Conventional therapeutic techniques treat the patient by delivering a biotherapeutic to the entire body rather than the target tissue. In the case of chemotherapy, the biotherapeutic is a drug that kills healthy and diseased cells indiscriminately which can lead to undesirable side effects. With targeted delivery, biotherapeutics can be delivered directly to the diseased tissue significantly reducing exposure to otherwise healthy tissue. Typical composite delivery devices are minimally composed of a stimuli responsive polymer, such as poly(N-isopropylacrylamide), allowing for triggered release when heated beyond approximately 32 °C, and magnetic nanoparticles which enable targeting as well as provide a mechanism for stimulus upon alternating magnetic field heating. Although more traditional methods, such as emulsion polymerization, have been used to realize these composite devices, the synthesis is problematic. Poisonous surfactants that are necessary to prevent agglomeration must be removed from the finished polymer, increasing the time and cost of the process. This study seeks to further explore non-toxic, biocompatible, non-residual, photochemical methods of creating stimuli responsive nanogels to advance the targeted biotherapeutic delivery field. Ultraviolet photopolymerization promises to be more efficient, while ensuring safety by using only biocompatible substances. The reactants selected for nanogel fabrication were N-isopropylacrylamide as monomer, methylene bisacrylamide as cross-linker, and Irgacure 2959 as ultraviolet photo-initiator. The superparamagnetic nanoparticles for encapsulation were approximately 10 nm in diameter and composed of magnetite to enable remote delivery and enhanced triggered release properties. Early investigations into the interactions of the polymer and nanoparticles employ a pioneering experimental setup, which allows for coincident turbidimetry and alternating magnetic field heating of an aqueous solution containing both materials. Herein, a low-cost, scalable, and rapid, custom ultraviolet photo-reactor with in-situ, spectroscopic monitoring system is used to observe the synthesis as the sample undergoes photopolymerization. This method also allows in-situ encapsulation of the magnetic nanoparticles simplifying the process. Size characterization of the resulting nanogels was performed by Transmission Electron Microscopy revealing size-tunable nanogel spheres between 50 and 800 nm by varying the ratio and concentration of the reactants. Nano-Tracking Analysis indicates that the nanogels exhibit minimal agglomeration as well as provides a temperature-dependent particle size distribution. Optical characterization utilized Fourier Transform Infrared and Ultraviolet Spectroscopy to confirm successful polymerization. When samples of the nanogels encapsulating magnetic nanoparticles were subjected to an alternating magnetic field a temperature increase was observed indicating that triggered release is possible. Furthermore, a model, based on linear response theory that innovatively utilizes size distribution data, is presented to explain alternating magnetic field heating results. The results presented here will advance targeted biotherapeutic delivery and have a wide range of applications in medical sciences like oncology, gene delivery, cardiology and endocrinology.

Der erste Teil dieser Arbeit beschäftigt sich mit der Frage, welchen Einfluss kurzzeitige Schwankungen der erneuerbaren Energiequellen auf die synchrone Netzfrequenz haben. Zu diesem Zweck wird eine lineare Antworttheorie für stochastische Störungen von dynamischen Systemen auf Netzwerken hergeleitet. Anschließend wird diese Theorie verwendet, um den Einfluss von kurzfristigen Wind- und Sonnenschwankungen auf die Netzdynamik zu analysieren. Hierbei wird gezeigt, dass die Frequenzantwort des Netzes weitestgehend homogen ist, aber die Anfälligkeit für Leistungsschwankungen aufgrund von Leitungsverlusten entlang des Leistungsflusses zunimmt. Der zweite Teil der Arbeit befasst sich mit der Modellierung von netzbildenden Wechselrichterregelungen. Bislang existiert kein universelles Modell zur Beschreibung der kollektiven Dynamik solcher Systeme. Um dies zu erreichen, wird unter Ausnutzung der inhärenten Symmetrie des synchronen Betriebszustandes eine Normalform für netzbildende Akteure abgeleitet. Anschließend wird gezeigt, dass dieses Modell eine gute Annäherung an typische Wechselrichter-Dynamiken bietet, aber auch für eine datengesteuerte Modellierung gut geeignet ist. Der letzte Teil der Arbeit befasst sich mit der Analyse des Risikos von Stromausfällen, welche durch Hurrikans verursacht werden. Hohe Windgeschwindigkeiten verursachen häufig Schäden an der Übertragungsinfrastruktur, welche wiederum zu Überlastungen anderer Komponenten führen und damit eine Kaskade von Ausfällen im gesamten Netz auslösen können. Simulationen solcher Szenarien werden durch die Kombination eines meteorologischen Windmodells sowie eines Modells für kaskadierende Leitungsausfälle durchgeführt. Durch Monte-Carlo-Simulationen in einer synthetischen Nachbildung des texanischen Übertragungsnetzes können einzelne kritische Leitungen identifiziert werden, welche zu großflächigen Stromausfällen führen. / The first part of this thesis addresses the question which impact short-term renewable fluctuations have on the synchronous grid frequency. For this purpose, a linear response theory for stochastic perturbations of networked dynamical systems is derived. This theory is then used to analyze the impact of short-term wind and solar fluctuations on the grid frequency. It is shown that while the network frequency response is mainly homogenous, the susceptibility to power fluctuations is increasing along the power flow due to transmission line losses. The second part of the thesis is concerned with modeling grid-forming inverter controls. So far there exists no universal model for studying the collective dynamics of such systems. By utilizing the inherent symmetry of the synchronous operating state, a normal form for grid-forming actors is derived. It is shown that this model provides a useful approximation of certain inverter control dynamics but is also well-suited for a data-driven modeling approach. The last part of the thesis deals with analyzing the risk of hurricane-induced power outages. High wind speeds often cause damage to transmission infrastructure which can lead to overloads of other components and thereby induce a cascade of failures spreading through the entire grid. Simulations of such scenarios are implemented by combining a meteorological wind field model with a model for cascading line failures. Using Monte Carlo simulations in a synthetic test case resembling the Texas transmission system, it is possible to identify critical lines that trigger large-scale power outages.

