Ansätze der mathematischen Modellierung ermöglichen die Analyse der dynamischen Eigenschaften biologischer Systeme und den Einfluß spezifischer Funktionen. Das Ziel dieser Arbeit ist es verschiedene Aspekte der Interaktionen zwischen Wirt und Krankheitserregern zu analysieren. In Kapitel 3 diskutiere ich ein Modell der zellulären Antwort auf Hitzeschockstress im Pilz Candida albicans. Das Modell in Form von gewöhnlichen Differentialgleichungen erörtert mehrere Aspekte des Systems, wie z.B. die erworbene Thermotoleranz und eine perfekte Anpassung an die Beanspruchung durch die Temperaturwechsel. Im Rahmen der Interaktionen zwischen Wirt und Krankheitserreger ist die Studie relevant, da die Entwicklung von Fieber eine primäre Antwort des Organismus auf eine Pilzinvasion ist. Die Dynamik von C. albicans Virulenzfaktoren, wie z.B. der Übergang vom Hefe- zum Hyphenstadium, und die Abwehrmechanismen des Wirts bestimmen den Zustand des Pilzes, d.h. ob er als Kommensale oder Krankheitserreger vorkommt. Mit Hilfe einer agenten-basierten Modellierungstechnik, in Kapitel 4, untersuche ich die Auswirkungen potenzieller medikamentöser Behandlungen von Pilzpopulationen und ihre Effektivität. In Kapitel 5 analysiere ich die Dynamik der C. albicans Hefe- und Hyphenpopulationen unter der Annahme, das zwischen den Individuen beider Populationen paarweise Wechselwirkungen bestehen, die zusätzlich von Fresszellen und Ernährungsbedingungen beeinflusst werden. Das erste Modell basiert auf den Prinzipien der Spieltheorie. Aus dieser Studie lässt sich die Hypothese aufstellen, dass sich im Verlauf der Infektion die evolutionäre Spieldynamik von der Snowdrift Spieldynamik in Richtung Gefangendilemma verschiebt. Im zweiten Modell untersuche ich die Umschaltraten zwischen Hefen und Hyphen. Das Modell zeigt, dass in Pilzpopulationen die Ausprägung verschiedener Phänotypen der Grund für die erhöhte Überlebensfähigkeit der Population sein könnte. / Mathematical modeling approaches facilitate the analysis of dynamic properties of mechanisms triggering specific functions of biological systems. Through this work I aim to shed light on various aspects of host-pathogen interactions. In Chapter 3, I discuss a model of heat shock stress response activated in the fungus Candida albicans. The model in form of ordinary differential equations reveals several features of the system, such as acquired thermotolerance and a perfect molecular adaptation to the thermal insult. The study is relevant in the context of host-pathogen interactions since development of fever is a primary host response to fungal invasion. The dynamics of C. albicans virulence factors, e.g., yeast to hypha transition, and defense mechanisms of the host determine the state of the fungi, i.e. whether to act as a commensal or as a foe. Through application of an agent-based modeling technique, in Chapter 4, I investigate effects of potential drug treatments on fungal populations and their effectivity in the fungal clearance. In Chapter 5, I analyze the dynamics of candida yeast and hyphal populations assuming pairwise interactions influenced by phagocytic cells and nutritional conditions. The first model is based on game theory principles. From the study it can be hypothesized that during the course of infection the evolutionary game dynamics shift from Snowdrift game dynamics toward Prisoners’ dilemma. In the second model, I examine switching rates between yeast and hypha. The model reveals that phenotypic variations may occur in order to increase the fitness of the population.

