimentaire en milieu torrentiel. L'activité sédimentaire du Manival, un système torrentiel actif des Alpes françaises, a été étudiée par relevés au laser scanner terrestre et complétée par une étude géostructurale ainsi qu'un suivi du transfert en sédiments du torrent. Une année de flux sédimentaire a pu être observée, coïncidant avec deux laves torrentielles et plusieurs phénomènes de charriages. Cette étude a révélé que les laves s'étaient générées dans le torrent et étaient précédées par une recharge de débris depuis les versants. La production de débris s'est passée principalement en l'hiver - début du printemps, causée par de grandes ruptures de pentes. Le transfert était plus étrange, se produisant presque exclusivement au début du printemps subordonné aux conditions d'écoulement et en automne lors de longues pluies. Les orages d'été n'affectèrent guère les dépôts, qui semblent dépendre de leur stabilité. Les implications morpho-géologiques dans l'apport sédimentaire ont été évaluées à l'aide de MNT et études de terrain. Une classification de la topographie basée sur la pente a permis de charactériser le mode de production et transfert. Une analyse de stabilité de pente à partir des structures de roches a permis d'estimer la susceptibilité à la rupture. Les zones sources modélisées comprennent plus de 97% des chutes de blocs observées et les bilans sédimentaires sont corrélés à la densité de ruptures potentielles. Ce travail d'analyses des morphologies du terrain et de susceptibilité à la rupture documente la dynamique sédimentaire pour l'estimation quantitative des zones érosives induisant l'activité torrentielle. Le développement des formes d'érosion a été évalué par l'analyse de leur géométrie avec celle des ruptures potentielles et avec la direction de la fréquence maximale des joints. Les structures de roches, mais en particulier les dièdres et les discontinuités dominantes, semblent être très influents dans les mécanismes d'érosion affectant les bassins rocheux. Ils représentent des zones de faiblesse exploitées en priorité par les processus de démantèlement et d'érosion, encourageant l'initiation de ravines et couloirs, mais aussi leur propagation. L'incorporation du control géologique dans les processus de surface contribue à une meilleure compréhension de l'évolution topographique de bassins actifs. Un algorithme de flux sédimentaire a été implémenté dans un modèle en cascade, lequel divise le bassin en biefs et en systèmes individuels répondant aux processus. Chaque unité inclut de façon simple les informations géomorpologiques et celles du flux sédimentaire dérivées à partir de SIG et de cartographie de terrain. Cet outil permet la simulation des transferts de masse dans les chenaux, considérants la variabilité de l'apport et son transport, et aide à réduire l'incertitude liée à la prédiction de bilans sédimentaires torrentiels. Ce travail vise très humblement d'éclairer quelques aspects de la dynamique sédimentaire en milieu torrentiel.

Modeling Merging Behavior at Lane Drops, InTrans Projects 13-466 and 06-277, 2015

In work-zone configurations where lane drops are present, merging of traffic at the taper presents an operational concern. In addition, as flow through the work zone is reduced, the relative traffic safety of the work zone is also reduced. Improving work-zone flow-through merge points depends on the behavior of individual drivers. By better understanding driver behavior, traffic control plans, work zone policies, and countermeasures can be better targeted to reinforce desirable lane closure merging behavior, leading to both improved safety and work-zone capacity. The researchers collected data for two work-zone scenarios that included lane drops with one scenario on the Interstate and the other on an urban arterial roadway. The researchers then modeled and calibrated these scenarios in VISSIM using real-world speeds, travel times, queue lengths, and merging behaviors (percentage of vehicles merging upstream and near the merge point). Once built and calibrated, the researchers modeled strategies for various countermeasures in the two work zones. The models were then used to test and evaluate how various merging strategies affect safety and operations at the merge areas in these two work zones.

Business Process Modeling in Software Requirements Engineering for Small and Medium Software Projects

Vaatimusmäärittelyn tavoitteena on luoda halutun järjestelmän kokonaisen, yhtenäisen vaatimusluettelon vaatimusten määrittämiseksi käsitteellisellä tasolla. Liiketoimintaprosessien mallintaminen on varsin hyödyllinen vaatimusmäärittelyn varhaisissa vaiheissa. Tämä työ tutkii liiketoimintaprosessien mallintamista tietojärjestelmien kehittämistä varten. Nykyään on olemassa erilaisia liiketoimintaprosessien mallintamiseen tarkoitettuja tekniikoita. Tämä työ tarkastaa liiketoimintaprosessien mallintamisen periaatteet ja näkökohdat sekä eri mallinnustekniikoita. Uusi menetelmä, joka on suunniteltu erityisesti pienille ja keskisuurille ohjelmistoprojekteille, on kehitetty prosessinäkökohtien ja UML-kaavioiden perusteella.

