Niche, distribution and global change : modeling insights into biogeography and conservation biology Olivier Broennimann

RESUME Les évidences montrant que les changements globaux affectent la biodiversité s'accumulent. Les facteurs les plus influant dans ce processus sont les changements et destructions d'habitat, l'expansion des espèces envahissantes et l'impact des changements climatiques. Une évaluation pertinente de la réponse des espèces face à ces changements est essentielle pour proposer des mesures permettant de réduire le déclin actuel de la biodiversité. La modélisation de la répartition d'espèces basée sur la niche (NBM) est l'un des rares outils permettant cette évaluation. Néanmoins, leur application dans le contexte des changements globaux repose sur des hypothèses restrictives et demande une interprétation critique. Ce travail présente une série d'études de cas investiguant les possibilités et limitations de cette approche pour prédire l'impact des changements globaux. Deux études traitant des menaces sur les espèces rares et en danger d'extinction sont présentées. Les caractéristiques éco-géographiques de 118 plantes avec un haut degré de priorité de conservation sont revues. La prévalence des types de rareté sont analysées en relation avec leur risque d'extinction UICN. La revue souligne l'importance de la conservation à l'échelle régionale. Une évaluation de la rareté à échelle globale peut être trompeuse pour certaine espèces car elle ne tient pas en compte des différents degrés de rareté que présente une espèce à différentes échelles spatiales. La deuxième étude test une approche pour améliorer l'échantillonnage d'espèces rares en incluant des phases itératives de modélisation et d'échantillonnage sur le terrain. L'application de l'approche en biologie de la conservation (illustrée ici par le cas du chardon bleu, Eryngium alpinum), permettrait de réduire le temps et les coûts d'échantillonnage. Deux études sur l'impact des changements climatiques sur la faune et la flore africaine sont présentées. La première étude évalue la sensibilité de 227 mammifères africains face aux climatiques d'ici 2050. Elle montre qu'un nombre important d'espèces pourrait être bientôt en danger d'extinction et que les parcs nationaux africains (principalement ceux situé en milieux xériques) pourraient ne pas remplir leur mandat de protection de la biodiversité dans le futur. La seconde étude modélise l'aire de répartition en 2050 de 975 espèces de plantes endémiques du sud de l'Afrique. L'étude propose l'inclusion de méthodes améliorant la prédiction des risques liés aux changements climatiques. Elle propose également une méthode pour estimer a priori la sensibilité d'une espèce aux changements climatiques à partir de ses propriétés écologiques et des caractéristiques de son aire de répartition. Trois études illustrent l'utilisation des modèles dans l'étude des invasions biologiques. Une première étude relate l'expansion de la laitue sáuvage (Lactuca serriola) vers le nord de l'Europe en lien avec les changements du climat depuis 250 ans. La deuxième étude analyse le potentiel d'invasion de la centaurée tachetée (Centaures maculosa), une mauvaise herbe importée en Amérique du nord vers 1890. L'étude apporte la preuve qu'une espèce envahissante peut occuper une niche climatique différente après introduction sur un autre continent. Les modèles basés sur l'aire native prédisent de manière incorrecte l'entier de l'aire envahie mais permettent de prévoir les aires d'introductions potentielles. Une méthode alternative, incluant la calibration du modèle à partir des deux aires où l'espèce est présente, est proposée pour améliorer les prédictions de l'invasion en Amérique du nord. Je présente finalement une revue de la littérature sur la dynamique de la niche écologique dans le temps et l'espace. Elle synthétise les récents développements théoriques concernant le conservatisme de la niche et propose des solutions pour améliorer la pertinence des prédictions d'impact des changements climatiques et des invasions biologiques. SUMMARY Evidences are accumulating that biodiversity is facing the effects of global change. The most influential drivers of change in ecosystems are land-use change, alien species invasions and climate change impacts. Accurate projections of species' responses to these changes are needed to propose mitigation measures to slow down the on-going erosion of biodiversity. Niche-based models (NBM) currently represent one of the only tools for such projections. However, their application in the context of global changes relies on restrictive assumptions, calling for cautious interpretations. In this thesis I aim to assess the effectiveness and shortcomings of niche-based models for the study of global change impacts on biodiversity through the investigation of specific, unsolved limitations and suggestion of new approaches. Two studies investigating threats to rare and endangered plants are presented. I review the ecogeographic characteristic of 118 endangered plants with high conservation priority in Switzerland. The prevalence of rarity types among plant species is analyzed in relation to IUCN extinction risks. The review underlines the importance of regional vs. global conservation and shows that a global assessment of rarity might be misleading for some species because it can fail to account for different degrees of rarity at a variety of spatial scales. The second study tests a modeling framework including iterative steps of modeling and field surveys to improve the sampling of rare species. The approach is illustrated with a rare alpine plant, Eryngium alpinum and shows promise for complementing conservation practices and reducing sampling costs. Two studies illustrate the impacts of climate change on African taxa. The first one assesses the sensitivity of 277 mammals at African scale to climate change by 2050 in terms of species richness and turnover. It shows that a substantial number of species could be critically endangered in the future. National parks situated in xeric ecosystems are not expected to meet their mandate of protecting current species diversity in the future. The second study model the distribution in 2050 of 975 endemic plant species in southern Africa. The study proposes the inclusion of new methodological insights improving the accuracy and ecological realism of predictions of global changes studies. It also investigates the possibility to estimate a priori the sensitivity of a species to climate change from the geographical distribution and ecological proprieties of the species. Three studies illustrate the application of NBM in the study of biological invasions. The first one investigates the Northwards expansion of Lactuca serriola L. in Europe during the last 250 years in relation with climate changes. In the last two decades, the species could not track climate change due to non climatic influences. A second study analyses the potential invasion extent of spotted knapweed, a European weed first introduced into North America in the 1890s. The study provides one of the first empirical evidence that an invasive species can occupy climatically distinct niche spaces following its introduction into a new area. Models fail to predict the current full extent of the invasion, but correctly predict areas of introduction. An alternative approach, involving the calibration of models with pooled data from both ranges, is proposed to improve predictions of the extent of invasion on models based solely on the native range. I finally present a review on the dynamic nature of ecological niches in space and time. It synthesizes the recent theoretical developments to the niche conservatism issues and proposes solutions to improve confidence in NBM predictions of the impacts of climate change and species invasions on species distributions.

