Processos de fragmentação são ferramentas fundamentais no estudo de íons por espectrometria de massas, pois permitem a obtenção de informação sobre a estrutura e termoquímica destes íons . Desenvolvemos uma técnica de dissociação de íons baseada na ativação destes através da absorção multifotônica sequencial de radiação infravermelha de um filamento incandescente. Nesta técnica, íons aprisionados na cela de um espectrômetro de massas por transformada de Fourier são submetidos a radiação do filamento por intervalos de tempo relativamente longos (da ordem de segundos), e passam por um processo de multíplos eventos de absorção e emissão de radiação, até a energia interna dos íons atingir um nível suficiente para a fragmentação. A partir deste modelo para o processo foram implementados métodos computacionais que permitem a simulação da dissociação. A realização destas simulações exige o conhecimento do espectro vibracional do íon, que normalmente tem que ser obtido por algum método teórico de cálculo, como foi feito neste trabalho paro o caso de alguns dos íons estudados. O método de dissociação unimolecular induzida por absorção de radiação infravermelha foi aplicado na determinação das energias de ativação e de dissociação dos íons moleculares de acetofenona, p-cimeno e cumeno. Este método também mostrou-se capaz de diferenciar diferentes estruturas isomericas, e foi com esta finalidade aplicado no estudo da isomerização ceto-enol do íon molecular de acetofenona. Demonstrou-se também a capacidade do método dissociar os íons moleculares de n-butilbenzeno e brometo de alila. / Fragmentation processes are fundamental tools for the mass spectrometric study of ions because they provide information on structure and termochemistry of these ions. We have developed a dissociation technique that is based on the multiphoton activation of trapped ions by infrared radiation emitted by an incandescent filament. In this technique, ions trapped in the cell of a Fourier Transform mass spectrometer are exposed to the filament radiation for long time periods (seconds), and a process of multiple absorption and emition events occurs, until the internal energy of the ions is high enough for fragmentation. Computational methods have been implemented from this model allowing for simulation of the dissociation process. For this simulation the ion vibrational spectra, that normally must be obtained from theoretical calculations, is also required, as has been done in this work for some of the studied ions. The method of unimolecular dissociation induced by infrared radiation was applied to the determination of activation and dissociation energies of the molecular ions of acetophenone, p-cymene and cumene. This method also proved to be capable in the differentiation of isomeric structures, and was so applied in the study for the keto-enol isomerization of the acetophenone molecular ion. It was also shown that the method can dissociate the molecular ions of n-butylbenzene an allyl bromide.

Dr. Kwan Hsu was neither a superstar nor a celebrity. Her name does not come up in conversations about important contributors to her field of biophysics nor is she instantly recognizable for her contributions to Portland State University's international program or the state of Oregon's business ties with China. Yet she was a contributor, a cog-in-the-wheel, at the very least, in all of these areas and more. She was a peripheral member of a well-known Chinese family, but few in the United States know of or perhaps have interest in, but otherwise, she had no great connections or family ties to generate interest in her story. How does one process a collection for a woman who does not meet the traditional criteria for excellence or success or public interest for an archive? Where is the value to the larger historical narrative of our time in preserving the memories of someone who was non-remarkable, or, conversely, someone who may be even too unique to contribute to that greater narrative? These are the questions I wrestled with when I first came to this collection. As my research progressed, I realized that I faced more questions, and that to come to any understanding that might answer them, I was going to have to research the history of archives and archival processes. Science, the Cold War, Communist China, women, the immigrant experience, all of these issues became part of my thesis, however shallowly I was able to investigate them. Questions of identity and historiography, of power and discourse were explored. In the end, what I found was that a collection that on the outside looked unimpressive and unenlightening, could indeed be very valuable, and provide insight into any number of areas of current interest in historical research. This is that story.

