<div>Researchers and scientists across various areas face the perennial challenge of selecting experimental conditions or inputs for computer simulations in order to achieve promising results.</div><div> The aim of conducting these experiments could be to study the production of a material that has great applicability.</div><div> One might also be interested in accurately modeling and analyzing a simulation of a physical process through a high-fidelity computer code.</div><div> The presence of noise in the experimental observations or simulator outputs, called aleatory uncertainty, is usually accompanied by limited amount of data due to budget constraints.</div><div> This gives rise to what is known as epistemic uncertainty. </div><div> This problem of designing of experiments with limited number of allowable experiments or simulations under aleatory and epistemic uncertainty needs to be treated in a Bayesian way.</div><div> The aim of this thesis is to extend the state-of-the-art in Bayesian optimal design of experiments where one can optimize and infer statistics of the expensive experimental observation(s) or simulation output(s) under uncertainty.</div>

Els mecanismes de regulaci o de les c el lules poden ser modelats per controlar i entendre la biologia cel lular. Diferents nivells d'abstracci o s'utilitzen per descriure els processos biol ogics. En aquest treball s'han utilitzat grafs i equacions diferencials per modelar les interaccions cel lulars tant qualitativament com quantitativa. En aquest treball s'han analitzat dades d'interacci o i activitat de diferents organismes, E. coli i S. cerevisiae: xarxes d'interacci o prote na-prote na, de regulaci o de la transcripci o, i metab oliques, aix com per ls d'expressi o gen omica i prote omica. De la rica varietat de mesures de grafs, una variable important d'aquestes xarxes biol ogiques es la distribuci o de grau, i he aplicat eines d'an alisi estad stica per tal de caracteritzar-la. En tots els casos estudiats les distribucions de grau tenen una forma de cua pesada, per o la majoria d'elles presenten difer encies signi catives respecte un model de llei de pot encia, d'acord amb proves estad stiques. D'altra banda, cap de les xarxes podrien ser assignades de forma inequvoca a cap distribuci o testejada. Pel que fa a un nivell m es microsc opic, hem utilitzat equacions diferencials per estudiar la din amica de models de diversos sistemes bioqu mics. En primer lloc, una eina de programari anomenada ByoDyn ha estat creada des de zero. L'eina permet realitzar simulacions deterministes i estoc astiques, analitzar models mitjan cant estimaci o de par ametres, sensibilitat i an alisi d'identi cabilitat, aix com dissenyar optimament experiments. S'ha creat una interf cie web que ofereix la possibilitat d'interactuar amb el programa d'una manera gr a ca, independentment de la con guraci o de l'usuari, permetent l'execuci o del programa en diferents entorns computacionals. Finalment, hem aplicat un protocol de disseny experimental optim en un model multicel lular de l'embriog enesi en vertebrats. / Regulatory mechanisms of cells can be modelled to control and under- stand cellular biology. Di erent levels of abstraction are used to describe biological processes. In this work we have used graphs and di erential equations to model cellular interactions qualitatively and quantitatively. From di erent organisms, E. coli and S. cerevisiae, we have analysed data available for they complete interaction and activity networks. At the level of interaction, the protein-protein interaction network, the tran- scriptional regulatory networks and the metabolic network have been studied; for the activity, both gene and protein pro les of the whole or- ganism have been examined. From the rich variety of graph measures, one of primer importance is the degree distribution. I have applied sta- tistical analysis tools to such biological networks in order to characterise the degree distribution. In all cases the studied degree distributions have a heavy-tailed shape, but most of them present signi cant di erences from a power-law model according to a statistical test. Moreover, none of the networks could be unequivocally assigned to any of the tested distribution. On the other hand, in a more ne-grained view, I have used di erential equations to model dynamics of biochemical systems. First, a software tool called ByoDyn has been created from scratch incorporating a fairly complete range of analysis methods. Both deterministic and stochas- tic simulations can be performed, models can be analysed by means of parameter estimation, sensitivity, identi ability analysis, and optimal ex- perimental design. Moreover, a web interface has been created that pro- vides with the possibility interact with the program in a graphical man- ner, independent of the user con guration, allowing the execution of the program at di erent computational environments. Finally, we have ap- plied a protocol of optimal experimental design on a multicellular model of embryogenesis.