Implicit methods for qualitative modeling of gene regulatory networks.

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

Modeling competencies and capabilities in knowledge intensive business environment

Tämän diplomityön päämääränä oli tutkia Perloksen teknologiaosaamisia. Perloksen tavoitteena on tulevaisuudessa yhdistää ja soveltaa uusia teknologioita ja älykkäitä materiaaleja muovimekaniikkaan.Ideana oli mallintaa Perloksen osaamisia ja osaamisgapeja ottaen huomioon heidän tulevaisuuden visionsa. Projektituotteena osaamisten mallintamisessa oli Perlos Healthcaren asiakkaan analysoiva mittauslaite. Tutkimuksen arvo on huomattava sillä tunnistamalla osaamisensa ja kyvykkyytensä yritys pystyy luomaan paremman tarjooman vastatessaan koko ajan kasvaviin asiakasvaatimuksiin. Tutkimus on osa TEKESin rahoittamaa LIIMA -projektia. Työn ensimmäisessä osassa esitellään osaamiseen ja partneroitumiseen liittyviä teorioita. Osaamisten mallintaminen tehtiin Excel -pohjaisella työkalulla. Se sisältää projektituotteeseen liittyen osaamisriippuvuuksien mallintamisen ja gap -analyysin. Yhtenä tutkimusmetodina käytettiin haastattelututkimusta. Työ ja sen tulokset antavat operatiivista hyötyä teknologioiden ja markkinoiden välisessä kentässä.