The research in the field of travel demand modeling is driven by the need to understand individuals’ behavior in the context of travel-related decisions as accurately as possible. In this regard, the activity-based approach to modeling travel demand has received substantial attention in the past decade, both in the research arena as well as in practice. At the same time, recent efforts have been focused on more fully realizing the potential of activity-based models by explicitly recognizing the multi-dimensional nature of activity-travel decisions. However, as more behavioral elements/dimensions are added, the dimensionality of the model systems tends to explode, making the estimation of such models all but infeasible using traditional inference methods. As a result, analysts and practitioners often trade-off between recognizing attributes that will make a model behaviorally more representative (from a theoretical viewpoint) and being able to estimate/implement a model (from a practical viewpoint). An alternative approach to deal with the estimation complications arising from multi-dimensional choice situations is the technique of composite marginal likelihood (CML). This is an estimation technique that is gaining substantial attention in the statistics field, though there has been relatively little coverage of this method in transportation and other fields. The CML approach is a conceptually and pedagogically simpler simulation-free procedure (relative to traditional approaches that employ simulation techniques), and has the advantage of reproducibility of the results. Under the usual regularity assumptions, the CML estimator is consistent, unbiased, and asymptotically normally distributed. The discussion above indicates that the CML approach has the potential to contribute in the area of travel demand modeling in a significant way. For example, the approach can be used to develop conceptually and behaviorally more appealing models to examine individuals’ travel decisions in a joint framework. The overarching goal of the current research work is to demonstrate the applicability of the CML approach in the area of activity-travel demand modeling and to highlight the enhanced features of the choice models estimated using the CML approach. The goal of the dissertation is achieved in three steps as follows: (1) by evaluating the performance of the CML approach in multivariate situations, (2) by developing multidimensional choice models using the CML approach, and (3) by demonstrating applications of the multidimensional choice models developed in the current dissertation. / text

No description available.

The general topic of our thesis is forward looking behavior in strategic situations. Mixing theoretical and experimental analysis, we document how strategic thinking is affected by the specific features of a dynamic interaction. The overarching result is that the information regarding decisions that are close to the current one, receive a qualitatively different consideration, with respect to distant ones. That is, the actual decisions are based on reasoning over a limited number of steps, close to actual decison node. We capture this feature of behavior both in a strategic (limited backward induction) and in a non-strategic (limited farsightedness) set up, and we identify relevant consequences on the outcome of the interaction, which powerfullly explain many observed experimental regularities.<p>In the first essay, we present a general out-of-equilibrium framework for strategic thinking in sequential games. It assumes the agents to take decisions on restricted game trees, according to their (limited) foresight level, following backward induction. Therefore we talk of limited backward induction (LBI). We test for LBI using a variant of the race game. Our design allows to identify restricted game trees and backward reasoning, thus properly disentangling LBI behavior. The results provide strong support in favor of LBI. Most players solve intermediate tasks - i.e. restricted games - without reasoning on the terminal histories. Only a small fraction of subjects play close to equilibrium, and (slow) convergence toward it appears, though only in the base game. An intermediate task keeps the subjects off the equilibrium path longer than in the base game. The results cannot be rationalized using the most popular models of strategic reasoning, let alone equilibrium analysis.<p>In the second essay, a subtle implication of the model is investigated: the sensitivity of the players’ foresight to the accessibility and completeness of the information they have, using a Centipede game. By manipulating the way in which information is provided to subjects, we show that reduced availability of information is sufficient to shift the distribution of take-nodes further from the equilibrium prediction. On the other hand, similar results are obtained in a treatment where reduced availability of information is combined with an attempt to elicit preferences for reciprocity, through the presentation of the centipede as a repeated trust game. Our results could be interpreted as cognitive limitations being more effective than preferences in determining (shifts in) behavior in our experimental centipede. Furthermore our results are at odds with the recent ones in Cox [2012], suggesting caution in generalizing their results. Reducing the availability of information may hamper backward induction or induce myopic behavior, depending on the strategic environment.<p>The third essay consists of an experimental investigation of farsighted versus myopic behavior in network formation. Pairwise stability Jackson and Wolinsky [1996] is the standard stability concept in network formation. It assumes myopic behavior of the agents in the sense that they do not forecast how others might react to their actions. Assuming that agents are perfectly farsighted, related stability concepts have been proposed. We design a simple network formation experiment to test these extreme theories, but find evidence against both of them: the subjects are consistent with an intermediate rule of behavior, which we interpret as a form of limited farsightedness. On aggregate, the selection among multiple pairwise stable networks (and the performance of farsighted stability) crucially depends on the level of farsightedness needed to sustain them, and not on efficiency or cooperative considerations. Individual behavior analysis corroborates this interpretation, and suggests, in general, a low level of farsightedness (around two steps) on the part of the agents. / Doctorat en Sciences économiques et de gestion / info:eu-repo/semantics/nonPublished