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The elimination of drugs from the body is in many cases performed by the liver. Much could be gained if an accurate prediction of this process could be made early in the development of new drugs. However, for the elimination to occur, the drug molecule needs first to get inside the liver cell. Disposition is the expression used to encapsulate both elimination and distribution. This thesis presents novel approaches and models based on simple in vitro systems for the investigation of processes involved in the hepatic drug disposition. An approach to the estimation of enzyme kinetics based on substrate depletion data from cell fractions was thoroughly evaluated through experiments and simulations. The results that it provided were confirmed to be accurate and robust. In addition, a new experimental setup suitable for a screening environment, i.e., for a reduced number of samples, was generated through optimal experimental design. The optimization suggested that sampling at late time points over a wide range of concentration was the most advantageous. A model, based on data from primary hepatocytes in suspension, for the investigation of cellular disposition of metabolized drugs was developed. Information on the relative importance of metabolism and membrane protein related distribution was obtained by analysis of changes in the kinetics by specific inhibition of the various processes. The model was evaluated by comparing the results to those obtained from an in vivo study analyzed with an especially constructed mechanistic PBPK model. These investigations showed that the suggested model produced good predictions of the relative importance of metabolism and carrier mediated membrane transport for hepatic disposition. In conclusion, new approaches for the investigation of processes involved in hepatic disposition were developed. These methods were shown to be robust and increased the output of information from already commonly implemented in vitro systems.

La répression catabolique désigne un mode de régulation très répandu chez les bactéries, par lequel les enzymes nécessaires à l'import et la digestion de certaines sources carbonées sont réprimées en présence d'une source carbonée avantageuse, par exemple le glucose dans le cas de la bactérie E. coli. Nous proposons une approche mathématique et expérimentale pour séparer et évaluer l'importance des différents mécanismes de la répression catabolique. En particulier, nous montrons que l'AMP cyclique et l'état physiologique de la cellule jouent tous deux un rôle important dans la régulation de gènes sujets à la ré- pression catabolique. Nous présentons également des travaux méthodologiques réalisés dans le cadre de cette étude et contribuant à l'étude des réseaux de régulation génique en général. En particulier, nous étudions l'applicabilité de l'approximation quasi-stationnaire utilisée pour la réduction de modèles, et présentons des méthodes pour l'estimation robuste de taux de croissance, activité de promoteur, et concentration de protéines à partir de données bruitées provenant d'expériences avec gènes rapporteur. / Carbon Catabolite Repression (CCR) is a wide-spread mode of regulation in bacteria by which the enzymes necessary for the uptake and utilization of some carbon sources are repressed in presence of a preferred carbon source, e.g., glucose in the case of Escherichia coli . We propose a joint mathematical and experimental approach to separate and evaluate the importance of the different components of CCR. In particular, we show that both cyclic AMP and the global physiology of the cell play a major role in the regulation of the cAMP-dependent genes affected by CCR. We also present methodological improvements for the study of gene regulatory networks in general. In partic- ular, we examine the applicability of the Quasi-Steady-State-Approximation to reduce mathematical gene expression models, and provide robust meth- ods for the robust estimation of growth rate, promoter activity, and protein concentration from noisy kinetic reporter experiments.

