Dissertations / Theses on the topic 'Binding phases'

Resorcinarenes can be functionalized at their upper and lower rims. In this work, the upper rim of a resorcinarene was functionalized with glutamic acids and the lower rim was functionalized with either methyl or undecyl alkyl groups. The cavitands were characterized by nuclear magnetic resonance (NMR), mass spectrometry (MS), UV-vis spectroscopy, dynamic light scattering (DLS) and electron microscopy. The binding of resorcinarene with amine guests was studied in DMSO by UV-vis titration. The obtained binding constants (K values) were in the range of 12,000-136000 M-1. The resorcinarenes were shown to form aggregates in a variety of solvents. The aggregates were spherical as confirmed by DLS, SEM and TEM experiments. Dynamic light scattering (DLS) experiments revealed the size of the aggregates could be controlled by cavitand concentration, pH, and temperature. The resorcinarene with undecyl alkyl group were adsorbed onto 55% cross-linked styrene-divinylbenzene resin to prepare a new stationary phases for ion chromatography (IC) columns. The new column packing material was applied in determination of uremic toxins and water contaminants. The new IC column afforded separation of the five uremic toxins : guanidinoacetic acid, guanidine, methylguanidine, creatinine, and guanidinobenzoic acid in 30 minutes. Detection and quantification of uremic toxins helps diagnose kidney problems and start patient care. Gradient elutions at ambient temperature with methanesulfonic acid (MSA) as eluent resulted in detection levels in water from 10 to 47 ppb and in synthetic urine from 28 to 180 ppb. Trace levels of creatinine (1 ppt) were detected in the urine of a healthy individual using the columns. The new IC stationary phase separated cationic pharmaceuticals including a group of guanidine compounds in surface water. Detection limits in the range of 5 - 32 µg L-1 were achieved using integrated pulsed amperometric detection (IPAD) for guanidine (G), methylguanidine (MG), 1,1-dimethylbiguanidine (DMG), agmatine (AGM), guanidinobenzoic acid (GBA) and cimetidine (CIM). Suppressed conductivity (CD) and UV-vis detection resulted in limits of detection similar to IPAD, in the range of 1.7 - 66 µg L-1, but were not able to detect all of the analytes. Three water sources, river, lake, and marsh, were analyzed and despite matrix effects, sensitivity for guanidine compounds was in the 100 µg L-1 range and apparent recoveries were 80-96 %. The peak area precision was 0.01 - 2.89% for IPAD, CD and UV-vis detection.

The recently developed technique of diffusive gradients in thin films (DGT) for speciation measurement of analytes in the environment was further developed through the development of series of new binding phases including poly(acrylamide-co-acrylic acid) copolymer hydrogel (PAM-PAA), poly(acrylamidoglycolic acid-co-acrylamide) (PAAGA-PAM) hydrogel, the Whatman P81 cellulose phosphate ion exchange membrane (P81) and a liquid binding phase of poly(4-styrenesulfonate) (PSS). A new diffusion layer, cellulose dialysis membrane, was also employed for the liquid binding phase DGT. PAM-PAA copolymer hydrogel was prepared by the controlled hydrolysis of polyacrylamide (PAM) in an alkaline solution of 10% sodium hydroxide. The capacity of the copolymer hydrogel to bind various metal ions was tested under a range of uptake conditions. Ions such as Cu2+ and Cd2+ were bound more strongly to the copolymer hydrogel than the competing ions such as Na+, K+, Ca2+ and Mg2+. Metals bound to the copolymer hydrogel can be efficiently eluted in 2 M HNO3 solution (>94%). Application of this new binding material to DGT technique was validated in a synthetic lake water (Windermere, Lake District, UK) with a recovery of 99.0% for Cu2+. PAAGA-PAM hydrogel was prepared by copolymerising 2-acrylamidoglycolic acid with acrylamide. The metal ion binding properties of the hydrogel were characterised for Cu2+, Cd2+ and competing ions under various experimental conditions. The hydrogel was shown to bind Cu2+ and Cd2+ strongly under non-competitive binding conditions, with binding capacities of 5.3 and 5.1 micromol cm-2, respectively. The binding capacity of each metal decreased, under competitive binding conditions (with a range of metal ions present at 17.8 mN), to 1.3 and 0.17 micromol cm-2, respectively, indicating a strong selective binding towards Cu2+. The metal ions were readily recovered (>94%) by eluting with 2 M HNO3. Finally, the copolymer hydrogel was tested as a binding phase with the DGT technique. A linear mass vs. time relationship was observed for Cu2+ in Windermere water with a recovery of close to 100%. The use of a commercially available solid ion exchange membrane (P81) as the binding phase in DGT analysis was demonstrated. P81 is a strong cation exchange membrane. Its performance characteristics as a new binding phase in DGT measurement of Cu2+ and Cd2+ were systematically investigated. Several advantages over the conventional ion exchange resin-embedded hydrogel based binding phases used in DGT were observed. These include: simple preparation, ease of handling, and reusability. The binding phase preferentially binds to transition metal ions rather than competing ions. Within the optimum pH range (pH 4.0 - 9.0), the maximum non-competitive binding capacities of the membrane for Cu2+ and Cd2+ were 3.22 and 3.07 micromol cm-2, respectively. The suitability of the new membrane-based binding phase for DGT applications was validated experimentally. The results demonstrated excellent agreement with theoretically predicted trends. The reusability of this binding phase was also investigated. Application of a liquid binding phase and a dialysis membrane diffusive layer were proposed for the first time. The binding phase was a 0.020 M solution of poly(4-styrenesulfonate) (PSS) polyelectrolyte using a specially designed DGT device. The binding properties of Cd2+, Cu2+, and a range of alkali and alkaline earth metal ions to the PSS solution were characterised. The PSS behaved like a cation exchanger with preferential binding to Cd2+ (6.0 micromole ml-1, log K = 9.0) and Cu2+ (2.5 micromole ml-1, log K = 8.1) under competitive binding conditions. The DGT devices were successfully validated for Cd2+ and Cu2+ in Windermere water. The speciation performance of the solid and liquid binding phases developed in this study was investigated in solutions containing ethylenediaminetetraacetic acid disodium salt (EDTA), humic acid (HA), glucose (GL), dodecylbenzenesulfonic acid (DBS) and tannic acid (TA) with Cu2+ and Cd2+. The ratios of labile metals over total metals were at good agreement with calculated theoretical values using Stability Constants Database. The results indicated that the DGT-labile concentration measured by DGT with these binding phases is essentially free metal ion concentration in the sample. All newly developed DGT binding phases were successfully applied for environmental speciation. The field deployments were carried out in both freshwater and salt-water test sites.

Fragment based lead discovery (FBLD), where libraries of small fragments are screened andlater on developed to lead compounds, is an alternative to the classical drug discovery methods such as high trough-put screening. Weak affinity chromatography (WAC) is a new promising approach to the screening process of FBLD. WAC is performed by injections of fragments onto a high performance liquid chromatography (HPLC) column in which a protein is immobilized to a silica support. The retention of the injected fragments is correlated to the binding affinity of the fragments towards the immobilized protein. Immobilization capacity of three different silica materials with varying pore size (Kromasil240 Å, Nucleosil 1000 Å and Kromasil 300 Å) was evaluated by immobilization of trypsin. Retention of benzamidines on the trypsin columns was evaluated with different mobile phases. Contribution of non-specific binding in the interaction between the 4-aminobenzamidine and thrombin was estimated by frontal chromatography on a capillary columnusing PBS and PBS/acetonitrile as mobile phases. This study showed that the Kromasil 300 Å had a superior immobilization capacity of trypsin compared to the Kromasil 240 Å andthe Nucleosil 1000 Å (100 mg compared to 87.4 mg and 15.1 mg trypsin/g silica, respectively). However, the Nucleosil 1000 Å might be a more suitable support for the immobilization of larger proteins. Adding 5 % methanol or acetonitrile to the mobile phase resulted in a significant (p < 0.05) decreased retention of benzamidine fragments on the trypsin 240 Å column. Non-specific binding between thrombin and 4-ABA was not statistically significantly altered when 5 % acetonitrile was added to the mobile phase.

Le système zirconium-hydrogène est très étudié dans le cadre de la sûreté nucléaire car la précipitation d'hydrures entraîne la fragilisation des gainages, à base d'alliage de zirconium. Il s'agit de la première barrière de confinement des produits radioactifs : son intégrité doit être maintenue tout au long de la vie des assemblages combustible, en centrale y compris en cas d'accident et post-centrale (transport et entreposage). De nombreuses incertitudes demeurent quant aux cinétiques de précipitation des hydrures et à l'impact des contraintes sur leur précipitation. La modélisation à l'échelle atomique de ce système permettrait d'apporter des clarifications sur les mécanismes en jeu. Les méthodes traditionnelles de modélisation atomistique sont basées sur des approches thermostatistiques, dont la précision et la fiabilité dépendent du potentiel interatomique qui les alimente. Or il n'existe pas de potentiel rendant possible une étude rigoureuse du système Zr-H. Cette thèse a permis de développer cet outil manquant en utilisant l'approximation des liaisons fortes. Au-delà de ce nouveau potentiel, ce travail donne un guide détaillé des nombreuses étapes d'une dérivation de tels potentiels avec la prise en compte de l'hybridation spd, ajustés ici sur des calculs DFT. Ce guide est établi tant pour un métal de transition pur que dans la perspective d'un couplage métal-covalent (carbures, nitrures et siliciures métalliques)
The zirconium-hydrogen system is of nuclear safety interest, as the hydride precipitation leads to the cladding embrittlement, which is made of zirconium-based alloys. The cladding is the first safety barrier confining the radioactive products: its integrity shall be kept during the entire fuel-assemblies life, in reactor, including accidental situation, and post-operation (transport and storage). Many uncertainties remain regarding the hydrides precipitation kinectics and the local stress impact on their precipitation. The atomic scale modeling of this system would bring clarifications on the relevant mechanisms. The usual atomistic modeling methods are based on thermostatistic approaches, whose precision and reliability depend on the interatomic potential used. However, there was no potential allowing a rigorous study of the Zr-H system. The present work has indeed addressed this issue: a new tight-binding potential for zirconium hydrides modeling is now available. Moreover, this thesis provides a detailed manual for deriving such potentials accounting for spd hybridization, and fitted here on DFT results. This guidebook has be written in light of modeling a pure transition metal followed by a metal-covalent coupling (metallic carbides, nitrides and silicides)

Il a été observé que l’altération des fonctions des granules de stress, entités cytoplasmiques non-membranaires composées d’ARN et de protéines liant l’ARN (RBPs), peut conduire au développement de maladies telles que la sclérose latérale amyotrophique, la démence fronto-temporale, la myopathie à inclusions et la maladie de Paget des os. Ces pathologies sont caractérisées par un dépôt cytoplasmique d’inclusions solides enrichies en RBPs et comprenant des fibrilles. Une connexion génétique a été suggérée entre la persistance des granules de stress et l’accumulation de ces inclusions pathologiques dans le cytoplasme des patients. Dans mon manuscrit de thèse, il est mis en évidence le fait que la protéine hnRNPA1, dont les mutations entrainent les maladies mentionnées plus haut, subit une séparation de phases entre deux liquides connue également sous l’appellation « Séparation de Phases Liquide-Liquide » (LLPS) dans des gouttelettes enrichies en protéines. Bien que le domaine composé d’une séquence à faible complexité (Low Complexity sequence Domains ou LCD) soit suffisant pour obtenir cette séparation de phases, les domaines de liaison à l’ARN y contribuent également en présence d’ARN. Cela a permis d’envisager l’existence de plusieurs mécanismes intervenant dans la régulation de l’assemblage de ces granules. Un autre résultat a mis en exergue le fait que la formation de fibrilles n’est pas une obligation pour permettre la séparation de phases mais que les gouttelettes, enrichies en protéines, entrainent, par ailleurs, une augmentation de la formation de ces fibrilles. La séparation de phases liquide-liquide induite par le domaine composé d’une séquence à faible complexité semble contribuer à l’assemblage des granules de stress et à leurs propriétés liquides. Finalement, cette étude propose d’établir une réelle corrélation entre la formation des granules de stress qui deviennent persistants et l’accumulation d’inclusions pathologiques dans le cytoplasme des patients
Stress granules are membrane-less organelles composed of RNA-binding proteins (RBPs) and RNA. Functional impairment of stress granules has been implicated in amyotrophic lateral sclerosis, inclusion body myopathy, Paget’s disease of bone and frontotemporal dementia; these diseases are characterized by solid, fibrillar, cytoplasmic inclusions that are rich in RNA binding proteins (RBPs). Genetic evidence suggests a link between persistent stress granules and the accumulation of pathological inclusions. In this thesis manuscript, I demonstrate that the disease-related RBP hnRNPA1 undergoes liquid-liquid phase separation (LLPS) into protein-rich droplets mediated by a low complexity sequence domain (LCD). While the LCD of hnRNPA1 is sufficient to mediate LLPS, the folded RNA recognition motifs contribute to LLPS in the presence of RNA, potentially giving rise to several mechanisms for regulating assembly of stress granules. Importantly, while not required for LLPS, fibrillization is enhanced in protein-rich droplets. I suggest that LCD-mediated LLPS contributes to the assembly of stress granules and their liquid properties, and provides a mechanistic link between persistent stress granules and fibrillar protein pathology in disease

