Atomic force microscopy assisted with electron and ion beam microscopy for the direct measurement of biostructures and DNA samples

Dissertation to obtain a Master degree in Biotechnology

The role of electron transfer in DNA building blocks: evaluation of strand breaks and their implications

Dissertação para obtenção do Grau de Doutor em Engenharia Física

Electron Transfer and Ligand Binding Properties of Cytochromes

Dissertation presented to obtain the Ph.D degree in Biochemistry

Analysis, testing and development of safe cleaning methods of rusted stone material

Three different treatments were applied on several specimens of dolomitic and calcitic marble, properly stained with rust to mimic real situations (the stone specimens were exposed to the natural environment for about six months in contact with rusted iron). Thirty six marble specimens, eighteen calcitic and eighteen dolomitic, were characterized before and after treatment and monitored throughout the cleaning tests. The specimens were characterized by SEM-EDS (Scanning Electron Microscopy coupled with Energy Dispersion System), XRD (XRay Diffraction), XRF (X-Ray Fluorescence), FTIR (Fourier Transform Infrared Spectroscopy) and color measurements. It was also made a microscopic and macroscopic analysis of the stone surface along with the tests of short and long term capillary absorption. A series of test trials were conducted in order to understand which concentrations and contact times best suits to this purpose, to confirm what had been written to date in the literature. We sought to develop new methods of treatment application, skipping the usual methods of applying chemical treatments on stone substrates, with the use of cellulose poultice, resorting to the agar, a gel already used in many other areas, being something new in this area, which possesses great applicability in the field of conservation of stone materials. After the application of the best methodology for cleaning, specimens were characterized again in order to understand which treatment was more effective and less harmful, both for the operator and the stone material. Very briefly conclusions were that for a very intense and deep penetration into the stone, a solution of 3.5% of SDT buffered with ammonium carbonate to pH around 7 applied with agar support would be indicated. For rust stains in its initial state, the use of Ammonium citrate at a concentration of 5% buffered with ammonium to pH 7 could be applied more than once until satisfactory results appear.

Desenvolvimento de um papel de filtro de baixo custo para tratamento de água

É sabido que devido à escassez de água potável, nomeadamente em países sub-desenvolvidos, morrem milhares de pessoas por ano, com a procura de fontes de água alternativas, que por sua vez se encontram contaminadas com microrganismos patogénicos; a este facto também se salienta a possibilidade de ocorrência de catástrofes naturais, tornando-se necessário o desenvolvimento de sistemas de desinfecção prácticos, de baixo custo e eficientes. O trabalho experimental desenvolvido focou-se nestas realidades, tendo por objectivo principal o desenvolvimento de um papel bactericida, em particular, um papel de baixo custo como é o caso do papel de filtro de café, para aplicação em desinfecção de água. Este papel foi funcionalizado com nanopartículas sintetizadas de prata, óxido de zinco e com ambas, assim como com nanopartículas comerciais, cuja caracterização foi feita por Microscopia Electrónica de Varrimento (SEM, Scanning Electron Microscopy), Energia Dispersiva de Raios-X (EDS, Energy-dispersive X-ray Spectroscopy), Espectroscopia de Ultravioleta-Visível (UV-VIS Uv-Visible Spectroscopy), Difracção de Raios-X (DRX, X-Rays Diffraction), Análise Termogravimétrica (TA, Thermal Analysis), e Calorimetria Diferencial de Varrimento (DSC, Differencial Scanning Calorimetry) e a actividade anti-bacteriana dos papéis foi avaliada através de Testes de Sensibilidade aos Antibióticos, pelo Método de Kirby-Bauer, contra as bactérias S.a.ATCC25923 e E.coli ATCC25922. No decorrer das sínteses variaram-se alguns parâmetros consoante o tipo de nanopartícula, para as np´s de prata variou-se essencialmente a metodologia de síntese e o tipo de redutor, para as np´s de óxido de zinco, dado ser um composto fotossensível, submeteu-se o papel á luz ultravioleta, o que, por outro lado também esterelizava o papel, e para ter uma comparação, esterelizou-se também o papel pela autoclave, constatando-se, pelas técnicas de caracterização, nomeadamente DRX, que os papeis não continham nanopartículas de óxido de zinco mas sim de acetato de zinco. Surpreendentemente, nos papéis autoclavados já se detectou a presença de óxido de zinco. Com os papéis que evidenciararam maior actividade anti-bacteriana realizaram-se filtrações de membrana com amostras de água contaminada e a determinação da concentração de metal no filtrado foi realizada pela técnica de Espectroscopia de Absorção Atómica de Chama (Flame Atomic Absorption Spectroscopy) conseguindo-se uma taxa de redução bacteriana de practicamente 100% para E.coli NCTC 9001 e E.f NCTC775 com os papéis contendo acetato de zinco numa concentração de 50 mM e np´sAg e acetato de zinco, numa concentração de 10 mM. De forma a validar o trabalho desenvolvido a parte final consistiu em testar os filtros com melhores propriedades em águas contaminadas, tendo esse trabalho sido feito no Laboratório de Água de Consumo dos Serviços Municipalizados de Água e Saneamento de Almada.