In this doctoral thesis, we theoretically investigate the propagation of sound waves in dilute Bose gases, in both the collisionless and hydrodynamic regimes. The study of sound wave is a topic of high relevance for the understanding of dynamical properties of any fluid, classical or quantum, and further provides insightful information about the equation of state of the system. In our work, we focus in particular on the two-dimensional (2D) Bose gas, in which the sound wave is predicted to give useful information about the nature of the superfluid phase transition. Recently, experimental measurement of sound wave in a uniform 2D Bose gas has become available, and we show that the measured data are quantitatively well explained by our collisionless theory. Finally, we study the mixtures of weakly interacting Bose gases, by developing a beyond mean-field theory, which includes the effects of thermal and quantum fluctuations in both the density and spin channels. Our new theory allows for the investigation of sound dynamics, as well as the fundamental problem of phase- separation.

The size and conformational complexity of proteins and other large systems represent major challenges for today's methods of quantum chemistry.This thesis is centered around the development of new computational tools to gain molecular-level insight into electronic transitions in such systems. To meet this challenge, we focus on the polarizable embedding (PE) model, which takes advantage of the fact that many electronic transitions are localized to a smaller part of the entire system.This motivates a partitioning of the large system into two regions that are treated at different levels of theory:The smaller part directly involved in the electronic process is described using accurate quantum-chemical methods, while the effects of the rest of the system, the environment, are incorporated into the Hamiltonian of the quantum region in an effective manner. This thesis presents extensions of the PE model with theaim of expanding its range of applicability to describe electronic transitions in large molecular systemsin the optical and X-ray regions. The developments cover both improvements with regardto the quantum region as well as the embedding potential representing the environment.Regarding the former, a damped linear response formulation has been implemented to allow for calculations of absorption spectra of large molecular systems acrossthe entire frequency range. A special feature of this development is its abilityto address core excitations that are otherwise not easily accessible.Another important development presented in this thesis is the coupling of the PE model to a multi-configuration self-consistent-field description of the quantum region and its further combination with response theory. In essence, this extends the PE model to the study of electronic transitions in large systems that are prone to static correlation --- a situation that is frequently encountered in biological systems. In addition to the direct environmental effects on the electronic structure of the quantum region, another important component of the description of electronic transitions in large molecular systems is an accurate account of the indirect effects of the environment, i.e., the geometrical distortions in the quantum region imposed by the environment. In thisthesis we have taken the first step toward the inclusion of geometry distortions in the PE frameworkby formulating and implementing molecular gradients for the quantum region. To identify critical points related to the environment description, we perform a theoretical analysis of the PE model starting from a full quantum-mechanicaltreatment of a composite system. Based on this, we present strategies for an accurate yet efficient construction of the embedding potentialcovering both the calculation of ground state and transition properties. The accurate representation of the environment makes it possible to reduce the size of the quantum region without compromising the overall accuracy of the final results. This further enables use of highly accurate quantum-chemical methods despite their unfavorable scaling with the size of the system. Finally, some examples of applications will be presented to demonstrate how the PE model may be applied as a tool to gain insight into and rationalize the factors influencing electronic transitions in large molecular systems of increasing complexity. / <p>The dissertation was awarded the best PhD thesis prize 2016 by the Danish Academy of Natural Sciences.</p><p></p><p>QC 20170209</p>