Single crystal nickel-based superalloys are used in modern gas turbines because of their remarkable resistance to creep deformation at elevated temperatures, which is ensured by the addition of significant amounts of refractory elements. Too high concentrations of refractory elements can lead to the formation of topologically-close packed (TCP) phases during exposure to conditions of high temperature and stress which result in the degradation of the creep properties. The traditional methods for predicting the occurrence of TCP phases in Ni-based superalloys have been based on the PHACOMP and newPHACOMP methodologies which are well-known to fail with respect to new generations of alloys. In this work a novel two-dimensional structure map (Nbar, deltaV/V) for TCP phases where Nbar is the valence-electron count and deltaV/V is a compositional dependent size factor. This map is found to separate the experimental data on the TCP phases of binary, ternary and multi-component TCP phases into well-defined regions corresponding to different structure types such as A15, sigma, chi, delta, P, R, mu, and Laves. In particular, increasing size factor separates the A15, sigma and chi phases from the delta, P, R, mu phases. The structure map is then also used in conjunction with CALPHAD computations of sigma phase stability to show that the predictive power of newPHACOMP for the seven component Ni–Co–Cr–Ta–W–Re–Al system is indeed poor. In order to gain a microscopic understanding of the observed structural trends, namely the differences between the two groups of TCP structures with increasing deltaV/V and the trend from A15 to sigma to chi with increasing Nbar, the electronic structure is coarse-grained from density functional theory (DFT) to tight-binding to bond-order potentials (BOPs). First, DFT is used to calculate the structural energy differences across the elemental 4d and 5d transition metal series and the heats of formation of the binary alloys Mo-Re, Mo-Ru, Nb-Re, and Nb-Ru. These calculations show that the valence electron concentration stabilizes A15, sigma and chi but destablizes mu and Laves phases. The latter are shown to be stabilized instead by relative size difference. Second, a simple canonical TB model and in combination with the structural energy difference theorem is found to qualitatively reproduce the energy differences predicted by the elemental DFT calculations. The structural energy difference theorem rationalizes the importance of the size factor for the stability of the mu and Laves binary phases as observed in the structure map and DFT heats of formation. Finally, analytic BOP theory, is employed to identify the structural origins of the energetic differences between TCP structure-types that lead to the trends found within the two-dimensional structure map.

Laves-Phasen sind intermetallische Verbindungen der Zusammensetzung AB2, die in den Strukturtypen C14 (MgZn2), C15 (MgCu2), C36 (MgNi2) oder deren Abkömmlingen kristallisieren. Diese sind Polytypen mit einem gemeinsamen grundlegenden Strukturmuster. Insgesamt sind über 1400 binäre und ternäre Laves-Phasen bekannt. Sie stellen damit die größte Gruppe der bislang bekannten intermetallischen Verbindungen dar. Laves-Phasen wurden intensiv untersucht um grundlegende Aspekte der Phasenstabilität zu verstehen. Geometrische und elektronische Faktoren haben sich in ihrer Vorhersagekraft bezüglich des Auftretens und der Stabilität einer Laves-Phase aber nur in wenigen Fällen als hilfreich erwiesen. Das Auftreten von Homogenitätsbereichen und damit einhergehender struktureller Defekte ist in den meisten Fällen immer noch unklar und spiegelt grundsätzliche Probleme in der Chemie intermetallischer Verbindungen wider: Das unvollständige Bild der chemischen Bindung, die Tendenz zur Bildung ausgedehnter Homogenitätsbereiche sowie der Einfluss von Minoritätskomponenten auf Struktur und Phasenstabilität ist bei intermetallischen Verbindungen größer als bei vielen anderen Verbindungsklassen. Daher sind die Informationen über Struktur, Stabiblität und physikalische Eigenschaften intermetallischer Verbindungen im Allgemeinen unvollständig und mitunter unzuverlässig oder widersprüchlich. Um diese Probleme anzugehen wurden in dieser Arbeit Laves-Phasen in den Systemen Nb--TM (TM = Cr, Mn, Fe, Co) und Nb--Cr--TM (TM = Co, Ni) als Modellsysteme ausgewählt. Das Ziel der Untersuchung ist, das Wechselspiel zwischen chemischer Bindung, Struktur und Phasenstabilität für die Laves-Phasen auf der Grundlage genauer experimenteller Daten sowie quantenmechanischer Rechnungen zu beleuchten. Die Untersuchungen des binären Systems Nb--Co nehmen hier eine Schlüsselposition ein. Eine Neubestimmung des Phasendiagramms des Systems Nb--Co im Bereich der Laves-Phasen bestätigt die Existenz von Phasen mit C14-, C15- und C36-Struktur. Dabei wurden schmale Zweiphasenfelder C15 + C36 und C15 + C14 sowie ein schmaler, aber signifikanter Homogenitätsbereich der C36-Phase experimentell nachgewiesen. Die Kristallstrukturen von C36-Nb(1-x)Co(2+x) (x = 0,265), C15-Nb(1-x)Co(2+x) (x = 0,12), C15-NbCo2 und C14-Nb(1+x)Co(2-x) (x = 0,07) wurden mittels Einkristall-Röntgenstrukturanalyse verfeinert. Im Falle von C36-Nb(1-x)Co(2+x) (x = 0,265) und C15-Nb(1-x)Co(2+x) (x = 0,12) wird bestätigt, dass der Homogenitätsbereich durch Substitution von Nb durch Co erzeugt wird. Im Fall von C14-Nb(1+x)Co(2-x) werden Abweichungen von der Zusammensetzung NbCo2 durch Substitution von Co durch überschüssiges Nb erzeugt, wobei nur eine der beiden Co-Lagen gemischt besetzt wird. Quantenmechanische Rechnungen zeigen, dass dieses Besetzungsmuster energetisch bevorzugt ist. Weder mittels Röntgenbeugung noch mittels hochauflösender Elektronenmikroskopie und Elektronenbeugeng wurden Ordnungsvarianten oder Stapelvarianten der Laves-Phasen beobachtet. In der Kristallstruktur von C36-Nb(1-x)Co(2+x) (x = 0,265) ist mehr als ein Viertel des Nb durch überschüssiges Co ersetzt. Von zwei kristallographischen Nb-Lagen wird eine bevorzugt von Co besetzt, so dass sich der Co-Anteil der beiden Lagen etwa wie 2:1 verhält. Co-Antistrukturatome sind relativ zu der Nb-Position verschoben. Triebkraft dieser Verschiebungen ist die Bildung von Nb--Co-Kontakten innerhalb der A-Teilstruktur. Gemischte Besetzung der Nb-Lagen, die Verteilung der Co-Antistrukturatome und mit der Substitution einhergehende Verzerrungen führen zu einer komplizierten Realstruktur. Zur Beschreibung der elektronischen Struktur von C36-Nb(1-x)Co(2+x) (x = 0,265) werden daher verschiedene Modelle verwendet, die Tendenzen sowohl zur beobachteten Mischbesetzung als auch zur Verzerrung der Kristallstruktur aufzeigen. Die elektronische Struktur und chemische Bindung von C14-, C15- und C36-NbCo2 wurde vergleichend untersucht. Berechnungen der Gesamtenergie zeigen sehr geringe Energiedifferenzen zwischen den drei Strukturen, die mit einer sehr ähnlichen Bindungssituation der Polytypen im Einklang ist. In den Systemen Nb--Cr und Nb--Fe wurde der Verlauf der Gitterparameter innerhalb des gesamten Homogenitätsbereichs der Laves-Phase bei ausgewählten Temperaturen untersucht. Die Kristallstrukturen von C15-NbCr2 und C14-NbFe2 wurden erstmals verfeinert. Vorläufige Untersuchungen bestätigen die Existenz von zwei Hochtemperaturmodifikationen (C14 und C36) von NbCr2. Im System Nb--Mn wurde die Mn-reiche Seite des Homogenitätsbereichs bei 800 °C und 1100 °C an aus zweiphasigen (Mn(Nb) + C14) Präparaten isolierten Einkristallen untersucht. Bei 800 °C wird ein Kristall der Zusammensetzung NbMn2 erhalten, während bei 1100 °C ausgeprägte Löslichkeit von Mn in der C14-Phase beobachtet wird. Die Summenformel kann als Nb(1-x)Mn(2+x) (x = 0,13) geschrieben werden. Die Substitution von Nb durch Mn führt zu Verschiebungen der Antistrukturatome bezüglich der Nb-Lagen und damit zur Bildung kurzer Nb--Mn-Abstände. In den ternären Systemen Nb--Cr--Co und Nb--Cr--Ni wurden die Kristallstrukturen der C14-Phasen C14-Nb(Cr(1-x)Co(x))2 und C14-Nb(Cr(1-x)Ni(x))2 am Einkristall untersucht. Neben den auch für die binären C14-Phasen beobachteten Verzerrungen zeigen die Kristallstrukturen eine teilweise geordnete Verteilung von Cr und Co bzw. Cr und Ni auf die beiden kristallographischen Lagen der B-Teilstruktur. Die bevorzugte Besetzung wurde auf der Grundlage von Extended-Hückel-Rechnungen untersucht. Zwar können diese Rechnungen kein quantitatives Bild liefern, jedoch werden Tendenzen im System Nb--Cr--Co richtig wiedergegeben. Im System Nb--Cr--Ni liefern die Rechnungen jedoch dem Experiment widersprechende Ergebnisse. Die Vorhersagekraft der Methode ist also begrenzt. Vergleichende Untersuchungen der Reihe NbTM2, TM = Cr, Mn, Fe, Co mittels Röntgenabsorptionsspektroskopie und Bandstrukturrechnungen zeigen, dass die chemische Bindung der untersuchten Verbindungen im wesentlichen ähnlich ist, aber dass durchaus Entwicklungen innerhalb der Reihe festgestellt werden können. Diese Entwicklung wird besonders in der Verzerrung der C14-Phasen und hier speziell der B-Teilstruktur deutlich, die in den experimentell zugänglichen C14-Phasen in NbMn2 deutlicher ausgeprägt ist als in NbFe2. Analysen der chemischen Bindung mit Hilfe der COHP-Methoden zeigen eine ähnliche Tendenz zur Verzerrung, die vereinfacht auch als Funktion der Valenzelektronenkonzentration aufgefasst werden kann. Berechnungen der Gesamtenergie unterstützen diese Interpretation. Im Gesamtbild der elektronischen Struktur ist eine leichte Zunahme des ionischen Bindungsanteils von TM = Cr zu TM = Co zu erkennen. Die Natur der Laves-Phasen in Systemen der Übergangsmetalle ist ein sehr vielschichtiges Problem, das weiterhin intensive und interdisziplinäre Forschung erfordert. Insbesondere mit der Charakterisierung nichtstöchiometrischer Laves-Phasen wurden aber bereits wichtige Beiträge zum Verständnis der Bildung der Homogenitätsbereiche erarbeitet.

