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Grasslands cover 40% of the earth’s land area and provide numerous valuable ecosystem services. However, climate change, global land use change and increasing intensive anthropogenic interventions make grasslands to one of the most endangered ecosystem types in the world. Effective protection in the future requires a fundamental understanding of the dynamics of grasslands and their major drivers. Field experiments have been conducted for impact analyses, for example, with different management intensities, plant community composition and altered climatic conditions. Complementary, ecological models allow to extend the analysis to long-term effects of changes as well as to a deeper understanding of the underlying ecological processes. In this thesis, an individual-based grassland model and network science were applied to understand the community structure and dynamics emerging from individual plant interactions – in relation to plant traits, ecological processes, environmental and anthropogenic impacts, and the small-scale spatial distribution of plants. In the first study, an individual-based process-oriented grassland model was parameterized to simulate field data of a local biodiversity experiment using the concept of plant functional types. The influence of various functional plant traits and ecological processes on grassland productivity and functional composition were analyzed. Different functional plant traits showed partly contrasting effects on plant growth. With regard to the modeled ecological processes, competition for space between plants affected grassland productivity more than shading of plants. In the second study, the parameterized grassland model was used to analyze the impact of functional diversity, mowing frequency and air temperature on ecological processes that lead to changes in grassland productivity. The model reproduced the increase of biomass yields with functional diversity as observed in the field experiment. Modeled plant competition for space showed to be the dominant process and was responsible for an increase in biomass yields in more frequently mown grasslands. In the third study, an approach to generate a regionally transferable parameterization of the grassland model is presented. The impact of management, environment and climate change on productivity and functional composition of grasslands was analyzed within a German-wide scenario analysis. Management intensity had more influence on grassland productivity than environmental factors and correlations of productivity with environmental factors become stronger in less managed grasslands. Climate change showed to have only a minor influence on simulated vegetation attributes. In the fourth study, network science was applied to forest megaplots to quantify the spatial neighborhood structure of species-rich ecosystems. Networks at the individual-tree and tree-species levels revealed similar structures at three investigated forest sites. Tropical tree species coexisted in small-scale networks and only up to 51% of all possible connections between species pairs were realized. A null community analysis showed that details on the tree position and tree size have no major influence on the network structures identified. In summary, this thesis presents the development of advanced methods and analysis tools as well as their application to vegetation ecosystems with high diversity. Thereby, complex structures and dynamics of ecological systems could be systematically explored by combining ecological models with extensive field measurements.

In today's network-dependent society, cyber attacks with network worms have become the predominant threat to confidentiality, integrity, and availability of network computing resources. Despite ongoing research efforts, there is still no comprehensive network-security solution aimed at controling large-scale worm propagation. The aim of this work is fivefold: (1) Developing an accurate combinatorial model of worm propagation that can facilitate the analysis of worm control strategies, (2) Building an accurate epidemiological model for the propagation of a worm employing local strategies, (3) Devising distributed architecture and algorithms for detection of worm scanning activities, (4) Designing effective control strategies against the worm, and (5) Simulation of the developed models and strategies on large, scale-free graphs representing real-world communication networks. The proposed pair-approximation model uses the information about the network structure--order, size, degree distribution, and transitivity. The empirical study of propagation on large scale-free graphs is in agreement with the theoretical analysis of the proposed pair-approximation model. We, then, describe a natural generalization of the classical cops-and-robbers game--a combinatorial model of worm propagation and control. With the help of this game on graphs, we show that the problem of containing the worm is NP-hard. Six novel near-optimal control strategies are devised: combination of static and dynamic immunization, reactive dynamic and invariant dynamic immunization, soft quarantining, predictive traffic-blocking, and contact-tracing. The analysis of the predictive dynamic traffic-blocking, employing only local information, shows that the worm can be contained so that 40\% of the network nodes are not affected. Finally, we develop the Detection via Distributed Blackholes architecture and algorithm which reflect the propagation strategy used by the worm and the salient properties of the network. Our distributed detection algorithm can detect the worm scanning activity when only 1.5% of the network has been affected by the propagation. The proposed models and algorithms are analyzed with an individual-based simulation of worm propagation on realistic scale-free topologies.