Optical scattering techniques are suitable probes for studying weak disordered refractive index media such as biological cells and tissues. Several brain diseases accompany the nano-to-submicron scales’ structural alterations of the basic building blocks of cells/tissues in the brain and skin fibroblasts. For example, several molecular modifications such as DNA methylation, and histone degradation occur in cells earlier than morphological changes detectable at a microscopic level. These alterations also change the refractive index structures of the cells/tissues at the nano-to-submicron scales. Unfortunately, traditional methods do not allow the detection of these alterations in the early stages of diseases. Recent developments in mesoscopic optical physics-based techniques can probe these alterations. Particularly, mesoscopic light transport and localization approaches enable the measurements and quantifications of the degree of structural alterations in the cells/tissues and unprecedented information on progressive brain diseases. This dissertation provides a detailed study of the structural changes at nano-to-submicron levels in human brain cells/tissues and human skin fibroblasts in two major neurodegenerative diseases, Alzheimer’s disease (AD) and Parkinson's disease (PD), using dual spectroscopic imaging techniques, namely partial wave spectroscopy (PWS) for light transport and inverse participation ratio (IPR) for weak light localization. In particular, a nanoscale-sensitive advanced PWS technique is used to quantify the structural alterations in cells/tissues. Further, the IPR technique is used to quantify molecular-specific mass density alterations within cells using their light localization properties via confocal imaging. These dual optical scattering techniques were utilized to measure the degree of structural disorders, termed ‘disorder strength’, by distinguishing the diseased cells/tissues from normal ones in the human brain and human skin fibroblasts due to neurodegenerative diseases. Our results show that the degree of structural disorder (����) increases in the affected cells and tissues relative to the normal, both at the cellular/tissue level and in the DNA molecular mass density structural levels. The results of the studies strongly reveal that the degree of structural disorder strength (����) is an effective biomarker/numerical indicator for brain disease diagnostics.

Les poêles à pétrole sont des appareils de chauffage dépourvus d'évacuation des gaz brûlés vers l'extérieur de la pièce. Ils ont été à l'origine de 49 cas d'intoxication aiguë au monoxyde de carbone en France en 2007. Ce type de chauffage est probablement responsable d'intoxications chroniques, mais celles-ci ne sont pas documentées. L'objectif de ce travail est d'une part la quantification en laboratoire des émissions gazeuses de poêles à pétrole récents et d'autre part l'élaboration de protocoles de mesure pour l'étude de la qualité de l'air à l'intérieur de logements du Nord-Pas-de-Calais. Deux types de poêles à pétrole (à mèche et électronique) ont été étudiés dans une enceinte expérimentale instrumentée de 8 m3. Ils émettent principalement NO, NO2, CO, CO2 et des particules. Trois COV préoccupants (formaldéhyde, benzène et 1,3-butadiène) ont également été quantifiés. Les facteurs d'émission dépendent du type de poêle et de la composition du carburant utilisé, en particulier de sa teneur en soufre et en esters méthyliques d'acides gras. L'accumulation de suies au cours de l'utilisation du poêle à mèche s'accompagne d'une forte augmentation des émissions de CO, qui peut conduire à des intoxications chroniques et aiguës. Des mesures de terrain chez six volontaires ont permis de tester nos protocoles dans un milieu plus complexe que celui du laboratoire. Le rôle prépondérant des poêles à pétrole sur les niveaux de pollution dans les logements a été mis en évidence. Ce travail servira de base à une future étude épidémiologique portant sur la santé respiratoire des utilisateurs de tels appareils de chauffage.

Dans le cadre de la séparation sélective pour le traitement et la valorisation des combustibles nucléaires usés, l'extraction liquide/liquide est largement utilisée au niveau industriel. Néanmoins, ce procédé est encore mal compris en ce qui concerne les phénomènes physico-chimiques qui se produisent à l'interface liquide/liquide. Ce travail porte sur la compréhension de la dynamique de l'interface liquide nanométrique durant le transfert d'une espèce entre une phase aqueuse et une phase organique. Deux techniques expérimentales ont principalement été utilisées: la mesure de tension interfaciale et l'optique non linéaire. Ce travail a également donné lieu au développement d'un modèle numérique de dynamique de transfert de phase prenant en compte à la fois des phénomènes de transport diffusif proche de l'interface et une cinétique chimique sur l'interface décrivant les processus d'adsorption/désorption. Des systèmes modèles constitués de molécules surfactantes et/ou chromophores et/ou complexantes ont été étudiés aux interfaces air/liquide et liquide/liquide. L'adsorption/désorption, l'agrégation en surface, la complexation d'ion à une interface liquide et la structuration des systèmes ont ainsi pu être étudiées tant d'un point de vue des états d'équilibre que de la dynamique. Enfin, ces études ont été appliquées à un système d'intérêt industriel utilisé dans le procédé de dépollution DIAMEX.