Laves-Phasen sind intermetallische Verbindungen der Zusammensetzung AB2, die in den Strukturtypen C14 (MgZn2), C15 (MgCu2), C36 (MgNi2) oder deren Abkömmlingen kristallisieren. Diese sind Polytypen mit einem gemeinsamen grundlegenden Strukturmuster. Insgesamt sind über 1400 binäre und ternäre Laves-Phasen bekannt. Sie stellen damit die größte Gruppe der bislang bekannten intermetallischen Verbindungen dar. Laves-Phasen wurden intensiv untersucht um grundlegende Aspekte der Phasenstabilität zu verstehen. Geometrische und elektronische Faktoren haben sich in ihrer Vorhersagekraft bezüglich des Auftretens und der Stabilität einer Laves-Phase aber nur in wenigen Fällen als hilfreich erwiesen. Das Auftreten von Homogenitätsbereichen und damit einhergehender struktureller Defekte ist in den meisten Fällen immer noch unklar und spiegelt grundsätzliche Probleme in der Chemie intermetallischer Verbindungen wider: Das unvollständige Bild der chemischen Bindung, die Tendenz zur Bildung ausgedehnter Homogenitätsbereiche sowie der Einfluss von Minoritätskomponenten auf Struktur und Phasenstabilität ist bei intermetallischen Verbindungen größer als bei vielen anderen Verbindungsklassen. Daher sind die Informationen über Struktur, Stabiblität und physikalische Eigenschaften intermetallischer Verbindungen im Allgemeinen unvollständig und mitunter unzuverlässig oder widersprüchlich. Um diese Probleme anzugehen wurden in dieser Arbeit Laves-Phasen in den Systemen Nb--TM (TM = Cr, Mn, Fe, Co) und Nb--Cr--TM (TM = Co, Ni) als Modellsysteme ausgewählt. Das Ziel der Untersuchung ist, das Wechselspiel zwischen chemischer Bindung, Struktur und Phasenstabilität für die Laves-Phasen auf der Grundlage genauer experimenteller Daten sowie quantenmechanischer Rechnungen zu beleuchten. Die Untersuchungen des binären Systems Nb--Co nehmen hier eine Schlüsselposition ein. Eine Neubestimmung des Phasendiagramms des Systems Nb--Co im Bereich der Laves-Phasen bestätigt die Existenz von Phasen mit C14-, C15- und C36-Struktur. Dabei wurden schmale Zweiphasenfelder C15 + C36 und C15 + C14 sowie ein schmaler, aber signifikanter Homogenitätsbereich der C36-Phase experimentell nachgewiesen. Die Kristallstrukturen von C36-Nb(1-x)Co(2+x) (x = 0,265), C15-Nb(1-x)Co(2+x) (x = 0,12), C15-NbCo2 und C14-Nb(1+x)Co(2-x) (x = 0,07) wurden mittels Einkristall-Röntgenstrukturanalyse verfeinert. Im Falle von C36-Nb(1-x)Co(2+x) (x = 0,265) und C15-Nb(1-x)Co(2+x) (x = 0,12) wird bestätigt, dass der Homogenitätsbereich durch Substitution von Nb durch Co erzeugt wird. Im Fall von C14-Nb(1+x)Co(2-x) werden Abweichungen von der Zusammensetzung NbCo2 durch Substitution von Co durch überschüssiges Nb erzeugt, wobei nur eine der beiden Co-Lagen gemischt besetzt wird. Quantenmechanische Rechnungen zeigen, dass dieses Besetzungsmuster energetisch bevorzugt ist. Weder mittels Röntgenbeugung noch mittels hochauflösender Elektronenmikroskopie und Elektronenbeugeng wurden Ordnungsvarianten oder Stapelvarianten der Laves-Phasen beobachtet. In der Kristallstruktur von C36-Nb(1-x)Co(2+x) (x = 0,265) ist mehr als ein Viertel des Nb durch überschüssiges Co ersetzt. Von zwei kristallographischen Nb-Lagen wird eine bevorzugt von Co besetzt, so dass sich der Co-Anteil der beiden Lagen etwa wie 2:1 verhält. Co-Antistrukturatome sind relativ zu der Nb-Position verschoben. Triebkraft dieser Verschiebungen ist die Bildung von Nb--Co-Kontakten innerhalb der A-Teilstruktur. Gemischte Besetzung der Nb-Lagen, die Verteilung der Co-Antistrukturatome und mit der Substitution einhergehende Verzerrungen führen zu einer komplizierten Realstruktur. Zur Beschreibung der elektronischen Struktur von C36-Nb(1-x)Co(2+x) (x = 0,265) werden daher verschiedene Modelle verwendet, die Tendenzen sowohl zur beobachteten Mischbesetzung als auch zur Verzerrung der Kristallstruktur aufzeigen. Die elektronische Struktur und chemische Bindung von C14-, C15- und C36-NbCo2 wurde vergleichend untersucht. Berechnungen der Gesamtenergie zeigen sehr geringe Energiedifferenzen zwischen den drei Strukturen, die mit einer sehr ähnlichen Bindungssituation der Polytypen im Einklang ist. In den Systemen Nb--Cr und Nb--Fe wurde der Verlauf der Gitterparameter innerhalb des gesamten Homogenitätsbereichs der Laves-Phase bei ausgewählten Temperaturen untersucht. Die Kristallstrukturen von C15-NbCr2 und C14-NbFe2 wurden erstmals verfeinert. Vorläufige Untersuchungen bestätigen die Existenz von zwei Hochtemperaturmodifikationen (C14 und C36) von NbCr2. Im System Nb--Mn wurde die Mn-reiche Seite des Homogenitätsbereichs bei 800 °C und 1100 °C an aus zweiphasigen (Mn(Nb) + C14) Präparaten isolierten Einkristallen untersucht. Bei 800 °C wird ein Kristall der Zusammensetzung NbMn2 erhalten, während bei 1100 °C ausgeprägte Löslichkeit von Mn in der C14-Phase beobachtet wird. Die Summenformel kann als Nb(1-x)Mn(2+x) (x = 0,13) geschrieben werden. Die Substitution von Nb durch Mn führt zu Verschiebungen der Antistrukturatome bezüglich der Nb-Lagen und damit zur Bildung kurzer Nb--Mn-Abstände. In den ternären Systemen Nb--Cr--Co und Nb--Cr--Ni wurden die Kristallstrukturen der C14-Phasen C14-Nb(Cr(1-x)Co(x))2 und C14-Nb(Cr(1-x)Ni(x))2 am Einkristall untersucht. Neben den auch für die binären C14-Phasen beobachteten Verzerrungen zeigen die Kristallstrukturen eine teilweise geordnete Verteilung von Cr und Co bzw. Cr und Ni auf die beiden kristallographischen Lagen der B-Teilstruktur. Die bevorzugte Besetzung wurde auf der Grundlage von Extended-Hückel-Rechnungen untersucht. Zwar können diese Rechnungen kein quantitatives Bild liefern, jedoch werden Tendenzen im System Nb--Cr--Co richtig wiedergegeben. Im System Nb--Cr--Ni liefern die Rechnungen jedoch dem Experiment widersprechende Ergebnisse. Die Vorhersagekraft der Methode ist also begrenzt. Vergleichende Untersuchungen der Reihe NbTM2, TM = Cr, Mn, Fe, Co mittels Röntgenabsorptionsspektroskopie und Bandstrukturrechnungen zeigen, dass die chemische Bindung der untersuchten Verbindungen im wesentlichen ähnlich ist, aber dass durchaus Entwicklungen innerhalb der Reihe festgestellt werden können. Diese Entwicklung wird besonders in der Verzerrung der C14-Phasen und hier speziell der B-Teilstruktur deutlich, die in den experimentell zugänglichen C14-Phasen in NbMn2 deutlicher ausgeprägt ist als in NbFe2. Analysen der chemischen Bindung mit Hilfe der COHP-Methoden zeigen eine ähnliche Tendenz zur Verzerrung, die vereinfacht auch als Funktion der Valenzelektronenkonzentration aufgefasst werden kann. Berechnungen der Gesamtenergie unterstützen diese Interpretation. Im Gesamtbild der elektronischen Struktur ist eine leichte Zunahme des ionischen Bindungsanteils von TM = Cr zu TM = Co zu erkennen. Die Natur der Laves-Phasen in Systemen der Übergangsmetalle ist ein sehr vielschichtiges Problem, das weiterhin intensive und interdisziplinäre Forschung erfordert. Insbesondere mit der Charakterisierung nichtstöchiometrischer Laves-Phasen wurden aber bereits wichtige Beiträge zum Verständnis der Bildung der Homogenitätsbereiche erarbeitet.

Physics
Ph.D.
The Random Phase Approximation and beyond Random Phase Approximation methods based on Adiabatic Connection Fluctuation Dissipation Theorem (ACFD) are tested for structural phase transitions of different groups of materials, including metal to metal, metal to semiconductor, semiconductor to semiconductor transitions. Also the performance assessment of semilocal density functionals with or without empirical long range dispersion corrections has been explored for the same cases. We have investigated the structural phase transitions of three broad group of materials, semi- conductor to metal transitions involving two symmetric structures, semiconductor to metal and wide bandgap semiconductor to semiconductor transitions involving at least one lower symmetric structure and lastly special cases comprising metal to metal transitions and transitions between energetically very close structural phases. The first group contains Si (diamond → β-tin), Ge (diamond → β-tin) and SiC (zinc blende → rocksalt), second group contains GaAs (zinc blende → cmcm) and SiO 2 (quartz → stishovite) and third group contains Pb (fcc → hcp), C(graphite → diamond) and BN (cubic → hexagonal) respectively. We have found that the difference in behavior of exchange and correlation in semilocal functionals and ACFD methods is striking. For the former, the exchange potential and energy often comprise the majority of the binding described by density functional approximations, and the addition of the correlation energy and potential often induce only a (relatively) small shift from the exchange- only results. For the ACFD, however, non self-consistent EXX typically underbinds by a considerable degree resulting in wildly inaccurate results. Thus the addition of correlation leads to very large shifts in the exchange-only results, in direct contrast to semilocal correlation. This difference in behavior is directly linked to the non-local nature of the EXX, and even though the exchange-only starting point is often nowhere close to experiment, the non-local correlation from the ACFD corrects this deficiency and yields the missing binding needed to produce accurate results. Thus we find the ACFD approach to be vital in the validation of semilocal results and recommend its use in materials where experimental results cannot be straightforwardly compared to other approximate electronic structure calculations. Utilizing the second-order approximation to Random Phase Approximation renormalized (RPAr) many-body perturbation theory for the interacting density-density response function, we have used a so-called higher-order terms (HOT) approximation for the correlation energy. In combination with the first-order RPAr correction, the HOT method faithfully captures the infinite- order correlation for a given exchange-correlation kernel, yielding errors of the total correlation energy on the order of 1% or less for most systems. For exchange-like kernels, our new method has the further benefit that the coupling-strength integration can be completely eliminated resulting in a modest reduction in computational cost compared to the traditional approach. When the correlation energy is accurately reproduced by the HOT approximation, structural properties and energy differences are also accurately reproduced, as confirmed by finding interlayer binding energies of several periodic solids and compared that to some molecular systems along with some phase transition parameters of SiC. Energy differences involving fragmentation have proved to be challenging for the HOT method, however, due to errors that do not cancel between a composite system and its constituent pieces which has been verified in our work as well.
Temple University--Theses

Biomolecular condensates act as indispensable membrane-less organelles for intracellular organization and regulation of biochemical reactions. Proteins and RNAs are known to phase separate into condensates, however the sequence domains that encode this process remain unclear. By means of computational tools and predictions, I systematically analysed the sequences of the human and yeast proteomes for phase separation ability. Furthermore, I experimentally evaluated the sequence domains of the yeast protein Pub1. My findings report that RNA-binding domains (RBDs) and prion-like domains (PrLDs) play different roles in the phase separation process. While one PrLD can lead the assembly, a combination of RBDs modulate the dynamicity of the condensate. The high interacting capacity of the PrLD explains the ability to recruit molecules into condensates but it also compromises homeostasis. This work sheds light on the principles behind formation and regulation of membrane-less organelles.
Els condensats biomoleculars actuen com a orgànuls sense membrana, organitzant el funcionament intern de la cèl·lula i regulant les reaccions bioquímiques que hi tenen lloc. Proteïnes i ARNs es separen en una fase diferent formant aquests condensats, però els dominis de les seves seqüències que propicien aquest procés encara no són clars. A través d’eines computacionals i de prediccions, he analitzat la habilitat de les seqüències del proteoma humà i de llevat de formar aquesta nova fase. A més, he avaluat experimentalment els dominis de la seqüència de Pub1, una proteïna de llevat. Els meus resultats indiquen que els dominis d’unió a ARN (RBDs) i els dominis similars a prions (PrLDs) tenen funcions diferents en el procés de separació de fases. Mentre que un PrLD pot liderar-ne la formació, diversos RBDs modulen les dinàmiques dintre del condensat. L’elevada capacitat d’interacció que tenen els PrLDs explica l’habilitat de reclutar molècules per formar condensats, però alhora compromet els equilibris i estabilitat cel·lulars (homeòstasi). La meva investigació revela informació sobre els principis que governen la formació i regulació d’orgànuls sense membrana.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1995.
Includes bibliographical references (leaves 109-114).
by Ariel Javier Sebastián Traiber.
Ph.D.

