abstract: DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with the recognition molecules, the analyte molecules generate stochastic signal trains accommodating their “electronic fingerprints”. Signal features are used to detect the molecules using a machine learning algorithm and different molecules can be identified with significantly high accuracy. This, in turn, paves the way for rapid, economical nanopore sequencing platform, overcoming the drawbacks of Next Generation Sequencing (NGS) techniques. To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day. In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition, Pyrene reader showed higher DNA base-calling accuracy compare to Imidazole reader, the workhorse in our previous projects. In my other projects, various amino acids and RNA nucleoside monophosphates were also classified with significantly high accuracy using RT. Twenty naturally occurring amino acids and various RNA nucleosides (four canonical and two modified) were successfully identified. Thus, we envision nanopore sequencing biomolecules using Recognition Tunneling (RT) that should provide comprehensive betterment over current technologies in terms of time, chemical and instrumental cost and capability of de novo sequencing. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

abstract: Richard Feynman said “There’s plenty of room at the bottom”. This inspired the techniques to improve the single molecule measurements. Since the first single molecule study was in 1961, it has been developed in various field and evolved into powerful tools to understand chemical and biological property of molecules. This thesis demonstrates electronic single molecule measurement with Scanning Tunneling Microscopy (STM) and two of applications of STM; Break Junction (BJ) and Recognition Tunneling (RT). First, the two series of carotenoid molecules with four different substituents were investigated to show how substituents relate to the conductance and molecular structure. The measured conductance by STM-BJ shows that Nitrogen induces molecular twist of phenyl distal substituents and conductivity increasing rather than Carbon. Also, the conductivity is adjustable by replacing the sort of residues at phenyl substituents. Next, amino acids and peptides were identified through STM-RT. The distribution of the intuitive features (such as amplitude or width) are mostly overlapped and gives only a little bit higher separation probability than random separation. By generating some features in frequency and cepstrum domain, the classification accuracy was dramatically increased. Because of large data size and many features, supporting vector machine (machine learning algorithm for big data) was used to identify the analyte from a data pool of all analytes RT data. The STM-RT opens a possibility of molecular sequencing in single molecule level. Similarly, carbohydrates were studied by STM-RT. Carbohydrates are difficult to read the sequence, due to their huge number of possible isomeric configurations. This study shows that STM-RT can identify not only isomers of mono-saccharides and disaccharides, but also various mono-saccharides from a data pool of eleven analytes. In addition, the binding affinity between recognition molecule and analyte was investigated by comparing with surface plasmon resonance. In present, the RT technique is applying to chip type sequencing device onto solid-state nanopore to read out glycosaminoglycans which is ubiquitous to all mammalian cells and controls biological activities. / Dissertation/Thesis / Doctoral Dissertation Physics 2016

<p> The nematic phases of liquid crystals have been the most thoroughly investigated since the founding of the liquid crystal field in the early 1900&rsquo;s. The resulting technologies, most notably the liquid crystal display, have changed our world and spawned an entire industry. Consequently, the recent identification of a new type of nematic &ndash; the twist-bend nematic &ndash; was met with as much surprise as excitement, as it melds the fluid properties and environmental responsiveness of conventional nematics with the intrinsic polarization and complex ordering of bent-core liquid crystals. I summarize the history of the twist-bend nematic phase, charting the development of our understanding from its first identification to the present day. Furthermore, I enumerate and highlight my own efforts in the field to characterize the behavior and nanoscale organization of the twist-bend phase.</p><p>

