Browsing by Subject "Nanofabrication"
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Item Open Access Multiplex Gene Synthesis and Error Correction from Microchips Oligonucleotides and High-throughput Gene Screening with Programmable Double Emulsion Microfluidics Droplets(2015) Ma, SiyingPromising applications in the design of various biological systems hold critical implications as heralded in the rising field of synthetic biology. But, to achieve these goals, the ability to synthesize and screen in situ DNA constructs of any size or sequence rapidly, accurately and economically is crucial. Today, the process of DNA oligonucleotide synthesis has been automated but the overall development of gene and genome synthesis and error correction technology has far lagged behind that of gene and genome sequencing. What even lagged behind is the capability of screening a large population of information on a single cell, protein or gene level. Compartmentalization of single cells in water-in-oil emulsion droplets provides an opportunity to screen vast numbers of individual assays with quantitative readouts. However these single-emulsion droplets are incompatible with aqueous phase analysis and are not controllable through molecule transports.
This thesis presents the development of a multi-tool ensemble platform targeted at high-throughput gene synthesis, error correction and screening. An inkjet oligonucleotide synthesizer is constructed to synthesize oligonucleotides as sub-arrays onto patterned and functionalized thermoplastic microchips. The arrays are married to microfluidic wells that provide a chamber to for enzymatic amplification and assembly of the DNA from the microarrays into a larger construct. Harvested product is then amplified off-chip and error corrected using a mismatch endonuclease-based reaction. Bacterial cells baring individual synthetic gene variants are encapsulated as single cells into double-emulsion droplets where cell populations are enriched by up to 1000 times within several hours of proliferation. Permeation of Isopropyl-D-1-thiogalactopyranoside (IPTG) molecules from the external solution allows induction of target gene expression. The induced expression of the synthetic fluorescent proteins from at least ~100 bacteria per droplet generates clearly distinguishable fluorescent signals that enable droplets sorting through fluorescence-activated cell sorting (FACS) technique. The integration of oligo synthesis and gene assembly on the same microchip facilitates automation and miniaturization, which leads to cost reduction and increases in throughput. The capacity of double emulsion system (millions discrete compartments in 1ml solution) combined with high-throughput sorting by FACS provide the basis for screening complex gene libraries for different functionality and activity, significantly reducing the cost and turn-around time.
Item Open Access Subwavelength-scale Light Localization in Complete Photonic Bandgap Materials(2010) Tang, LinglingThe objective of this dissertation work is to examine light localization in semiconductors provided by a complete photonic bandgap via three-dimensional (3D) woodpile photonic crystals. A 3D photonic crystal is a periodic nanostructure that demonstrates omni-directional Bragg reflection. These materials are anticipated to become a powerful tool for engineering light propagation and localization within subwavelength scales due to their complete photonic bandgap and the distinctive dispersion relation.
The approach of realizing microcavities in this dissertation is to combine multi-directional etching fabrication methods with mode gap design. Modulation of unit cell size along a line-defect 3D waveguide could bring a guiding mode into the mode gap region of the waveguide and form a microcavity with a resonance inside the complete photonic bandgap. The designed microcavities could be fabricated by multi-directional etching methods because they can structurally be decomposed into two sets of connected and straight dielectric rods.
Ultra-high-quality factor microcavities and sub-wavelength-scale waveguides are designed without introduction of local disorders. Monopole, dipole, and quadrupole resonant modes are demonstrated with a small modal volume. The smallest modal volumes obtained are 0.36 cubic half-wavelengths for a resonance field in vacuum, and 2.88 cubic half-wavelengths for a resonance field in a dielectric. Direct metal contacts with the microcavities do not significantly deteriorate the quality factors because the resonant fields are located inside the microcavities. Single-mode woodpile waveguides are also designed in both lateral and vertical propagation directions.
The multi-directional etching method is a simple approach to the fabrication of woodpile photonic crystals and designed optical components with a variety of crystal orientations and surfaces, including (110), (001), (100), and (010) planes. An arbitrary surface plane (mn0) is obtained with this method, where m and n are integers. Moreover, it can also produce large area woodpile photonic crystals with high precision in silicon and GaAs materials.
These optical components in woodpile photonic crystals would be building blocks of high-density, low-loss 3D integrated optics, cavity quantum electrodynamics (QED), nonlinear optics, and enable the realization of current-injection optical devices.