Thesis advisor: Eranthie Weerapana
Antibiotic resistance of bacterial pathogens poses an increasing threat to the wellbeing of our society and urgently calls for new strategies for infection diagnosis and antibiotic discovery. The overuse and misuse of broad-spectrum antibiotics has contributed to the antibiotic resistance crisis. Additionally, treatment of infections with broad-spectrum antibiotics can cause disruption to the host gut microbiome. The development of narrow-spectrum antibiotics would be ideal to avoid unnecessary cultivation of antibiotic resistance and damage to the human microbiota. Bacteria present many mechanisms of resistance, including modulating their cell surface with amine functionalities. In an age where infections are no longer responding to typical antibiotic treatments, novel drugs that target the characteristics of antibiotic resistance would be beneficial to remedy these defiant infections. Herein, we describe the utility of iminoboronate formation to target the amine- presenting surface modifications on bacteria, particularly those that display antibiotic resistance. Specifically, multiple 2-acetylphenylboronic acid warheads were incorporated into a peptide scaffold to develop potent peptide probes of bacterial cells. Further, by engineering a phage display library presenting the 2-acetylphenylboronic acid moieties, we were able to perform peptide library screens against live bacterial cells to develop reversible covalent peptide probes of target strains of bacteria. These peptide probes, which were developed for clinical strains of Staphylococcus aureus and Acinetobacter baumannii which display resistance, can label the target bacterium at submicromolar concentrations in a highly specific manner and in complex biological milieu. We further show that the identified peptide probes can be readily converted to bactericidal agents that deliver generic toxins to kill the targeted bacterial strain with high specificity. It is conceivable that this phage display platform is applicable to a wide array of bacterial strains, paving the way to facile diagnosis and development of strain-specific antibiotics. Furthermore, it is intriguing to speculate that even higher potency binding could be accomplished with better designed phage libraries with dynamic covalent warheads. This work is currently underway in our laboratory
Thesis (PhD) — Boston College, 2018
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry

Plasmodium vivax Duffy binding protein (DBP) is an essential ligand for reticulocyte invasion making it a premier asexual blood stage vaccine candidate. However, strain-specific immunity due to DBPII allelic variation may complicate vaccine efficacy, suggesting that an effective DBPII vaccine needs to target immune responses to conserved epitopes that are potential targets of strain-transcending neutralizing immunity. Anti DBPII monoclonal antibodies, which were previously characterized by COS7 cell binding assay as inhibitory and non-inhibitory to DBPII-erythrocyte binding, were mapped to DBPII gene fragment libraries using phage display. Inhibitory mAb 3C9 binds to a conserved conformation-dependent epitope in subdomain 3 while non-inhibitory mAb 3D10 binds to a linear epitope in subdomain 1 of DBPII. More definitive epitope mapping of mAb 3D10 was achieved using a random peptide library displayed on phage. Since DBP region II is mostly made up of alpha-helices, we used a randomized helical scaffold library, the Affibody library, displayed on phage, to determine epitope of conformation-dependent antibodies. The immunogenicity of the identified epitopes was evaluated in mice and the immune sera evaluated for binding to DBPII by ELISA and inhibition of DBPII-erythrocyte binding by the COS7 cell assay. Immune serum from the mAb3C9 epitope blocked DBPII-erythrocyte, suggesting this epitope could be a good subunit vaccine target.

En plus d’être l’intermédiaire entre l’ADN et les protéines, l’ARN est impliqué dans plusieurs processus biologiques : régulation et expression des gènes (riboswitches, ARNm et ARNt) ou encore catalyse (ribozymes). La fonction de chaque ARN est liée à sa structure et à sa dynamique de repliement. Des cations tel que le magnésium se lient à l’ARN et peuvent être essentiels au bon repliement et à la stabilité de ces structures. L’obtention de détails structuraux et thermodynamiques sur l’interaction avec le magnésium a donc une grande importance dans la compréhension de la relation structure-fonction. La première partie de ce travail a consisté en la caractérisation des équilibres de liaison entre le magnésium et des motifs d’ARN modèles, appelés « kissing complexes », par spectrométrie de masse native (SM). Grâce à la SM, il est possible de distinguer les stoechiométries de liaison du magnésium. Le travail présenté ici a permis l’élaboration d’une méthode pour quantifier chaque espèce en prenant en compte la distribution d’adduits non-spécifiques. Afin d’aller plus loin dans la localisation du magnésium, nous avons utilisé la spectrométrie de masse en tandem (SM/SM). Nous avons également étudié le comportement des complexes d’ARN en phase gazeuse en utilisant la spectrométrie de mobilité ionique (SMI), avec pour but de détecter des changements de conformation dus à la liaison de cations ou ligands. Contrairement à ce qui était anticipé, nous avons démontré que les duplexes d’ADN et ARN ainsi que les « kissing complexes » subissaient une compaction significative en phase gazeuse aux états de charge initialement obtenus par SM native, ce qui pourrait cacher l’effet des cations. Notre travail a montré comment la spectrométrie de masse peut apporter de nouvelles indications sur les stoechiométries et affinités entre ARN et cations, et discute de certaines limitations quant à l’utilisation de techniques en phase gazeuse pour explorer les structures en solution
Besides being the molecular intermediate between DNA and proteins, RNA can have many other functions such as gene regulation (riboswitches), gene expression (mRNA and tRNA) or catalysis (ribozymes). RNA function is linked to its structure and its folding dynamics. Cations such as magnesium bind to RNA and are in some instances essential for proper folding and for stability. The need of structural and thermodynamic details about Mg2+ interactions is then of upmost importance in the study of the structurefunction relationships. The first part of our work consists in characterizing the binding equilibria between magnesium and RNA model motifs, called kissing complexes, using native mass spectrometry (MS). MS makes it possible to distinguish individual binding stoichiometries, and the present work consisted in developing a method to quantify each species, taking into account the contribution of nonspecific adducts. We also explored how tandem mass spectrometry (MS/MS) could further help localizing magnesium ions. Further, we explored the structures of RNA complexes in the gas phase using ion mobility mass spectrometry (IMMS), with the aim to detect shape changes upon cation or ligand binding. But in contrast with anticipations, we found that DNA and RNA duplexes as well as RNA kissing complexes undergo a significant compaction at charge states naturally produced by native ESI-MS, which may hide the effect of cations. Our work showcases how mass spectrometry can bring novel information on RNA-cation binding stoichiometries and affinities, but also discusses some limitations of a gas-phase method to probe solution structures

Colonisation by many bacteria and viruses is now thought to depend upon their ability to adhere to host cells via proteinacious surface appendages called adhesins. Information relevant to the prevention and cure of many diseases therefore is supplied by knowledge of this adhesive process, especially the chemistry of the binding and the structure of the binding molecules. At this time, the structure of very few adhesin receptors is known. Similarly, the quaternary and primary structure of only a small number of adhesins is currently available. Those associated with Escherichia coli are known in some cases to be arranged as helical coils with repeating proteinacious subunits with molecular weights of 10-30 kDa, however there is conflicting information on the distribution along these coils of the polypeptide involved in adhesion. Thermodynamic binding studies have not yet been used to clarify this problem because of the size of the receptors for the adhesins. This thesis presents a thermodynamic study of the binding between the adhesin from an F41+ E.coli and its receptor, glycophorin, from the human red blood cell membrane using an aqueous polymer two-phase system. The study shows that 2.4±0.8 glycophorin molecules bind to the predominant subunit of this adhesin, suggesting that this subunit has one binding site, since glycophorin dissolves as a dimer. It is proposed that the assay could be used, in addition, to obtain information on the chemical specificity and the thermodynamics of this particular reaction, in order to obtain a broader understanding of the colonisation and infection by this particular pathogen.
Science, Faculty of
Chemistry, Department of
Graduate

The objective of this study was to identify peptide ligands, using phage display techniques, which bind sites on mouse embryos, ovaries, cytoplasmic membranes and/or intracytoplasmic components. Specifically, M13 coliphage 7-mer, 12-mer and 15-mer random peptide libraries were used separately for biopanning. Peptides derived from the amplified pools were sequenced and studied. The phage display for in vivo ovary experiments yielded no pool of peptides after two cycles of biopanning and re-amplification. With the same initial concentration of a random 7-mer or 12-mer library, there were repeating sequences derived after three and four biopanning cycles on mouse embryos and unfertilized ova. The sequences were not distinguishable from a control group. Subsequent experimentation using a random 15-mer library to select for internalized phage-peptides yielded two apparent consensus sequences, RNVPPIFNDVYWIAF (9/32 or 28%) and HGRFILPWWYAFSPS (11/32 or 34%). The 15-mer control group yielded no clones. The deduced peptide sequences were compared to known sequences to ascertain their uniqueness. No significant similarities were found, yielding two possible novel motifs. Through this adapted process of phage display and further research, the phage display technology may be used as a tool in the recognition of specific mouse gamete sites. By identifying binding sites of mouse gametes, the peptides might be exploited as a means of studying the embryo cell surface or cytoplasmic components and mouse sperm-egg interactions. Such peptides may also be used for macromolecule delivery in transfection or transgenesis.
Master of Science

