Polyglutamine monomer structure and its implications for molecular self-assembly

Polyglutamine is a naturally occurring peptide found within several proteins in neuronal cells of the brain, and its aggregation has been implicated in several neurodegenerative diseases, including Huntington's disease. The resulting aggregates have been demonstrated to possess ~-sheet structure, and aggregation has been shown to start with a single misfolded peptide. The current project sought to computationally examine the structural tendencies of three mutant poly glutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing, and were analyzed quantitatively by various geometry- and energy-based methods. According to the results, the experimentally-observed inhibition of aggregation appears to be due to localized conformational restraint placed on the peptide backbone by inserted prolines, which in tum confines the peptide to native coil structure, discouraging transition towards the ~sheet structure required for aggregation. Such knowledge could prove quite useful to the design of future treatments for Huntington's and other related diseases.

The Fast Regulation of Photosynthesis in Diatoms: an inquiry into the physiological and physical origins of non-photochemical chlorophyll fluorescence quenching.

Diatoms are renowned for their robust ability to perform NPQ (Non-Photochemical Quenching of chlorophyll fluorescence) as a dissipative response to heightened light stress on photosystem II, plausibly explaining their dominance over other algal groups in turbulent light environs. Their NPQ mechanism has been principally attributed to a xanthophyll cycle involving the lumenal pH regulated reversible de-epoxidation of diadinoxanthin. The principal goal of this dissertation is to reveal the physiological and physical origins and consequences of the NPQ response in diatoms during short-term transitions to excessive irradiation. The investigation involves diatom species from different originating light environs to highlight the diversity of diatom NPQ and to facilitate the detection of core mechanisms common among the diatoms as a group. A chiefly spectroscopic approach was used to investigate NPQ in diatom cells. Prime methodologies include: the real time monitoring of PSII excitation and de-excitation pathways via PAM fluorometry and pigment interconversion via transient absorbance measurements, the collection of cryogenic absorbance spectra to measure pigment energy levels, and the collection of cryogenic fluorescence spectra and room temperature picosecond time resolved fluorescence decay spectra to study excitation energy transfer and dissipation. Chemical inhibitors that target the trans-thylakoid pH gradient, the enzyme responsible for diadinoxanthin de-epoxidation, and photosynthetic electron flow were additionally used to experimentally manipulate the NPQ response. Multifaceted analyses of the NPQ responses from two previously un-photosynthetically characterised species, Nitzschia curvilineata and Navicula sp., were used to identify an excitation pressure relief ‘strategy’ for each species. Three key areas of NPQ were examined: (i) the NPQ activation/deactivation processes, (ii) how NPQ affects the collection, dissipation, and usage of absorbed light energy, and (iii) the interdependence of NPQ and photosynthetic electron flow. It was found that Nitzschia cells regulate excitation pressure via performing a high amplitude, reversible antenna based quenching which is dependent on the de-epoxidation of diadinoxanthin. In Navicula cells excitation pressure could be effectively regulated solely within the PSII reaction centre, whilst antenna based, diadinoxanthin de-epoxidation dependent quenching was implicated to be used as a supplemental, long-lasting source of excitation energy dissipation. These strategies for excitation balance were discussed in the context of resource partitioning under these species’ originating light climates. A more detailed investigation of the NPQ response in Nitzschia was used to develop a comprehensive model describing the mechanism for antenna centred non-photochemical quenching in this species. The experimental evidence was strongly supportive of a mechanism whereby: an acidic lumen triggers the diadinoxanthin de-epoxidation and protonation mediated aggregation of light harvesting complexes leading to the formation of quencher chlorophyll a-chlorophyll a dimers with short-lived excited states; quenching relaxes when a rise in lumen pH triggers the dispersal of light harvesting complex aggregates via deprotonation events and the input of diadinoxanthin. This model may also be applicable for describing antenna based NPQ in other diatom species.

Factor models, VARMA processes and parameter instability with applications in macroeconomics