A System-Level Simulation Model for a Protocol Processor

As the development of integrated circuit technology continues to follow Moore’s law the complexity of circuits increases exponentially. Traditional hardware description languages such as VHDL and Verilog are no longer powerful enough to cope with this level of complexity and do not provide facilities for hardware/software codesign. Languages such as SystemC are intended to solve these problems by combining the powerful expression of high level programming languages and hardware oriented facilities of hardware description languages. To fully replace older languages in the desing flow of digital systems SystemC should also be synthesizable. The devices required by modern high speed networks often share the same tight constraints for e.g. size, power consumption and price with embedded systems but have also very demanding real time and quality of service requirements that are difficult to satisfy with general purpose processors. Dedicated hardware blocks of an application specific instruction set processor are one way to combine fast processing speed, energy efficiency, flexibility and relatively low time-to-market. Common features can be identified in the network processing domain making it possible to develop specialized but configurable processor architectures. One such architecture is the TACO which is based on transport triggered architecture. The architecture offers a high degree of parallelism and modularity and greatly simplified instruction decoding. For this M.Sc.(Tech) thesis, a simulation environment for the TACO architecture was developed with SystemC 2.2 using an old version written with SystemC 1.0 as a starting point. The environment enables rapid design space exploration by providing facilities for hw/sw codesign and simulation and an extendable library of automatically configured reusable hardware blocks. Other topics that are covered are the differences between SystemC 1.0 and 2.2 from the viewpoint of hardware modeling, and compilation of a SystemC model into synthesizable VHDL with Celoxica Agility SystemC Compiler. A simulation model for a processor for TCP/IP packet validation was designed and tested as a test case for the environment.

Mathematical simulation parameters for drying of cassava starch pellets

Based on experimental tests, it was obtained the equations for drying, equilibrium moisture content, latent heat of vaporization of water contained in the product and the equation of specific heat of cassava starch pellets, essential parameters for realizing modeling and mathematical simulation of mechanical drying of cassava starch for a new technique proposed, consisting of preformed by pelleting and subsequent artificial drying of starch pellets. Drying tests were conducted in an experimental chamber by varying the air temperature, relative humidity, air velocity and product load. The specific heat of starch was determined by differential scanning calorimetry. The generated equations were validated through regression analysis, finding an appropriate correlation of the data, which indicates that by using these equations, can accurately model and simulate the drying process of cassava starch pellets.

Power cycling lifetime estimation of IGBT power modules based on chip temperature modeling

In this doctoral thesis, methods to estimate the expected power cycling life of power semiconductor modules based on chip temperature modeling are developed. Frequency converters operate under dynamic loads in most electric drives. The varying loads cause thermal expansion and contraction, which stresses the internal boundaries between the material layers in the power module. Eventually, the stress wears out the semiconductor modules. The wear-out cannot be detected by traditional temperature or current measurements inside the frequency converter. Therefore, it is important to develop a method to predict the end of the converter lifetime. The thesis concentrates on power-cycling-related failures of insulated gate bipolar transistors. Two types of power modules are discussed: a direct bonded copper (DBC) sandwich structure with and without a baseplate. Most common failure mechanisms are reviewed, and methods to improve the power cycling lifetime of the power modules are presented. Power cycling curves are determined for a module with a lead-free solder by accelerated power cycling tests. A lifetime model is selected and the parameters are updated based on the power cycling test results. According to the measurements, the factor of improvement in the power cycling lifetime of modern IGBT power modules is greater than 10 during the last decade. Also, it is noticed that a 10 C increase in the chip temperature cycle amplitude decreases the lifetime by 40%. A thermal model for the chip temperature estimation is developed. The model is based on power loss estimation of the chip from the output current of the frequency converter. The model is verified with a purpose-built test equipment, which allows simultaneous measurement and simulation of the chip temperature with an arbitrary load waveform. The measurement system is shown to be convenient for studying the thermal behavior of the chip. It is found that the thermal model has a 5 C accuracy in the temperature estimation. The temperature cycles that the power semiconductor chip has experienced are counted by the rainflow algorithm. The counted cycles are compared with the experimentally verified power cycling curves to estimate the life consumption based on the mission profile of the drive. The methods are validated by the lifetime estimation of a power module in a direct-driven wind turbine. The estimated lifetime of the IGBT power module in a direct-driven wind turbine is 15 000 years, if the turbine is located in south-eastern Finland.