Modernization has brought about steady increase in the consumption of goods and services by human societies across the globe, which mostly driven by both population growth and the change of individual living standards. This, of course, leads to an ever-increasing waste production that ends up in landfills and very often as a source of pollution on natural ecosystems, especially in the low and middle-income countries where waste management is almost inexistent. The management of waste streams is a huge challenge for developed countries as well, where societal and environmental impacts are visible despite massive investments in waste management. One of the most problematic waste materials is plastic, which can remain in nature for over 100 years without degradation, leading to serious environmental concerns. As one of the most significant innovations of the 20th century, plastic is a widely used and cost-effective material for many applications. After their useful lifetimes, their management is problematic. Thus, robust and innovative approaches of managing such waste material are needed in order to mitigate the problem. One of the innovative approaches of tackling the menace cause by plastic waste is through its incorporation into the construction materials. This thesis seeks to address this problem by exploring the use of melted plastic wastes (High Density Poly Ethylene, HDPE and Low Density Poly Ethylene, LDPE) as binder in developing new construction materials (mortar with melted plastic as the only binder, MPB and Plastic Waste Crete, PWC) as an alternative to partially replace traditional concrete and mortar, or finding other engineering uses for this type of waste. Worldwide, about 190 m3 of concrete is poured every second, which translates to 6 billion m3 per year and making it, one of the most widely used manufactured materials. However, the production of concrete requires water and cement. Cement is expensive, and its production contributes to the emission of environmentally polluting gases. Replacing this binding element with recycled plastic derivatives would have significant economic and environmental benefits. In addition to the elimination of cement cost, this will result in water savings, which is especially important for areas without fresh water scarcity. Some researchers have used plastics in concrete and mortars as additives and/or replacement for fine and coarse aggregates. In addition, different types of plastics have been used in bitumen as an additive to reduce construction cost and improve sustainability by adding value to wastes materials. However, there is paucity of technical information about the use of the melted HDPE and LDPE plastic wastes as the only binding phase in concrete- or mortar-like materials. Moreover, many parameters such as preparation conditions, field variables, constituent elements, and final applications have impacts on the performance of construction materials Thus, the key objective of this PhD research is to develop the mortar with plastic binder (MPB) and PlasticWasteCrete (PWC) by using molten HDPE and LDPE plastic wastes as the only binder as well as to investigate the engineering properties of these new types of construction materials. The plastic contents of 45%, 50%, 60% and 65% and HDPE to LDPE ratios of 40/60, 50/50, and 60/40 were selected for the experimental tests. Clean river sand was used as the only aggregate for the MPB, while both sand and gravel were used for the PWC. Various tests were then performed on prepared MPB and PWC samples at different curing times from early to advanced ages to assess their engineering properties. These tests were conducted in accordance with the ASTM standards to evaluate the mechanical properties (compressive strength and splitting tensile strength), permeability and density of the MPB and PWC materials. Additional tests were carried out to analyze the products at the microstructural level (optical microscope, SEM, MIP and thermogravimetric analysis) to gain an insight into the microstructural properties of the developed materials and how that affect their engineering properties. The compressive strength tests revealed the optimal plastic content for the MPB and PWC with the best strength performance. The average compressive strength values for various optimal formulations after 28 days were found to be in the range of 9 to 18 MPa. The splitting tensile strength for the new materials from 1 to 28 days of curing time, were found to be between 1 and 5 MPa. The average hardened density of the MPB and PWC is about 2 g/cm3, which makes them lightweight material according to RILEM classification. In addition, various absorption tests (capillary and immersion) were performed on different MPB and PWC samples, and the obtained results showed that they are porous materials having lower rate of absorption than the traditional cementitious materials (mortar, concrete). This observation was supported by the results from both MIP and SEM analyses. Finally, thermogravimetric analysis provided interesting details on the thermal decomposition of the new materials, with significant changes or mass loss for these products being observed only at temperatures higher than 300°C. The findings from this study suggest MPB and PWC made with melted plastic waste as the only binder have a promising potentials for use in construction. The research conducted in this PhD study offers a good understanding of the engineering properties of the materials as well as the optimal formulations that yield best performance in terms of strength and durability. In summary, it provides useful technical information and tools on the MPB and PWC that will contribute in setting guidelines on the optimal applications of these products in the field of construction in order to have safe, durable and cost-effective structures. Résumé Avec la modernisation de nos sociétés, les habitudes ont considérablement changé, ainsi, on observe une forte consommation des biens et services, due à l’augmentation de la population et l’amélioration de leurs conditions de vie. Ce qui conduit à une augmentation considérable des quantités des déchets qui terminent leurs cycles au niveau des décharges ou dans les océans/fleuves devenant ainsi une source de source de pollution des écosystèmes naturels, surtout dans les pays à revenu faible et intermédiaire avec des systèmes défaillants ou moins performants de gestion des déchets. La gestion des flux de déchets est aussi un défi pour certains pays développés, où les impacts sociaux et environnementaux sont visibles en dépit des investissements massifs dans ce secteur. Parmi ces déchets, nous avons les plastiques, l’une des innovations du 20e siècle avec des qualités versatiles et coût faible, se trouve partout dans nos vies quotidiennes. Après leur utilisation, les plastiques deviennent des déchets qui peuvent rester dans la nature plus de 100 ans sans aucune dégradation, avec des conséquences néfastes sur l’Homme et l’environnement. Ainsi, une approche robuste et innovante de gestion de ces déchets est nécessaire afin d'atténuer leurs impacts. L'une des approches innovantes pour réduire l’impact causé par les déchets plastiques consiste à les incorporer dans les matériaux de construction. Ainsi, le problème est abordé dans cette thèse en développant des technologies permettant de recycler les plastiques fondus comme liant dans les nouveaux matériaux de construction (MPB et PWC), afin d’offrir une alternative pour remplacer partiellement le béton / mortier traditionnel. Le béton est l’un des matériaux les plus utilisés au monde, avec environ 190 m3 coulés chaque seconde, correspondant à 6 milliards de m3 par an. Cependant, la production de béton nécessite de l'eau et du ciment. Le ciment coûte cher et sa production contribue à l'émission de gaz polluants l'environnement. Le remplacement d'une partie du béton traditionnel par un matériau à base des déchets plastique aura des avantages économiques, sociaux et environnementaux importants. Allant dans ce sens, certains chercheurs ont utilisé les plastiques dans le béton et le mortier comme additifs et / ou substituts des matériaux granulaires tels que le sable et le gravier. Aussi, différents types de plastiques ont été utilisé dans le bitume comme additif pour réduire les coûts de construction et améliorer la durabilité, ainsi contribuer à donner de la valeur aux déchets. Cependant, jusqu'à présent, il existe peu d’informations techniques sur l'utilisation de déchets plastiques (HDPE et LDPE) fondus comme seuls liants pour développer de nouveaux types de matériaux de construction. En plus, plusieurs facteurs (les conditions de préparation, les éléments constitutifs, les applications finales, etc.) ont un impact sur les caractéristiques des matériaux de construction. Ainsi, l'objectif de cette recherche doctorale est de développer des nouveaux matériaux de construction (MPB et PWC) en utilisant les déchets plastiques fondus (HDPE et LDPE) comme seul liant, puis déterminer les propriétés caractéristiques de ces matériaux afin de trouver la formulation optimale conduisant à la meilleure résistance. En plus de l'élimination du coût du ciment, cette technologie permet aussi de faire des économies d'eau, bénéfique surtout pour les zones avec des difficultés d'accès à l’eau potable. Cela contribuera à la réduction des coûts de la construction en utilisant les produits innovants comme alternative au béton / mortier conventionnel. Un vaste programme expérimental, comprenant des tests à petite et grande échelle, a été développé afin d'atteindre les objectifs de cette étude de doctorat. La campagne expérimentale a comporté différentes étapes comprenant la sélection des matériaux, la détermination de la formulation optimale et les conditions appropriées pour la préparation des matériaux susmentionnés. Par la suite, pour une meilleure compréhension du comportement technique et des propriétés du produit final, divers tests ont été effectué sur les matériaux préparés à différents temps de durcissement. Ces tests ont été menés conformément aux normes ASTM pour évaluer les propriétés mécaniques (résistance à la compression et à la traction), la perméabilité et la densité des nouveaux matériaux. Les expériences ont été approfondies en analysant les produits au niveau microstructural (microscope optique, SEM, MIP et analyse thermique) pour avoir un aperçu des propriétés microstructurales des matériaux développés et essayer de comprendre les relations avec leur comportement mécanique. Les essais de compression ont permis de trouver la teneur en plastique optimale pour les matériaux (MPB et PWC) avec les meilleures valeurs de résistance. Les résistances moyennes à la compression à 28 jours pour diverses formulations étaient comprises entre 9 et 18 MPa. La résistance à la traction par fendage des nouveaux matériaux entre 1 et 28 jours se situait entre 1 et 5 MPa. La densité moyenne du béton et mortier écologique est proche de 2 g / cm3, ils peuvent donc être considérés comme des matériaux légers selon la classification RILEM. De plus, divers tests d'absorption (capillaire et par immersion) ont été réalisé sur différents échantillons de MPB et PWC, les résultats obtenus ont montré qu'il s'agit de matériaux poreux ayant un taux d'absorption plus faible que les matériaux traditionnels contenant du ciment. Plusieurs analyses microstructurales ont été réalisées sur différents échantillons des nouveaux produits (MPB et PWC) et les matériaux cimentaires traditionnels ont été utilisés pour renforcer notre compréhension. Enfin, l'analyse thermique a fourni des détails intéressants sur la décomposition thermique de ces nouveaux matériaux ; des changements significatifs avec une perte de masse considérable ont été observés seulement pour des températures supérieures à 300 ° C. Les résultats de ces essais permettent d'acquérir une bonne compréhension des propriétés techniques des nouveaux matériaux (MPB et PWC) ainsi que de déterminer les teneurs optimales en plastique conduisant aux meilleures performances en termes de résistance et de durabilité. Ainsi, les recherches menées dans cette étude de doctorat fournissent des informations techniques et des outils utiles sur le MPB et le PWC; et contribueront à installer des bases pour guider les applications optimales de ces nouveaux produits dans le domaine de la construction afin d'avoir des structures sûres, durables et rentables.

The chemical and electrochemical functionalisation of surfaces is of great importance in the construction of electrodes modified with biomolecules. Besides fundamental investigations, research is driven by numerous important applications including biosensing, biofuel cells or molecular electronics. While significant developments have been made some key problems remain, particularly the stability, orientation and electrical communication of the immobilised biomolecule with the conducting support. In order to address these issues a modular approach to electrode modification has been developed, allowing simple variation of the key elements of the tether. After electrochemical attachment of a mono-Boc-protected diamine linker, deprotection followed by amide coupling can be used to introduce a spacer to control the length of the structure. A reactive group may then be introduced and the enzyme coupled. In this work the reactive group chosen was maleimide. A maleimide group will react 1000 times faster with a thiol than an amine at neutral pH, allowing selective attachment to a free cysteine residue in a biomolecule. The initial modification of the electrode surface with linker has been modified to create a partial coverage of the linker on the electrode surface The oxidation of a mixture of amines, using a Boc-protected diamine and a capping group allowed the Boc amine to be spaced out on the surface for optimal enzyme attachment. The developed methods have been used to successfully couple Cytochrome C and two engineered variants of glucose dehydrogenase from Glomerella cingulate to modified electrodes.

Proteins perform an incredible array of functions facilitated by a diverse set of biochemical properties. Changing these properties is an essential molecular mechanism of evolutionary change, with major questions in protein evolution surrounding this topic. How do new functional biochemical features evolve? How do proteins change following gene duplication events? I used the S100 protein family as a model to probe these aspects of protein evolution. The S100s are signaling proteins that play a diverse range of biological roles binding Calcium ions, transition metal ions, and other proteins. Calcium drives a conformational change allowing S100s to bind to diverse peptide regions of target proteins. I used a phylogenetic approach to understand the evolution of these diverse biochemical features. Chapter I comprises an introduction to the disseration. Chapter II is a co-authored literature review assessing available evidence for global trends in protein evolution. Chapter III describes mapping of transition metal binding onto a maximum likelihood S100 phylogeny. Transition metal binding sites and metal-driven structural changes are a conserved, ancestral features of the S100s. However, they are highly labile at the amino acid level. Chapter IV further characterizes the biophysics of metal binding in the S100A5 lineage, revealing that the oft–cited Ca2+/Cu2+ antagonism of S100A5 is likely due to an experimental artifact of previous studies. Chapter V uses the S100 family to investigate the evolution of binding specificity. Binding specificity for a small set of peptides in the duplicate S100A5 and S100A6 clades. Ancestral sequence reconstruction reveals a pattern of clade-level conservation and apparent subfunctionalization along both lineages. In chapter VI, peptide phage display, deep-sequencing, and machine-learning are combined to quantitatively reconstruct the evolution of specificity in S100A5 and S100A6. S100A5 has subfunctionalized from the ancestor, while S100A6 specificity has shifted. The importance of unbiased approaches to measure specificity are discussed. This work highlights the lability of conserved functions at the biochemical level, and measures changes in specificity following gene duplication. Chapter VII summarizes the results of the dissertation, considers the implications of these results, and discusses limitations and future directions. This dissertation includes both previously published/unpublished and co- authored material.

The family 1 cellulose-binding modules (CBM1) form a groupof small, stable carbohydrate-binding proteins. These modulesare essential for fungal cellulosedegradation. This thesisdescribes both functional studies of the CBM1s as well asprotein engineering of the modules for several objectives.