Avec les avancements de la technologie de l'information, les données temporelles économiques et financières sont de plus en plus disponibles. Par contre, si les techniques standard de l'analyse des séries temporelles sont utilisées, une grande quantité d'information est accompagnée du problème de dimensionnalité. Puisque la majorité des séries d'intérêt sont hautement corrélées, leur dimension peut être réduite en utilisant l'analyse factorielle. Cette technique est de plus en plus populaire en sciences économiques depuis les années 90. Étant donnée la disponibilité des données et des avancements computationnels, plusieurs nouvelles questions se posent. Quels sont les effets et la transmission des chocs structurels dans un environnement riche en données? Est-ce que l'information contenue dans un grand ensemble d'indicateurs économiques peut aider à mieux identifier les chocs de politique monétaire, à l'égard des problèmes rencontrés dans les applications utilisant des modèles standards? Peut-on identifier les chocs financiers et mesurer leurs effets sur l'économie réelle? Peut-on améliorer la méthode factorielle existante et y incorporer une autre technique de réduction de dimension comme l'analyse VARMA? Est-ce que cela produit de meilleures prévisions des grands agrégats macroéconomiques et aide au niveau de l'analyse par fonctions de réponse impulsionnelles? Finalement, est-ce qu'on peut appliquer l'analyse factorielle au niveau des paramètres aléatoires? Par exemple, est-ce qu'il existe seulement un petit nombre de sources de l'instabilité temporelle des coefficients dans les modèles macroéconomiques empiriques? Ma thèse, en utilisant l'analyse factorielle structurelle et la modélisation VARMA, répond à ces questions à travers cinq articles. Les deux premiers chapitres étudient les effets des chocs monétaire et financier dans un environnement riche en données. Le troisième article propose une nouvelle méthode en combinant les modèles à facteurs et VARMA. Cette approche est appliquée dans le quatrième article pour mesurer les effets des chocs de crédit au Canada. La contribution du dernier chapitre est d'imposer la structure à facteurs sur les paramètres variant dans le temps et de montrer qu'il existe un petit nombre de sources de cette instabilité. Le premier article analyse la transmission de la politique monétaire au Canada en utilisant le modèle vectoriel autorégressif augmenté par facteurs (FAVAR). Les études antérieures basées sur les modèles VAR ont trouvé plusieurs anomalies empiriques suite à un choc de la politique monétaire. Nous estimons le modèle FAVAR en utilisant un grand nombre de séries macroéconomiques mensuelles et trimestrielles. Nous trouvons que l'information contenue dans les facteurs est importante pour bien identifier la transmission de la politique monétaire et elle aide à corriger les anomalies empiriques standards. Finalement, le cadre d'analyse FAVAR permet d'obtenir les fonctions de réponse impulsionnelles pour tous les indicateurs dans l'ensemble de données, produisant ainsi l'analyse la plus complète à ce jour des effets de la politique monétaire au Canada. Motivée par la dernière crise économique, la recherche sur le rôle du secteur financier a repris de l'importance. Dans le deuxième article nous examinons les effets et la propagation des chocs de crédit sur l'économie réelle en utilisant un grand ensemble d'indicateurs économiques et financiers dans le cadre d'un modèle à facteurs structurel. Nous trouvons qu'un choc de crédit augmente immédiatement les diffusions de crédit (credit spreads), diminue la valeur des bons de Trésor et cause une récession. Ces chocs ont un effet important sur des mesures d'activité réelle, indices de prix, indicateurs avancés et financiers. Contrairement aux autres études, notre procédure d'identification du choc structurel ne requiert pas de restrictions temporelles entre facteurs financiers et macroéconomiques. De plus, elle donne une interprétation des facteurs sans restreindre l'estimation de ceux-ci. Dans le troisième article nous étudions la relation entre les représentations VARMA et factorielle des processus vectoriels stochastiques, et proposons une nouvelle classe de modèles VARMA augmentés par facteurs (FAVARMA). Notre point de départ est de constater qu'en général les séries multivariées et facteurs associés ne peuvent simultanément suivre un processus VAR d'ordre fini. Nous montrons que le processus dynamique des facteurs, extraits comme combinaison linéaire des variables observées, est en général un VARMA et non pas un VAR comme c'est supposé ailleurs dans la littérature. Deuxièmement, nous montrons que même si les facteurs suivent un VAR d'ordre fini, cela implique une représentation VARMA pour les séries observées. Alors, nous proposons le cadre d'analyse FAVARMA combinant ces deux méthodes de réduction du nombre de paramètres. Le modèle est appliqué dans deux exercices de prévision en utilisant des données américaines et canadiennes de Boivin, Giannoni et Stevanovic (2010, 2009) respectivement. Les résultats montrent que la partie VARMA aide à mieux prévoir les importants agrégats macroéconomiques relativement aux modèles standards. Finalement, nous estimons les effets de choc monétaire en utilisant les données et le schéma d'identification de Bernanke, Boivin et Eliasz (2005). Notre modèle FAVARMA(2,1) avec six facteurs donne les résultats cohérents et précis des effets et de la transmission monétaire aux États-Unis. Contrairement au modèle FAVAR employé dans l'étude ultérieure où 510 coefficients VAR devaient être estimés, nous produisons les résultats semblables avec seulement 84 paramètres du processus dynamique des facteurs. L'objectif du quatrième article est d'identifier et mesurer les effets des chocs de crédit au Canada dans un environnement riche en données et en utilisant le modèle FAVARMA structurel. Dans le cadre théorique de l'accélérateur financier développé par Bernanke, Gertler et Gilchrist (1999), nous approximons la prime de financement extérieur par les credit spreads. D'un côté, nous trouvons qu'une augmentation non-anticipée de la prime de financement extérieur aux États-Unis génère une récession significative et persistante au Canada, accompagnée d'une hausse immédiate des credit spreads et taux d'intérêt canadiens. La composante commune semble capturer les dimensions importantes des fluctuations cycliques de l'économie canadienne. L'analyse par décomposition de la variance révèle que ce choc de crédit a un effet important sur différents secteurs d'activité réelle, indices de prix, indicateurs avancés et credit spreads. De l'autre côté, une hausse inattendue de la prime canadienne de financement extérieur ne cause pas d'effet significatif au Canada. Nous montrons que les effets des chocs de crédit au Canada sont essentiellement causés par les conditions globales, approximées ici par le marché américain. Finalement, étant donnée la procédure d'identification des chocs structurels, nous trouvons des facteurs interprétables économiquement. Le comportement des agents et de l'environnement économiques peut varier à travers le temps (ex. changements de stratégies de la politique monétaire, volatilité de chocs) induisant de l'instabilité des paramètres dans les modèles en forme réduite. Les modèles à paramètres variant dans le temps (TVP) standards supposent traditionnellement les processus stochastiques indépendants pour tous les TVPs. Dans cet article nous montrons que le nombre de sources de variabilité temporelle des coefficients est probablement très petit, et nous produisons la première évidence empirique connue dans les modèles macroéconomiques empiriques. L'approche Factor-TVP, proposée dans Stevanovic (2010), est appliquée dans le cadre d'un modèle VAR standard avec coefficients aléatoires (TVP-VAR). Nous trouvons qu'un seul facteur explique la majorité de la variabilité des coefficients VAR, tandis que les paramètres de la volatilité des chocs varient d'une façon indépendante. Le facteur commun est positivement corrélé avec le taux de chômage. La même analyse est faite avec les données incluant la récente crise financière. La procédure suggère maintenant deux facteurs et le comportement des coefficients présente un changement important depuis 2007. Finalement, la méthode est appliquée à un modèle TVP-FAVAR. Nous trouvons que seulement 5 facteurs dynamiques gouvernent l'instabilité temporelle dans presque 700 coefficients.