In chemical and energy engineering, it is crucial to understand the thermodynamic properties of fluids and solids and their phase behavior. Equations of state have been proven to be extremely helpful in representing these properties. Today, the most accurate modeling approaches for equations of state are empirical methods. These methods typically depend on the expert knowledge of the modeler, as well as on the quantity and quality of the available data. To accelerate the modeling process, the potential of symbolic regression, a method that not only fits the parameters of a given model, but also seeks its functional form, is investigated. Accurate modeling of thermodynamic properties is impossible, without a reliable data base. While different data acquisition methods exist, carefully conducted measurements are the most important data acquisition method. However, setting up experiments and conducting the measurements are often time-consuming and expensive. Therefore, reducing the experimental effort without sacrificing information for model development is highly desirable. Optimal experimental design is a methodology for planning measurements that aims to be the most informative regarding the uncertainty in parameter estimates or predictions of a given model. In the present thesis, the optimal experimental design algorithm was adapted to consider different equilibrium times for changes in temperature and pressure. The main problems for the individual application of symbolic regression and optimal experimental design are that for symbolic regression, there are often not enough data available, and for optimal experimental design, the underlying model is rarely known. For this reason, the potential of combining optimal experimental design with symbolic regression for efficient thermodynamic property modeling was investigated within an iterative data acquisition and modeling process. Optimal experimental design and symbolic regression, individually and together, were found to have the potential to accelerate the data acquisition and modeling of thermodynamic properties, which is also of interest for other applications.:Nomenclature Abstract Kurzfassung Introduction Results Summary and Outlook Bibliography Appendix / In der Chemie- und Energietechnik ist es von entscheidender Bedeutung, die thermodynamischen Eigenschaften von Flüssigkeiten und Feststoffen und ihr Phasenverhalten zu verstehen. Zustandsgleichungen haben sich bei der Darstellung dieser Eigenschaften als äußerst hilfreich erwiesen. Die genauesten Modellierungsansätze für Zustandsgleichungen sind heute empirische Methoden. Diese Methoden hängen in der Regel vom Fachwissen des Modellierers sowie von der Menge und Qualität der verfügbaren Daten ab. Um den Modellierungsprozess zu beschleunigen, wird das Potenzial der symbolischen Regression untersucht, einer Methode, die nicht nur die Parameter eines gegebenen Modells anpasst, sondern auch dessen funktionale Form sucht. Eine genaue Modellierung der thermodynamischen Eigenschaften ist ohne eine zuverlässige Datenbasis nicht möglich. Zwar gibt es verschiedene Methoden der Datenerfassung, doch sind sorgfältig durchgeführte Messungen die wichtigste Methode der Datenerfassung. Der Aufbau von Experimenten und die Durchführung der Messungen sind jedoch oft zeitaufwändig und teuer. Daher ist es äußerst wünschenswert, den experimentellen Aufwand zu verringern, ohne dabei Informationen für die Modellentwicklung zu verlieren. Optimale Versuchsplanung ist eine Methodik zur Planung von Messungen die darauf abzielt, die Unsicherheit in den Parameterschätzungen oder Vorhersagen eines gegebenen Modells so informativ wie möglich zu gestalten. In der vorliegenden Arbeit wurde der Algorithmus für die optimale Versuchsplanung so angepasst, dass unterschiedliche Gleichgewichtszeiten für Temperatur- und Druckänderungen berücksichtigt werden. Die Hauptprobleme bei der individuellen Anwendung von symbolischer Regression und optimaler Versuchsplanung sind, dass für die symbolische Regression oft nicht genügend Daten zur Verfügung stehen und bei der optimalen Versuchsplanung das zugrunde liegende Modell selten bekannt ist. Aus diesem Grund wurde das Potenzial der Kombination von optimaler Versuchsplanung und symbolischer Regression für eine effiziente Modellierung thermodynamischer Eigenschaften im Rahmen eines iterativen Datenerfassungs- und Modellierungsprozesses untersucht. Es wurde festgestellt, dass die optimale Versuchsplanung und die symbolische Regression, sowohl einzeln als auch zusammen, das Potenzial haben, die Datenerfassung und Modellierung thermodynamischer Eigenschaften zu beschleunigen, was auch für andere Anwendungen von Interesse ist.:Nomenclature Abstract Kurzfassung Introduction Results Summary and Outlook Bibliography Appendix