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on this, we extend the mapping of protein sequence not only to a fixed stable structure but also to an ensemble of protein conformations, which help us explain the complex interaction within a cell that was otherwise obscured. The objective of this dissertation is to develop effective ab initio methods and tools for protein un/structure prediction by developing effective statistical energy function, conformational search method, and disulfide connectivity patterns predictor. The key outcomes of this dissertation research are: i) a sequence and structure-based energy function for structured proteins that includes energetic terms extracted from hydrophobic-hydrophilic properties, accessible surface area, torsion angles, and ubiquitously computed dihedral angles uPhi and uPsi, ii) an ab initio protein structure predictor that combines optimal energy function derived from sequence and structure-based properties of proteins and an effective conformational search method which includes angular rotation and segment translation strategies, iii) an SVM with RBF kernel-based framework to predict disulfide connectivity pattern, iv) a hydrophobic-hydrophilic property based energy function for unstructured proteins, and v) an ab initio conformational ensemble generator that combines energy function and conformational search method for unstructured proteins which can help understand the biological systems involving IDPs and assist in rational drugs design to cure critical diseases such as cancer or cardiovascular diseases caused by challenging states of IDPs.

La première partie de ce manuscrit concerne l'étude en monocouches à l'interface air-eau de mélanges lipidiques susceptibles de former des "rafts" dans les membranes cellulaires, c'est-à-dire des domaines enrichis spécifiquement en certains lipides (glycolipides, sphingolipides, cholestérol) et certaines protéines. Du fait de leur composition spécifique, ces domaines sont caractérisés par une phase particulière ("liquid ordered phase") présentant des caractéristiques intermédiaires entre celles des phases fluides et condensées. Les principales méthodes mises en oeuvre dans cette étude sont des mesures de pression de surface (isothermes de compression, analyse des aires moléculaires moyennes, études de désorption en présence de beta-cyclodextrine), la microscopie de fluorescence (après marquage de la monocouche à l'aide d'une sonde fluorescente), ou la microscopie à l'angle de Brewster. Une des parties les plus importantes de ce travail concerne le comportement de monocouches constituées d'un glycolipide, le GM3, en présence de phospholipides (phase fluide), de sphingomyéline ou de cholestérol (phase "raft"). Les mesures montrent que le GM3 n'a pas d'affinité particulière pour la sphingomyéline. De même, son interaction avec le cholestérol induit une condensation de la monocouche similaire à celle observée avec les phospholipides en phase fluide, et ne permet pas le maintien du cholestérol dans la monocouche lors d'une désorption induite par la beta-cyclodextrine. Ce manque d'interaction spécifique du GM3 avec des lipides présents dans les "rafts" permet donc d'expliquer sa répartition assez large dans les membranes d'adipocytes, tant dans la phase fluide que dans les "rafts". La seconde partie concerne l'étude de molécules organiques de type hémicyanine organisées en monocouches de Langmuir et films de Langmuir-Blodgett, étudiés par des méthodes complémentaires (absorption, spectroscopie de fluorescence stationnaire et résolue en temps), mesures de pression de surface et microscopie de fluorescence. Ces hémicyanines comportent une chaîne hydrophobe nécessaire à la réalisation de films organisés stables. Ces derniers peuvent avoir de multiples applications dans la collecte et le transfert de l'énergie lumineuse ou les analyses chimiques ou biochimiques (reconnaissance sélective de cations lors de pollutions par exemple).

Le domaine du rayonnement extrême ultraviolet (EUV) offre de grandes possibilités scientifiques et technologiques en photolithographie, en astrophysique, en spectrométrie de photoélectron, etc. Ainsi, de nombreux miroirs multicouches sont développés pour fonctionner dans ce domaine spectral, qui joue un rôle important pour les applications optiques. L'objectif de ce travail est de concevoir, réaliser, caractériser et proposer des multicouches (Mg/Co, Al/SiC, ...). Puis le but est d'appliquer une méthode capable de distinguer entre interdiffusion et rugosité géométrique afin de corréler les performances optiques de la multicouche à sa qualité structurale. Nous proposons de caractériser les miroirs multicouches en employant une méthodologie combinant plusieurs techniques (Spectroscopie d'émission X, Réflectométrie EUV, ...). La combinaison de ces méthodes permet d'obtenir une description chimique et structurale de l'empilement multicouche et de comprendre les phénomènes prenant place aux interfaces. Il est en effet important de connaître les phénomènes interfaciaux, comme la formation de composés ou le développement de la rugosité, car ils gouvernent les propriétés optiques des multicouches.