A simulation model of the optimal maintenance strategy: conceptual agent-based approach

In this Master’s thesis agent-based modeling has been used to analyze maintenance strategy related phenomena. The main research question that has been answered was: what does the agent-based model made for this study tell us about how different maintenance strategy decisions affect profitability of equipment owners and maintenance service providers? Thus, the main outcome of this study is an analysis of how profitability can be increased in industrial maintenance context. To answer that question, first, a literature review of maintenance strategy, agent-based modeling and maintenance modeling and optimization was conducted. This review provided the basis for making the agent-based model. Making the model followed a standard simulation modeling procedure. With the simulation results from the agent-based model the research question was answered. Specifically, the results of the modeling and this study are: (1) optimizing the point in which a machine is maintained increases profitability for the owner of the machine and also the maintainer with certain conditions; (2) time-based pricing of maintenance services leads to a zero-sum game between the parties; (3) value-based pricing of maintenance services leads to a win-win game between the parties, if the owners of the machines share a substantial amount of their value to the maintainers; and (4) error in machine condition measurement is a critical parameter to optimizing maintenance strategy, and there is real systemic value in having more accurate machine condition measurement systems.

Gas-solid two-phase flow in the riser of circulating fluidized beds: mathematical modelling and numerical simulation

A mathematical model is developed for gas-solids flows in circulating fluidized beds. An Eulerian formulation is followed based on the two-fluids model approach where both the fluid and the particulate phases are treated as a continuum. The physical modelling is discussed, including the formulation of boundary conditions and the description of the numerical methodology. Results of numerical simulation are presented and discussed. The model is validated through comparison to experiment, and simulation is performed to investigate the effects on the flow hydrodynamics of the solids viscosity.

Towards sustainable Iron- and steelmaking with economic optimization

The iron and steelmaking industry is among the major contributors to the anthropogenic emissions of carbon dioxide in the world. The rising levels of CO2 in the atmosphere and the global concern about the greenhouse effect and climate change have brought about considerable investigations on how to reduce the energy intensity and CO2 emissions of this industrial sector. In this thesis the problem is tackled by mathematical modeling and optimization using three different approaches. The possibility to use biomass in the integrated steel plant, particularly as an auxiliary reductant in the blast furnace, is investigated. By pre-processing the biomass its heating value and carbon content can be increased at the same time as the oxygen content is decreased. As the compression strength of the preprocessed biomass is lower than that of coke, it is not suitable for replacing a major part of the coke in the blast furnace burden. Therefore the biomass is assumed to be injected at the tuyere level of the blast furnace. Carbon capture and storage is, nowadays, mostly associated with power plants but it can also be used to reduce the CO2 emissions of an integrated steel plant. In the case of a blast furnace, the effect of CCS can be further increased by recycling the carbon dioxide stripped top gas back into the process. However, this affects the economy of the integrated steel plant, as the amount of top gases available, e.g., for power and heat production is decreased. High quality raw materials are a prerequisite for smooth blast furnace operation. High quality coal is especially needed to produce coke with sufficient properties to ensure proper gas permeability and smooth burden descent. Lower quality coals as well as natural gas, which some countries have in great volumes, can be utilized with various direct and smelting reduction processes. The DRI produced with a direct reduction process can be utilized as a feed material for blast furnace, basic oxygen furnace or electric arc furnace. The liquid hot metal from a smelting reduction process can in turn be used in basic oxygen furnace or electric arc furnace. The unit sizes and investment costs of an alternative ironmaking process are also lower than those of a blast furnace. In this study, the economy of an integrated steel plant is investigated by simulation and optimization. The studied system consists of linearly described unit processes from coke plant to steel making units, with a more detailed thermodynamical model of the blast furnace. The results from the blast furnace operation with biomass injection revealed the importance of proper pre-processing of the raw biomass as the composition of the biomass as well as the heating value and the yield are all affected by the pyrolysis temperature. As for recycling of CO2 stripped blast furnace top gas, substantial reductions in the emission rates are achieved if the stripped CO2 can be stored. However, the optimal recycling degree together with other operation conditions is heavily dependent on the cost structure of CO2 emissions and stripping/storage. The economical feasibility related to the use of DRI in the blast furnace depends on the price ratio between the DRI pellets and the BF pellets. The high amount of energy needed in the rotary hearth furnace to reduce the iron ore leads to increased CO2 emissions.

