Nanostructures fabricated by different methods have become increasingly important for various applications at the cellular level. In order to understand how these nanostructures “behave” and for studying their internalization kinetics, several attempts have been made at tagging and investigating their interaction with living cells. In this study, magnetic iron nanowires with an iron oxide layer are coated with (3-Aminopropyl)triethoxysilane (APTES), and subsequently labeled with a fluorogenic pH-dependent dye pHrodo™ Red, covalently bound to the aminosilane surface. Time-lapse live imaging of human colon carcinoma HCT 116 cells interacting with the labeled iron nanowires is performed for 24 hours. As the pHrodo™ Red conjugated nanowires are non-fluorescent outside the cells but fluoresce brightly inside, internalized nanowires are distinguished from non-internalized ones and their behavior inside the cells can be tracked for the respective time length. A machine learning-based computational framework dedicated to automatic analysis of live cell imaging data, Cell Cognition, is adapted and used to classify cells with internalized and non-internalized nanowires and subsequently determine the uptake percentage by cells at different time points. An uptake of 85 % by HCT 116 cells is observed after 24 hours incubation at NW-to-cell ratios of 200. While the approach of using pHrodo™ Red for internalization studies is not novel in the literature, this study reports for the first time the utilization of a machine-learning based time-resolved automatic analysis pipeline for quantification of nanowire uptake by cells. This pipeline has also been used for comparison studies with nickel nanowires coated with APTES and labeled with pHrodo™ Red, and another cell line derived from the cervix carcinoma, HeLa. It has thus the potential to be used for studying the interaction of different types of nanostructures with potentially any live cell types.

GaAs nanowires (NW) have been grown on Si (111) substrates by the self-assisted vapor-liquid-solid (VLS) mechanism using molecular beam epitaxy (MBE). Substrates were prepared with nano-patterned oxide templates using electron beam lithography (EBL) in order to achieve position controlled NW growth. Early experiments uncovered several key issues with regards to the patterning process. Cross-sectional lamella prepared using the focused-ion beam (FIB) technique were used to study the NW-substrate interface using transmission electron microscopy (TEM). Undesirable growth outcomes were found to be caused in part by an unintended residual layer of oxide. Uniform NW dimensions were then obtained by improving the pattern transfer method. The effects of deposition parameters on the growth results were then explored in further experiments. The first systematic study of the axial and radial growth rates of vertical NWs in the positioned array was conducted. It was proposed that the observed expansion of the Ga droplet in Ga-rich growth conditions results in a slight inverse tapered morphology, promoting significant radial growth. While the growth rates were shown to be approximately constant in time, their measured values were found to increase with increasing pattern pitch and decrease with increasing hole diameter. A phenomenological model was then developed based on the principle of mass conservation. A fit to the experimental data was obtained by calculating the collection of growth material supplied by a secondary flux of both gallium and arsenic species desorbing from the oxide surface between the NWs, subsequently impinging on the liquid droplet and NW sidewalls. The reduction of this contribution due to shading of the incident and scattered flux by neighboring NWs in the array was able to account for the differences in final NW morphologies observed with increasing pattern pitch. This model demonstrates the significant impact of secondary adsorption in patterned self-assisted NW growth. / Thesis / Doctor of Science (PhD)