Utilisation of Coir Geotextiles for Unpaved Roads and Embankments

The increasing tempo of construction activity the world over creates heavy pressure on existing land space. The quest for new and competent site often points to the needs for improving existing sites, which are otherwise deemed unsuitable for adopting conventional foundations. This is accomplished by ground improvement methods, which are employed to improve the quality of soil incompetent in their natural state. Among the construction activities, a well-connected road network is one of the basic infrastructure requirements, which play a vital role for the fast and comfortable movement of inter- regional traffic in countries like India.One of the innovative ground improvement techniques practised all over the world is the use of geosynthetics, which include geotextiles, geomembranes, geogrids, etc . They offer the advantages such as space saving, enviromnental sensitivity, material availability, technical superiority, higher cost savings, less construction time, etc . Because of its fundamental properties, such as tensile strength, filtering and water permeability, a geotextile inserted between the base material and sub grade can function as reinforcement, a filter medium, a separation layer and as a drainage medium. Though polymeric geotextiles are used in abundant quantities, the use of natural geotextiles (like coir, jute, etc.) has yet to get momentum. This is primarily due to the lack of research work on natural geotextilcs for ground improvement, particularly in the areas of un paved roads. Coir geotextiles are best suited for low cost applications because of its availability at low prices compared to its synthetic counterparts. The proper utilisation of coir geotextilcs in various applications demands large quantities of the product, which in turn can create a boom in the coir industry. The present study aims at exploring the possibilities of utilising coir geotextiles for unpaved roads and embankments.The properties of coir geotextiles used have been evaluated. The properties studied include mass per unit area, puncture resistance, tensile strength, secant modulus, etc . The interfacial friction between soils and three types of coir geotextiles used was also evaluated. It was found that though the parameters evaluated for coir geotextiles have low values compared to polymeric geotextiles, the former are sufficient for use in unpaved roads and embankments. The frictional characteristics of coir geotextile - soil interfaces are extremely good and satisfy the condition set by the International Geosynthetic Society for varied applications.The performance of coir geotextiles reinforced subgrade was studied by conducting California Bearing Ratio (CBR) tests. Studies were made with coir geotextiles placed at different levels and also in multiple layers. The results have shown that the coir geotextile enhances the subgrade strength. A regression analysis was perfonned and a mathematical model was developed to predict the CBR of the coir geotextile reinforced subgrade soil as a function of the soil properties, coir geotextile properties, and placement depth of reinforcement.The effects of coir geotextiles on bearing capacity were studied by perfonning plate load tests in a test tan1e This helped to understand the functioning of geotextile as reinforcement in unpaved roads and embankments. The perfonnance of different types of coir geotextiles with respect to the placement depth in dry and saturated conditions was studied. The results revealed that the bearing capacity of coir-reinforced soil is increasing irrespective of the type of coir geotextiles and saturation condition.The rut behaviour of unreinforced and coir reinforced unpaved road sections were compared by conducting model static load tests in a test tank and also under repetitive loads in a wheel track test facility. The results showed that coir geotextiles could fulfill the functions as reinforcement and as a separator, both under static and repetitive loads. The rut depth was very much reduced whik placing coir geotextiles in between sub grade and sub base.In order to study the use of Coir geotextiles in improving the settlement characteristics, two types of prefabricated COlf geotextile vertical drains were developed and their time - settlement behaviour were studied. Three different dispositions were tried. It was found that the coir geotextile drains were very effective in reducing consolidation time due to radial drainage. The circular drains in triangular disposition gave maximum beneficial effect.In long run, the degradation of coir geotextile is expected, which results in a soil - fibre matrix. Hence, studies pertaining to strength and compressibility characteristics of soil - coir fibre composites were conducted. Experiments were done using coir fibres having different aspect ratios and in different proportions. The results revealed that the strength of the soil was increased by 150% to 200% when mixed with 2% of fibre having approximately 12mm length, at all compaction conditions. Also, the coefficient of consolidation increased and compression index decreased with the addition of coir fibre.Typical design charts were prepared for the design of coir geotextile reinforced unpaved roads. Some illustrative examples are also given. The results demonstrated that a considerable saving in subase / base thickness can he achieved with the use of eoir geotextiles, which in turn, would save large quantities of natural aggregates.

