Spontaneous Unfolding and Refolding of FNIII Domains Assayed by Thiol Exchange

Fibronectin (FN) is a large extracellular matrix (ECM) protein that is made up of

type I (FNI), type II (FNII), & type III (FNIII) domains. It assembles into an insoluble

supra-­‐‑molecular structure: the fibrillar FN matrix. FN fibrillogenesis is a cell‐‑mediated process, which is initiated when FN binds to integrins on the cell surface. The FN matrix plays an important role in cell migration, proliferation, signaling & adhesion. Despite decades of research, the FN matrix is one of the least understood supra-­‐‑molecular protein assemblies. There have been several attempts to elucidate the exact mechanism of matrix assembly resulting in significant progress in the field but it is still unclear as to what are FN-­‐‑FN interactions, the nature of these interactions and the domains of FN that

are in contact with each other. FN matrix fibrils are elastic in nature. Two models have been proposed to explain the elasticity of the fibrils. The first model: the ‘domain unfolding’ model postulates that the unraveling of FNIII domains under tension explains fibril elasticity.

The second model relies on the conformational change of FN from compact to extended to explain fibril elasticity. FN contain 15 FNIII domains, each a 7-­‐‑strand beta sandwich. Earlier work from our lab used the technique of labeling a buried Cys to study the ‘domain unfolding’ model. They used mutant FNs containing a buried Cys in a single FNIII domain and found that 6 of the 15 FNIII domains label in matrix fibrils. Domain unfolding due to tension, matrix associated conformational changes or spontaneous folding and unfolding are all possible explanation for labeling of the buried Cys. The present study also uses the technique of labeling a buried Cys to address whether it is spontaneous folding and unfolding that labels FNIII domains in cell culture. We used thiol reactive DTNB to measure the kinetics of labeling of buried Cys in eleven FN III domains over a wide range of urea concentrations (0-­‐‑9M). The kinetics data were globally fit using Mathematica. The results are equivalent to those of H-­‐‑D exchange, and

provide a comprehensive analysis of stability and unfolding/folding kinetics of each

domain. For two of the six domains spontaneous folding and unfolding is possibly the reason for labeling in cell culture. For the rest of the four domains it is probably matrix associated conformational changes or tension induced unfolding.

A long-­‐‑standing debate in the protein-­‐‑folding field is whether unfolding rate

constants or folding rate constants correlate to the stability of a protein. FNIII domains all have the same ß sandwich structure but very different stabilities and amino acid sequences. Our study analyzed the kinetics of unfolding and folding and stabilities of eleven FNIII domains and our results show that folding rate constants for FNIII domains are relatively similar and the unfolding rates vary widely and correlate to stability. FN forms a fibrillar matrix and the FN-­‐‑FN interactions during matrix fibril formation are not known. FNI 1-­‐‑9 or the N-­‐‑ terminal region is indispensible for matrix formation and its major binding partner has been shown to be FNIII 2. Earlier work from our lab, using FRET analysis showed that the interaction of FNI 1-­‐‑9 with a destabilized FNIII 2 (missing the G strand, FNIII 2ΔG) reduces the FRET efficiency. This efficiency is restored in the presence of FUD (bacterial adhesion from S. pyogenes) that has been known to interact with FNI 1-­‐‑9 via a tandem ß zipper. In the present study we

use FRET analysis and a series of deletion mutants of FNIII 2ΔG to study the shortest fragment of FNIII 2ΔG that is required to bind FNI 1-­‐‑9. Our results presented here are qualitative and show that FNIII 2ΔC’EFG is the shortest fragment required to bind FNI 1-­‐‑9. Deletion of one more strand abolishes the interaction with FNI 1-­‐‑9.