Orientador: Fauze Ahmad Aouada / Banca: José Antonio Malmonge / Banca: Elson Longo da Silva / Resumo: Portadores de cadeias macromoleculares flexíveis e interligadas covalentemente, os hidrogéis são polímeros hidrofílicos, e quando sintetizados a partir da junção de polímeros sintéticos e naturais possuem excelente biocompatibilidade, biodegradabilidade e porosidade. O que amplia sua aplicabilidade desde liberação controlada, tanto de medicamentos quanto de nutrientes para o solo, implantes terapêuticos, cultura de células e cartilagens, dentre outros. Nesse trabalho, os hidrogéis nanocompósitos foram sintetizados via polimerização radical livre a partir de poliacrilamida (PAAm), carboximetilcelulose (CMC) e zeólita. A caracterização desses nanocompósitos foi realizada a partir de estudos de grau de intumescimento, no qual foram utilizados 4 meio diferentes (água destilada, NaCl (variando- se a concentração em 0,05; 0,10; 0,15 e 0,20 mol/L), CaCl 2 (a 0,15 mol/L) e AlCl 3 (a 0,15 mol/L)); propriedades cinéticas (n e k); espectroscopia de absorção no infravermelho (FTIR); microscopia eletrônica de varredura (MEV) e análises térmicas (TG, DTG e DSC). Concluímos que os hidrogéis de PAAm, CMC e zeólita apresentaram menor capacidade de absorção quando comparados a hidrogéis de PAAm e CMC. Percebemos que a concentração de catalisador N, N, N', N' -tetrametiletilenodiamina (TEMED) tem forte influência sobre o grau de intumescimento dos hidrogéis, pois age diretamente na velocidade e na formação das reações que originam os hidrogéis nanocompósitos. As soluções salinas contendo cargas iônicas maiores (CaCl 2 e AlCl 3 ) apresentam menor desempenho no grau de intumescimento; enquanto que soluções com carga menor (NaCl) apresentam melhor desempenho, sendo que sua concentração não provocou grandes variações no grau de intumescimento. Como visto nas análises de FTIR, MEV e EDS, pode-se afirmar que houve interação entre os hidrogéis de PAAm e CMC... / Abstract: Carriers and flexible macromolecular chains covalently linked, hydrogels are highly hydrophilic polymers, and when synthesized from the junction of synthetic and natural polymers have excellent biocompatibility, biodegradability and porosity. What expands its applicability from controlled release of both drugs as nutrients to the soil, therapeutic implants, cell culture and cartilage, and others. In this work, nanocomposite hydrogels formed from polyacrylamide (PAAm), carboxymethylcellulose (CMC) and zeolite were synthesized via free radical polymerization. The characterizations of these nanocomposites were made from swelling degree studies in four different media (distilled water, NaCl (varying the concentration of 0.05; 0.10; 0, 15 and 0.20 mol / L), CaCl 2 (0.15 mol / L) and AlCl 3 (0.15 mol / L); kinetic properties (n and k); fourier transform infrared spectroscopy (FTIR); scanning electron microscopy (SEM) and thermal analysis (TG, DTG and DSC). It was possible to conclude that the PAAm, CMC and zeolite hydrogels had lower absorption capacity when compared to hydrogels without zeolite. Also, the concentration of N, N, N', N' - tetramethylethylenediamine TEMED catalyst has strong influence on the degree of swelling of hydrogels, because it acts directly on the speed and in the polymerization reactions. Saline solutions containing large ionic charges (CaCl 2 and AlCl 3 ) have lower performance in the swelling degree when compared to solutions with small charge (NaCl), being that its variation no provoked significant changes in the swelling degree. As seen in the FTIR, SEM and EDS techniques, there was interaction between hydrogels PAAm and CMC with the zeolite, decreasing the matrix pore sizes which directly influences the degree of swelling and structure of hydrogels. From thermal analysis, it was possible to conclude that the zeolite increased the thermal stability of nanocomposites. Thus ... / Mestre