Physicochemical and Biochemical Characterization of Enzymes Immobilized on lnorganic Matrices

Biotechnology is currently considered as a useful altemative to conventional process technology in industrial and catalytic fields. The increasing awareness of the need to create green and sustainable production processes in all fields of chemistry has stimulated materials scientists to search for innovative catalysts supports. lmmobilization of enzymes in inorganic matrices is very useful in practical applications due to the preserved stability and catalytic activity of the immobilized enzymes under extreme conditions. Nanostructured inorganic, organic or hybrid organic-inorganic nanocomposites present paramount advantages to facilitate integration and miniaturization of the devices (nanotechnologies), thus affording a direct connection between the inorganic, organic and biological worlds. These properties, combined with good chemical stability, make them competent candidates for designed biocatalysts, protein-separation devices, drug delivery systems, and biosensors Aluininosilicate clays and layered double hydroxides, displaying, respectively, cation and anion exchange properties, were found to be attractive materials for immobilization because of their hydrophilic, swelling and porosity properties, as well as their mechanical and thermal stability.The aim of this study is the replacement of inorganic catalysts by immobilized lipases to obtain purer and healthier products.Mesocellular silica foams were synthesized by oil-in-water microemulsion templating route and were functionalized with silane and glutaraldehyde. " The experimental results from IR spectroscopy and elemental analysis demonstrated the presence of immobilized lipase and also functionalisation with silane and glutaraldehyde on the supports.The present work is a comprehensive study on enzymatic synthesis of butyl isobutyrate through esterification reaction using lipase immobilized onto mesocellular siliceous foams and montmorillonite K-10 via adsorption and covalent binding. Moreover, the irnrnobil-ization does not modify the nature of the kinetic mechanism proposed which is of the Bi-Bi Ping—Pong type with inhibition by n-butanol. The immobilized biocatalyst can be commercially exploited for the synthesis of other short chain flavor esters. Mesocellular silica foams (MCF) were synthesized by microemusion templating method via two different routes (hydrothermal and room temperature). and were functionalized with silane and glutaraldehyde. Candida rugosa lipase was adsorbed onto MCF silica and clay using heptane as the coupling medium for reactions in non-aqueous media. I From XRD results, a slight broadening and lowering of d spacing values after immobilization and modification was observed in the case of MCF 160 and MCF35 but there was no change in the d-spacing in the case of K-10 which showed that the enzymes are adsorbed only on the external surface. This was further confirmed from the nitrogen adsorption measurements

Competing tunneling and capacitive paths in Co-ZrO2 granular thin films

The ac electrical response is studied in thin films composed of well-defined nanometric Co particles embedded in an insulating ZrO2 matrix which tends to coat them, preventing the formation of aggregates. In the dielectric regime, ac transport originates from the competition between interparticle capacitive Cp and tunneling Rt channels, the latter being thermally assisted. This competition yields an absorption phenomenon at a characteristic frequency 1/(RtCp), which is observed in the range 1010 000 Hz. In this way, the effective ac properties mimic the universal response of disordered dielectric materials. Temperature and frequency determine the complexity and nature of the ac electrical paths, which have been successfully modeled by an Rt-Cp network.