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Essay #1 – Factors influencing the risk of falls in the construction industry: a review of the evidence Falls are a significant public health risk and a leading cause of nonfatal and fatal injuries among construction workers worldwide. A more comprehensive understanding of casual factors leading to fall incidents is essential to prevent falls in the construction industry. However, an extensive overview of causal factors is missing from the literature. In this paper, 536 articles on factors contributing to the risk of falls were retrieved. One hundred twenty-one (121) studies met the criteria for relevance and quality to be coded, and were synthesized to provide an overview. In lieu of the homogeneity needed across studies to conduct a structured meta-analysis, a literature synthesis method based on macro-variables was advanced. This method provides a flexible approach to aggregating previous findings and assessing agreement across those studies. Factors commonly associated with falls included working surfaces and platforms, workers’ safety behaviors and attitudes, and construction structure and facilities. Significant differences across qualitative and quantitative studies were found in terms of focus, and areas with limited agreement in previous research were identified. Findings contribute to research on the causes of falls in construction, developing engineering controls, informing policy and intervention design to reduce the risk of falls, and improving research synthesis methods. Essay #2 – Review of quantitative studies of interventions for responding to infectious disease outbreaks We reviewed the modeling and retrospective literature on responding to outbreaks of infectious diseases in humans and animals. Unlike routine immunization and control efforts, outbreak response activities require rapid reactive actions to address an urgent or emergent situation. We focused our review on characterizing the types of diseases analyzed, the interventions used, and the models employed. Out of the 211 studies identified, we find that the majority focus on a few diseases (influenza, foot and mouth disease, smallpox, measles, and hepatitis). We identified 34 distinct interventions explored in these studies that fall under the general categories of vaccination, prophylaxis, quarantine/isolation, contact restriction, exposure reduction, killing/slaughtering, and surveillance. A large number of studies (141) use simulation/analytical models to analyze outbreak response strategies. We identify key factors contributing to the effectiveness of different interventions that target high-risk individuals, trace infected contacts, or use a ring to delineate geographical boundaries for an intervention. Essay #3 – Development of an individual-based model for polioviruses: implications of the selection of network type and outcome metrics We developed an individual-based (IB) model to explore the stochastic attributes of state transitions, the heterogeneity of the individual interactions, and the impact of different network structure choices on the poliovirus transmission process in the context of understanding the dynamics of outbreaks. We used a previously published differential equation-based model to develop the IB model and inputs. To explore the impact of different types of networks, we implemented a total of 26 variations of six different network structures in the IB model. We found that the choice of network structure plays a critical role in the model estimates of cases and the dynamics of outbreaks. This study provides insights about the potential use of an IB model to support policy analyses related to managing the risks of polioviruses and shows the importance of assumptions about network structure. / Ph. D.

Computational modelling of populations of cells has been applied to further understanding in a range of biological fields, from cell sorting to tumour development. The ability to analyse the emergent population-level effects of variation at the cellular and subcellular level makes it a powerful approach. As more detailed models have been proposed, the demand for computational power has increased. While developments in microchip technology continue to increase the power of individual compute units available to the research community, the use of parallel computing offers an immediate increase in available computing power. To make full use of parallel computing technology it is necessary to develop specialised algorithms. To that end, this thesis is concerned with the development, implementation and application of a novel parallel algorithm for the simulation of an off-lattice individual-based model of a population of cells. We first use the Message Passing Interface to develop a parallel algorithm for the overlapping spheres model which we implement in the Chaste software library. We draw on approaches for parallelising molecular dynamics simulations to develop a spatial decomposition approach to dividing data between processors. By using functions designed for saving and loading the state of simulations, our implementation allows for the parallel simulation of all subcellular models implemented in Chaste, as well as cell-cell interactions that depend on any of the cell state variables. Our implementation allows for faithful replication of model cells that migrate between processors during a simulation. We validate our parallel implementation by comparing results with the extensively tested serial implementation in Chaste. While the use of the Message Passing Interface means that our algorithm may be used on shared- and distributed-memory systems, we find that parallel performance is limited due to high communication costs. To address this we apply a series of optimisations that improve the scaling of our algorithm both in terms of compute time and memory consumption for given benchmark problems. To demonstrate an example application of our work to a biological problem, we extend our algorithm to enable parallel simulation of the Subcellular Element Model (S.A. Sandersius and T.J. Newman. Phys. Biol., 5:015002, 2008). By considering subcellular biomechanical heterogeneity we study the impact of a stiffer nuclear region within cells on the initiation of buckling of a compressed epithelial layer. The optimised parallel algorithm decreases computation time for a single simulation in this study by an order of magnitude, reducing computation time from over a week to a single day.