An increase in the co-operativity in the motion of particles and a growth of a suitably defined dynamical correlation length seem to be generic features exhibited by all liquids upon supercooling. These features have been observed both in experiments and in numerical simulations of glass-forming liquids. Specially designed NMR experiments have estimated that the rough magnitude of this correlation length is of the order of a few nanometers near the glass transition. Simulations also predict that there are regions in the system which are more liquid-like than other regions. A complete theoretical understanding of this behaviour is not available at present. In recent calculations, Berthier, Biroli and coworkers [1, 2] extended the simple mode coupling theory (MCT) to incorporate the effects of dynamic heterogeneity and predicted the existence of a growing dynamical correlation length associated with the cooperativity of the dynamics. MCT also predicts a power law divergence of different dynamical quantities at the mode coupling temperature and at temperatures somewhat higher than the mode coupling temperature, these predictions are found to be consistent with experimental and simulation results. The system size dependence of these quantities should exhibit finite size scaling (FSS) similar to that observed near a continuous phase transition in the temperature range where they show power law growth. Hence we have used the method of finite size scaling in the context of the dynamics of supercooled liquids. In chapter 2, we present the results of extensive molecular dynamics simulations of a model glass forming liquid and extract a dynamical correlation length ξ associated with dynamic heterogeneity by performing a detailed finite size scaling analysis of a four-point dynamic susceptibility χ4(t) [3] and the associated Binder cumulant. We find that although these quantities show the “normal” finite size scaling behaviour expected for a system with a growing correlation length, the relaxation time τ does not. Thus glassy dynamics can not be fully understood in terms of “standard” critical phenomena. Inspired by the success of the empirical Adam-Gibbs relation [4] which relates dynamics with the configurational entropy, we have calculated the configurational entropy for different system sizes and temperatures to explain the nontrivial scaling behaviour of the relaxation time. We find that the behaviour of the relaxation time τ can be explained in terms of the Adam-Gibbs relation [4] for all temperatures and system sizes. This observation raises serious questions about the validity of the mode coupling theory which does not include the effects of the potential energy (or free energy) landscape on the dynamics. On the other hand, in the “random first order transition” theory (RFOT), introduced by Wolynes and coworkers [5], the configurational entropy plays a central role in determining the dynamics. So we also tried to explain our simulation results in terms of RFOT. However, this interpretation has the drawback that the value of one of the exponents of this theory extracted from our numerical results does not satisfy an expected physical bound, and there is no clear explanation for the obtained values of other exponents. Thus we find puzzling values for the exponents relevant to the applicability of RFOT, which are in need of explanation. This can be due to the fact that RFOT focuses only near the glass transition, while all our simulation results are for temperatures far above the glass transition temperature (actually, above the mode coupling temperature). Interestingly, results similar to ours were obtained in a recent analysis [6] of experimental data near the laboratory glass transition, on a large class of glass-forming materials. Thus right now we do not have any theory which can explain our simulation data consistently from all perspectives. There have been some attempts to extend the RFOT analysis to temperatures above the mode coupling temperature [7, 8] and to estimate a length scale associated with the configurational entropy at such temperatures. We compare our results with the predictions arising from these analyses. In chapter 3, we present simulation results that suggest that finite size scaling analysis is probably the only feasible method for obtaining reliable estimates of the dynamical correlation length for supercooled liquids. As mentioned before, although there exists a growing correlation length, the behaviour of all measured quantities (specifically, the relaxation time) is not in accordance with the behaviour expected in “standard” critical phenomena. So one might suspect the results for the correlation length extracted from the scaling analysis. To find out whether the results obtained by doing finite size scaling are correct, we have done simulations of very large system sizes for the same model glass forming liquid. In earlier studies, the correlation length has been extracted from the wave vector dependence of the dynamic susceptibility in the limit of zero wave vector, but to estimate the correlation length with reasonable accuracy one needs data in the small wave vector range. This implies that one needs to simulate very large systems. But as far as we know, in all previous studies typical system sizes of the order of 10, 000 particles have been used to do this analysis. In this chapter we show by comparing results for systems of 28, 000 and 350, 000 particles that these previous estimates are not reliable. We also show that one needs to simulate systems with at least a million particles to estimate the correlation length correctly near the mode coupling temperature and this size increases with decreasing temperature. We compare the correlation length obtained by analyzing the wave vector dependence of the dynamic susceptibility for a 350, 000particle system with the results obtained from the finite size scaling analysis. We were only able to compare the results in the high temperature range due to obvious reasons. However the agreement in the high temperature range shows that the finite size scaling analysis is robust and also establishes the fact that finite size scaling is the only practical method to extract reliable correlation lengths in supercooled liquids. In chapter 4, we present a free energy landscape analysis of dynamic heterogeneity for a monodisperse hard sphere system. The importance of the potential energy landscape for particles interacting with soft potentials is well known in the glass community from the work of Sastry et al. [9] and others, but the hard sphere system which does not have any well defined potential energy landscape also exhibits similar slow dynamics in the high density limit. Thus it is not clear how to treat the hard sphere systems within the same energy landscape formalism. Dasgupta et al. [10, 11, 12, 13, 14, 15] showed that one can explain the slow dynamics of these hard core systems in term of a free energy landscape picture. They and other researchers showed that these system have many aperiodic local minima in its free energy landscape, with free energy lower than that of the liquid. Using the Ramkrishnan-Yussouff free energy functional, we have performed multi parameter variational minimizations to map out the detailed density distribution of glassy free energy minima. We found that the distribution of the widths of local density peaks at glassy minima is spatially heterogeneous. By performing hard sphere event driven molecular dynamics simulation, we show that there exists strong correlation between these density inhomogeneity and the local Debye-Waller factor which provides a measure of the dynamic heterogeneity observed in simulations. This result unifies the system of hard core particles with the other soft core particles in terms of a landscapebased description of dynamic heterogeneity. In chapter 5, we extend the same free energy analysis to a polydisperse system and show that there is a critical polydispersity beyond which the crystal state is not stable and glassy states are thermodynamically stable. We also found a reentrant behaviour in the liquid-solid phase transition within this free-energy based formalism. These results are in qualitative agreement with experimental observations for colloidal systems.