Design and study of self-assembled functional organic and hybrid systems for biological applications

The focus of self-assembly as a strategy for the synthesis has been confined largely to molecules, because of the importance of manipulating the structure of matter at the molecular scale. We have investigated the influence of temperature and pH, in addition to the concentration of the capping agent used for the formation of the nano-bio conjugates. For example, the formation of the narrower size distribution of the nanoparticles was observed with the increase in the concentration of the protein, which supports the fact that γ-globulin acts both as a controller of nucleation as well as stabiliser. As analyzed through various photophysical, biophysical and microscopic techniques such as TEM, AFM, C-AFM, SEM, DLS, OPM, CD and FTIR, we observed that the initial photoactivation of γ-globulin at pH 12 for 3 h resulted in small protein fibres of ca. Further irradiation for 24 h, led to the formation of selfassembled long fibres of the protein of ca. 5-6 nm and observation of surface plasmon resonance band at around 520 nm with the concomitant quenching of luminescence intensity at 680 nm. The observation of light triggered self-assembly of the protein and its effect on controlling the fate of the anchored nanoparticles can be compared with the naturally occurring process such as photomorphogenesis.Furthermore,our approach offers a way to understand the role played by the self-assembly of the protein in ordering and knock out of the metal nanoparticles and also in the design of nano-biohybrid materials for medicinal and optoelectronic applications. Investigation of the potential applications of NIR absorbing and water soluble squaraine dyes 1-3 for protein labeling and anti-amyloid agents forms the subject matter of the third chapter of the thesis. The study of their interactions with various proteins revealed that 1-3 showed unique interactions towards serum albumins as well as lysozyme. 69%, 71% and 49% in the absorption spectra as well as significant quenching in the fluorescence intensity of the dyes 1-3, respectively. Half-reciprocal analysis of the absorption data and isothermal titration calorimetric (ITC) analysis of the titration experiments gave a 1:1 stoichiometry for the complexes formed between the lysozyme and squaraine dyes with association constants (Kass) in the range 104-105 M-1. We have determined the changes in the free energy (ΔG) for the complex formation and the values are found to be -30.78, -32.31 and -28.58 kJmol-1, respectively for the dyes 1, 2 and 3. Furthermore, we have observed a strong induced CD (ICD) signal corresponding to the squaraine chromophore in the case of the halogenated squaraine dyes 2 and 3 at 636 and 637 nm confirming the complex formation in these cases. To understand the nature of interaction of the squaraine dyes 1-3 with lysozyme, we have investigated the interaction of dyes 1-3 with different amino acids. These results indicated that the dyes 1-3 showed significant interactions with cysteine and glutamic acid which are present in the side chains of lysozyme. In addition the temperature dependent studies have revealed that the interaction of the dye and the lysozyme are irreversible. Furthermore, we have investigated the interactions of these NIR dyes 1-3 with β- amyloid fibres derived from lysozyme to evaluate their potential as inhibitors of this biologically important protein aggregation. These β-amyloid fibrils were insoluble protein aggregates that have been associated with a range of neurodegenerative diseases, including Huntington, Alzheimer’s, Parkinson’s, and Creutzfeldt-Jakob diseases. We have synthesized amyloid fibres from lysozyme through its incubation in acidic solution below pH 4 and by allowing to form amyloid fibres at elevated temperature. To quantify the binding affinities of the squaraine dyes 1-3 with β-amyloids, we have carried out the isothermal titration calorimetric (ITC) measurements. The association constants were determined and are found to be 1.2 × 105, 3.6× 105 and 3.2 × 105 M-1 for the dyes, 1-3, respectively. To gain more insights into the amyloid inhibiting nature of the squaraine dyes under investigations, we have carried out thioflavin assay, CD, isothermal titration calorimetry and microscopic analysis. The addition of the dyes 1-3 (5μM) led to the complete quenching in the apparent thioflavin fluorescence, thereby indicating the destabilization of β-amyloid fibres in the presence of the squaraine dyes. Further, the inhibition of the amyloid fibres by the squaraine dyes 1-3, has been evidenced though the DLS, TEM AFM and SAED, wherein we observed the complete destabilization of the amyloid fibre and transformation of the fibre into spherical particles of ca. These results demonstrate the fact that the squaraine dyes 1-3 can act as protein labeling agents as well as the inhibitors of the protein amyloidogenesis. The last chapter of the thesis describes the synthesis and investigation of selfassembly as well as bio-imaging aspects of a few novel tetraphenylethene conjugates 4-6.Expectedly, these conjugates showed significant solvatochromism and exhibited a hypsochromic shift (negative solvatochromism) as the solvent polarity increased, and these observations were justified though theoretical studies employing the B3LYP/6-31g method. We have investigated the self-assembly properties of these D-A conjugates though variation in the percentage of water in acetonitrile solution due to the formation of nanoaggregates. Further the contour map of the observed fluorescence intensity as a function of the fluorescence excitation and emission wavelength confirmed the formation of J-type aggregates in these cases. To have a better understanding of the type of self-assemblies formed from the TPE conjugates 4-6, we have carried out the morphological analysis through various microscopic techniques such as DLS, SEM and TEM. 70%, we observed rod shape architectures having ~ 780 nm in diameter and ~ 12 μM in length as evidenced through TEM and SEM analysis. We have made similar observations with the dodecyl conjugate 5 at ca. 70% and 50% water/acetonitrile mixtures, the aggregates formed from 4 and 5 were found to be highly crystalline and such structures were transformed to amorphous nature as the water fraction was increased to 99%. To evaluate the potential of the conjugate as bio-imaging agents, we have carried out their in vitro cytotoxicity and cellular uptake studies though MTT assay, flow cytometric and confocal laser scanning microscopic techniques. Thus nanoparticle of these conjugates which exhibited efficient emission, large stoke shift, good stability, biocompatibility and excellent cellular imaging properties can have potential applications for tracking cells as well as in cell-based therapies. In summary we have synthesized novel functional organic chromophores and have studied systematic investigation of self-assembly of these synthetic and biological building blocks under a variety of conditions. The investigation of interaction of water soluble NIR squaraine dyes with lysozyme indicates that these dyes can act as the protein labeling agents and the efficiency of inhibition of β-amyloid indicate, thereby their potential as anti-amyloid agents.