Dispositifs optoélectroniques à base de semi-conducteurs organiques en couches minces

Les petites molécules de type p à bandes interdites étroites sont de plus en plus perçues comme des remplaçantes possibles aux polymères semi-conducteurs actuellement utilisés conjointement avec des dérivés de fullerènes de type n, dans les cellules photovoltaïques organiques (OPV). Par contre, ces petites molécules tendent à cristalliser facilement lors de leur application en couches minces et forment difficilement des films homogènes appropriés. Des dispositifs OPV de type hétérojonction de masse ont été réalisés en ajoutant différentes espèces de polymères semi-conducteurs ou isolants, agissant comme matrices permettant de rectifier les inhomogénéités des films actifs et d’augmenter les performances des cellules photovoltaïques. Des polymères aux masses molaires spécifiques ont été synthétisés par réaction de Wittig en contrôlant précisément les ratios molaires des monomères et de la base utilisée. L’effet de la variation des masses molaires en fonction des morphologies de films minces obtenus et des performances des diodes organiques électroluminescentes reliées, a également été étudié. La microscopie électronique en transmission (MET) ou à balayage (MEB) a été employée en complément de la microscopie à force atomique (AFM) pour suivre l’évolution de la morphologie des films organiques minces. Une nouvelle méthode rapide de préparation des films pour l’imagerie MET sur substrats de silicium est également présentée et comparée à d’autres méthodes d’extraction. Motivé par le prix élevé et la rareté des métaux utilisés dans les substrats d’oxyde d’indium dopé à l’étain (ITO), le développement d’une nouvelle méthode de recyclage eco-responsable des substrats utilisés dans ces études est également présenté.

Materiais à base de Sr(Ti,Nb)O3 para sensores lambda

Os sensores lambda resistivos possuem as vantagens de simplicidade e menor custo relativamente à utilização generalizada de sensores potenciométricos de oxigénio. Nesse sentido, os titanatos de estrôncio têm sido alvo de diversos estudos. Para a produção de uma relação inequívoca entre a condutividade destes materiais e a pressão parcial de oxigénio é necessária a adição de um dopante dador que suprime a condução eletrónica do tipo-p na região de pressões parciais de oxigénio próximas de ar. Contudo, a adição de um dopante dador produz respostas lentas destes materiais quando densos a variações da pressão parcial de oxigénio. Além da preparação usual dos pós por reação do estado sólido, foram preparadas diversas composições por mecanossíntese. Tal relaciona-se com o fato exaustivamente reportado de as amostras destes materiais, especialmente quando dopados com dadores, apresentarem comportamentos dependentes das condições de processamento. Teve ainda o intuito de avaliar a viabilidade da sua preparação por este método, e consequentemente verificar se este método de preparação, que presumivelmente produzirá pós com composição mais homogénea e mais reativos, permite alterar/manipular a resposta obtida por amostras com eles produzidas. Foram preparados diversos filmes, tipologia muito usada na produção de sensores resistivos, e amostras porosas com diversas composições à base de titanato de estrôncio produzidos com variadas condições de processamento. Foram realizadas diversas caracterizações sobre estes espécimes numa tentativa de melhor compreender as propriedades destes materiais e a dependência destas com parâmetros microestruturais como o tamanho de grão e a porosidade. Foi verificado que os exemplares de titanato de estrôncio não dopado, quer em filmes quer em amostras porosas, apresentam um comportamento elétrico semelhante ao apresentado por amostras densas deste material. Apurou-se ainda, que as suas características apresentam uma variação ténue com a alteração das condições de processamento. Já espécimes de titanato de estrôncio dopados com dador revelam uma forte dependência das suas propriedades com as condições de processamento utilizadas, nomeadamente, a temperatura de sinterização e o tempo de permanência a essa temperatura. Para o fabrico de sensores resistivos de oxigénio poderá ser preferível o recurso a amostras porosas pelo facto de mais facilmente se manipularem as suas características microestruturais e devido à exclusão dos problemas associados à interação entre o substrato de alumina e o filme. As composições não dopadas são as indicadas para esta função se a gama de pressões de oxigénio a avaliar for relativamente pouco extensa sendo aconselhadas as composições dopadas com dador se for pretendida uma medição da pressão parcial de oxigénio em zonas mais extensas correspondentes à queima com deficiência ou excesso de oxigénio. Mesmo em amostras de elevada porosidade poderá ocorrer resposta transiente do material dopado com dador.