Modeling of fractal antennas

In this Master Thesis the characteristics of the chosen fractal microstrip antennas are investigated. For modeling has been used the structure of the square Serpinsky fractal curves. During the elaboration of this Master thesis the following steps were undertaken: 1) calculation and simulation of square microstrip antennа, 2) optimizing for obtaining the required characteristics on the frequency 2.5 GHz, 3) simulation and calculation of the second and third iteration of the Serpinsky fractal curves, 4) radiation patterns and intensity distribution of these antennas. In this Master’s Thesis the search for the optimal position of the port and fractal elements was conducted. These structures can be used in perspective for creation of antennas working at the same time in different frequency range.

Coolability of porous core debris beds : Effects of bed geometry and multi-dimensional flooding

This thesis addresses the coolability of porous debris beds in the context of severe accident management of nuclear power reactors. In a hypothetical severe accident at a Nordic-type boiling water reactor, the lower drywell of the containment is flooded, for the purpose of cooling the core melt discharged from the reactor pressure vessel in a water pool. The melt is fragmented and solidified in the pool, ultimately forming a porous debris bed that generates decay heat. The properties of the bed determine the limiting value for the heat flux that can be removed from the debris to the surrounding water without the risk of re-melting. The coolability of porous debris beds has been investigated experimentally by measuring the dryout power in electrically heated test beds that have different geometries. The geometries represent the debris bed shapes that may form in an accident scenario. The focus is especially on heap-like, realistic geometries which facilitate the multi-dimensional infiltration (flooding) of coolant into the bed. Spherical and irregular particles have been used to simulate the debris. The experiments have been modeled using 2D and 3D simulation codes applicable to fluid flow and heat transfer in porous media. Based on the experimental and simulation results, an interpretation of the dryout behavior in complex debris bed geometries is presented, and the validity of the codes and models for dryout predictions is evaluated. According to the experimental and simulation results, the coolability of the debris bed depends on both the flooding mode and the height of the bed. In the experiments, it was found that multi-dimensional flooding increases the dryout heat flux and coolability in a heap-shaped debris bed by 47–58% compared to the dryout heat flux of a classical, top-flooded bed of the same height. However, heap-like beds are higher than flat, top-flooded beds, which results in the formation of larger steam flux at the top of the bed. This counteracts the effect of the multi-dimensional flooding. Based on the measured dryout heat fluxes, the maximum height of a heap-like bed can only be about 1.5 times the height of a top-flooded, cylindrical bed in order to preserve the direct benefit from the multi-dimensional flooding. In addition, studies were conducted to evaluate the hydrodynamically representative effective particle diameter, which is applied in simulation models to describe debris beds that consist of irregular particles with considerable size variation. The results suggest that the effective diameter is small, closest to the mean diameter based on the number or length of particles.