abstract: Engineered nanoparticles (NPs) pose risk potentials, if they exist in water systems at significant concentrations and if they remain reactive to cause toxicity. Three goals guided this study: (1) establishing NP detecting methods with high sensitivity to tackle low concentration and small sizes, (2) achieving assays capable of measuring NP surface reactivity and identifying surface reaction mechanisms, and (3) understanding the impact of surface adsorption of ions on surface reactivity of NPs in water. The size detection limit of single particle inductively coupled plasma spectrometry (spICP-MS) was determined for 40 elements, demonstrating the feasibility of spICP-MS to different NP species in water. The K-means Clustering Algorithm was used to process the spICP-MS signals, and achieved precise particle-noise differentiation and quantitative particle size resolution. A dry powder assay based on NP-catalyzed methylene blue (MB) reduction was developed to rapidly and sensitively detect metallic NPs in water by measuring their catalytic reactivity. Four different wet-chemical-based NP surface reactivity assays were demonstrated: “borohydride reducing methylene blue (BHMB)”, “ferric reducing ability of nanoparticles (FRAN)”, “electron paramagnetic resonance detection of hydroxyl radical (EPR)”, and “UV-illuminated methylene blue degradation (UVMB)”. They gave different reactivity ranking among five NP species, because they targeted for different surface reactivity types (catalytic, redox and photo reactivity) via different reaction mechanisms. Kinetic modeling frameworks on the assay outcomes revealed two surface electron transfer schemes, namely the “sacrificial reducing” and the “electrode discharging”, and separated interfering side reactions from the intended surface reaction. The application of NPs in chemical mechanical polishing (CMP) was investigated as an industrial case to understand NP surface transformation via adsorbing ions in water. Simulation of wastewater treatment showed CMP NPs were effectively removed (>90%) by lime softening at high pH and high calcium dosage, but 20-40% of them remained in water after biomass adsorption process. III/V ions (InIII, GaIII, and AsIII/V) derived from semiconductor materials showed adsorption potentials to common CMP NPs (SiO2, CeO2 and Al2O3), and a surface complexation model was developed to determine their intrinsic complexation constants for different NP species. The adsorption of AsIII and AsV ions onto CeO2 NPs mitigated the surface reactivity of CeO2 NPs suggested by the FRAN and EPR assays. The impact of the ion adsorption on the surface reactivity of CeO2 NPs was related to the redox state of Ce and As on the surface, but varied with ion species and surface reaction mechanisms. / Dissertation/Thesis / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2018

<p> Direct coagulation printing (DCP) is a new approach to extrusion-based additive manufacturing, developed during this thesis project using alumina nanopowder. The fabrication of complex ceramic parts, sintered to full density, was achieved and the details of this invention are described. With the use of additive manufacturing, complex features can be generated that are either very difficult or unattainable by conventional subtractive manufacturing methods. Three unique approaches were taken to create a slurry suitable for extrusion 3D-printing. Each represented a different method of suspending alumina nanopowder in a liquid; a bio-polymer gel based on chitosan, a synthetic polymer binder using poly-vinyl acetate (PVA), and electrostatic stabilization with the dispersant tri-ammonium citrate (TAC). It was found that TAC created a slurry with viscosity and coagulation rate that were tuneable through pH adjustment with nitric acid. This approach led to the most promising printing and sintering results, and is the basis of DCP. Taguchi and fractional factorial design of experiments models were used to optimize mixing of the alumina slurry, rheological properties, print quality, and sinterability. DCP was characterized by measuring the mechanical properties and physical characteristics of printed parts. Features as small as ~450 ?m in width were produced, in parts with overhangs and enclosed volumes, in both linear and radial geometries. After sintering, these parts exhibited little to no porosity, with flexural modulus and hardness comparing favorably with conventionally manufactured alumina parts. A remarkable aspect of DCP is that it is a completely binderless process, requiring no binder removal step. In addition, DCP can employ nanopowders, allowing for enhanced mechanical properties as observed in nano-grained materials. Perhaps most importantly, any material that acquires a surface charge when in aqueous media has the potential to be used in DCP, making it a method of additive manufacturing using many metals and ceramics other than alumina.</p><p>