Reactive electron scattering from biomolecules and technologically relevant molecules

The role of a set of gases relevant within the context of biomolecules and technologically relevant molecules under the interaction of low-energy electrons was studied in an effort to contribute to the understanding of the underlying processes yielding negative ion formation. The results are relevant within the context of damage to living material exposed to energetic radiation, to the role of dopants in the ion-molecule chemistry processes, to Electron Beam Induced Deposition (EBID) and Ion Beam Induced Deposition (IBID) techniques. The research described in this thesis addresses dissociative electron attachment (DEA) and electron transfer studies involving experimental setups from the University of Innsbruck, Austria and Universidade Nova de Lisboa, Portugal, respectively. This thesis presents DEA studies, obtained by a double focusing mass spectrometer, of dimethyl disulphide (C2H6S2), two isomers, enflurane and isoflurane (C3F5Cl5) and two chlorinated ethanes, pentachloroethane (C2HCl5) and hexachloroethane (C2Cl6), along with quantum chemical calculations providing information on the molecular orbitals as well as thermochemical thresholds of anion formation for enflurane, isoflurane, pentachloroethane and hexachloroethane. The experiments represent the most accurate DEA studies to these molecules, with significant differences from previous work reported in the literature. As far as electron transfer studies are concerned, negative ion formation in collisions of neutral potassium atoms with N1 and N3 methylated pyrimidine molecules were obtained by time-of-flight mass spectrometry (TOF). The results obtained allowed to propose concerted mechanisms for site and bond selective excision of bonds.

Electron driven reactions in sulphur containing biological prototypes

The interaction of ionising radiation with living tissues may direct or indirectly generate several secondary species with relevant genotoxic potential. Due to recent findings that electrons with energies below the ionisation threshold can effectively damage DNA, radiation-induced damage to biological systems has increasingly come under scrutiny. The exact physico-chemical processes that occur in the first stages of electron induced damage remain to be explained. However, it is also known that free electrons have a short lifetime in the physiological medium. Hence, electron transfer processes studies represent an alternative approach through which the role of "bound" electrons as a source of damage to biological tissues can be further explored. The thesis work consists of studying dissociative electron attachment (DEA) and electron transfer to taurine and thiaproline. DEA measurements were executed in Siedlce University with Prof. Janina Kopyra under COST action MP1002 (Nanoscale insights in ion beam cancer therapy). The electron transfer experiments were conducted in a crossed atom(potassium)-molecule beam arrangement. In these studies the anionic fragmentation patterns were obtained. The results of both mechanisms are shown to be significantly different, unveiling that the damaging potential of secondary electrons can be underestimated. In addition, sulphur atoms appear to strongly influence the dissociation process, demonstrating that certain reactions can be controlled by substitution of sulphur at specific molecular sites.