The Surface Plasmon Resonance of Supported Noble Metal Nanoparticles: Characterization, Laser Tailoring, and SERS Application

This work deals with the optical properties of supported noble metal nanoparticles, which are dominated by the so-called Mie resonance and are strongly dependent on the particles’ morphology. For this reason, characterization and control of the dimension of these systems are desired in order to optimize their applications. Gold and silver nanoparticles have been produced on dielectric supports like quartz glass, sapphire and rutile, by the technique of vapor deposition under ultra-high vacuum conditions. During the preparation, coalescence is observed as an important mechanism of cluster growth. The particles have been studied in situ by optical transmission spectroscopy and ex situ by atomic force microscopy. It is shown that the morphology of the aggregates can be regarded as oblate spheroids. A theoretical treatment of their optical properties, based on the quasistatic approximation, and its combination with results obtained by atomic force microscopy give a detailed characterization of the nanoparticles. This method has been compared with transmission electron microscopy and the results are in excellent agreement. Tailoring of the clusters’ dimensions by irradiation with nanosecond-pulsed laser light has been investigated. Selected particles are heated within the ensemble by excitation of the Mie resonance under irradiation with a tunable laser source. Laser-induced coalescence prevents strongly tailoring of the particle size. Nevertheless, control of the particle shape is possible. Laser-tailored ensembles have been tested as substrates for surface-enhanced Raman spectroscopy (SERS), leading to an improvement of the results. Moreover, they constitute reproducible, robust and tunable SERS-substrates with a high potential for specific applications, in the present case focused on environmental protection. Thereby, these SERS-substrates are ideally suited for routine measurements.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Effects of different tillage treatments on labile soil organic matter pools and stabilization processes