Group-III-nitrides have been intensively investigated for optoelectronics and power electronics and are uniquely suitable for energy-related applications, such as solar hydrogen generation and nanogenerators. Compared to planar group-III-nitrides, their nanostructures offer a high surface-to-volume ratio, increased light absorption cross-section, and improved carrier transportation behavior. This thesis focuses on molecular-beam-epitaxy-grown group-III-nitrides, specifically nanowires and membranes, and applications in renewable energy harvesting and conversion. A Mo2C-decorated (In,Ga)N nanowire-based photocathode was demonstrated for nitrogen fixation. The conventional Haber-Bosch method demands high reaction pressure and temperature while releasing a considerable amount of greenhouse gas. The proposed photoelectrocatalytic method can utilize solar energy to generate ammonia without carbon emissions. The proposed photocathodes can achieve maximum faradaic efficiency of 12 %, ammonia yield of 8.9 µg/h/cm2, and excellent stability for over 12 hrs. Moreover, group-III-nitrides were fabricated into a freestanding membrane through a novel method combining electrochemical porosification and controlled spalling. The novel method is reproducible and scalable, which can significantly reduce the consumption of sacrificial substrates compared to existing nitride membrane exfoliation techniques, thus promising a scalable platform. The as-fabricated GaN membranes were demonstrated for photoelectrocatalytic methylene blue degradation. Through laboratory tests and rooftop field tests, we proved the feasibility of our wafer-scale GaN membranes in achieving a dye degradation efficiency of 92%, a total organic carbon removal rate of 50.2%, and extraordinary stability for ~ 50 hours under solar illumination. The membrane can also degrade ~87% of MB under visible-light illumination. Furthermore, the (Al,Ga)N membranes were fabricated into flexible transparent piezoelectric devices. The devices can sense compression pressure and bending strain while giving a comparable compression sensitivity to other thin film piezotronics devices of ~ 2.41 mV/kPa and 42.36 pA/kPa, a maximum bending gauge factor of ~ 1271, and an output power density of ~ 5.38 nW/cm2. The sensors can withstand over 35000 cycles of operation and can be utilized for sensing and harvesting mechanical energies from human motions and environmental signals. This research utilized nanowires and membrane-based group-III-nitrides for different photoelectrocatalytic reactions and piezotronics devices, from material preparation and characterizations, and demonstrated practical devices for clean energy-related applications.

We analyze a toy model for p-n junction photovoltaic devices by simulating photoexcited state dynamics in silicon nanowires. One nanowire is approximately circular in cross section with a diameter of d = 1.17 nm. The other has an approximately rhombic cross-section with d1 = 1.16 nm and d2 = 1.71 nm. Both nanowires have been doped with aluminum and phosphorus atoms and capped with gold leads. We use Boltzmann transport equation (BE) that includes phonon emission, carrier multiplication (CM), and exciton transfer. BE rates are computed using non-equilibrium finite-temperature many-body perturbation theory (MBPT) based on Density Functional Theory (DFT) simulations, including excitonic effects from Bethe-Salpeter Equation. We compute total charge transfer amount generated from the initial photoexcitation and find an enhancement when CM is included. In particular, we see between 78% and 79% enhancement in the smaller wire, while we see 116% enhancement in the larger nanowire

Geobacter sulfurreducens possesses type IV pili that are considered to be conductive nanowires and a crucial structural element in biofilm formation, enabling electron transfer to insoluble metal oxides in anaerobic sediments and to graphite anodes in microbial fuel cells. The molecular mechanism by which electrons are transferred through the nanowires to the electron acceptor is not fully understood. Prior to the work described in this thesis, the gene (pilA) encoding the structural pilus subunit had been identified, but little was known about the functional translation start codon, the length of the mature secreted protein, or what renders the pili conductive. Using mass spectrometry, I found that a tyrosine residue (Y32) near the carboxyl terminus of the mature PilA protein is posttranslationally modified by attachment of glycerophosphate. I studied the significance of Y32 for biofilm formation on various surfaces and for growth of G. sulfurreducens with insoluble electron acceptors. A mutant in which Y32 was replaced by phenylalanine lacked the glycerophosphate; biofilm formation on graphite surfaces was severely diminished and current production in microbial fuel cells was initiated only after a long lag phase. Moreover, cells with Y32F mutation in the pilA gene exhibited growth deficiency when Fe(III) oxide was the sole electron acceptor. My data confirm the role of G. sulfurreducens pili in biofilm formation and electron transfer to Fe(III) oxide and identify an amino acid in the PilA protein that is essential for these two processes. I also confirmed the existence of two functional translation start codons for the pilA gene and identified two isoforms (short and long) of the PilA preprotein by series of genetic complementation experiments. The short PilA isoform is found predominantly in an intracellular fraction, and seems to stabilize the long isoform and influence the secretion of several outer surface c-type cytochromes. The long PilA isoform, on the other hand, is required for secretion of PilA to the outer surface of the cell, a process that requires co-expression of pilA and the nine genes on its 3’ side. The long isoform is essential for biofilm formation on various surfaces, for optimum current production in microbial fuel cells, and for growth on insoluble Fe(III) oxide. This study provides new insight concerning the function and biogenesis of Geobacter type IV PilA, as well as a foundation for further research that will be conducted on microbial nanowires.