Horizontal Slug Flow in a Large-Size Pipeline: Experimentation and Modeling

The knowledge of the slug flow characteristics is very important when designing pipelines and process equipment. When the intermittences typical in slug flow occurs, the fluctuations of the flow variables bring additional concern to the designer. Focusing on this subject the present work discloses the experimental data on slug flow characteristics occurring in a large-size, large-scale facility. The results were compared with data provided by mechanistic slug flow models in order to verify their reliability when modelling actual flow conditions. Experiments were done with natural gas and oil or water as the liquid phase. To compute the frequency and velocity of the slug cell and to calculate the length of the elongated bubble and liquid slug one used two pressure transducers measuring the pressure drop across the pipe diameter at different axial locations. A third pressure transducer measured the pressure drop between two axial location 200 m apart. The experimental data were compared with results of Camargo's1 algorithm (1991, 1993), which uses the basics of Dukler & Hubbard's (1975) slug flow model, and those calculated by the transient two-phase flow simulator OLGA.

Large-Size AlGaN/GaN HEMT Large-Signal Electrothermal Characterization and Modeling for Wireless Digital Communications

The rapid growth in high data rate communication systems has introduced new high spectral efficient modulation techniques and standards such as LTE-A (long term evolution-advanced) for 4G (4th generation) systems. These techniques have provided a broader bandwidth but introduced high peak-to-average power ratio (PAR) problem at the high power amplifier (HPA) level of the communication system base transceiver station (BTS). To avoid spectral spreading due to high PAR, stringent requirement on linearity is needed which brings the HPA to operate at large back-off power at the expense of power efficiency. Consequently, high power devices are fundamental in HPAs for high linearity and efficiency. Recent development in wide bandgap power devices, in particular AlGaN/GaN HEMT, has offered higher power level with superior linearity-efficiency trade-off in microwaves communication. For cost-effective HPA design to production cycle, rigorous computer aided design (CAD) AlGaN/GaN HEMT models are essential to reflect real response with increasing power level and channel temperature. Therefore, large-size AlGaN/GaN HEMT large-signal electrothermal modeling procedure is proposed. The HEMT structure analysis, characterization, data processing, model extraction and model implementation phases have been covered in this thesis including trapping and self-heating dispersion accounting for nonlinear drain current collapse. The small-signal model is extracted using the 22-element modeling procedure developed in our department. The intrinsic large-signal model is deeply investigated in conjunction with linearity prediction. The accuracy of the nonlinear drain current has been enhanced through several issues such as trapping and self-heating characterization. Also, the HEMT structure thermal profile has been investigated and corresponding thermal resistance has been extracted through thermal simulation and chuck-controlled temperature pulsed I(V) and static DC measurements. Higher-order equivalent thermal model is extracted and implemented in the HEMT large-signal model to accurately estimate instantaneous channel temperature. Moreover, trapping and self-heating transients has been characterized through transient measurements. The obtained time constants are represented by equivalent sub-circuits and integrated in the nonlinear drain current implementation to account for complex communication signals dynamic prediction. The obtained verification of this table-based large-size large-signal electrothermal model implementation has illustrated high accuracy in terms of output power, gain, efficiency and nonlinearity prediction with respect to standard large-signal test signals.

The use of public participation and economic appraisal for public involvement in large-scale hydropower projects: Case study of the Nam Theun 2 Hydropower Project

Gaining public acceptance is one of the main issues with large-scale low-carbon projects such as hydropower development. It has been recommended by the World Commission on Dams that to gain public acceptance, publicinvolvement is necessary in the decision-making process (WCD, 2000). As financially-significant actors in the planning and implementation of large-scale hydropowerprojects in developing country contexts, the paper examines the ways in which publicinvolvement may be influenced by international financial institutions. Using the casestudy of the NamTheun2HydropowerProject in Laos, the paper analyses how publicinvolvement facilitated by the Asian Development Bank had a bearing on procedural and distributional justice. The paper analyses the extent of publicparticipation and the assessment of full social and environmental costs of the project in the Cost-Benefit Analysis conducted during the projectappraisal stage. It is argued that while efforts were made to involve the public, there were several factors that influenced procedural and distributional justice: the late contribution of the Asian Development Bank in the projectappraisal stage; and the issue of non-market values and discount rate to calculate the full social and environmental costs.

Fractional order modeling of large three-dimensional RC networks

An incidence matrix analysis is used to model a three-dimensional network consisting of resistive and capacitive elements distributed across several interconnected layers. A systematic methodology for deriving a descriptor representation of the network with random allocation of the resistors and capacitors is proposed. Using a transformation of the descriptor representation into standard state-space form, amplitude and phase admittance responses of three-dimensional random RC networks are obtained. Such networks display an emergent behavior with a characteristic Jonscher-like response over a wide range of frequencies. A model approximation study of these networks is performed to infer the admittance response using integral and fractional order models. It was found that a fractional order model with only seven parameters can accurately describe the responses of networks composed of more than 70 nodes and 200 branches with 100 resistors and 100 capacitors. The proposed analysis can be used to model charge migration in amorphous materials, which may be associated to specific macroscopic or microscopic scale fractal geometrical structures in composites displaying a viscoelastic electromechanical response, as well as to model the collective responses of processes governed by random events described using statistical mechanics.