The purpose of this research is to study the detection of temporal changes between two (or more) multimodal images satellites, i.e., between two different imaging modalities acquired by two heterogeneous sensors, giving for the same scene two images encoded differently and depending on the nature of the sensor used for each acquisition. The two (or multiple) multimodal satellite images are acquired and coregistered at two different dates, usually before and after an event. In this study, we propose new models belonging to different categories of multimodal change detection in remote sensing imagery. As a first contribution, we present a new constraint scenario expressed on every pair of pixels existing in the before and after image change. A second contribution of our work is to propose a spatio-temporal textural gradient operator expressed with complementary norms and also a new filtering strategy of the difference map resulting from this operator. Another contribution consists in constructing an observation field from a pair of pixels and to infer a solution maximum a posteriori sense. A fourth contribution is proposed which consists to build a common feature space for the two heterogeneous images. Our fifth contribution lies in the modeling of patterns of change by anomalies and on the analysis of reconstruction errors which we propose to learn a non-supervised model from a training base consisting only of patterns of no-change in order that the built model reconstruct the normal patterns (non-changes) with a small reconstruction error. In the sixth contribution, we propose a pairwise learning architecture based on a pseudosiamese CNN network that takes as input a pair of data instead of a single data and constitutes two partly uncoupled CNN parallel network streams (descriptors) followed by a decision network that includes fusion layers and a loss layer in the sense of the entropy criterion. The proposed models are enough flexible to be used effectively in the monomodal change detection case. / Cette recherche a pour objet l’étude de la détection de changements temporels entre deux (ou plusieurs) images satellitaires multimodales, i.e., avec deux modalités d’imagerie différentes acquises par deux capteurs hétérogènes donnant pour la même scène deux images encodées différemment suivant la nature du capteur utilisé pour chacune des prises de vues. Les deux (ou multiples) images satellitaires multimodales sont prises et co-enregistrées à deux dates différentes, avant et après un événement. Dans le cadre de cette étude, nous proposons des nouveaux modèles de détection de changement en imagerie satellitaire multimodale semi ou non supervisés. Comme première contribution, nous présentons un nouveau scénario de contraintes exprimé sur chaque paire de pixels existant dans l’image avant et après changement. Une deuxième contribution de notre travail consiste à proposer un opérateur de gradient textural spatio-temporel exprimé avec des normes complémentaires ainsi qu’une nouvelle stratégie de dé-bruitage de la carte de différence issue de cet opérateur. Une autre contribution consiste à construire un champ d’observation à partir d’une modélisation par paires de pixels et proposer une solution au sens du maximum a posteriori. Une quatrième contribution est proposée et consiste à construire un espace commun de caractéristiques pour les deux images hétérogènes. Notre cinquième contribution réside dans la modélisation des zones de changement comme étant des anomalies et sur l’analyse des erreurs de reconstruction dont nous proposons d’apprendre un modèle non-supervisé à partir d’une base d’apprentissage constituée seulement de zones de non-changement afin que le modèle reconstruit les motifs de non-changement avec une faible erreur. Dans la dernière contribution, nous proposons une architecture d’apprentissage par paires de pixels basée sur un réseau CNN pseudo-siamois qui prend en entrée une paire de données au lieu d’une seule donnée et est constituée de deux flux de réseau (descripteur) CNN parallèles et partiellement non-couplés suivis d’un réseau de décision qui comprend de couche de fusion et une couche de classification au sens du critère d’entropie. Les modèles proposés s’avèrent assez flexibles pour être utilisés efficacement dans le cas des données-images mono-modales.

<p>In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.