<p> Using gold as seed particles, the vapour-liquid-solid (VLS) growth of GaAs nanowires by molecular beam epitaxy on GaAs (100) substrates was investigated with a view to understanding and controlling the growth directions of nanowires. The crystallographic orientation as well as surface density of nanowires was found to be significantly affected by surface topography resulting from surface preparation prior to nanowire growth. Elongated pits of varying dimensions and orientation were formed on GaAs (100) substrates depending on the interaction of GaAs with gold or surface oxide. An in-depth analysis was carried out regarding the formation of pits as well as chemical composition of the oxide layer during the seed particle formation process. </p> <p> By analyzing the orientation-dependent structural properties of nanowires at different stages of growth, the origin of multi-directionality of nanowires on GaAs (100) substrates has been explored, and it has been shown that the growth directionality of nanowires can be significantly triggered to either the <011> or <111> direction by optimizing the growth rate as well as size of seed particles. Crystallographic properties of nanowires have also been discussed with reference to their growth directions.</p> / Thesis / Doctor of Philosophy (PhD)

The functionality of a novel 3-dimensional betavoltaic battery design will be investigated to improve conversion efficiency over existing planar devices. A beta-emitting isotope of nickel, Ni-63, is embedded in the volume of empty space between self-assisted p-i-n junction gallium phosphide nanowires to improve the beta capture efficiency. Parameters such as nanowire pitch, diameter, and height will influence the efficiency and were investigated thoroughly. Material selection was performed based on the following considerations. Gallium phosphide is chosen to achieve a high open circuit voltage under beta exposure. Ni-63 has an optimal beta energy spectrum for a nanowire device and a half-life of 101 years for long term application. The majority of the work focused on the development of the fabrication process, particularly the radioactive source deposition. The method used for embedding the source was a citrate-based sol-gel which was spun onto the sample. This method was modified for this nanowire application and specific challenges to the process are outlined. Furthermore, the obstacles of working with radioactive materials will be discussed. The first nanowire-based betavoltaic device is reported to produce beta-generated current and achieved a beta conversion efficiency of 0.03%. Investigation of the junction was performed to provide future improvements to the efficiency. Additionally, simulated IV curves for a non-active sample exhibited a possible conversion efficiency of 1.92%. / Thesis / Master of Applied Science (MASc)

This research provides a method of using a mixed powder in tube approach for producing and characterizing large quantities of highly oriented, high aspect ratio semiconductor nanowires in an inherently safe and contained manner. This work modifies the previously used mixed powder method to produce significantly smaller features below 100nm in diameter. For the first time SiGe alloys are produced in optical fiber from a mixture of the two powders across the entire compositional range. A discussion of the properties of silicon and germanium and their alloys is given with emphasis on the differences between properties at the bulk scale and at the nanoscale. The limitations of silicon and germanium for photonic applications, due to their indirect band gap nature, is removed when these materials are reduced to the nanoscale. A brief discussion of ways that these properties can be modified is given with size, composition, and strain all being viable factors of control. The optical and electrical properties of these nanowire arrays is evaluated as a function of the size, number of wires, and composition. A clear dependence between size and quantity of wires was observed with respect to composition. The nanowires were found to have complex interactions with light showing high absorption as well as unique transmission characteristics. Arrays of these fibers were able to create a measurable photocurrent and provide potential uses for detection of light and other photonic applications. An understanding of the etching necessary to both expose these nanowires for analysis as well as completely remove them from the glass matrix was developed. Etch rates in these areas was observed to be higher than reported etch values. Etching with dilute solutions was found to allow removal of the wires cleanly and allow recovery of them for other applications. / Master of Science / This research provides a method of using a mixed powder in tube approach for producing and characterizing large quantities of highly oriented, high aspect ratio semiconductor nanowires in an inherently safe and contained manner. These wires are over 1000 times smaller than thickness of a human hair are made using traditional fiber drawing methods or pulling at high temperatures. These fibers differ from traditional optical fibers in that they are produced from a tube filled with powder instead of a solid glass rod. This is similar to the same method used to produce wires in other materials such as copper. The use of the glass to contain the semiconductor material allows us to increase the temperature it is pulled at above the melting point. The liquid material is then drawn into the very small sizes using pores in the glass powder it is mixed with. This allows these wires to be produced in much longer lengths, larger quantities, and easier than previous methods. These nanowires are produced from silicon and germanium, which are two of the most important materials currently used in electronics. These semiconductors are used in most electronics, solar cells, and LEDs that are used in everyday life. Silicon and germanium while very important materials have limitations in photonic applications, interactions with light. The properties of the materials for these applications can be improved by reducing them in size to the nanoscale. The wires produced in this research were evaluated to determine if they possessed the more ideal properties. The wires were found to have detectable photocurrent, electricity generated from light. This is the primary property that is needed in solar cells. The wires produced in this method are an important early step to improving solar cells efficiency and reliability. These v wires have benefits over other forms of silicon because they are produced with protective glass coating in a single step.