Les travaux de cette thèse présentent la synthèse par une polymérisation RAFT en miniémulsion de nanoparticules fluorescentes (NPFs) polymères à coeur BODIPY copolymérisé au styrène et à couronne hydrophile biocompatible et fonctionnalisable à base de poly(oxyde d'éthylène) et de poly(acide acrylique). Les propriétés de fluorescence de ces NPFs ont été étudiées par spectroscopie de fluorescence stationnaire et résolue en temps. L'élaboration de la synthèse de ce type de NPFs, et la mise au point d'un procédé "one-pot" sont présentés dans un premier temps. Ensuite, les propriétés spectroscopiques de ces NPFs sont étudiées, notamment l'influence de la concentration en monomères de BODIPY au coeur des NPFs pouvant mener à la formation d'agrégats peu ou pas fluorescents. Les propriétés spectroscopiques (longueur d'onde d'émission de fluorescence et rendement quantique) du coeur des NPFs ont été modulées. Cela est rendu possible en réalisant la synthèse de monomères de BODIPY portant des groupements aromatiques encombrés, ou présentant différentes fonctions polymérisables. La couronne hydrophile des NPFs a également été modifiée afin d'obtenir différentes répartitions des unités acide acrylique et oxyde d'éthylène dans les chaînes de copolymères en surface. Ces nouvelles NPFs sont également synthétisées par un procédé "one-pot". Enfin, des molécules à fonctions amine (fluorophores, protéines) ont été introduites dans la couronne hydrophile de ces diverses NPFs par une chimie de couplage peptidique sur les fonctions acides carboxyliques. Des nano-senseurs de pH ratiométriques ont ainsi pu être élaborés.