Cette thèse est un recueil de trois articles sur la théorie microéconomique. Les deux premiers traitent de la question de la course vers le bas lorsque les gouvernements se livrent à la concurrence pour certains facteurs mobiles. Le troisième article propose une extension du problème d'appariement plusieurs-à-un en y introduisant des agents de tailles différentes. Dans le premier article, nous montrons comment le résultat standard de course vers le bas (race-to-the-bottom) peut être évité en introduisant du bien public dans un modèle de compétition fiscale. Notre économie comporte deux juridictions peuplées par de la main-d’œuvre parfaitement mobile répartie en deux catégories : qualifiée et non-qualifiée. Les gouvernements, en poursuivant un objectif Rawlsien (max-min), annoncent simultanément leur projet d'investissement en bien public avant d'adopter une politique de taxation non-linéaire du revenu. Les travailleurs, après avoir observé la politique de taxation des différents gouvernements et leurs promesses d'investissement en bien publique, choisissent chacun un lieu de résidence et une offre de travail. Ainsi, les gouvernements atteignent leurs objectifs de redistribution en cherchant à attirer de la main-d’œuvre productive à travers la fourniture de bien public en plus d'une politique de taxation favorable. Nous montrons qu'il existe des équilibres où les travailleurs qualifiés paient une taxe strictement positive. En outre, lorsque l'information sur le type des travailleurs est privée, il existe, pour certaines valeurs des paramètres, des équilibres où la main-d’œuvre non-qualifiée bénéficie d'un transfert net (ou subvention) de la part du gouvernement. Dans le second article, nous étudions comment le modèle standard de compétition des prix à la Bertrand avec des produits différenciés pourrait fournir des informations utiles pour les programmes de citoyenneté par investissement dans les Caraïbes. Nous montrons que lorsque les pays peuvent être classés en deux types en fonction de la taille de leur demande, l'imposition d'un prix minimum uniforme et d'un quota maximum appropriés amène les pays à un résultat efficace qui Pareto domine l'équilibre de Nash non coopératif. Enfin, le troisième article explore une extension du problème standard d'appariement plusieurs-à-un en y incorporant des agents de tailles différentes (familles de réfugiés) d'un côté, à assigner à des foyers de capacités différentes de l'autre. La taille d'une famille de réfugiés représente le nombre de membres qui la compose. Une caractéristique spécifique à ce modèle est qu'il n'autorise pas de répartir les membres d'une même famille entre différents foyers. Il est bien connu que, dans ces conditions, bon nombre de propriétés désirables des règles d'appariement s'effondrent. Nous faisons donc l'hypothèse des priorités croissantes avec la taille pour chaque foyer, c'est-à-dire qu'une famille d'accueil préférerait toujours un plus grand nombre de réfugiés tant que la capacité de son foyer le permet. Nous montrons qu'un appariement stable par paire existe toujours sous cette hypothèse et nous proposons un mécanisme pour le trouver. Nous montrons que notre mécanisme est non-manipulable du point de vue des réfugiés : aucun groupe de réfugiés ne pourrait tirer profit d'une déclaration truquée de leurs préférences. Notre mécanisme est également optimal pour les réfugiés en ce sens qu'il n'existe aucun autre mécanisme stable par paire qui serait plus profitable à tous les réfugiés. / This thesis is a collection of three articles on microeconomic theory. The first two articles are concerned with the issue of race-to-the-bottom when governments engage in competition for some mobile factor. The third article proposes an extension for the many-to-one matching problem by introducing different-size agents. In the first article, we show how the standard race-to-the-bottom result can be avoided by introducing public good into a tax competition model. Our economy has two jurisdictions populated by perfectly mobile workers divided into two categories: skilled and unskilled. Governments, in pursuit of a Rawlsian objective (max-min), simultaneously announce their plans for investing in public good before deploying a nonlinear income tax schedule. After observing the tax schedules of the governments and their promises to invest in public good, each worker chooses a place of residence and a supply of labour. Thus, governments achieve their redistribution objectives by seeking to attract productive labour through the provision of public goods in addition to favorable taxation policy. We show that there exist equilibria where skilled workers pay a strictly positive tax. In addition, when information on the type of workers is private, there are equilibria for certain parameter values in which unqualified workers receive a net transfer (or subsidy) from the government. In the second article, we investigate how the Bertrand standard price competition with differentiated products could provide useful insight for Citizenship By Investment programs in the Caribbean. We show that when countries can be classified into two types according to the size of their demand, imposing appropriate uniform minimum price and maximum quota brings countries to an efficient outcome that Pareto dominates the Non-Cooperative Nash Equilibrium. Finally. in the third article, we explore an extension of the standard many-to-one matching problem by incorporating different-size agents (refugee families) on the many side of the market, to be assigned to entities (homes) with different capacities on the other side. A specific feature of this model is that it does not allow refugee families to be split between several homes. It is well known that many of the desirable properties of matching rules are unachievable in this framework. We introduce size-monotonic priority ranking over refugee families for each home, that is, a host family (home) would always prefer a greater number of members of refugee families until its capacity constraint binds. We show that a pairwise stable matching always exists under this assumption and we propose a mechanism to find it. We show that our mechanism is strategy-proof for refugees: no refugee family could benefit from misrepresenting his preferences. Our mechanism is also refugees optimal pairwise stable in the sense that there is no other pairwise stable mechanism that would be more profitable to all refugees.

Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.