NiSi is an attractive material in the production of CMOS devices. The problem with the utilization of NiSi, is that there is no proper method of cleaning the oxide on the surface. Sputtering is the most common method used for the cleaning, but it has its own complications. Dry cleaning methods include the reactions with radicals and these processes are not well understood and are the focus of the project. Dissociated NF3 and NH3 were used as an alternative and XPS is the technique to analyze the reactions of atomic fluorine and nitrogen with the oxide on the surface. A thermal cracker was used to dissociate the NF3 and NH3 into NFx+F and NHx+H. There was a formation of a NiF2 layer on top of the oxide and there was no evidence of nitrogen on the surface indicating that the fluorine and hydrogen are the reacting species. XPS spectra, however, indicate that the substrate SiO2 layer is not removed by the dissociated NF3 and NiF2 growth process. The NiF2 over layer can be reduced to metallic Ni by reacting with dissociated NH3 at room temperature. The atomic hydrogen from dissociated ammonia reduces the NiF2 but it was determined that the atomic hydrogen from the ammonia does not react with SiO2.

Générer des carburants solaires, comme l’hydrogène via la photoélectrolyse de l’eau, est une stratégie à explorer pour notre futur énergétique. Pour éviter l’emploi du platine en tant que catalyseur de production d’hydrogène, des métaux abondants peuvent être utilisés. Au laboratoire, le complexe diimine-dioxime de cobalt, catalyseur moléculaire de réduction des protons, a pu être immobilisé pour créer une cathode produisant de manière stable de l’hydrogène en milieu aqueux. Dans ces travaux, nous avons étudié l’introduction du catalyseur dans des dispositifs photoélectrocatalytiques. Différentes conditions opératoires dans l’eau, solvant de choix, ont été examinées. Le complexe se dégrade s’il est en solution mais son activité est maintenue, même en présence d’oxygène, s’il est supporté sur électrode. Cette électrode a ainsi pu être intégrée en cellule tandem. De nouveaux dérivés du complexe ont aussi été développés pour l’attachement sur oxydes transparents conducteurs. Un dérivé a été co-immobilisé avec des photosensibilisateurs sur une surface de NiO, oxyde de type p. Les photocathodes co-greffées obtenues ont été caractérisées par un ensemble de techniques analytiques et ont démontré la production d’hydrogène en conditions photoélectrocatalytiques. Des entités colorant-catalyseur pouvant s’ancrer sur surface ont également été synthétisées et ouvrent de nouvelles voies pour élaborer des photocathodes moléculaires. / Solar fuels generated from the light-induced splitting of water into H2 and O2 is an appealing strategy for securing future energy. The use of platinum for catalyzing hydrogen evolution may be bypassed with earth-abundant catalysts. In a previous study, our lab realized the immobilization of a proton reduction catalyst, the cobalt diimine-dioxime molecular complex, within a cathode material steadily evolving H2 from fully aqueous media. In this work, we report on the implementation of this catalyst into light-driven devices. Operating conditions in the solvent of interest, water, were screened. The molecular catalyst degrades when free in solution, but retains activity when supported on an electrode, even in the presence of O2, and could thus be integrated into a tandem cell. Further on, new derivatives of the catalyst were developed for the attachment onto transparent conducting oxides. Co-grafted photocathodes were constructed by anchoring a functionalized catalyst along with photosensitizers onto p-type NiO. These architectures were checked by a whole set of analytical techniques and light-driven catalytic hydrogen evolution was achieved by photocathodes assessed under device-related photoelectrochemical conditions. Immobilizable dye-catalyst dyads were also successfully synthetized as alternative derivatives and open up new possibilities to develop molecular photocathodes.

V této závěrečné práci bylo popsáno časné reologické chování alkalicky aktivované strusky, anorganického materiálu, který vzniká aktivací mleté granulované vysokopecní strusky alkalickým roztokem. Vliv typu aktivačního roztoku (hydroxidů, křemičitanů a uhličitanů) a jeho koncentrace na časné reologické parametry byl zkoumán pomocí amplitudových oscilačních měření. Bylo pozorováno, že typ aktivátoru je hlavním faktorem ovlivňujícím reologické chování alkalicky aktivované strusky. Dále bylo pozorováno, že aktivátory na bázi draslíku vedou ke slabší struktuře (nižší mez kluzu, mez toku a nižší hodnoty viskoelastických modulů) oproti použití aktivátorů na bázi sodíku. To lze vysvětlit rozdíly ve velikosti alkalických iontů. Na rozdíl od ostatních aktivátorů křemičitany způsobovaly zvýšení ztrátového faktoru, přičemž vykazovaly spíše kapalné chování. Z výsledků vyplynulo, že většina aktivátorů má tzv. kritickou hodnotu koncentrace, po jejímž dosažení mají reologické vlastnosti vzorků tendenci se měnit s rostoucí koncentrací. Získané výsledky korelovaly s výstupy zeta potenciálu.