An improved understanding of soil organic carbon (Corg) dynamics in interaction with the mechanisms of soil structure formation is important in terms of sustainable agriculture and reduction of environmental costs of agricultural ecosystems. However, information on physical and chemical processes influencing formation and stabilization of water stable aggregates in association with Corg sequestration is scarce. Long term soil experiments are important in evaluating open questions about management induced effects on soil Corg dynamics in interaction with soil structure formation. The objectives of the present thesis were: (i) to determine the long term impacts of different tillage treatments on the interaction between macro aggregation (>250 µm) and light fraction (LF) distribution and on C sequestration in plots differing in soil texture and climatic conditions. (ii) to determine the impact of different tillage treatments on temporal changes in the size distribution of water stable aggregates and on macro aggregate turnover. (iii) to evaluate the macro aggregate rebuilding in soils with varying initial Corg contents, organic matter (OM) amendments and clay contents in a short term incubation experiment. Soil samples were taken in 0-5 cm, 5-25 cm and 25-40 cm depth from up to four commercially used fields located in arable loess regions of eastern and southern Germany after 18-25 years of different tillage treatments with almost identical experimental setups per site. At each site, one large field with spatially homogenous soil properties was divided into three plots. One of the following three tillage treatments was carried in each plot: (i) Conventional tillage (CT) with annual mouldboard ploughing to 25-30 cm (ii) mulch tillage (MT) with a cultivator or disc harrow 10-15 cm deep, and (iii) no tillage (NT) with direct drilling. The crop rotation at each site consisted of sugar beet (Beta vulgaris L.) - winter wheat (Triticum aestivum L.) - winter wheat. Crop residues were left on the field and crop management was carried out following the regional standards of agricultural practice. To investigate the above mentioned research objectives, three experiments were conducted: Experiment (i) was performed with soils sampled from four sites in April 2010 (wheat stand). Experiment (ii) was conducted with soils sampled from three sites in April 2010, September 2011 (after harvest or sugar beet stand), November 2011 (after tillage) and April 2012 (bare soil or wheat stand). An incubation study (experiment (iii)) was performed with soil sampled from one site in April 2010. Based on the aforementioned research objectives and experiments the main findings were: (i) Consistent results were found between the four long term tillage fields, varying in texture and climatic conditions. Correlation analysis of the yields of macro aggregate against the yields of free LF ( ≤1.8 g cm-3) and occluded LF, respectively, suggested that the effective litter translocation in higher soil depths and higher litter input under CT and MT compensated in the long term the higher physical impact by tillage equipment than under NT. The Corg stocks (kg Corg m−2) in 522 kg soil, based on the equivalent soil mass approach (CT: 0–40 cm, MT: 0–38 cm, NT: 0–36 cm) increased in the order CT (5.2) = NT (5.2) < MT (5.7). Significantly (p ≤ 0.05) highest Corg stocks under MT were probably a result of high crop yields in combination with reduced physical tillage impact and effective litter incorporation, resulting in a Corg sequestration rate of 31 g C-2 m-2 yr-1. (ii) Significantly higher yields of macro aggregates (g kg-2 soil) under NT (732-777) and MT (680-726) than under CT (542-631) were generally restricted to the 0-5 cm sampling depth for all sampling dates. Temporal changes on aggregate size distribution were only small and no tillage induced net effect was detectable. Thus, we assume that the physical impact by tillage equipment was only small or the impact was compensated by a higher soil mixing and effective litter translocation into higher soil depths under CT, which probably resulted in a high re aggregation. (iii) The short term incubation study showed that macro aggregate yields (g kg-2 soil) were higher after 28 days in soils receiving OM (121.4-363.0) than in the control soils (22.0-52.0), accompanied by higher contents of microbial biomass carbon and ergosterol. Highest soil respiration rates after OM amendments within the first three days of incubation indicated that macro aggregate formation is a fast process. Most of the rebuilt macro aggregates were formed within the first seven days of incubation (42-75%). Nevertheless, it was ongoing throughout the entire 28 days of incubation, which was indicated by higher soil respiration rates at the end of the incubation period in OM amended soils than in the control soils. At the same time, decreasing carbon contents within macro aggregates over time indicated that newly occluded OM within the rebuilt macro aggregates served as Corg source for microbial biomass. The different clay contents played only minor role in macro aggregate formation under the particular conditions of the incubation study. Overall, no net changes on macro aggregation were identified in the short term. Furthermore, no indications for an effective Corg sequestration on the long term under NT in comparison to CT were found. The interaction of soil disturbance, litter distribution and the fast re aggregation suggested that a distinct steady state per tillage treatment in terms of soil aggregation was established. However, continuous application of MT with a combination of reduced physical tillage impact and effective litter incorporation may offer some potential in improving the soil structure and may therefore prevent incorporated LF from rapid decomposition and result in a higher C sequestration on the long term.

Adsorption kinetic investigations of phthalocyanine derivatives self assembled monolayers (SAMs) on gold: Temperature influence on the SAM formation process and quality

The ordered nano-structured surfaces, like self-assembled monolayers (SAMs) are of a great scientific interest, due to the low cost, simplicity, and versatility of this method. SAMs found numerous of applications in molecular electronics, biochemistry and optical devices. Phthalocyanine (Pc) complexes are of particular interest for the SAM preparation. These molecules exhibit fascinating physical properties and are chemically and thermally stable. Moreover their complex structure is advantageous for the fabrication of switchable surfaces. In this work the adsorption process of Pcs derivatives, namely, subphthalocyanines (SubPcB) and terbium (2TbPc) sandwich complexes on gold has been investigated. The influence of the molecular concentration, chain length of peripheral groups, and temperature on the film formation process has been examined using a number of techniques. The SAMs formation process has been followed in situ and in real time by means of second harmonic generation (SHG) and surface plasmon resonance (SPR) spectroscopy. To investigate the quality of the SAMs prepared at different temperatures atomic force microscopy (AFM) and X-Ray photoelectron spectroscopy (XPS)measurements were performed. Valuable information about SubPcB and 2TbPc adsorbtion process has been obtained in the frame of this work. The kinetic data, obtained with SHG and SPR, shows the best conformance with the first order Langmuir kinetic model. Comparing SHG and SPR results, it has been found, that the film formation occurs faster than the formation of chemical bonds. Such, the maximum amount of molecules on the surface is reached after 6 min for SubPcB and 30 min for 2TbPc. However, at this time the amount of formed chemicals bonds is only 10% and 40% for SubPcB and 2TbPc, respectively. The most intriguing result, among others, was obtained at T = 2 °C, where the formation of the less dense SAMs have been detected with SHG.However, analyzing XPS and AFM data, it has been revealed, that there is the same amount of molecules on the surface at both temperature T = 2 °C, and T = 21 °C, but the amount of formed chemicals bond is different. At T = 2 °C molecules form aggregates, therefore many of available anchor groups stay unattached.