Timing verification in transaction modeling

Les systèmes Matériels/Logiciels deviennent indispensables dans tous les aspects de la vie quotidienne. La présence croissante de ces systèmes dans les différents produits et services incite à trouver des méthodes pour les développer efficacement. Mais une conception efficace de ces systèmes est limitée par plusieurs facteurs, certains d'entre eux sont: la complexité croissante des applications, une augmentation de la densité d'intégration, la nature hétérogène des produits et services, la diminution de temps d’accès au marché. Une modélisation transactionnelle (TLM) est considérée comme un paradigme prometteur permettant de gérer la complexité de conception et fournissant des moyens d’exploration et de validation d'alternatives de conception à des niveaux d’abstraction élevés. Cette recherche propose une méthodologie d’expression de temps dans TLM basée sur une analyse de contraintes temporelles. Nous proposons d'utiliser une combinaison de deux paradigmes de développement pour accélérer la conception: le TLM d'une part et une méthodologie d’expression de temps entre différentes transactions d’autre part. Cette synergie nous permet de combiner dans un seul environnement des méthodes de simulation performantes et des méthodes analytiques formelles. Nous avons proposé un nouvel algorithme de vérification temporelle basé sur la procédure de linéarisation des contraintes de type min/max et une technique d'optimisation afin d'améliorer l'efficacité de l'algorithme. Nous avons complété la description mathématique de tous les types de contraintes présentées dans la littérature. Nous avons développé des méthodes d'exploration et raffinement de système de communication qui nous a permis d'utiliser les algorithmes de vérification temporelle à différents niveaux TLM. Comme il existe plusieurs définitions du TLM, dans le cadre de notre recherche, nous avons défini une méthodologie de spécification et simulation pour des systèmes Matériel/Logiciel basée sur le paradigme de TLM. Dans cette méthodologie plusieurs concepts de modélisation peuvent être considérés séparément. Basée sur l'utilisation des technologies modernes de génie logiciel telles que XML, XSLT, XSD, la programmation orientée objet et plusieurs autres fournies par l’environnement .Net, la méthodologie proposée présente une approche qui rend possible une réutilisation des modèles intermédiaires afin de faire face à la contrainte de temps d’accès au marché. Elle fournit une approche générale dans la modélisation du système qui sépare les différents aspects de conception tels que des modèles de calculs utilisés pour décrire le système à des niveaux d’abstraction multiples. En conséquence, dans le modèle du système nous pouvons clairement identifier la fonctionnalité du système sans les détails reliés aux plateformes de développement et ceci mènera à améliorer la "portabilité" du modèle d'application.

Application du concept des transactions pour la modélisation et la simulation multicoeur des systèmes sur puce

Avec la complexité croissante des systèmes sur puce, de nouveaux défis ne cessent d’émerger dans la conception de ces systèmes en matière de vérification formelle et de synthèse de haut niveau. Plusieurs travaux autour de SystemC, considéré comme la norme pour la conception au niveau système, sont en cours afin de relever ces nouveaux défis. Cependant, à cause du modèle de concurrence complexe de SystemC, relever ces défis reste toujours une tâche difficile. Ainsi, nous pensons qu’il est primordial de partir sur de meilleures bases en utilisant un modèle de concurrence plus efficace. Par conséquent, dans cette thèse, nous étudions une méthodologie de conception qui offre une meilleure abstraction pour modéliser des composants parallèles en se basant sur le concept de transaction. Nous montrons comment, grâce au raisonnement simple que procure le concept de transaction, il devient plus facile d’appliquer la vérification formelle, le raffinement incrémental et la synthèse de haut niveau. Dans le but d’évaluer l’efficacité de cette méthodologie, nous avons fixé l’objectif d’optimiser la vitesse de simulation d’un modèle transactionnel en profitant d’une machine multicoeur. Nous présentons ainsi l’environnement de modélisation et de simulation parallèle que nous avons développé. Nous étudions différentes stratégies d’ordonnancement en matière de parallélisme et de surcoût de synchronisation. Une expérimentation faite sur un modèle du transmetteur Wi-Fi 802.11a a permis d’atteindre une accélération d’environ 1.8 en utilisant deux threads. Avec 8 threads, bien que la charge de travail des différentes transactions n’était pas importante, nous avons pu atteindre une accélération d’environ 4.6, ce qui est un résultat très prometteur.