<p> III-V optoelectronic device integration in a CMOS post-process compatible manner is important for the intimate integration of silicon-based electronic and photonic integrated circuits. The low temperature, self-catalyzed growth of high crystalline quality Wurtzite-phase InP nanopillars directly on silicon presents a viable approach to integrate high performance nano-optoelectronic devices. </p><p> For the optical transmitter side of the photonic link, InGaAs quantum wells have been grown in a core-shell manner within InP nanopillars. Position-controlled growth with varying pitch is used to systematically control emission wavelength across the same growth substrate. These nanopillars have been fabricated into electrically-injected quantum well in nanopillar LEDs operating within the silicon transparent 1400&ndash;1550 nm spectral window and efficiently emitting micro-watts of power. A high quality factor (Q ~ 1000) undercut cavity quantum well nanolaser is demonstrated, operating in the silicon-transparent wavelength range up to room temperature under optical excitation. </p><p> We also demonstrate an InP nanopillar phototransistor as a sensitive, low-capacitance photoreceiver for the energy-efficient operation of a complete optical link. Efficient absorption in a compact single nanopillar InP photo-BJT leads to a simultaneously high responsivity of 9.5 A/W and high 3dB-bandwidth of 7 GHz. </p><p> For photovoltaic energy harvesting, a sparsely packed InP nanopillar array can absorb ~90% of the incident light because of the large absorption cross section of these near-wavelength nanopillars. Experimental data based on wavelength and angle resolved integrating sphere measurements will be presented to discuss the nearly omnidirectional absorption properties of these nanopillar arrays.</p><p>

<p> Nanofabrication through multiphoton absorption has generated considerable interest because of its unique ability to generate 2D and 3D structures in a single laser-direct-write step as well as its ability to generate feature sizes well below the diffraction limited laser spot size. The majority of multiphoton fabrication has been used to create 3D structures of photopolymers which have applications in a wide variety of fields, but require additional post-processing steps to fabricate conductive structures. It has been shown that metal ions can also undergo multiphoton absorption, which reduces the metal ions to stable atoms/nanoparticles which are formed at the laser focal point. When the focus is located at the substrate surface, the reduced metal is deposited on the surface, which allows arbitrary 2D patterning as well as building up 3D structures from this first layer. Samples containing the metal ions can be prepared either in a liquid solution, or in a polymer film. The polymer film approach has the benefit of added support for the 3D metallic structures; however it is difficult to remove the polymer after fabrication to leave a free standing metallic structure. With the ion solution method, free standing metallic structures can be fabricated but need to be able to withstand surface tension forces when the remaining unexposed solution is washed away.</p><p> So far, silver nanowires with resistivity on the order of bulk silver have been fabricated, as well as a few small 3D structures. This research focuses on the surfactant assisted multiphoton reduction of silver ions in a liquid solution. The experimental setup consists of a Coherent Micra 10 Ultrafast laser with 30fs pulse length, 80MHz repetition rate, and a wavelength centered at 800nm. This beam is focused into the sample using a 100x objective with a N.A. of 1.49. Silver structures such as nanowires and grid patterns have been produced with minimum linewidth of 180nm. Silver nanowires with resistivity down to 6x bulk silver have been fabricated. Three-dimensional structures have also been fabricated with up to a 10&micro;m height at a thickness of 500nm. This method can fabricate structures with the possible applications in plasmonic metamaterials, photonic crystals, MEMS/NEMS and micro/nanocircuitry. </p><p>

<p> We present a versatile biosensing strategy that uses nucleic acids programmed to undergo an isothermal toehold mediated strand displacement in the presence of analyte. This rearrangement results in a double biotinylated duplex formation that induces the rapid aggregation of streptavidin decorated quantum dots (QDs). As biosensor reporters, QDs are advantageous to organic fluorophores and fluorescent proteins due to their enhanced spectral and fluorescence properties. Moreover, the nanoscale regime aids in an enhanced surface area that increase the number of binding of macromolecules, thus making cross-linking possible. The biosensing transduction response, in the current approach, is dictated by the analysis of the natural single particle phenomenon known as fluorescence intermittency, or blinking is the stochastic switching of fluorescence intensity ON (bright) and OFF (dark) states observed in single QD or other fluorophores. In contrast to binary blinking that is typical for single QDs, aggregated QDs exhibit quasi-continuous emission. This change is used as an output for the novel biosensing techniques developed by us. Analysis of blinking traces that can be measured by laser scanning confocal microscopy revealed improved detection of analytes in the picomolar ranges. Additionally, this unique biosensing approach does not require the analyte to cause any fluorescence intensity or color changes. Lastly, this biosensing method can be coupled with therapeutics, such as RNA interference inducers, that can be conditionally released and thus used as a theranostic probes.</p><p>