Concurrent Aggregates (CA): An Object-Oriented Language for Fine-Grained Message-Passing Machines

Fine-grained parallel machines have the potential for very high speed computation. To program massively-concurrent MIMD machines, programmers need tools for managing complexity. These tools should not restrict program concurrency. Concurrent Aggregates (CA) provides multiple-access data abstraction tools, Aggregates, which can be used to implement abstractions with virtually unlimited potential for concurrency. Such tools allow programmers to modularize programs without reducing concurrency. I describe the design, motivation, implementation and evaluation of Concurrent Aggregates. CA has been used to construct a number of application programs. Multi-access data abstractions are found to be useful in constructing highly concurrent programs.

Responsive Azobenzene-Containing Polymers and Gels

The photoviscosity effect in aqueous solutions of novel poly(4-methacryloyloxyazobenzene-co-N,N-dimethyl acrylamide) (MOAB-DMA) was demonstrated. The observed significant reduction in the zero-shear viscosity upon UV-irradiation of MOAB-DMA aqueous solutions was due to the dissociation of the interchain azobenzene aggregates. Such phenomena can be advantageously used in photoswitchable fluidic devices and in protein separation. Introduction of enzymatically degradable azo cross-links into Pluronic-PAA microgels allowed for control of swelling due to degradation of the cross-links by azoreductases from the rat intestinal cecum. Dynamic changes in the cross-link density of stimuli-responsive microgels enable novel opportunities for the control of gel swelling, of importance for drug delivery and microgel sensoric applications.

Synthesis and Aggregation Behavior of Pluronic F87/Poly(acrylic acid) Block Copolymer with Doxorubicin

Poly(acrylic acid) (PAA) was grafted onto both termini of Pluronic F87 (PEO₆₇-PPO₃₉-PEO₆₇) via atom transfer radical polymerization to produce a novel muco-adhesive block copolymer PAA₈₀-b-F₈₇-b-PAA₈₀. It was observed that PAA₈₀-F₈₇-PAA₈₀ forms stable complexes with weakly basic anti-cancer drug, Doxorubicin. Thermodynamic changes due to the drug binding to the copolymer were assessed at different pH by isothermal titration calorimetry (ITC). The formation of the polymer/drug complexes was studied by turbidimetric titration and dynamic light scattering. Doxorubicin and PAA-b-F87-b-PAA block copolymer are found to interact strongly in aqueous solution via non-covalent interactions over a wide pH range. At pH>4.35, drug binding is due to electrostatic interactions. Hydrogen-bond also plays a role in the stabilization of the PAA₈₀-F₈₇-PAA₈₀/DOX complex. At pH 7.4 (α=0.8), the size and stability of polymer/drug complex depend strongly on the doxorubicin concentration. When CDOX <0.13mM, the PAA₈₀-F₈₇-PAA₈₀ copolymer forms stable inter-chain complexes with DOX (110 ~ 150 nm). When CDOX >0.13mM, as suggested by the light scattering result, the reorganization of the polymer/drug complex is believed to occur. With further addition of DOX (CDOX >0.34mM), sharp increase in the turbidity indicates the formation of large aggregates, followed by phase separation. The onset of a sharp enthalpy increase corresponds to the formation of a stoichiometric complex.

Internal structure of chlorosomes from brown-colored Chlorobium species and the role of carotenoids in their assembly

Chlorosomes are the main light harvesting complexes of green photosynthetic bacteria. Recently, a lamellar model was proposed for the arrangement of pigment aggregates in Chlorobium tepidum chlorosomes, which contain bacteriochlorophyll (BChl) c as the main pigment. Here we demonstrate that the lamellar organization is also found in chlorosomes from two brown-colored species (Chl. phaeovibrioides and Chl. phaeobacteroides) containing BChl e as the main pigment. This suggests that the lamellar model is universal among green sulfur bacteria. In contrast to green-colored Chl. tepidum, chlorosomes from the brown-colored species often contain domains of lamellar aggregates that may help them to survive in extremely low light conditions. We suggest that carotenoids are localized between the lamellar planes and drive lamellar assembly by augmenting hydrophobic interactions. A model for chlorosome assembly, which accounts for the role of carotenoids and secondary BChl homologs, is presented