Uma efetiva ação de conservação depende de um claro entendimento de como as espécies respondem às características ambientais, em particular à cobertura, configuração espacial e qualidade do habitat. No entanto, nem sempre esses dados estruturais da paisagem estão disponíveis em extensão e escala compatíveis com o planejamento ambiental. Ademais, a obtenção de dados empíricos sobre as respostas das espécies à estrutura da paisagem é longa e custosa, o que exige abordagens alternativas para o entendimento destas relações. Esta tese teve dois objetivos principais: i. gerar informações atualizadas sobre as características espaciais dos remanescentes de Mata Atlântica, estimando a quantidade e distribuição de mata existente ao longo de todo o Domínio fitogeográfico, além de avaliar a distribuição da floresta em relação a características do relevo; ii. avaliar, através de modelos de simulação, o efeito da estrutura da paisagem, qualidade de habitat e atributos das espécies, em processos associados à movimentação de aves. A Mata Atlântica é uma das florestas com maior biodiversidade do planeta, mas está também entre as mais ameaçadas, dado o avançado estágio de perda e fragmentação do hábitat, o que a coloca entre os principais hotspots do planeta. Na primeira parte desta tese, estimamos que a cobertura da Mata Atlântica está entre 12 a 16% (em função de erros de mapeamento), o que representa um valor intermediário em relação às estimativas anteriores (7-8%, ou 22-23%). Os dados de configuração mostram uma situação pouco favorável para conservação das espécies. Mais de 80% dos fragmentos remanescentes são menores que 50 hectares, tamanho extremamente reduzido e incapaz de preservar a maioria das espécies florestais. Ademais, quase a metade da floresta existente está a menos de 100 m de ambientes antropizados, sendo que as áreas mais distantes da borda ficam a aproximadamente 12 km da matriz. Outro fato alarmante é a grande distância média entre os remanescentes de mata (1.440 m), o que torna difícil a movimentação de indivíduos entre fragmentos. A quantidade de unidades de conservação é extremamente reduzida, correspondendo apenas a aproximadamente 1% da Mata Atlântica original, bem abaixo dos 10% sugeridos como mínimo para a manutenção de espécies. As faixas de altitude acima de 1200 m mantêm mais de 20% da cobertura original, enquanto as faixas mais baixas conservam somente 10% da floresta. Algumas diretrizes de conservação e restauração por sub-regiões biogeográficas foram propostas, porém tais regiões apresentaram-se muito extensas para a definição de ações de manejo. Este fato nos levou a sugerir a subdivisão do domínio em 55 novos compartimentos, considerando características de clima e relevo, além dos aspectos biogeográficos. Na segunda parte desta tese, foi desenvolvido o BioDIM (Biologically scaled dispersal model), um modelo baseado em indivíduos que simula a movimentação de aves florestais calibradas para espécies encontradas na Mata Atlântica. O BioDIM inclui vários perfis (i.e. sensibilidades) de espécies, permitindo simular desde espécies muito sensíveis (preferência pelo interior dos fragmentos), até espécies moderadamente generalistas (cruzam até 120 m através de ambientes abertos). Além da sensibilidade a ambientes abertos ou de borda, a área de vida (i.e. requerimento de habitat), e o deslocamento máximo diário ou explorativo (i.e. quando o indivíduo está dispersando) também foram considerados. As simulações com o BioDIM foram feitas para 10.000 paisagens simuladas, apresentando grande variação de porcentagem (de 5 a 70%), agregação e qualidade do habitat, o que nos permitiu estudar uma ampla gama de paisagens, o que não seria viável em estudos empíricos. Os resultados sugerem as características das espécies e a estrutura da paisagem foram igualmente importantes para explicar os processos ecológicos analisados, porém a qualidade de habitat foi pouco influente. A sensibilidade das espécies foi o fator mais importante para explicar a mortalidade de indivíduos e a taxa de dispersão, sendo um fator de efeito secundário para o custo de movimentação e para a taxa de encontros entre indivíduos. A porcentagem de cobertura foi o fator mais influente para custo de movimentação, enquanto para a taxa de encontros o efeito primário foi o tamanho da área de vida. Uma surpresa foi que, ao se avaliar os efeitos para cada perfil de espécie, observou-se que a agregação de habitat foi tão importante quanto a quantidade de habitat para explicar alguns processos, independente da quantidade de habitat, oposto do que tem sido sugerido na literatura. Isto sugere que as variáveis