The characteristics and specificity of CBM1s from theTrichoderma reeseiCel7A and Cel6A, along with severalother wild type and mutated CBMs, were studied using bindingexperiments and transmission electron microscopy (TEM). Datafrom the binding studies confirmed that the presence of onetryptophan residue on the CBM1 binding face enhances itsbinding to crystalline cellulose. The twoT. reeseiCBM1s as well as the CBM3 from theClostridium thermocellumCipA were investigated by TEMexperiments. All three CBMs were found to bind in lineararrangements along the sides of the fibrils. Further analysesof the bound CBMs indicated that the CBMs bind to the exposedhydrophobic surfaces, the so called (200) crystalline face ofValoniacellulose crystals.

The function and specificity of CBM1s as a part of an intactenzyme were studied by replacing the CBM from the exo-actingCel7A by the CBM1 from the endoglucanase Cel7B. Apart fromslightly improved affinity of the hybrid enzyme, the moduleexchange did not significantly influence the function of theCel7A. This indicates that the two CBM1s are analogous in theirbinding properties and function during cellulosehydrolysis.

The CBM1 was also used for immobilization studies. Toimprove heterologous expression of a CBM1-lipase fusionprotein, a linker stability study was carried out inPichia pastoris. A proline/threonine rich linker peptidewas found to be stable for protein production in this host. Forwhole bacterial cell immobilization, theT. reeseiCel6A CBM1 was expressed on the surface of thegram-positive bacteria,Staphylococcus carnosus. The engineeredS. carnosuscells were shown to bind cellulosefibers.

To exploit the stable CBM1 fold as a starting point forgenerating novel binders, a phage display library wasconstructed. Binding proteins against an amylase as well asagainst a metal ion were selected from the library. Theamylase-binding proteins were found to bind and inhibit thetarget enzyme. The metal binding proteins selected from thelibrary were cloned on the surface of theS. carnosusand clearly enhanced the metal bindingability of the engineered bacteria.

Keywords: cellulose-binding, family 1carbohydrate-binding module, phage display, bacterial surfacedisplay, combinatorial protein library, metal binding, proteinengineering,Trichoderma reesei, Staphyloccus carnosus.

Standard purification processes in large scale antibody production are largely dependent on Protein A chromatography. Protein A binds specifically to many subclasses of IgG with high affinity. However, in order to elute the proteins, the pH needs to be lowered. Since lowering of the pH can be detrimental to some antibodies, a milder purification process is of great interest. A variant of Protein A, called ZCa, has previously been engineered to bind to IgG in a calcium-dependent manner. The antibody binds to ZCa when calcium is present and releases when calcium is removed. For the IgG1 subclass, the elution still requires a slight lowering of the pH, which is why there is room for improvement of the molecule. A phage display selection has been performed with the aim to obtain calcium-dependent IgG1 binders that are able to release the antibodies upon calcium depletion at neutral pH. In addition, an attempt on increasing the alkaline stability of the binders was made. Sequence analysis of the selection output showed almost no indications of increased alkaline stability. Instead, M13K07 helper phages were exposed to new selections for increased alkaline tolerance which might be useful in future phage display selections. Even though the binders selected for in this project did show some promising characteristics, none of them were able to elute upon calcium depletion at neutral pH as aimed for. However, one of the variants did show promising results during most of the performed characterizations. Most interestingly, the elution properties of this variant could indicate a higher calcium-dependence in the interaction with the target than that of ZCa, although further characterizations need to be performed in order to draw any conclusions about possible improvements of this protein domain.

Small robust affinity proteins have shown great potential for use in therapy, in vivo diagnostics, and various biotechnological applications. However, the affinity proteins often need to be modified or functionalized to be successful in many of these applications. The use of chemical synthesis for the production of the proteins can allow for site-directed functionalization not achievable by recombinant routes, including incorporation of unnatural building blocks. This thesis focuses on chemical engineering of Affibody molecules and an albumin binding domain (ABD), which both are three-helix bundle proteins of 58 and 46 amino acids, respectively, possible to synthesize using solid phase peptide synthesis (SPPS). In the first project, an alternative synthetic route for Affibody molecules using a fragment condensation approach was investigated. This was achieved by using native chemical ligation (NCL) for the condensation reaction, yielding a native peptide bond at the site of ligation. The constant third helix of Affibody molecules enables a combinatorial approach for the preparation of a panel of different Affibody molecules, demonstrated by the synthesis of three different Affibody molecules using the same helix 3 (paper I). In the next two projects, an Affibody molecule targeting the amyloid-beta peptide, involved in Alzheimer’s disease, was engineered. Initially the N-terminus of the Affibody molecule was shortened resulting in a considerably higher synthetic yield and higher binding affinity to the target peptide (paper II). This improved variant of the Affibody molecule was then further engineered in the next project, where a fluorescently silent variant was developed and successfully used as a tool to lock the amyloid-beta peptide in a β-hairpin conformation during studies of copper binding using fluorescence spectroscopy (paper III). In the last two projects, synthetic variants of ABD, interesting for use as in vivo half-life extending partners to therapeutic proteins, were engineered. In the first project the possibility to covalently link a bioactive peptide, GLP-1, to the domain was investigated. This was achieved by site-specific thioether bridge-mediated cross-linking of the molecules via a polyethylene glycol (PEG)-based spacer. The conjugate showed retained high binding affinity to human serum albumin (HSA) and a biological activity comparable to a reference GLP-1 peptide (paper IV). In the last project, the possibility to increase the proteolytic stability of ABD through intramolecular cross-linking, to facilitate its use in e.g. oral drug delivery applications, was investigated. A tethered variant of ABD showed increased thermal stability and a considerably higher proteolytic stability towards pepsin, trypsin and chymotrypsin, three important proteases found in the gastrointestinal (GI) tract (paper V). Taken together, the work presented in this thesis illustrates the potential of using chemical synthesis approaches in protein engineering.

QC 20140207

Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au premier abord, de telles structures sont rendues possibles par l’existence de protéines bivalentes, capable d’apparier des régions parfois très éloignées sur la séquence d’ADN. Le système physique ainsi constitué du chromosome et de protéines bivalentes peut être très complexe. C’est pourquoi les mécanismes régissant le repliement du chromosome sont restés majoritairement incompris.Nous avons étudié des modèles d’architecture du chromosome en utilisant le formalisme de la physique statistique. Notre point de départ est la représentation du chromosome sous la forme d’un polymère rigide, pouvant interagir avec une solution de protéines liantes. Les structures résultant de ces interactions ont été caractérisées à l’équilibre thermodynamique. De plus, nous avons utilisé des simulations de dynamique Brownienne en complément des méthodes théoriques, car elles permettent de prendre en considération une plus grande complexité dans les phénomènes biologiques étudiés.Les principaux aboutissements de cette thèse ont été : (i) de fournir un modèle pour l’existence des usines de transcriptions caractérisées in vivo à l’aide de microscopie par fluorescence ; (ii) de proposer une explication physique pour une conjecture portant sur un mécanisme de régulation de la transcription impliquant la formation de boucles d’ADN en tête d’épingle sous l’effet de la protéine H-NS, qui a été émise suite à l’observation de ces boucles au microscope à force atomique ; (iii) de proposer un modèle du chromosome qui reproduise les contacts mesurés à l’aide des techniques Hi-C. Les conséquences de ces mécanismes sur la régulation de la transcription ont été systématiquement discutées
Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies

Protein engineering and in vitro selection systems are powerful methods to generate binding proteins. In nature, antibodies are the primary affinity proteins and their usefulness has led to a widespread use both in basic and applied research. By means of combinatorial protein engineering and protein library technology, smaller antibody fragments or alternative non-immunoglobulin protein scaffolds can be engineered for various functions based on molecular recognition. In this thesis, a 46 amino acid small albumin-binding domain derived from streptococcal protein G was evaluated as a scaffold for the generation of affinity proteins. Using protein engineering, the albumin binding has been complemented with a new binding interface localized to the opposite surface of this three-helical bundle domain. By using in vitro selection from a combinatorial library, bispecific protein domains with ability to recognize several different target proteins were generated. In paper I, a bispecific albumin-binding domain was selected by phage display and utilized as a purification tag for highly efficient affinity purification of fusion proteins. The results in paper II show how protein engineering, in vitro display and multi-parameter fluorescence-activated cell sorting can be used to accomplish the challenging task of incorporating two high affinity binding-sites, for albumin and tumor necrosis factor-alpha, into this new bispecific protein scaffold. Moreover, the native ability of this domain to bind serum albumin provides a useful characteristic that can be used to extend the plasma half-lives of proteins fused to it or potentially of the domain itself. When combined with a second targeting ability, a new molecular format with potential use in therapeutic applications is provided. The engineered binding proteins generated against the epidermal growth factor receptors 2 and 3 in papers III and IV are aimed in this direction. Over-expression of these receptors is associated with the development and progression of various cancers, and both are well-validated targets for therapy. Small bispecific binding proteins based on the albumin-binding domain could potentially contribute to this field. The new alternative protein scaffold described in this thesis is one of the smallest structured affinity proteins reported. The bispecific nature, with an inherent ability of the same domain to bind to serum albumin, is unique for this scaffold. These non-immunoglobulin binding proteins may provide several advantages as compared to antibodies in several applications, particularly when a small size and an extended half-life are of key importance.

QC 20121122

Mass spectrometry is a versatile, sensitive and fast technique with which to probe biophysical properties in biological systems and one of the most important analytical tools in the multidisciplinary field of proteomics. The study of nativestate proteins and their complexes in the gas-phase is well established and direct infusion electrospray ionisation mass spectrometry (DI-ESI-MS) techniques are becoming increasingly popular as a tool for screening and determining quantitative information on protein-protein and protein-ligand interactions. However, complexes retained by ESI-MS are not always representative of those in solution and care must be taken in interpreting purely gas-phase results. This thesis details modification and advancement of solution phase techniques devised by Gross et al. utilising ESI-MS and Fitzgerald et al. applying matrix assisted laser desorption ionisation (MALDI)-MS termed PLIMSTEX (protein-ligand interactions by mass spectrometry, titration and hydrogen-deuterium-exchange)[1] and SUPREX (Stability of unpurified proteins from rates of H/D exchange)[2] to quantify these interactions with regards to high throughput analysis. The first part of this thesis describes the different developmental stages of the devised HPLC-front ends and their optimisation with myoglobin and insulin. The successfully developed HPLC-front end in conjunction with PLIMSTEX and SUPREX and ESI-MS then gets tested with self expressed and purified cyclophilin A(CypA)- cyclosporin A (CsA) system, followed by a test screen with potential CypA binding ligands. Dissociation constants (Kd’s) within one order of magnitude to reported values are determined. In the third part of this thesis the application of the devised ESI-SUPREX methodology has been applied to anterior gradient 2 (AGr2) and the factor H complement control proteins module 19-20 (fH19-20) exhibiting binding potential to a taggedhexapeptide and a synthetic pentasaccharide, respectively, resulting in thermodynamical data for these protein-ligand interactions. For the AGr2 system another dimension of investigation has been added by temperature controlling the devised ESI-SUPREX approach, revealing a phase transition in the protein at higher temperatures. The final part of this thesis describes the application of the ESI-SUPREX methodology to probe folding properties of CypA in the presence of the self expressed and purified E. coli chaperonin groEL. Thereby the denaturing properties of groEL have been emphasised along with the stabilisation of a denatured CypA species.