Approximate ab initio calculations and the method of molecular fragments

A two stage approach to performing ab initio calculations on medium and large sized molecules is described. The first step is to perform SCF calculations on small molecules or molecular fragments using the OPIT Program. This employs a small basis set of spherical and p-type Gaussian functions. The Gaussian functions can be identified very closely with atomic cores, bond pairs, lone pairs, etc. The position and exponent of any of the Gaussian functions can be varied by OPIT to produce a small but fully optimised basis set. The second stage is the molecular fragments method. As an example of this, Gaussian exponents and distances are taken from an OPIT calculation on ethylene and used unchanged in a single SCF calculation on benzene. Approximate ab initio calculations of this type give much useful information and are often preferable to semi-empirical approaches, since the nature of the approximations involved is much better defined.

Dosimetria in vivo em tumores de mama: comparação entre a dose medida e calculada

Introdução – A dosimetria in vivo é útil na medição da dose administrada aos doentes durante o tratamento, avaliando diferenças significativas entre a dose prescrita e a dose administrada no volume alvo, bem como nos órgãos de risco. Objetivo – Comparar a dose medida com a dose calculada em doentes com tumores de mama com e sem filtro físico. Métodos – Realizaram-se medições da dose na pele, utilizando díodos tipo–p, para os campos tangenciais e respetivos field-in-field em 38 doentes. Resultados – Verificaram-se diferenças estatisticamente significativas nos campos tangenciais open (ρ=0,000). Discussão – Estudos reportam desvios sistemáticos significativos entre a dose calculada e a dose medida. Conclusão – Com este estudo conclui-se que não existe influência nas doses devido à presença do filtro físico.

Low temperature magneto-photoluminescence characterization of high purity gallium arsenide and indium phosphide

Low-temperature magneto-photoluminescence is a very powerful technique to characterize high purity GaAs and InP grown by various epitaxial techniques. These III-V compound semiconductor materials are used in a wide variety of electronic, optoelectronic and microwave devices. The large binding energy differences of acceptors in GaAs and InP make possible the identification of those impurities by low-temperature photoluminescence without the use of any magnetic field. However, the sensitivity and resolution provided by this technique rema1ns inadequate to resolve the minute binding energy differences of donors in GaAs and InP. To achieve higher sensitivity and resolution needed for the identification of donors, a magneto-photoluminescence system 1s installed along with a tunable dye laser, which provides resonant excitation. Donors 1n high purity GaAs are identified from the magnetic splittings of "two-electron" satellites of donor bound exciton transitions 1n a high magnetic field and at liquid helium temperature. This technique 1s successfully used to identify donors 1n n-type GaAs as well as 1n p-type GaAs in which donors cannot be identified by any other technique. The technique is also employed to identify donors in high purity InP. The amphoteric incorporation of Si and Ge impurities as donors and acceptors in (100), (311)A and (3ll)B GaAs grown by molecular beam epitaxy is studied spectroscopically. The hydrogen passivation of C acceptors in high purity GaAs grown by molecular beam epitaxy (MBE) and metalorganic chemical vapor deposition (MOCVD) 1s investigated using photoluminescence. Si acceptors ~n MBE GaAs are also found to be passivated by hydrogenation. The instabilities in the passivation of acceptor impurities are observed for the exposure of those samples to light. Very high purity MOCVD InP samples with extremely high mobility are characterized by both electrical and optical techniques. It is determined that C is not typically incorporated as a residual acceptor ~n high purity MOCVD InP. Finally, GaAs on Si, single quantum well, and multiple quantum well heterostructures, which are fabricated from III-V semiconductors, are also measured by low-temperature photoluminescence.

