Researchers discovered the existence of non-coding RNA while unraveling the secrets of the human genome. Non-coding RNA molecules are never translated into proteins, yet they are highly abundant and serve critical functions within all cells. Imbalances in one class of regulatory non-coding RNA, known as microRNA (miRNA), lead to diseases such as cancer and cardiovascular disease. MiRNA inhibition is a potent therapeutic strategy because single miRNAs can regulate hundreds of different disease-associated genes. Peptide nucleic acids (PNA) are excellent miRNA inhibitors, yet they have no innate ability to reach miRNA targets in the body. This worksâ central hypothesis is that therapeutic anti-miRNA activity can be improved by engineering nanoparticles to increase PNA blood circulation half-life, cellular uptake, and targeted delivery to the cytoplasm of diseased cells. In this thesis, two highly tunable biomaterials (porous silicon and âsmartâ polymers) are combined to form composite nanoparticles that improve the PNA therapeutic delivery. These nanocomposites are shown to be non-toxic, increase PNA blood-circulation half-life from <1 min to 70 min, and improve PNA delivery to its site of action in target cells. This thesis demonstrates how nanotechnology can aid the clinical translation of a promising new class of therapeutics.

Porous silicon, a nanostructured material formed by electrochemical etching of a silicon substrate, is an ideal candidate for constructing optical biosensors due to its large internal surface area, straightforward fabrication, and tunable optical properties that can be exploited to form numerous photonic structures. A major challenge for porous silicon biosensors is its reactive surface that is highly susceptible to oxidation and corrosion in an aqueous environment. In DNA sensing applications, porous silicon corrosion can mask the DNA binding signal as the dissolution of porous silicon is accelerated by the negative charges on the phosphate backbone of the DNA molecules. This corrosion process can be mitigated through surface passivation of porous silicon and the use of charge neutral peptide nucleic acid molecules as capturing probes for DNA targets. Complete mitigation can be achieved by additionally introducing Mg2+ ions to shield the negative charges on the DNA targets. Another key challenge facing porous silicon biosensors is the inefficient analyte transport through nanopores, which can be as slow as a few molecules per pore per second for molecules whose size approaches that of the pore opening. An open-ended porous silicon membrane is demonstrated to overcome the mass transport challenge by allowing analytes to flow through the pores in microfluidic-based assays. The flow-through approach for biosensing using porous silicon membranes enables a 6-fold improvement in sensor response time compared to closed-ended, flow-over porous silicon sensors when detecting high molecular weight analytes (e.g., streptavidin). For small analytes, little to no sensor performance improvement is observed as the closed-ended porous silicon films do not suffer significant mass transport challenges with these molecules. Experimental results and finite element method simulations also indicate that the flow-through scheme enables more reasonable response times for the detection of dilute analytes and reduces the volume of solution required for analysis. Overall, the improvement of surface stabilization and analyte transport efficiency in porous silicon photonic structures opens the door to a fast and reliable optical biosensing platform.

This research is focused on developing a new type of gamma-ray scintillator and is motivated by the need for more accurate positron emission tomography (PET) imaging. PET scans are used to display regions of high-metabolic activity within the body and can indicate the presence of tumors, so clear images are essential for accurate diagnoses and treatment options. Scintillation detectors currently used for PET scans typically have a time resolution of hundreds of ps that yields images with poorly defined and blurred boundaries. Conversely, ZnO nanowires have a response time that is an order of magnitude faster with the potential for an analogous improvement to spatial resolution. Moreover, initial experiments show ZnO nanowires are radiation hardened with highly transient lattice defects. To optimize overall scintillator efficiency, the emission can be enhanced through a combination of optical-cavity effects (15x enhancement) and plasmon-exciton coupling (3x enhancement), while the low interaction volume of the nanowires can be addressed by adding a high-Z backing layer to attenuate incoming gamma rays. The ability to decouple, and address separately, emission efficiency and gamma-ray interaction provides a unique materials workbench and establishes ZnO nanowires as a highly promising PET scan scintillator material.