Modern drug development is an astronomically expensive and time consuming undertaking. Because of this, studying the pharmacokinetic properties of drugs in vitro has become an integral step early in the process of drug development, with the goal of preventing costly failures late in the process, and dangerous side effects. Artificial phospholipid bilayers known as droplet interface bilayers (DIBs) have the potential to be used for these pharmacokinetics assays, combining the low cost of cell-free assays with the ability to more closely mimic structures found in life than current cell-free in vitro techniques. Combined with the reproducibility, ease of use, and low reagent consumption found with microfluidic methods, disruptive new low cost techniques for assessing pharmacokinetics in drug development may be possible using DIBs as an artificial cell membrane model. In this work, I establish the potential of DIBs to be used as a pharmacokinetics modelling platform, and advance the use of microfluidic methods for carrying out pharmacokinetics assays in drug discovery. I first developed a new microfluidic platform for the formation of DIBs, which sought to solve some of the shortcomings of current microfluidic methods for DIB formation (Chapter 2). This device is the first that can be used to form DIB networks from dissimilar droplets in parallel, without use of active controls, and with droplet contact gentle enough to enable use of biomimetic lipid mixtures. I examine for the first time the behaviour of phospholipids on microfluidic devices, and characterise the interaction that they have with a common material used to construct microfluidic devices (Chapter 3). Not only has this interaction never been studied before, but my unexpected findings indicate a new area requiring further study in order to advance the adoption of DIBs on microfluidic devices. In collaboration with my colleague Jaime Korner, I use my newly developed microfluidic platform to carry out an on-chip permeation assay for the first time using biomimetic lipid formulations and bespoke compartments modelled after the human intestine. We demonstrate that this on-chip assay has predictive accuracy greater than that of a current widely used cell-free technique (Chapter 4). Finally, I demonstrate that a DIB based microfluidic platform enables, and is critical for, characterising the effect of structural features such as membrane asymmetry on drug permeation. With this, I find measurable, previously unknown effects of membrane asymmetry on the absorption of the chemotherapy drug doxorubicin, highlighting a possible contributing factor to chemoresistance in some cancers (Chapter 5). I find, and demonstrate throughout the body of this work that microfluidic methods and DIBs can not only provide alternatives to current cell-free in vitro pharmacokinetics assays, but that they can exceed the performance of existing assays, and be used for entirely new ways of examining pharmacokinetics. Through building bespoke artificial cell membranes from the ground up, I hope to demonstrate herein the great potential of these powerful new cell-free methods. / Graduate / 2022-09-12

This study was intended to provide a fuller understanding of the surface chemical processes which result in the corrosion of ferrous materials.

The focus of the following research was to (1) understand the chemistry involved in nitriding an organosilicate glass substrate prior to tantalum deposition, as well as the effect nitrogen incorporation plays on subsequent tantalum deposition and (2) the reduction of a native oxide, the removal of surface contaminants, and the etching of a HgCdTe surface utilizing atomic hydrogen. These studies were investigated utilizing XPS, TEM and AFM. XPS data show that bombardment of an OSG substrate with NH3 and Ar ions results in the removal of carbon species and the incorporation of nitrogen into the surface. Tantalum deposition onto a nitrided OSG surface results in the initial formation of tantalum nitride with continued deposition resulting in the formation of tantalum. This process is a direct method for forming a thin TaN/Ta bilayer for use in micro- and nanoelectronic devices. Exposure to atomic hydrogen is shown to increase the surface roughness of both air exposed and etched samples. XPS results indicate that atomic hydrogen reduces tellurium oxide observed on air exposed samples via first-order kinetics. The removal of surface contaminants is an important step prior to continued device fabrication for optimum device performance. It is shown here that atomic hydrogen effectively removes adsorbed chlorine from the HgCdTe surface.