Ion-beam sources based on superionic solid electrolytes

An ion emitter consisting of a sharp silver tip covered in RbAg4I5 solid electrolyte film has been developed and studied. An accelerating potential is applied and Ag+ ions are emitted from the tip’s apex by field evaporation. The emitted ions are collected by a Faraday cup, producing a current on the pico/nanoampere level which is read by an electrometer. The tips were produced mechanically by sandpaper polishing. The sharpest tip produced had a 2:4 m apex radius. Two deposition methods were studied: thermal vacuum and pulsed laser deposition. The best tip produced a peak current value of 96nA at 180oC, and a quasi-stable 4nA emission current at 160oC, both using an extraction potential of 10kV . The emission dependence on time, temperature and accelerating potential has been studied. Deposited films were characterized by X-ray diffraction (XRD), profilometry, optical and Scanning Electron Microscope (SEM) and Secondary Ion Mass Spectroscopy (SIMS) measurements. Several ion emitters were developed, the latter ones were all able to maintain stable high ion emissions for long periods of time. This investigation was a continuation of an ongoing project backed by the European Space Agency, with the objective of making a proof of concept of this kind of ion emitter with potential application on ion thrusters for orbiting satellites. Going forward, it would be interesting to make a finer analysis of the electrolyte’s conductivity at high temperatures, explore Wien Effect-based emission and to further develop a multi-tip ion emitter prototype.

Field-effect transistors based on Zinc oxide nanoparticles

This work reports the development of field-effect transistors (FETs), whose channel is based on zinc oxide (ZnO) nanoparticles (NPs). Using screen-printing as the primary deposition technique, different inks were developed, where the semiconducting ink is based on a ZnO NPs dispersion in ethyl cellulose (EC). These inks were used to print electrolyte-gated transistors (EGTs) in a staggered-top gate structure on glass substrates, using a lithium-based polymeric electrolyte. In another approach, FETs with a staggered-bottom gate structure on paper were developed using a sol-gel method to functionalize the paper’s surface with ZnO NPs, using zinc acetate dihydrate (ZnC4H6O4·2H2O) and sodium hydroxide (NaOH) as precursors. In this case, the paper itself was used as dielectric. The various layers of the two devices were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), Fourier Transform Infrared spectroscopy (FTIR), thermogravimetric and differential scanning calorimetric analyses (TG-DSC). Electrochemical impedance spectroscopy (EIS) was used in order to evaluate the electric double-layer (EDL) formation, in the case of the EGTs. The ZnO NPs EGTs present electrical modulation for annealing temperatures equal or superior to 300 ºC and in terms of electrical properties they showed On/Off ratios in the order of 103, saturation mobilities (μSat) of 1.49x10-1 cm2(Vs)-1 and transconductance (gm) of 10-5 S. On the other hand, the ZnO NPs FETs on paper exhibited On/Off ratios in the order of 102, μSat of 4.83x10- 3 cm2(Vs)-1and gm around 10-8 S.

Perylene Diimide acceptors: Fabrication and characterization of electron-only, hole-only devices and solar cells