Twins are a pair of adjoining crystal grains related to each other by a special symmetry. They are frequently observed in bulk materials and nanomaterials. The formation of twins is an important topic in materials science and engineering because it affects material behaviors such as plastic deformation of metals, yield strength, and band gap energy in nanoscale semiconductors. Because of these unique phenomena and properties that the twinning can bring to the materials, it is of interest to investigate the formation of twins. Our primary objective in this dissertation is to study twinning in nanowires. Both gold and platinum <111> oriented nanowires were fabricated by similar solution-phase chemical synthesis methods. High-resolution transmission electron microscopy and electron diffraction patterns were carried out to analyze the structures of the nanowires. Nanodiffraction was used to demonstrate twinning is a general structural feature of the growth of gold nanowires growing in a <111> direction.  A model was proposed to explain the conditions under which twinning is energetically favored during nanowire growth. The model, which is based on a maximum rate hypothesis, considers the nanowire geometry and the relative surface and stacking fault energies and predicts twins should appear in gold nanowires but not in platinum nanowires, in agreement with experimental observations. During the structural characterization of gold nanowires, our interest is to resolve 3D structure of twinning. However, the structure of twinning in gold nanowires is very fine and the average spacing between twin boundaries is only 0.57nm (+/- 0.38 nm); therefore, regular 3D electron microscopy technique is unable to reconstruct these defected structures. Here we present a stereo vision technique to reconstruct 3D atomic non-periodic structures containing defects. The technique employs intrinsic atomic planes as epipolar planes to achieve the alignment accuracy needed to reconstruct a crystal with atomic resolution. We apply it to determine the 3D geometry and atomic arrangements of twinning in gold nanowire. In addition, an iterated cross-correlation algorithm was developed to analyze electron diffraction fully automatically to facilitate structural analysis of nanowires. A time-temperature-transformation diagram of platinum nanowires in chemical synthesis was determined to help optimize the fabrication process of the nanowires. / Ph. D.

Work on individually constructed devices has demonstrated that nanowires (NWs) offer great promise for applications such as sensing and optoelectronics. Despite this work, reliable large scale alignment and integration of these individual nanostructures into a lithographically defined process remains a challenge. Dielectrophoresis (DEP) is a promising alignment method in which a nonuniform electric field is used to exert force on and manipulate NWs in solution. DEP offers the possibility of rapid, large area room-temperature assembly of NWs across opposing electrodes. DEP structures were fabricated on Si substrates and consisted of pairs of parallel Al electrodes on a 100nm insulating SiO2 film. ZnO NWs were suspended in isopropyl alcohol (IPA) and flowed across the electrodes. Alignment yield and angle of alignment were investigated as a function voltage and frequency. A method to remove excess nanowires through frequency tuning and IPA flushing is also investigated. The electrical properties of the formed ZnO NW devices will be reported. / Graduation date: 2010