<p>The role of mechanical forces in the fate and function of adherent cells has been revealed to be a pivotal factor in understanding cell biology. Cells require certain physical cues to be present in their microenvironment or the cell will begin apoptosis. Mechanical signals from the environment are interpreted at the cellular level and biochemical responses are made due to the information from outside the cell, this process is known as mechanotransduction. Misinterpretation of physical cues has been indicated in many disease states, including heart disease and asthma. When a cell is bound to the ECM, proteins such as integrins are engaged at static and stable adhesion sites. These tight and static anchoring points found at the ECM exist in stark contrast to the dynamic conditions seen at intercellular junctions. Intercellular junctions, such as gap and adherens junctions, are formed between cells to act as a mechanism to relay information and exchange material. Due to the important role intercellular junctions play in processes of wound healing, epithelial-mesenchymal transition and cancer metastasis developing more sophisticated levels of understanding of these mechanisms would provide valuable insight.</p> <p>Complex biological processes, including immune cell signaling and cellular ECM adhesions, have been effectively replicated in model systems. These model systems have included the use of solid supported lipid bilayers and polymeric hydrogels that display cell adhesion molecules. Studies of cellular mechanotransduction at ECM adhesion sites has also been completed with covalently functionalized polymeric substrates of adjustable elasticity. However, developing model systems that allow the accurate reproduction of properties seen at intercellular junctions, while also allowing the investigation of cellular mechanosensitivity has proven to be a difficult task. Previous work has shown that polymer-tethered lipid bilayers (PTLBs) are a viable material to allow the replication of the dynamics and adhesion seen at intercellular junctions. Although efforts have been made to produce PTLBs with different mechanical properties, there is currently not a material with sufficient tunable elastic properties for the study of cellular mechanotransduction.</p> <p>To establish a system that allows the study of stiffness effects across a biologically relevant range (~0.50 – 40 kPa) while maintaining the dynamic properties seen at cell-to-cell junctions, polymer gel-tethered bilayers (PGTBs) were developed. A fabrication strategy was established to allow the incorporation of a hydrogel support with easily tunable stiffness and a tethered lipid bilayer coating, which produced a powerful platform to study the effects of stiffness at intercellular junctions. Careful attention was given to maintain the beneficial properties of membrane diffusion, and it was shown that on different linking architectures lipid bilayers could be established and diffusion was preserved. Microscopy-based FCS and FRAP methodology were utilized to measure lipid diffusion in these systems, while confocal microscopy was used to analyze cell spreading and adhesion. Three distinct architectures to link the lipid membrane to the underlying polyacrylamide hydrogel were pursued in this work, a non-covalent biotin-streptavidin system, a covalently linked design with fibronectin, and a direct covalent linkage utilizing crosslinker chemistry. In this work, it was shown that cells were able to spread and adhere on these substrates, with cell adhesion zones visualized under plated cells that demonstrate the capability of the cell to rearrange the presented linkers, while maintaining a stable material. Also confirmed is the tunability of the polymer hydrogel across a wide range of stiffness, this was shown by quantitative changes in cell spreading area in response to polymer properties.</p>