Dispositifs optoélectroniques à base de semi-conducteurs organiques en couches minces

Les petites molécules de type p à bandes interdites étroites sont de plus en plus perçues comme des remplaçantes possibles aux polymères semi-conducteurs actuellement utilisés conjointement avec des dérivés de fullerènes de type n, dans les cellules photovoltaïques organiques (OPV). Par contre, ces petites molécules tendent à cristalliser facilement lors de leur application en couches minces et forment difficilement des films homogènes appropriés. Des dispositifs OPV de type hétérojonction de masse ont été réalisés en ajoutant différentes espèces de polymères semi-conducteurs ou isolants, agissant comme matrices permettant de rectifier les inhomogénéités des films actifs et d’augmenter les performances des cellules photovoltaïques. Des polymères aux masses molaires spécifiques ont été synthétisés par réaction de Wittig en contrôlant précisément les ratios molaires des monomères et de la base utilisée. L’effet de la variation des masses molaires en fonction des morphologies de films minces obtenus et des performances des diodes organiques électroluminescentes reliées, a également été étudié. La microscopie électronique en transmission (MET) ou à balayage (MEB) a été employée en complément de la microscopie à force atomique (AFM) pour suivre l’évolution de la morphologie des films organiques minces. Une nouvelle méthode rapide de préparation des films pour l’imagerie MET sur substrats de silicium est également présentée et comparée à d’autres méthodes d’extraction. Motivé par le prix élevé et la rareté des métaux utilisés dans les substrats d’oxyde d’indium dopé à l’étain (ITO), le développement d’une nouvelle méthode de recyclage eco-responsable des substrats utilisés dans ces études est également présenté.

Effect of oxygen on the electrical characteristics of field effect transistors formed from electrochemically deposited films of poly(3-methylthiophene)

Field effect devices have been formed in which the active layer is a thin film of poly(3-methylthiophene) grown electrochemically onto preformed source and drain electrodes. Although a field effect is present after electrochemical undoping, stable device characteristics with a high modulation ratio are obtained only after vacuum annealing at an elevated temperature, and only then if the devices are held in vacuo. The polymer is shown to be p type and the devices operate in accumulation only. The hole mobility in devices thermally annealed under vacuum is around 10 -3 cm 2 V -1 s -1. On exposure to ambient laboratory air, the device conductance increases by several orders of magnitude. This increase may be reversed by subjecting the device to a further high-temperature anneal under vacuum. Subsidiary experiments show that these effects are caused by the reversible doping of the polymer by gaseous oxygen.

Fabrication and characterization of a nanostructured TiO2/In2S3-Sb2S3/CuSCN extremely thin absorber (eta) solar cell

CuSCN extremely thin absorber solar cell. Nanostructured TiO2 deposited by screen printing on an ITO substrate was used as an n-type electrode. An ∼80 nm extremely thin layer of the system In2S3-Sb2S3 deposited by successive ionic layer adsorption and a reaction (silar) method was used as an absorber. The voids were filled with p-type CuSCN and the entire assembly was completed with a gold contact. The solar cell fabricated with this heterostructure showed an energy conversion efficiency of 4.9%, which is a promising result in the development of low cost and simple fabrication of solar cells.

Materials design for ambipolar devices: tuning orbital energetics in oligothiophene-naphthalimides semiconductors