Les perovskites hybrides organique-halogénure de plomb représentent une classe de matériaux émergents, proposés en tant qu'absorbeur de lumière dans le cadre d'une nouvelle génération de cellules solaires. La formule chimique de ces composés est APbX3, où A est un cation organique, X représente un anion halogénure (normalement Cl-, Br-, ou l-, ou alors un alliage composé par ces éléments). Les perovskite hybrides combinent d'excellentes propriétés d'absorption avec une grande longueur de diffusion et de longues durées de vie des porteurs de charge, ce qui permet d'atteindre des efficacités de conversion de photons de 22%. Un autre avantage réside dans leur bas coût de fabrication. Par conséquent, avec le développement de cette classe de matériaux, le photovoltaïque basé sur les perovskites sera potentiellement capable de fortement améliorer les performances de la technologie photovoltaïque actuelle, basée sur le silicium. Dans cette thèse, nous utilisons des méthodes optiques afin d'étudier les propriétés électroniques de base et la morphologie de couches minces de plusieurs représentants des perovskites. Nous étudions notamment des composés ayant le methylammonium et le formamidinium en tant que cations organiques ainsi que les iodures et les bromures à large bande interdite et nous montrons de quelle manière la composition chimique influence les paramètres étudiés. Par magnéto-transmission, nous déterminons directement l'énergie de liaison de l'exciton et sa masse réduite. Nous avons trouvé que les énergies de liaison à T = 2K sont comprises de 14 à 25 meV, plus petites ou comparables à l'énergie thermique moyenne à la température ambiante (25meV). De plus, ces valeurs diminuent à T=160K jusqu'à 10-24meV. Suite à ces résultats, nous concluons que les porteurs photocréés dans les perovksites peuvent être considérés ionisés thermiquement à la température ambiante. Les valeurs de masse effective sont comprises entre 0.09-0.13 fois la masse de l'électron libre. Nous montrons également que l'énergie de liaison de l'exciton ainsi que la masse effective dépendent linéairement de la valeur de la bande interdite. Nos résultats permettent donc d'estimer la valeur des paramètres de ces nouveaux composés perovksites. Nous avons étudié la morphologie de couches minces de perovskite par photoluminescence résolue spatialement avec une résolution micrométrique. Cette technique nous a permis d'observer des grains cristallins uniques. Nous démontrons que la transition de la phase tétragonale à orthorhombique à basse température est incomplète dans tous les matériaux étudiés, comme montré par les résidus de phase tétragonale trouvés à T =4K. En étudiant structurellement certaines régions endommagées et photo-recuites, nous montrons que la présence de la phase tétragonale à basse température augmente, causée par une déplétion de l'halogène
The hybrid organo-lead halide perovskites are an emerging class of materials, proposed for use as light absorbers in a new generation of photovoltaic solar cells. The chemical formula for these materials is APbX3, where A is an organic cation and X represents halide anions (most commonly Br-, Cl- or I-, or alloyed combination of these). The hybrid perovskies combine excellent absorption properties with large diffusion lengths and long lifetime of the carriers, resulting in photon conversion efficiencies as high as 22%. Another advantage is the inexpensiveness of the fabrication process. Therefore, with the rapid development of this class of materials, the perovskite photovoltaics has perspectives to outperform the well-established silicon technology. Here, we use optical methods to investigate the basic electronic properties and morphology in the thin films of several representatives of the hybrid perovskites. We study the compounds based on Methylammonium and Formamidinium organic cations; the iodides and wide band-gap bromides, showing how the chemical composition influences the investigated parameters. Using magneto-transmission, we directly determine the values of exciton binding energy and reduced mass. We find that the exciton binding energies at T = 2 K, varying from 14 to 25 meV, are smaller or comparable to the average thermal energy at room temperature (˜25 meV). Moreover, these values fall further at T = 160 K, to 10-24 meV. Based on that we conclude that the carriers photocreated in a perovskite material can be considered to be thermally ionized at room temperature. The measured reduced masses are in the range of 0.09-0.13 of the electron rest mass. We also show that both exciton binding energy and reduced mass depend linearly on the band gap energy. Therefore, the values of these parameters can be easily estimated for the synthesis of new perovskite compounds. With the spatially resolved photoluminescence, we probe the morphology of perovskite films with micrometer resolution, which enables us to observe single crystalline grains. The resulting maps show that all investigated thin films are composed from the dark and bright crystalline grains. We demonstrate that the low temperature phase transition from tetragonal to orthorhombic phase is incomplete in all studied materials, as the remains of the tetragonal phase are found even at T = 4 K. By investigating structurally damaged and photo annealed regions, where the occurrence of the tetragonal phase at low temperatures is enhanced, we attribute its presence to the depleted halide content

The thesis presents work regarding amphiphilic molecules associated in aqueous solution or at the liquid/solid interface. Two main topics are included: the temperature-dependent behavior of micelles and the adsorption of dispersants on carbon nanotube (CNT) surfaces. Various NMR methods were used to analyze those systems, such as chemical shift detection, spectral intensity measurements, spin relaxation and, in particular, self-diffusion experiments. Besides this, small angle X-ray scattering (SAXS) was also applied for structural characterization.   A particular form of phase transition, core freezing, was detected as a function of temperature in micelles composed by a single sort of Brij-type surfactants. In mixed micelles, that phase transition still occurs accompanied by a reversible segregation of different surfactants into distinct aggregates. Adding a hydrophobic solubilizate shifts the core freezing point to a lower temperature. Upon lowering the temperature to the core freezing point, the solubilizate is released. The temperature course of the release curves with different initial solubilizate loadings is rationalized in terms of a temperature-dependent loading capacity.   The behavior of amphiphilic dispersant molecules in aqueous dispersions of carbon nanotubes (CNTs) has been investigated with a Pluronic-type block copolymer as frequent model dispersant. Detailed dispersion curves were recorded and the distribution of the dispersant among different available environments was analyzed. The amount of dispersed CNT was shown to be defined by a complex interplay of several factors during the dispersion process such as dispersant concentration, sonication time, centrifugation and CNT loading. In the dispersion process, high amphiphilic concentration is required because the pristine CNT surfaces made available by sonication must be rapidly covered by dispersants to avoid their re-attachment. In the prepared dispersions, the competitive adsorption of possible dispersants was investigated that provided information about the relative strength of the interaction of those with the nanotube surfaces. Anionic surfactants were found to have a strong tendency to replace Pluronics, which indicates a strong binding of those surfactants.   CNTs were dispersed in an epoxy resin to prepare nanotube-polymer composites. The molecular mobility of epoxy was investigated and the results demonstrated the presence of loosely associated CNT aggregates within which the molecular transport of epoxy is slow because of strong attractive intermolecular interactions between epoxy and the CNT surface. The rheological behavior is dominated by aggregate-aggregate jamming.

QC 20180103

A cell integrates mitogenic signals received at the plasma membrane with intracellular biochemical changes to direct the events of cell division. Oocytes from Xenopus laevis offer a system that allows molecular dissection of pathways controlling cell growth and division in response to extracellular cues. Xenopus oocytes, physiologically arrested in a G2 like state, respond to the hormone progesterone to reinitiate meiosis and mature into a fertilizable egg. Signals received at the oocyte membrane induce translation of dormant maternal mRNAs that not only drive meiotic entry but also maintain the cell cycle arrest in an egg. A major pathway controlling the translation of these mRNAs is cytoplasmic polyadenylation, facilitated by the Cytoplasmic Polyadenylation Element Binding protein (CPEB) through cis-acting elements in their 3'untranslated regions (3'UTRs). Cytoplasmic polyadenylation requires the phosphorylation of serine174 on CPEB by Aurora-A as well as the translation of a hitherto unknown mRNA. The transcript of the RINGO/Spy gene is a putative candidate for this unknown upstream regulator of CPEB function. RINGO/Spy mRNA is translationally repressed in immature oocytes by a ribonucleoprotein (RNP) complex consisting of the repressor Pumilio-2, the putative activator Deleted in Azoospermia-like (DAZl) and embryonic poly A binding protein (ePAB). Progesterone signaling leads to the dissociation of Pumilio-2 from the mRNP and the ensuing RINGO/Spy protein synthesis, in turn, promotes cytoplasmic polyadenylation and oocyte maturation. Pumilio and its associated proteins, such as Drosophila Brain tumor (Brat) and DAZl, in addition to their cytoplasmic roles have ill-defined functions within the nucleus. We detected DAZl within the nucleoli of telomerase-immortalized human retinal pigment epithelial (RPE) cells in interphase and on acrocentric chromosomes during mitosis. DAZl colocalizes with the RNA polymerase I associated Upstream Binding transcription Factor (UBF), most likely through pre-ribosomal RNA and is a likely component of the Nucleolar Organization Region (NOR). Stably knocking down DAZl in RPEs using short hairpin RNAs results in loss of nucleolar segregation, the physiological outcome of which is under investigation. These preliminary findings indicate an additional role for DAZl within the nucleolus, one likely to be independent from cytoplasmic translational control.

A cell integrates mitogenic signals received at the plasma membrane with intracellular biochemical changes to direct the events of cell division. Oocytes from Xenopus laevis offer a system that allows molecular dissection of pathways controlling cell growth and division in response to extracellular cues. Xenopus oocytes, physiologically arrested in a G2 like state, respond to the hormone progesterone to reinitiate meiosis and mature into a fertilizable egg. Signals received at the oocyte membrane induce translation of dormant maternal mRNAs that not only drive meiotic entry but also maintain the cell cycle arrest in an egg. A major pathway controlling the translation of these mRNAs is cytoplasmic polyadenylation, facilitated by the Cytoplasmic Polyadenylation Element Binding protein (CPEB) through cis-acting elements in their 3'untranslated regions (3'UTRs). Cytoplasmic polyadenylation requires the phosphorylation of serine174 on CPEB by Aurora-A as well as the translation of a hitherto unknown mRNA. The transcript of the RINGO/Spy gene is a putative candidate for this unknown upstream regulator of CPEB function. RINGO/Spy mRNA is translationally repressed in immature oocytes by a ribonucleoprotein (RNP) complex consisting of the repressor Pumilio-2, the putative activator Deleted in Azoospermia-like (DAZl) and embryonic poly A binding protein (ePAB). Progesterone signaling leads to the dissociation of Pumilio-2 from the mRNP and the ensuing RINGO/Spy protein synthesis, in turn, promotes cytoplasmic polyadenylation and oocyte maturation. Pumilio and its associated proteins, such as Drosophila Brain tumor (Brat) and DAZl, in addition to their cytoplasmic roles have ill-defined functions within the nucleus. We detected DAZl within the nucleoli of telomerase-immortalized human retinal pigment epithelial (RPE) cells in interphase and on acrocentric chromosomes during mitosis. DAZl colocalizes with the RNA polymerase I associated Upstream Binding transcription Factor (UBF), most likely through pre-ribosomal RNA and is a likely component of the Nucleolar Organization Region (NOR). Stably knocking down DAZl in RPEs using short hairpin RNAs results in loss of nucleolar segregation, the physiological outcome of which is under investigation. These preliminary findings indicate an additional role for DAZl within the nucleolus, one likely to be independent from cytoplasmic translational control.

Interferon regulatory factor 1 (IRF-1) is a tumour suppressor protein and transcription factor. It has been shown to modulate target gene expression in response to stimuli, which include viral infection and DNA damage, and to be down-regulated in several forms of cancer. This thesis details the development of an intrabody, an intracellular antibody, that binds specifically to endogenous IRF-1. The binding of the intrabody to IRF-1 enhanced transcription from IRF-1-responsive reporter gene constructs and endogenous promoters, thus it was shown to activate IRF-1. Intrabody binding also increased the rate at which IRF-1 was degraded, suggesting that the intrabody epitope may be regulating both IRF-1 activity and turnover. These results were supported point mutation within the intrabody epitope (P325 to A) as the resultant mutant also displayed both a higher transcriptional activity and increased rate of degradation. In an effort to understand the mechanisms which regulate IRF-1 activity a search for novel IRF-1-interacting proteins was carried out using phage peptide display. This in vitro technique enables the identification of peptides able to bind a specific target protein. The sequence of these peptides can then be used to search protein databases for homologous, full-length proteins that could also bind the target protein. This led to the identification of an IRF-1-binding peptide that held sequence similar to a region of Zinc Finger 350 (ZNF350), a transcription factor involved in regulating the DNA damage response. Subsequently, endogenous ZNF350 and IRF-1 were co-immunoprecipitated from a human cancer cell line. The extreme C-terminus of IRF-1 was shown to be sufficient for an interaction with ZNF350, although a second, more N-terminal site was also shown to be essential for a stable intracellular interaction. This data sheds new light on the role of the extreme C-terminus of IRF-1 in modulating the protein‟s activity. This study also provides new and IRF-1-specific molecular tools, in the form of intrabodies and IRF-1-binding peptides, which could be used in the future to further characterise the activity and regulation of this tumour suppressor protein.