The thrust towards energy conservation and reduced environmental footprint has fueled intensive research for alternative low cost sources of renewable energy. Organic photovoltaic cells (OPVs), with their low fabrication costs, easy processing and flexibility, represent a possible viable alternative. Perylene diimides (PDIs) are promising electron-acceptor candidates for bulk heterojunction (BHJ) OPVs, as they combine higher absorption and stability with tunable material properties, such as solubility and position of the lowest unoccupied molecular orbital (LUMO) level. A prerequisite for trap free electron transport is for the LUMO to be located at a level deeper than 3.7 eV since electron trapping in organic semiconductors is universal and dominated by a trap level located at 3.6 eV. Although the mostly used fullerene acceptors in polymer:fullerene solar cells feature trap-free electron transport, low optical absorption of fullerene derivatives limits maximum attainable efficiency. In this thesis, we try to get a better understanding of the electronic properties of PDIs, with a focus on charge carrier transport characteristics and the effect of different processing conditions such as annealing temperature and top contact (cathode) material. We report on a commercially available PDI and three PDI derivatives as acceptor materials, and its blends with MEH-PPV (Poly[2-methoxy 5-(2-ethylhexyloxy)-1,4-phenylenevinylene]) and P3HT (Poly(3-hexylthiophene-2,5-diyl)) donor materials in single carrier devices (electron-only and hole-only) and in solar cells. Space-charge limited current measurements and modelling of temperature dependent J-V characteristics confirmed that the electron transport is essentially trap-free in such materials. Different blend ratios of P3HT:PDI-1 (1:1) and (1:3) show increase in the device performance with increasing PDI-1 ratio. Furthermore, thermal annealing of the devices have a significant effect in the solar cells that decreases open-circuit voltage (Voc) and fill factor FF, but increases short-circuit current (Jsc) and overall device performance. Morphological studies show that over-aggregation in traditional donor:PDI blend systems is still a big problem, which hinders charge carrier transport and performance in solar cells.

Desenvolvimento e caracterização tribológica de hidrogéis poliméricos de PVA reforçados com fosfato tricálcico para aplicação como cartilagem articular para implantes articulares

Dissertação de mestrado integrado em Engenharia de Materiais

Otimização dos parâmetros de processamento em Laser Melting

Dissertação de mestrado integrado em Engenharia Mecânica

Thermal characterization of polyhydroxyalkanoates and poly(lactic acid) blends obtained by injection molding

In this work we present the thermal characterization of the full scope of polyhydroxyalcanoate and poly(lactic acid) blends obtain by injection molding. Blends of polyhydroxyalcanoate and poly(lactic acid) (PHA/PLA) were prepared in different compositions ranging from 0–100% in steps of 10%. The blends were injection molded and then characterized by differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and wide angle X-ray diffraction (WAXD). The increment of PHA fraction increased the degree of crystallinity of the blend and the miscibility of the base polymers as verified by the Fox model. The WAXD analysis indicates that the presence of PHA hindered the PLA crystallization. The crystallization evolution trough PHA weight fraction (wf) shows a phase inversion around 50-60%. SEM analyses confirmed that the miscibility of PHA/PLA blends increased with the incorporation of PHA and became total for values of PHA higher that 50%.

Mechanism of extracellular silver nanoparticles synthesis by Stereum hirsutum and Fusarium oxysporum

The increasing interest for greener and biological methods of synthesis has led to the development of non-toxic and comparatively more bioactive nanoparticles. Unlike physical and chemical methods of nanoparticle synthesis, microbial synthesis in general and mycosynthesis in particular is cost-effective and environment-friendly. However, different aspects, such as the rate of synthesis, monodispersity and downstream processing, need to be improved. Many fungal-based mechanisms have been proposed for the formation of silver nanoparticles (AgNPs), mainly those involving the presence of nitrate reductase, which has been detected in filtered fungus cell used for AgNPs production. There is a general acceptance that nitrate reductase is the main responsible for the reduction of Ag ions for the formation of AgNPs. However, this generally accepted mechanism for fungal AgNPs production is not totally understood. In order to elucidate the molecules participating in the mechanistic formation of metal nanoparticles, the current study is focused on the enzymes and other organic compounds involved in the biosynthesis of AgNPs. The use of each free fungal mycelium of both Stereum hirsutum and Fusarium oxysporum will be assessed. In order to identify defective mutants on the nitrate reductase structural gene niaD, fungal cultures of S.hirsutum and F.oxysporum will be selected by chlorate resistance. In addition, in order to verify if each compound identified as key-molecule influenced on the production of nanoparticles, an in vitro assay using different nitrogen sources will be developed. Lately, fungal extracellular enzymes will be measured and an in vitro assay will be done. Finally, The nanoparticle formation and its characterization will be evaluated by UV-visible spectroscopy, electron microscopy (TEM), X-ray diffraction analysis (XRD), Fourier transforms infrared spectroscopy (FTIR), and LC-MS/MS.