Ambipolar organic field-effect transistors (OFETs), which can efficiently transport both holes and electrons, using a single type of electrode, are currently of great interest due to their possible applications in complementary metal oxide semiconductor (CMOS)-like circuits, sensors, and in light-emitting transistors. Several theoretical and experimental studies have argued that most organic semiconductors should be able to transport both types of carrier, although typically unipolar behavior is observed. One factor that can compromise ambipolar transport in organic semiconductors is poor solid state overlap between the HOMO (p-type) or LUMO (n-type) orbitals of neighboring molecules in the semiconductor thin film. In the search of low-bandgap ambipolar materials, where the absence of skeletal distortions allows closer intermolecular π-π stacking and enhanced intramolecular π-conjugation, a new family of oligothiophene-naphthalimide assemblies have been synthesized and characterized, in which both donor and acceptor moieties are directly conjugated through rigid linkers. In previous works we found that oligothiophene-napthalimide assemblies connected through amidine linkers (NDI derivates) exhibit skeletal distortions (50-60º) arising from steric hindrance between the carbonyl group of the arylene core and the sulphur atom of the neighbored thiophene ring (see Figure 1). In the present work we report novel oligo- and polythiophene–naphthalimide analogues NAI-3T, NAI-5T and poly-NAI-8C-3T, in which the connections of the amidine linkage have been inverted in order to prevent steric interactions. Thus, the nitrogen atoms are directly connected to the naphthalene moiety in NAI derivatives while they were attached directly to the thiophene moiety in the previously investigated NDI-3T and NDI-5T. In Figure 1 is depicted the calculated molecular structure of NAI-3T together with that of NDI-3T showing how the steric interactions are not present in the novel NAI derivative. The planar skeletons in these new family induce higher degree of crystallinity and the carrier charge transport can be switched from n-type to ambipolar behaviour. The highest FET performance is achieved for vapor-deposited films of NAI-3T with mobilities of 1.95x10-4cm2V-1s-1 and 2.00x10-4cm2V-1s-1 for electrons and holes, respectively. Finally, these planar semiconductors are compared with their NDI derivates analogues, which exhibit only n-type mobility, in order to understand the origin of the ambipolarity in this new series of molecular semiconductors.

Effect of oxygen on the electrical characteristics of field effect transistors formed from electrochemically deposited films of poly(3-methylthiophene)

Field effect devices have been formed in which the active layer is a thin film of poly(3-methylthiophene) grown electrochemically onto preformed source and drain electrodes. Although a field effect is present after electrochemical undoping, stable device characteristics with a high modulation ratio are obtained only after vacuum annealing at an elevated temperature, and only then if the devices are held in vacuo. The polymer is shown to be p type and the devices operate in accumulation only. The hole mobility in devices thermally annealed under vacuum is around 10 -3 cm 2 V -1 s -1. On exposure to ambient laboratory air, the device conductance increases by several orders of magnitude. This increase may be reversed by subjecting the device to a further high-temperature anneal under vacuum. Subsidiary experiments show that these effects are caused by the reversible doping of the polymer by gaseous oxygen.

ELECTRON TRANSPORT IN LOW-DIMENSIONAL NANOSTRUCTURES - THEORETICAL STUDY WITH APPLICATION

Graphene as a carbon monolayer has attracted extensive research interest in recent years. My research work within the frame of density functional theory has suggested that positioning graphene in proximity to h-BN may induce a finite energy gap in graphene, which is important for device applications. For an AB-stacked graphene/BN bilayer, a finite gap is induced at the equilibrium configuration. This induced gap shows a linear relationship with the applied strain. For a graphene/BN/graphene trilayer, a negligible gap is predicted in the ground state due to the overall symmetry of the system. When an electric field is applied, a tunable gap can be obtained for both AAA and ABA stackings. Enhanced tunneling current in the AA-stacked bilayer nanoribbons is predicted compared to either single-layer or AB-stacked bilayer nanoribbons. Interlayer separation between the nanoribbons is shown to have a profound impact on the conducting features. The effect of boron or nitrogen doping on the electronic transport properties of C60 fullerene is studied. The BC59 fullerene exhibits a considerably higher current than the pristine or nitrogen doped fullerenes beyond the applied bias of 1 V, suggesting it can be an effective semiconductor in p-type devices. The interaction between nucleic acid bases - adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U) - and a hydrogen-passivated silicon nanowire (SiNW) is investigated. The binding energy of the bases with the SiNW shows the order: G > A~C~T~U. This suggests that the interaction strength of a hydrogen passivated SiNW with the nucleic acid bases is nearly the same-G being an exception. The nature of the interaction is suggested to be electrostatic.