Within the immune system, Y-shaped proteins known as antibodies play crucial roles in detecting and blocking the harmful effects of foreign pathogens. Antibodies are naturally synthesized in our bodies by plasma B-cells, but they can also be synthesized and manufactured in labs through methods of recombinant antibody technology. Today, the field of antibody research and development is a competitive area of study due to the great promise it carries. In this study, 4 clones were developed as phage linked and soluble scFv proteins in order to be tested for their specificity against an RTK antigen, T1. T1 was of interest due to its hypothesized involvement in a breast cancer causing pathway. Subsequent selection assays in the form of ELISA and Western Blot were performed in order to identify a promising antibody candidate both robust in expression and specific in binding. The ELISA results pointed to Clone A1 as having the greatest potency and specificity for the T1 target antigen when it was presented as a phage linked and soluble scFv protein. Evaluation of the expression profiles for the 4 soluble and phage linked clones also pointed to clone A1 as being the most robust and potent. In conclusion, clone A1 exhibited the greatest ability in expression and detection of the T1 antigen and was thereby determined to be the most promising candidate in further development and optimization procedures. A1’s results in the preliminary tests also suggests strong performance in its translation into a successful therapeutic drug.

The thesis is focused on site-specific labeling of affinity molecules for different applications where two types of binding proteins, Affibody molecules and antibodies, have been used. For the purpose of improving the properties of Affibody molecules for in vivo imaging, novel bi-functional chelators for radiolabeling using the radionuclide 111In were evaluated. In a first study, two chelators denoted NOTA and DOTA, respectively, were separately conjugated via maleimide chemistry to a C-terminal cysteine residue in a HER2-binding Affibody molecule (ZHER2:2395). In vivo evaluation using mice with prostate carcinoma cell line xenografts showed that the 111In-NOTA-MMA-ZHER2:2395 tracer exhibited faster clearance from blood than the 111In-DOTA-MMA-ZHER2:2395 counterpart,resulting in improved tumor-to-organ ratios. In a second study the in vivo imaging properties of a third tracer, 111In-NODAGA-MMA-ZHER2:2395, was investigated in tumor-bearing mice. While the tumor uptake was lower than seen for the 111In-DOTA-MMA-ZHER2:2395 tracer, a low uptake in non-targeted organs and a fast clearance from blood resulted in higher tumor-to-organ ratios for 111In-NODAGA-MMA-ZHER2:2395 compared to the DOTA variant. In a following study, a synthetically produced HER2-targeting affibody variant, denoted ZHER2:S1, was used where NODAGA, NOTA and DOTA chelators instead were conjugated via an amide bond to the N-terminus. In vivo evaluation in mice showed an unfavorable uptake in liver for 111In-NOTA-ZHER2:S1, resulting in a discontinuation. The study showed faster clearance of 111In-NODAGA-ZHER2:S1 from blood, but also an increased uptake in bone in comparison to 111In-DOTA-ZHER2:S1. As bone is a common metastatic site in prostate cancer, the favorable tumor-to-bone ratio for 111In-DOTA-ZHER2:S1 suggests it as the tracer of choice for prostate cancer. Further, the DOTA chelator was also evaluated as conjugated to either N- or C-terminus or to the back of helix 3 via an amide bond, where the in vivo evaluation showed that that C-terminal conjugation resulted in the highest contrast. Site specificity is also of great importance for labeling antibodies, as conjugation in the antigen-binding regions might influence the affinity. A method for site-specific labeling of antibodies using an IgG-binding domain that becomes covalently attached to the Fc-region of an antibody by photoconjugation was optimized. By investigation of positions most suitable for incorporation of the photoreactive probe, the conjugation efficiencies were increased for antibody subclasses important for both diagnostic and therapeutic applications. In addition, optimized variants were used in combination with an incorporated click-reactive handle for selective labeling of the antibody with a detection molecule.

QC 20140929

L'épigénétique est un composant essentiel du fonctionnement des génomes eucaryotes. Les divers phénomènes épigénétiques modifient l’état chromatinien et participent à la plasticité du génome, mais aussi au maintien de son identité fonctionnelle à travers les générations cellulaires. Parmi ces processus, la méthylation de l’ADN joue un rôle fondamental dans la régulation de l’expression des gènes.Chez les mammifères, la méthylation de l'ADN est associée à la répression transcriptionnelle, et elle remplit au moins trois fonctions essentielles. Premièrement, elle permet de réprimer les séquences répétées afin de préserver l’intégrité du génome. Deuxièmement, la méthylation contrôle l’expression des gènes soumis à l’empreinte parentale, qui sont des régulateurs cruciaux du développement et de la vie adulte. Enfin, la méthylation permet de réprimer certains gènes tissu-spécifiques dans les organes où ils doivent être silencieux. En plus de ces rôles physiologiques, la méthylation est liée au cancer. En effet, des patrons de méthylation anormaux sont fréquemment observés dans les cellules tumorales, et ces anomalies participent à la transformation cellulaire par plusieurs mécanismes.La méthylation exerce ces effets par l'intermédiaire de protéines dédiées, qui reconnaissent spécifiquement l'ADN méthylé et contrôlent la transcription en modulant la chromatine. Trois familles de protéines liant l'ADN méthylé sont connues chez les mammifères, et elles totalisent entre elles neuf membres. De nombreux arguments suggèrent que cette liste est encore incomplète, et que des protéines humaines liant l'ADN méthylé restent à découvrir. Dans cette optique, nous avons opté pour deux types d’approches distinctes, une approche basée sur la littérature et une approche génétique. L’étude des protéines candidates ne nous a pas permis d’identifier de nouvelles protéines liant l’ADN méthylé et l’approche génétique par phage display a révélé deux protéines intéressantes, CHD3 et HMGB1 qui doivent désormais être validées par des approches in vivo et in vitro.Par ailleurs, nous avons entrepris l’étude de la régulation des éléments répétés par la protéine Zbtb4 chez la souris. Les expériences préliminaires indiquent une possible régulation des satellites mineurs par Zbtb4. Le rôle de cette régulation sera, par la suite, approfondi
Epigenetic phenomena are key contributors to the function of eukaryotic genomes. These processes act on chromatin, and they are used to render the genome dynamic, but also stable throughout successive rounds of cell division. Among epigenetic processes, DNA methylation is especially well known for its role in the regulation of gene expression.In mammals, DNA methylation is strongly correlated with transcriptional repression, and fulfills at least three essential roles. First, it maintains repeated sequences transcriptionally silenced, thus ensuring the stability of the genome. Second, it is responsible for the proper regulation of parentally imprinted genes, which are crucial regulators of embryonic development and adult life. Finally, DNA methylation ensures that some tissue-specific genes are kept inactive in the organs in which they should be repressed. Besides these roles in the physiology of normal cells, DNA methylation has strong links to cancer. Indeed the pattern of DNA methylation on the genome is frequently altered in cancer cells, and these anomalies contribute to transformation by several mechanisms.DNA methylation does not control transcription directly, but instead acts via a set of dedicated proteins that specifically recognize methylated DNA and repress transcription by acting at the chromatin level. At present, three families of such proteins, totalling 9 members altogether, are known in humans. However, several lines of evidence suggest that the list is not exhaustive, and that other human proteins that bind methylated DNA remain to be found. This was the goal of the current project.To this end, we opted for two distinct types approaches, an approach based on literature and a genetic approach. The study of candidate proteins does not allow us to identify new methylated DNA binding proteins and the genetic approach by phage display revealed two proteins of interest, HMGB1 and CHD3 that must now be validated by in vivo and in vitro approaches.Furthermore, we studied the regulation of DNA repeats by Zbtb4 in mice. Preliminary results show a regulation of minor satellites by Zbtb4. The role of this regulation will be analyse further in the future

The causative agent of the most devastating honeybee disease, American foulbrood (AFB), is the spore-forming bacterium Paenibacillus larvae. To prevent AFB outbreaks beekeepers prophylactically treat their hives with antibiotics even though it decreases the overall health of uninfected hives. A new treatment for AFB is needed due to recent legislation against using antibiotics, antibiotic resistance developing in P. larvae, and the resilience of P. larvae spores. Bacteriophages, or phages, are an attractive alternative to traditional antibiotics because of their specificity and ability to evolve alongside their target bacterium. In this study, two phage cocktails were developed for the treatment of AFB. The first cocktail was comprised of Brevibacillus laterosporus phages. B. laterosporus is a commensal microbe in most honeybee guts. When treated with B. laterosporus phages, B. laterosporus is induced to produce an antimicrobial toxin to which P. larvae is highly sensitive. Treating AFB infected hives with B. laterosporus phages was able to clear active infections at a rate of 75% as opposed to untreated hives that did not recover. However, B. laterosporus phages did not clear latent P. larvae spores and recovered hives relapsed after treatment. The second cocktail was comprised of P. larvae phages and hives treated with the second cocktail recovered at a rate of 100%, protected 100% of at-risk hives, and treated hives did not relapse with AFB suggesting neutralization of P. larvae spores. A P. larvae phage used in the second cocktail was examined to identify any spore-phage interactions. Results from modified plaque assays, fluorescence from FITC-labeled phages bound to spores, and electron microscopy images all confirm that phages bind to P. larvae spores. Phage therapy for the treatment of AFB is an exciting avenue not only as an alternative to chemical antibiotics, but rather a treatment that can neutralize P. larvae spores.

Thesis (Ph. D.)--University of Toledo, 2008.
Typescript. "Submitted as partial fulfillment of the requirements for the Doctor of Philosophy in Chemistry." Includes bibliographical references (leaves 305-309).

Chloride-induced corrosion of reinforcing steel in concrete is a worldwide problem. In order to predict how chlorides penetrate in concrete and how other ionic species in con-crete pore solution affect the penetration of chlorides, this thesis presents a numerical study on multi-phase modelling of ionic transport in concrete dominated by migration process. There are many advantages in rapid chloride migration test (RCM) method and numeri-cal approach. However, most of models in the literature predicting chloride diffusivity in concrete are diffusion models, which not consider the action of externally applied electric field. In view of this, the specific aim of this thesis is to develop a rational nu-merical migration model to simulate chloride migration tests. By using this model, the diffusion coefficient of chlorides in concrete will be efficiently predicted. Furthermore, other mechanisms of ionic transportation in composite materials can be scientifically in-vestigated in the meantime. In most existing work, researchers tend to use the assumption of electro-neutrality con-dition, which ensures that no external charge can be imported (Bockris and Reddy, 1998), to determine the electrostatic potential within concrete as well as considering a 1-D problem with only one phase structure and single species (i.e. the chlorides) for pre-dicting the ionic migration. In contrast, this thesis presents a number of sets of multi-phase migration models in more than one dimension and uses the Poisson’s equation for controlling the multi-species interactions. By solving both mass conservation and Pois-son’s equations, the distribution profiles of each ionic species and electrostatic potential at any required time are successfully obtained. Some significant factors, i.e. the influ-ence of dimensions, aggregates, interfacial transition zones (ITZs), cracks and binding effect have also been discussed in detail. The results reveal a series of important features which may not be seen from existing numerical models. For quantitative study, this thesis also provides the prediction method of chloride diffu-sivity not only by the traditional stationary diffusion models but also by the migration models presented in the thesis. The obtained results are compared with three proven analytical models, i.e., Maxwell’s model (Dormieux and Lemarchand, 2000), Brug-geman’s equation (Bruggeman’s, 1935) and the lower bound of the effective diffusion coefficient proposed by Li et al. (2012) as well as validated against experimental data sets of an accelerated chloride migration test (ACMT) brought by Yang and Su (2002).

Thesis (Ph.D.)--University of Western Sydney, 2008.
A thesis presented to the University of Western Sydney, College of Health and Science, School of Biomedical and Health Sciences, in fulfilment of the requirements for the degree of Doctor of Philosophy. Includes bibliographies.