<p> Bioinspired design has been crucial in the development of new types of hierarchical nanocomposites. Particularly, the nacre-mimetic brick-and-mortar structure has shown excellent mechanical properties as well as gas barrier properties and optical transparency. Along with these intrinsic properties, the layered structure has been designed to serve as sensing devices. Here we expand the multi-functionality of nacre-mimetics by designing an optically transparent and electron conductive coating that reacts to high-pressure based on PEDOT:PSS and nanoclay. The main objectives of this project are: (i) to develop a multifunctional nanocomposite and evaluate the effect of high-pressure applied at the surface and (ii) to establish protocols for the morphological and structural characterization, and electro-mechanical testing of the nanocomposites based on a combination of atomic force microscopy (AFM), scanning electron microscopy (SEM) and transmittance spectroscopy. </p><p> The synthesis of the nanocomposite, containing PEDOT:PSS (conductive polymer) and nanoclay, was achieved using the self-assembly of core/shell platelets. Two different types of nanoclay, Cloisite Na+ and Laponite RD, are used and their properties compared. The reduction of thickness in PEDOT:PSS has been shown to increase the light transmittance across a film. Similarly, the thickness of the nanocomposite was reduced and compared to PEDOT:PSS. The measured optical transmittance for both nanocomposites is comparable to the bare polymer, demonstrating that the addition of the nanoclay does not affect the transparency of PEDOT:PSS significantly. The layered structure of the nanocomposites is investigated by imaging the fracture surface with SEM. The fracture surface of the Laponite RD based nanocomposite is much flatter than the Cloisite Na+ nanocomposite, since the particle size in Cloisite Na+ is about 10 times larger than Laponite RD. The characterization of electro-mechanical properties of the nanocomposites was performed using the correlation of conductive atomic force microscopy and contact resonance force microscopy to measure the local variations. The analysis shows that in thin and transparent films, there is segregation in the response of Cloisite Na+ based nanocomposites compared to the bare polymer or Laponite RD nanocomposite, hence the investigation focuses on Laponite RD. </p><p> For Laponite RD, we investigate the 3-D distribution of nanoclay in the coating. The distribution of nanoclay at the surface is elucidated by mapping the dissipative and conservative interactions between tip and sample in bimodal AFM. Measuring the strain produced by the tip, the 3-D structure is inferred using models for mechanical properties of nanocomposites. Single platelet measurements are used to infer the inter-platelet distance. It is known that the free amplitude of the higher eigenmode can be modulated to produce large forces in bimodal AFM. The pressure estimated for the typical cantilever parameters used are in the range 1.2-3.3 GPa, which is used to apply high-pressure to the subsurface structure of the nanocomposite. </p><p> We show that the tip-surface interaction modifies the subsurface morphology of the nanocomposite and results in changes of the out-of-plane current. Also, the structural modification caused by the bimodal AFM treatment results in local changes in mechanical properties. This behavior is obtained for the Laponite RD nanocomposite, but it is not observed for the Cloisite Na+ nanocomposite or the bare polymer. Laponite RD has a platelet size similar to the tip, while Cloisite Na+ is much larger leading to a reduction in pressure. By modelling the transmission probability of electrons, geometrical changes in the structure are examined and shown to modify the tunneling of the electrons through the coating. Specifically, parallel compression of the nanoclay (modelled as barriers for electrons) leads to a change in the transmission probability of the electrons. Depending on the kinetic energy of the electrons, the transmission probability could either increase or decrease.</p><p>