Dans la modélisation de la matière dense, et partiellement ionisée, une question importante concerne le traitement des électrons libres. Vis-à-vis des électrons liés, la nature délocalisée et non discrète de ces électrons est responsable d’une différence de traitement, qui est souvent effectuée dans les modélisations des propriétés radiatives des plasmas. Cependant, afin d’éviter les incohérences dans le calcul des spectres d’absorption, tous les électrons devraient, en principe, être décrits dans un même formalisme.Nous utilisons deux modèles variationnels d’atome-moyen : un modèle semi-classique, et un modèle quantique, qui permettent cette égalité de traitement pour tous les électrons. Nous calculons la section-efficace de photo-extinction, en appliquant le cadre de la théorie de la réponse linéaire dynamique à chacun de ces modèles d’atome dans un plasma. Pour cette étude, nous développons et utilisons une approche auto-cohérente, de type random-phase-approximation (RPA), qui, en allant au-delà de la réponse des électrons indépendants, permet d’évaluer les effets collectifs, par l’introduction de la polarisation dynamique. Cette approche s’inscrit dans le formalisme de la théorie de la fonctionnelle de la densité dépendant du temps (TDDFT), appliquée au cas d’un système atomique immergé dans un plasma.Pour les deux modèles, semi-classique et quantique, nous dérivons, et vérifions dans nos calculs, une nouvelle règle de somme, qui permet d’évaluer le dipôle atomique à partir d’un volume fini dans le plasma. Cette règle de somme s’avère être un outil de premier ordre pour le calcul des propriétés radiatives des atomes dans les plasmas denses. / In modeling dense and partially ionized matter, the treatment of the free electrons remains an important issue. Compared to bound electrons, the delocalized and non-discrete nature of these electrons is responsible to treat them differently, which is usually adopted in the modelings of radiative properties of plasmas. However, in order to avoid inconsistencies in the calculation of absorption spectra, all the electrons should be described in the same formalism.We use two variational average-atom models: a semi-classical and a quantum model, which allow this common treatment for all the electrons. We calculate the photo-extinction cross-section, by applying the framework of the linear dynamical response theory to each of these models of an atom in a plasma. For this study, we develop and use a self-consistent approach, of random-phase-approximation (RPA) type, which, while going beyond the independent electron response, permits to evaluate the collective effects by the introduction of the dynamical polarization. This approach uses the formalism of the time dependent density functional theory (TDDFT), applied in the case of an atomic system immersed in a plasma.For both models, semi-classical and quantum, we derive and verify in our calculations, a new sum rule, which allows the evaluation of the atomic dipole from a finite volume in the plasma. This sum rule turns out to be a crucial device in the calculation of radiative properties of atoms in dense plasmas.

Tous les systèmes biologiques sont formés d’atomes et de molécules qui interagissent et dont émergent des propriétés subtiles et complexes. Par ces interactions, les organismes vivants peuvent subvenir à toutes leurs fonctions vitales. Ces propriétés apparaissent dans tous les systèmes biologiques à des niveaux différents, du niveau des molécules et gènes jusqu’aux niveau des cellules et tissus. Ces dernières années, les physiciens se sont impliqués dans la compréhension de ces aspects particulièrement intrigants, en particulier en étudiant les systèmes vivants dans le cadre de la théorie des réseaux, théorie qui offre des outils d’analyse très puissants. Il est possible aujourd’hui d’identifier deux classes d’approches qui sont utilisée pour étudier ces types de systèmes complexes : les méthodes directes de modélisation et les approches inverses d’inférence. Dans cette thèse, mon travail est basé sur les deux types d’approches appliquées à trois niveaux de systèmes biologiques. Dans la première partie de la thèse, je me concentre sur les premières étapes du développement des tissus biologiques des plantes. Je propose un nouveau modèle pour comprendre la dynamique collective des transporteurs de l’hormone auxine et qui permet la croissance non-homogène des tissu dans l’espace et le temps. Dans la deuxième partie de la thèse, j’analyse comment l’évolution contraint la diversité́ de séquence des protéines tout en conservant leur fonction dans différents organismes. En particulier, je propose une nouvelle méthode pour inférer les sites essentiels pour la fonction ou la structure de protéines à partir d’un ensemble de séquences biologiques. Finalement, dans la troisième partie de la thèse, je travaille au niveau cellulaire et étudie les réseaux de signalisation associés à l’auxine. Dans ce contexte, je reformule un modèle préexistant et propose une nouvelle technique qui permet de définir et d’étudier la réponse du système aux signaux externes pour des topologies de réseaux différentes. J’exploite ce cadre théorique pour identifier le rôle fonctionnel de différentes topologies dans ces systèmes. / All biological systems are made of atoms and molecules interacting in a non- trivial manner. Such non-trivial interactions induce complex behaviours allow- ing organisms to fulfill all their vital functions. These features can be found in all biological systems at different levels, from molecules and genes up to cells and tissues. In the past few decades, physicists have been paying much attention to these intriguing aspects by framing them in network approaches for which a number of theoretical methods offer many powerful ways to tackle systemic problems. At least two different ways of approaching these challenges may be considered: direct modeling methods and approaches based on inverse methods. In the context of this thesis, we made use of both methods to study three different problems occurring on three different biological scales. In the first part of the thesis, we mainly deal with the very early stages of tissue development in plants. We propose a model aimed at understanding which features drive the spontaneous collective behaviour in space and time of PINs, the transporters which pump the phytohormone auxin out of cells. In the second part of the thesis, we focus instead on the structural properties of proteins. In particular we ask how conservation of protein function across different organ- isms constrains the evolution of protein sequences and their diversity. Hereby we propose a new method to extract the sequence positions most relevant for protein function. Finally, in the third part, we study intracellular molecular networks that implement auxin signaling in plants. In this context, and using extensions of a previously published model, we examine how network structure affects network function. The comparison of different network topologies provides insights into the role of different modules and of a negative feedback loop in particular. Our introduction of the dynamical response function allows us to characterize the systemic properties of the auxin signaling when external stimuli are applied.