de paisagem são importantes ao longo de todo o processo de conversão do habitat, e devem ser cuidadosamente consideradas na tomada de decisão voltada ao manejo para a conservação de espécies. / Effective conservation actions depend on a clear understanding of how species respond to environmental factors, particularly to the amount of habitat and the spatial arrangement and quality of this habitat. However, landscape structure information is not always available to the extent and scale needed to promote effective conservation planning. Additionally, acquiring biological information of how species respond to landscape structure is particularly expensive in time and money. This thesis has two main goals: i. to generate updated information about the amount and spatial distribution of the remnants of the Brazilian Atlantic Forest, combining information on the remaining forest and landscape relief; ii. untangle the effects of landscape structure, habitat quality, and species traits on ecological processes related to the movements of Atlantic Forest bird species, using simulation models. The Atlantic Forest is one of the most biodiverse regions on the planet, but is also among the most threatened because of the high degree of habitat loss and fragmentation, which confer the status of biodiversity \"hotspot\" on the region. In the first part of the thesis, I estimated that the remaining Brazilian Atlantic Forest occupies between 12-16% of its original extent (considering mapping errors), which is an intermediate estimate compared to previous ones (7-8%, or 22-23%). The spatial distribution of this forest indicates poor conditions for species conservation. More than 80% of the remaining forest is distributed in patches smaller than 50 ha, which is extremely reduced in size and incapable of preserving most of the forest species. Additionally, half of the remaining forest is less than 100 m distant from any edge, and the farthest point within any forest is about 12 km from the surrounding matrix. Another critical point is the high degree of isolation between patches (mean 1 440 m), which impedes the movement of individuals between forest fragments. Protected areas are extremely small, approximately 1% of the original extent, which is below the 10% suggested as the minimum amount for species maintenance. Higher-altitude areas (> 1200 m) retain more than 20% of the original cover; whereas in lower altitudes, such as from 400 to 800 m, only about 10% of the original forest still exists. Some conservation and restoration measures for the entire region and within biogeographical sub-regions are suggested, but I consider the subregions too extensive for defining appropriate management actions. Thus, I refined the subdivision of the entire region into 55 new sub-regions, considering climate and relief characteristics, as well as biogeographical aspects. In the second part of this thesis I developed a program called BioDIM (Biologically scaled dispersal model), an individual-based model calibrated to simulate the movement of Atlantic Forest bird species in fragmented landscapes. Five species profiles (i.e., species sensitivity) are already available in BioDIM, which allows us to simulate movements from highly sensitive species (which avoid forest edges), to moderately generalist ones (capable of crossing 120 m of open matrix). Home-range size (a surrogate for habitat amount requirement) and maximum routine and explorative distances per day can also be set. I generated 10 000 simulated landscapes, varying in habitat amount (5 to 70%), aggregation, and quality, which made it possible to evaluate landscape variability to a degree that would not be possible in real conditions. The results suggest that species traits and landscape structure were both important to explain the ecological processes, but habitat quality contributed relatively little. Species sensitivity was the prime factor in explaining dispersal rate and mortality, and had a secondary effect on movement cost and encounter rate. Habitat amount was the most influential factor to explain movement cost, and home-range size was the prime factor for encounter rate. Astonishingly, we observed that, within species profiles, habitat aggregation was as important as habitat amount to explain several ecological processes, independently of the percentage of forest amount. This is the opposite of what has been observed in the literature. These results indicate that landscape variables are important for all habitat conversion processes, and that they must be carefully considered in decision-making for species conservation management.