This thesis addresses issues related to the simulation and optimization of the injection molding of short fiber-reinforced plastics (SFRPs). The injection molding process is modeled by a two phase flow problem. The simulation of the two phase flow is accompanied by the solution of the Folgar-Tucker equation (FTE) for the simulation of the moments of fiber orientation densities. The FTE requires the solution of the so called 'closure problem'', i.e. the representation of the 4th order moments in terms of the 2nd order moments. In the absence of fiber-fiber interactions and isotropic initial fiber density, the FTE admits an analytical solution in terms of elliptic integrals. From these elliptic integrals, the closure problem can be solved by a simple numerical inversion. Part of this work derives approximate inverses and analytical inverses for special cases of fiber orientation densities. Furthermore a method is presented to generate rational functions for the computation of arbitrary moments in terms of the 2nd order closure parameters. Another part of this work treats the determination of effective material properties for SFRPs by the use of FFT-based homogenization methods. For these methods a novel discretization scheme, the 'staggered grid'' method, was developed and successfully tested. Furthermore the so called 'composite voxel'' approach was extended to nonlinear elasticity, which improves the approximation of material properties at the interfaces and allows the reduction of the model order by several magnitudes compared to classical approaches. Related the homogenization we investigate optimal experimental designs to robustly determine effective elastic properties of SFRPs with the least number of computer simulations. Finally we deal with the topology optimization of injection molded parts, by extending classical SIMP-based topology optimization with an approximate model for the fiber orientations. Along with the compliance minimization by topology optimization we also present a simple shape optimization method for compensation of part warpage for an black-box production process.:Acknowledgments v Abstract vii Chapter 1. Introduction 1 1.1 Motivation 1 1.2 Nomenclature 3 Chapter 2. Numerical simulation of SFRP injection molding 5 2.1 Introduction 5 2.2 Injection molding technology 5 2.3 Process simulation 6 2.4 Governing equations 8 2.5 Numerical implementation 18 2.6 Numerical examples 25 2.7 Conclusions and outlook 27 Chapter 3. Numerical and analytical methods for the exact closure of the Folgar-Tucker equation 35 3.1 Introduction 35 3.2 The ACG as solution of Jeffery's equation 35 3.3 The exact closure 36 3.4 Carlson-type elliptic integrals 37 3.5 Inversion of R_D-system 40 3.6 Moment tensors of the angular central Gaussian distribution on the n-sphere 49 3.7 Experimental evidence for ACG distribution hypothesis 54 3.8 Conclusions and outlook 60 Chapter 4. Homogenization of SFRP materials 63 4.1 Introduction 63 4.2 Microscopic and macroscopic model of SFRP materials 63 4.3 Effective linear elastic properties 65 4.4 The staggered grid method 68 4.5 Model order reduction by composite voxels 80 4.6 Optimal experimental design for parameter identification 93 Chapter 5. Optimization of parts produced by SFRP injection molding 103 5.1 Topology optimization 103 5.2 Warpage compensation 110 Chapter 6. Conclusions and perspectives 115 Appendix A. Appendix 117 A.1 Evaluation of R_D in Python 117 A.2 Approximate inverse for R_D in Python 117 A.3 Inversion of R_D using Newton's/Halley's method in Python 117 A.4 Inversion of R_D using