Orientador: Glaucia Amorim Faria / Resumo: Considerando que a intensidade de infestação (I.I.%) é um importante dado sobre o dano causado pela Diatraea saccharalis em cana-de-açúcar e que existem poucos trabalhos na literatura relacionados ao tamanho de ótimo de parcela para este tipo de amostragem, o objetivo deste trabalho foi estimar o tamanho ótimo de parcela em hectares e número de colmos que deverá ser utilizado no processo de amostragem de modo que represente a intensidade de infestação causada pelo ataque da D. saccharalis em cana-de-açúcar. Para os cálculos relativos ao tamanho da área a ser amostrada foram utilizados quatro métodos para o cálculo do tamanho de parcela: método de inspeção visual da curvatura máxima, método da máxima curvatura modificado, modelo linear segmentado com platô e modelo quadrático segmentado com platô. Para os cálculos referentes ao número de entrenós foi utilizado o método da estimativa da suficiência amostral. O método da máxima curvatura modificado foi o que proporcionou melhores resultados. De acordo com os resultados encontrados neste trabalho, podemos concluir que o número mínimo a ser amostrado é o de 36 entrenós por hectare e a área máxima a ser amostrada é a de 27,5 hectares. / Abstract: Infestation intensity (II%) is an important data on the damage caused by Diatraea saccharalis in sugarcane. There are few studies in the literature related to the optimal plot size for this type of sampling. The objective of this work is to estimate the optimal plot size in hectares and number of stems to be used in the sampling process to represent the intensity of infestation caused by D. saccharalis attack on sugarcane. For the calculation of the size of the minimum sampled area, four methods were used: 1. visual inspection method of maximum curvature; 2. modified maximum curvature method; 3. segmented linear model with plateau and; 4. quadratic segmented model with plateau. For the calculations referring to the number of internodes, the method of estimating the sample adequacy was used. The modified maximum curvature method presented the best results. According this study, the minimum number to be sampled is 36 trains per hectare and the maximum area to be sampled is 27.5 hectares. / Mestre

<p>The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.</p><p>For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.</p><p>A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.</p><p>A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.</p><p>The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.</p>

The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions. A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands. A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding. The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.

The charge and spin density correlations in a one dimensional electron gas (1DEG) confined in a semiconductor quantum wire structure at zero temperature are studied. The dielectric formulation of the many--body problem is employed and the longitudinal dielectric function, local-field correction, static structure factor, pair correlation function, ground state energy, compressibility, spin-dependent effective interaction potentials, paramagnon dispersion and static spin response function of the 1DEG are computed within the self-consistent field approximations of Singwi et al., known as the STLS and SSTL. The results are compared with those of other groups, and those obtained for two-dimensional electron gas systems whenever it is possible. It is observed that the SSTL satisfies the compressibility sum rule better than the STLS. Calculating the ground state energy of the 1DEG in unpolarized and fully polarized states, it is shown that both STLS and SSTL predict a Bloch transition for 1DEG systems at low electron densities. Finally, the coupled plasmon-phonon modes in semiconductor quantum wires are calculated within the Fermi and Luttinger liquid theories. The coupling of electrons to bulk longitudinal optical phonons without dispersion and to acoustic phonons via deformation potential with a linear dispersion are considered. Using the dielectric formalism, a unified picture of the collective coupled plasmon-phonon modes is presented. Considerable differences between the predictions of the Fermi and Luttinger liquid approaches at large wave vector values, which may be observed experimentally, are found.