Gallium arsenide and other III-V materials are well known for their excellent optical and electronic properties and have led to the development of high-performance optoelectronics. Several combinations of III-V semiconductors are now being considered as potentially attractive alternatives to silicon for these applications. However, further development requires fundamental understanding of processes that govern light-matter interactions. Specifically, surface strain and ultrafast dynamics are of great interest to the optoelectronic industry. The research of this dissertation represents an initial exploration of the factors influencing nonlinear optical responses on semiconductor surfaces. The results of this research have the potential to inform the field of nonlinear optics about which lattice behaviors are most likely to contribute to static and transient second harmonic generation (SHG). This information allows for future work to focus on the connection between SHG, dipole contributions, and interatomic potentials in semiconductors under different conditions. This research also provides information about whether strain, resonances, and subpicosecond lattice behaviors can be fit with a simple analytical solution. The results of this research reveal that an analytical fit of polarization-resolved SHG is sensitive to interatomic potential and dipole variations in all three dimensions simultaneously.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Interdisciplinary Science, 1996. / Includes bibliographical references (p. 362-403). / by William J. Hartnett. / Ph.D.

Thesis (Ph. D.)--Texas A&M University, 2005. / "Major Subject: Interdisciplinary Engineering" Title from author supplied metadata (automated record created on Sep. 15, 2006.) Vita. Abstract. Includes bibliographical references.

Thesis (M.Ed.)--Regis University, Denver, Colo., 2006. / Title from PDF title page (viewed on Feb. 14, 2007). Includes bibliographical references.

Thesis (Ph. D.)--Texas A&M University, 2005. / "Major Subject: Interdisciplinary Engineering" Title from author supplied metadata (automated record created on Feb. 23, 2007.) Vita. Abstract. Includes bibliographical references.

The interaction of electrons and phonons with the properties of semiconducting crystals continues to be a fascinating and highly fruitful field of study. This dissertation addresses two research problems under the general heading of electron and phonon effects on the optical properties of indirect gap semiconductors. The first problem concerns nonlinear (multi-photon) absorption in germanium crystals, a topic of interest for the telecommunications industry as well as to the basic scientist. Using a combination of infrared transmittance experiments and numerical analysis, the two- and three-photon absorption coefficients β and γ for germanium have been evaluated over the range of wavelengths from 2.8 µm to 5.2 μm. The ratios of the coefficients across the direct/indirect gap transitions and between the two-and three-photon cases, which are less susceptible to experimental uncertainties than the absolute coefficients, have also been determined. Comparison with theoretical studies shows excellent agreement. The second problem addresses the optical characteristics of ion-bombarded diamond crystals, which is a swiftly developing field due to diamonds current status as the material of choice for hosting photonic and quantum information devices. The ultrafast optical technique known as coherent acoustic phonon interferometry has been applied to He ion irradiated diamond crystals for the purpose of determining the optical modification induced by the implantation damage. The experimental results provide information about the variation at in the complex refractive indices of the implanted specimens as well as the variation in the photoelastic tensor. A simple phenomenological model quantitatively describing the damage-induced optical modification has been developed which accurately predicts the experimental observations, and may prove to be a useful tool for quantum device design.

INTERDISCIPLINARY MATERIALS SCIENCE PHOTOSYSTEM I FROM HIGHER PLANTS ENHANCE ELECTRODE PERFORMANCE DARLENE GUNTHER Thesis under the direction of Professor G. Kane Jennings Photosystem I (PSI) is a supramolecular protein complex found in the thylakoid membranes of higher plants, algae, and cyanobacteria. Recently, researchers from across the world have been interested in extracting PSI from its source and integrating it with electrodes to investigate biologically inspired solar energy conversion. There are two main investigations involving PSI in this thesis. First, adsorbing PSI monolayers onto atomically thin graphene creates a transparent, photoactive electrode that is less than 10 nm thick. Experiments utilizing PSI extracted from spinach and deposited onto graphene results in an enhanced photocurrent density over bare graphene electrodes. Furthermore, choice of opaque mediator with higher concentrations combined with highly transparent graphene produced larger photocurrents than the use of transparent mediator counterparts. Second, PSI is extracted from Pueraria lobata (kudzu) and deposited onto silicon electrodes for the first time. This study investigates the potential for transitioning from traditional food sources, such as spinach, to non-traditional food sources, such as kudzu, as a renewable resource for PSI. The kudzu-PSI-modified-silicon electrodes double the electrical output over bare silicon electrodes. Approved: G. Kane Jennings