This dissertation examines aspects of the relationship between connectivity and the development of genetic structure in subdivided coral reef populations using both simulation and algebraic methods. The first chapter develops an object-oriented, individual based method of simulating the dynamics of genes in subdivided populations. The model is then used to investigate how changes to different components of population structure (e.g., connectivity, birth rate, population size) influence genetic structure through the use of autocorrelation analysis. The autocorrelograms also demonstrate how relationships between populations change at different spatial and temporal scales. The second chapter uses discrete multivariate distributions to model the relationship between connectivity, selection and resource use in subdivided populations. The equations provide a stochastic basis for multiple-niche polymorphism through differential resource use, and the role of scale in changing selective weightings is also considered. The third chapter uses matrix equations to study the expected development of genetic structure among Caribbean coral reefs. The results show an expected break between eastern and western portions of the Caribbean, as well as additional nested structure within the Bahamas, the central Caribbean (Jamaica and the reefs of the Nicaraguan Rise) and the Mesoamerican Barrier Reef. The matrix equations provide an efficient means of modeling the development of genetic structure in subdivided populations through time. The fourth chapter uses matrix equations to examine the expected development of genetic structure among Southeast Asian coral reefs. Projecting genetic structure reveals an expected unidirectional connection from the South China Sea into the Coral Triangle region via the Sulu Sea. Larvae appear to be restricted from moving back into the South China Sea by a cyclonic gyre in the Sulu Sea. Additional structure is also evident, including distinct clusters within the Philippines, in the vicinity of the Makassar Strait, in the Flores Sea, and near Halmahera and the Banda Sea. The ability to evaluate the expected development of genetic structure over time in subdivided populations offers a number of potential benefits, including the ability to ascertain the expected direction of gene flow, to delineate natural regions of exchange through clustering, or to identify critical areas for conservation or for managing the spread of invasive material via elasticity analysis.

La malària és encara avui en dia una malaltia que causa aproximadament un milió de morts a l'any a tot el món. La seva eradicació suposa un gran repte per a la humanitat i per a la comunitat científica, en particular. El cultiu in vitro del paràsit és essencial per al desenvolupament de nous medicaments. Els mètodes de cultiu actuals es basen en l'heurística i requereixen millores.En aquesta tesi es presenta una aproximació teòrica al procés d'infecció a eritròcits en cultius in vitro amb Plasmodium falciparum, un dels protozous paràsits causants de la malària. El treball està centrat en la construcció i avaluació de models d'una complexitat adequada per tractar els problemes específics detectats pels experts en l'àmbit, i inclou també la formulació d'algorismes de simulació i el disseny de protocols experimentals.Aquest tipus de treball requereix de la col·laboració multidisciplinària. La visió dels experts en malària es complementa amb la modelització i simulació, que permet la comprovació dels supòsits preestablerts, la comprensió de fenòmens observats i la millora dels mètodes de cultiu actuals. Així doncs, cal establir i desenvolupar eines que permetin crear, analitzar i compartir models amb grups que estudien la malària des d'altres perspectives. En aquesta tesi, s'ha optat per la modelització basada en l'individu (IbM) i orientada a la reproducció de múltiples patrons (PoM). El model s'ha formulat seguint l'ODD, un protocol estàndard en el camp de l'ecologia teòrica, que s'ha adaptat a la representació de comunitats microbianes.Els models basats en l'individu (IbMs) defineixen un conjunt de normes que regeixen el comportament de cada cèl·lula i les seves interaccions amb les altres cèl·lules i amb el seu entorn immediat. A partir d'aquestes regles, i tenint en compte una certa diversitat dins de la població i un cert grau d'aleatorietat en els processos individuals, els IbMs mostren explícitament el comportament emergent del sistema en conjunt. Complementàriament, s'han aplicat conceptes propis de la termodinàmica per tal d'entendrel'aparició de patrons macroscòpics a partir de l'estructura de la població (per exemple de la distribució de les fases d'infecció entre els glòbuls vermells infectats).Aquesta recerca ha comportat la la creació i aplicació