<p>  </p> <p>A staggering number of problems in materials chemistry relate to controlling the assembly of matter at <10 nm scales, including those with applications in nanoelectronics, energy harvesting, and biomedical device design. It is difficult to achieve precise chemical patterning at the short length scales required for such applications using traditional top-down fabrication methods (<em>e.g., </em>lithographic techniques). On the other hand, biological systems create high-resolution chemical patterns with remarkable efficiency, by assembling simple molecular building blocks with nm-scale features (<em>e.g.,</em> nucleotides, amino acids, lipids) into structurally complex motifs capable of carrying out the diverse functions required for life. </p> <p>Drawing inspiration from the diverse structures and functions of lipids in biological membranes, this work uses lipids to create high-resolution chemical patterns at interfaces, control the growth and self-assembly of nanocrystals, and to facilitate interactions that precisely template nanocrystals at chemically patterned surfaces.</p> <p>Functional alkanes assemble into striped phase monolayers on highly oriented pyrolytic graphite (HOPG), in which the alkyl chains are oriented parallel to the substrate, expressing both the polar and nonpolar regions of the amphiphile at the environmental interface. The same is true for diyne phosphoethanolamine (dPE), a phospholipid with a zwitterionic headgroup. When assembled into striped phases on HOPG, the headgroup zwitterions of dPE are confined in 1-nm-wide rows of functional groups with a pitch of ~7 nm, resulting in ordered arrays of orientable dipoles at the HOPG surface. The chemistry of dimensionally confined functional groups is distinct from bulk solution phase chemistry, and in this case enables powerful directing effects which can be used to template the adsorption of ultranarrow gold nanowires (AuNWs) in precise alignment with the template stripes. </p> <p>Technical grade oleylamine (<em>cis</em>-9-octadecen-1-amine, OLAm, 70% purity) serves as the capping ligand for the AuNWs used in this work, and additionally plays an important role in the assembly of AuNWs at dPE/HOPG surfaces. While technical-grade reagents enable cost-effective and scalable production of materials, variation in the composition of impurities between different batches have significant impacts on nanocrystal morphology and assembly. We show that thermal transitions of alkyl chain impurities (<em>trans</em> and saturated chains) in AuNW ligand shells can be used to regulate AuNW assembly at chemically patterned interfaces. </p> <p>Characterization of OLAm reagents by 1H NMR and mass spectrometry reveals significant and highly variable fractions elaidylamine (ELAm, <em>trans</em>-9-octadecen-1-amine) and octadecylamine (ODAm) between different batches of OLAm. To understand the phase behavior of mixtures of the C18 alkylamines commonly found in technical grade OLAm, we synthesize isomerically pure OLAm and its <em>trans</em> isomer, elaidylamine (ELAm), to generate binary and ternary mixtures with (ODAm), which is commercially available in high purity. Differential scanning calorimetry reveals limited miscibility of the C18 chains, and demonstrates the significant impact of chain composition on the physical properties of mixtures of alkyl chains (<em>e.g.,</em> tech. grade OLAm). Finally, we examine the impacts of <em>trans</em> and saturated alkyl chains on AuNW synthesis. We find that inclusion of ODAm and ELAm in the ligand blend used for AuNW synthesis each result in shorter AuNWs than those synthesized with pure OLAm. We also observe enhanced stability of surface adsorbed AuNWs conferred by <em>trans </em>and saturated chains. </p>

<p>  </p> <p>As monoclonal antibodies (mAbs) become a more important part of the pharmaceutical industry, the need for better quicker analysis of then will also increase. To do this, better stationary phases specifically designed for mAbs need to be developed to analyze the quality of mAbs by their critical control attributes. The three main critical control attributes are size, charge, and glycosylation. This work focuses mainly on the development of stationary phases to analyze critical control attributes in size and charge through using a non-porous silica base and surface confined atom transfer radical polymerization to grow improved stationary phases that minimize undesired interactions and maximize desired interactions.</p>

Exploiting the functional diversity of proteins for fundamental research and biotechnological applications requires their functional organization into micro- and nanostructures while preserving their functional integrity to the highest possible level. My PhD research aimed to establish generic techniques based on photolithography which could be used to control the spatial as well as temporal organization of recombinantly expressed proteins on surfaces. My thesis describes in detail four strategies that I developed for achieving this goal. In the first approach a photo-induced Fenton reaction was used to selectively destroy tris(nitrilotriacetic acid) (tris-NTA) moieties on a surface. UV-irradiation through a photomask allowed localized photo-destruction and targeting of His-tagged proteins to non-irradiated regions. Photo-destruction could also be achieved by scanning selected regions with the UV laser of a confocal laser scanning microscope (CLSM) thus allowing flexible creation and modification of protein patterns. The second strategy was based on the photosensitive nitroveratryloxycarbonyl (NVOC) protection group, which was used to cage amine groups on a surface. Sequential uncaging by UV-irradiation through a photomask followed by reactions with biotin and coenzyme A was used to pattern streptavidin and ybbR-tagged proteins into microstructures. In the third approach a photo-fragmentable Histidine peptide was used to block tris-NTA surfaces against binding of His-tagged proteins. UV-irradiation through a photomask or by using a UV laser in a CLSM cleaved the peptide into short fragments which quickly dissociated from the surface due to loss in multivalency. His-tagged proteins could be efficiently targeted into irradiated regions even from a complex cell lysate. Sequential uncaging and immobilization allowed the construction of multiplexed protein patterns with a high degree of temporal control. The fourth strategy used combined peptide tags comprising of a His-tag as well as a Halo- or ybbR-tag to achieve rapid covalent immobilization of recombinant fusion proteins on surfaces functionalized with specific ligands. In combination with a photo-fragmentable histidine peptide as described above, stable spatio-temporal organization of proteins carrying these combined tags was possible. The techniques developed in this thesis enabled the photolithographical micropatterning of recombinant proteins carrying specific peptide or protein tags on surfaces in a functional manner. Owing to the generic nature of immobilization strategies, coupled with the ease of patterning, highly versatile applications of these methods both in fundamental research as well as bio-technological and analytical applications can be envisioned.