Synthesis of novel organic semiconductors for optoelectronic devices

This thesis describes the synthesis and characterisation of novel conjugated organic materials with optoelectronic application. The first chapter provides an introduction about organic semiconductors and in particular about their working principle from a physical and chemical point of view. An overview of the most common types of solar cells is provided, including examples of some of the best performing materials. The second chapter describes the synthesis of a new library of flavin derivatives as potential active materials for optoelectronic applications. Flavins are natural redox-active molecules, which show potential application in optoelectronics, thanks to their stability and versatility. FPF-Flavins, for instance, could be used either as acceptor units in push-pull polyconjugated systems or as acceptor unit in dyes for DSSCs. In the same chapter a first attempt of synthesising bis-flavins to be used as N-type semiconductors in BHJ devices is described. The third chapter describes the successful synthesis and characterization of a series of conjugated organic molecules based on the benzothiadiazole moiety. Among these, three molecules containing ferrocene as donor unit were tested as sensitizers for DSSCs, reporting a PCE of 0.3% as the best result. Further studies indicated a significant problem of charge recombination which limits the performance. A near-infrared absorbing push-pull polymer, based on BbT as acceptor unit, was also synthesised and tested in BHJ devices as P-type semiconductor in blend with PC71BM, showing a VOC of 0.71 V. Finally, the last chapter describes the synthesis of several tetrathiafulvalene derivatives in order to explore this moiety as donor unit in dyes for DSSCs and as HTM for perovskite-based solar cells. In particular, two very simple dyes were synthesised and implemented in DSSCs reporting a PCE 0.2% and 0.4%, respectively. The low efficiency was associated to the tendency to aggregate at the solid state, with the absorption shifting from the visible to the infrared range. A conjugated molecule, containing a DPP core, was also synthesised and tested as HTM for perovskite solar cells. The best reported PCE of 7.7% was obtained without any additives. A case study about dehalogenation and “halogen dance” in TTF iodide is also presented.

Cálculo de constantes ópticas de películas delgadas de Cu3BiS3 a través del método de Wolfe

Se calculó la obtención de las constantes ópticas usando el método de Wolfe. Dichas contantes: coeficiente de absorción (α), índice de refracción (n) y espesor de una película delgada (d ), son de importancia en el proceso de caracterización óptica del material. Se realizó una comparación del método del Wolfe con el método empleado por R. Swanepoel. Se desarrolló un modelo de programación no lineal con restricciones, de manera que fue posible estimar las constantes ópticas de películas delgadas semiconductoras, a partir únicamente, de datos de transmisión conocidos. Se presentó una solución al modelo de programación no lineal para programación cuadrática. Se demostró la confiabilidad del método propuesto, obteniendo valores de α = 10378.34 cm−1, n = 2.4595, d =989.71 nm y Eg = 1.39 Ev, a través de experimentos numéricos con datos de medidas de transmitancia espectral en películas delgadas de Cu3BiS3.

Hall Effect and transient surface photovoltage (SPV) study of Cu3BiS3 thin films

Se presentan las propiedades eléctricas del compuesto Cu3BiS3 depositado por co-evaporación. Este es un nuevo compuesto que puede tener propiedades adecuadas para ser utilizado como capa absorbente en celdas solares. Las muestras fueron caracterizadas a través de medidas de efecto Hall y fotovoltaje superficial transiente (SPV). A través de medidas de efecto Hall se encontró que la concentración de portadores de carga n es del orden de 1016 cm-3 independiente de la relación de masas de Cu/Bi. También se encontró que la movilidad de este compuesto (μ del orden de 4 cm2V -1s-1) varía de acuerdo con los mecanismos de transporte que la gobiernan en dependencia con la temperatura. A partir de las medidas de SPV se encontró alta densidad de defectos superficiales, defectos que son pasivados al superponer una capa buffer sobre el compuesto Cu3BiS3.