fixed point method in Python 119 A.5 Moment computation using SymPy 120 A.6 Fiber collision test 122 A.7 OED calculation of the weighting matrix 123 A.8 OED Jacobian of objective and constraints 123 Appendix B. Theses 125 Bibliography 127 / Diese Arbeit befasst sich mit Fragen der Simulation und Optimierung des Spritzgießens von kurzfaserverstärkten Kunststoffen (SFRPs). Der Spritzgussprozess wird durch ein Zweiphasen-Fließproblem modelliert. Die Simulation des Zweiphasenflusses wird von der Lösung der Folgar-Tucker-Gleichung (FTE) zur Simulation der Momente der Faserorientierungsdichten begleitet. Die FTE erfordert die Lösung des sogenannten 'Abschlussproblems'', d. h. die Darstellung der Momente 4. Ordnung in Form der Momente 2. Ordnung. In Abwesenheit von Faser-Faser-Wechselwirkungen und anfänglich isotroper Faserdichte lässt die FTE eine analytische Lösung durch elliptische Integrale zu. Aus diesen elliptischen Integralen kann das Abschlussproblem durch eine einfache numerische Inversion gelöst werden. Ein Teil dieser Arbeit leitet approximative Inverse und analytische Inverse für spezielle Fälle von Faserorientierungsdichten her. Weiterhin wird eine Methode vorgestellt, um rationale Funktionen für die Berechnung beliebiger Momente in Bezug auf die Abschlussparameter 2. Ordnung zu generieren. Ein weiterer Teil dieser Arbeit befasst sich mit der Bestimmung effektiver Materialeigenschaften für SFRPs durch FFT-basierte Homogenisierungsmethoden. Für diese Methoden wurde ein neuartiges Diskretisierungsschema 'staggerd grid'' entwickelt und erfolgreich getestet. Darüber hinaus wurde der sogenannte 'composite voxel''-Ansatz auf die nichtlineare Elastizität ausgedehnt, was die Approximation der Materialeigenschaften an den Grenzflächen verbessert und die Reduzierung der Modellordnung um mehrere Größenordnungen im Vergleich zu klassischen Ansätzen ermöglicht. Im Zusammenhang mit der Homogenisierung untersuchen wir optimale experimentelle Designs, um die effektiven elastischen Eigenschaften von SFRPs mit der geringsten Anzahl von Computersimulationen zuverlässig zu bestimmen. Schließlich beschäftigen wir uns mit der Topologieoptimierung von Spritzgussteilen, indem wir die klassische SIMP-basierte Topologieoptimierung um ein Näherungsmodell für die Faserorientierungen erweitern. Neben der Compliance-Minimierung durch Topologieoptimierung stellen wir eine einfache Formoptimierungsmethode zur Kompensation von Teileverzug für einen Black-Box-Produktionsprozess vor.:Acknowledgments v Abstract vii Chapter 1. Introduction 1 1.1 Motivation 1 1.2 Nomenclature 3 Chapter 2. Numerical simulation of SFRP injection molding 5 2.1 Introduction 5 2.2 Injection molding technology 5 2.3 Process simulation 6 2.4 Governing equations 8 2.5 Numerical implementation 18 2.6 Numerical examples 25 2.7 Conclusions and outlook 27 Chapter 3. Numerical and analytical methods for the exact closure of the Folgar-Tucker equation 35 3.1 Introduction 35 3.2 The ACG as solution of Jeffery's equation 35 3.3 The exact closure 36 3.4 Carlson-type elliptic integrals 37 3.5 Inversion of R_D-system 40 3.6 Moment tensors of the angular central Gaussian distribution on the n-sphere 49 3.7 Experimental evidence for ACG distribution hypothesis 54 3.8 Conclusions and outlook 60 Chapter 4. Homogenization of SFRP materials 63 4.1 Introduction 63 4.2 Microscopic and macroscopic model of SFRP materials 63 4.3 Effective linear elastic properties 65 4.4 The staggered grid method 68 4.5 Model order reduction by composite voxels 80 4.6 Optimal experimental design for parameter identification 93 Chapter 5. Optimization of parts produced by SFRP injection molding 103 5.1 Topology optimization 103 5.2 Warpage compensation 110 Chapter 6. Conclusions and perspectives 115 Appendix A. Appendix 117 A.1 Evaluation of R_D in Python 117 A.2 Approximate inverse for R_D in Python 117 A.3 Inversion of R_D using Newton's/Halley's method in Python 117 A.4 Inversion of R_D using fixed point method in Python 119 A.5 Moment computation using SymPy 120 A.6 Fiber collision test 122 A.7 OED calculation of the weighting matrix 123 A.8 OED Jacobian of objective and constraints 123 Appendix B. Theses 125 Bibliography 127