del model i simulador INDISIM-RBC, que ha demostrat ser una bona eina per millorar la comprensió dels cultius estudiats. Es tracta d'un model mecanicista, basat en l'individu, que reprodueix quantitativament els patrons observats en cultius reals a diferents nivells de descripció, i que en prediu el comportament sota determinades condicions.Hem demostrat que INDISIM-RBC pot ser emprat per a estudiar en detall alguns aspectes del cultiu del paràsit causant de la malària que calia aclarir. Permet realitzar experiments virtuals i així impulsar noves línies de recerca i explorar noves tècniques de cultiu. En particular, INDISIM-RBC s'ha utilitzat per millorar els protocols experimentals actuals del cultius estàtics, definint la geometria òptima de l'hematòcrit i els protocols de subcultiu més adequats per als cultius continus.El treball realitzat en malària s'ha comparat amb la investigació duta a terme pel grup de recerca em relació amb d'altres comunitats microbianes. D'aquesta manera, podem estudiar les propietats emergents dels sistemes microbians en general en relació als efectes de la individualitat de la cèl·lula, la diversitat de les poblacions, l'heterogeneïtat en el medi, o el caràcter local de les interaccions, entre d'altres. Aquesta visió general proporciona eines conceptuals que poden ser emprades per refinar l'anàlisi dels processos d'infecció sota estudi. / Malaria is still a major burden that causes approximately one million deaths annually worldwide. Its eradication supposes a great challenge to the humanity and to the scientific community, in particular. In vitro cultivation of the parasite is essential for the development of new drugs. Current culture methods are based on heuristics and demand for specific improvements.The present thesis is a theoretical approach to in vitro cultivation of the protozoan parasite Plasmodium falciparum infecting human red blood cells. It mainly focuses on the process of building a model of appropriate complexity to deal with the specific demands above mentioned, but it also includes the formulation and implementation of algorithms, and the design and execution of experimental trials.This kind of work requires multidisciplinary collaboration: the insight of the experts in malaria research is complemented with modeling and simulation, which allows for checking settled assumptions, increasing the understanding on the system and improving the current culturing methods.The use of tools for building, analyzing and sharing models is an imperative to this end. In this thesis, Pattern-oriented Modeling (PoM) has been adopted as the most appropriate way for raising of models and the ODD protocol (Objectives, Design Concepts and Details) has been proposed as the standard tool for communicating them.Individual-based Modeling (IbM) has been used to tackle malaria culture systems. IbMs define a set of rules governing each cell, its interactions with others and with its immediate surroundings. From this set of rules, and taking into account diversity within the population and a certain degree of randomness in the individual processes, IbMs explicitly show the emerging behavior of the system as a whole. Methods from statistical thermodynamics have been applied to understand the emergence of macroscopic patterns from the population structure (e.g. distribution of infection stages among infected red blood cells).The research resulted in the development of the model and simulator INDISIM-RBC, which has proved to be a good tool to improve understanding of the cultures under study. It is a mechanistically rich individual-based model and it quantitatively reproduces and predicts several patterns observed in real cultures at different levels of description.We demonstrated that INDISIM-RBC can be used to study in detail several aspects of malaria cultivation that remained unclear, as well as to perform virtual experiments. Consequently, it can be used to open novel lines of research and to examine potential experimental techniques. INDISIM-RBC has also been used to improve the current experimental culturing protocols in static cultivation by obtaining the optimal geometry of the hematocrit layer and subcultivation periods in the continuous cultures.This study on malaria has been compared to the research carried out by the group regarding other microbial communities. Thereby studying general emerging properties of microbial systems in general, with regard to the effect of cell individuality, heterogeneity and diversity, the local nature of interactions; and biological and spatial complexity. In doing so, the acquired holistic view has been used to develop tools that allow for a better characterization and study of the infection process, in particular.

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