CU Dissertations
-
- Development and Use of Novel Transverse Magnetic Tweezers for Single-Molecule Studies of DNA-Protein Interactions
- Degree Awarded: Ph.D. Biomedical Engineering. The Catholic University of America, I describe several contributions to single molecule experiments. A transverse magnetic tweezers is presented that enables in-plane micromechanical manipulation of a single DNA molecule. This includes a new method for tethering DNA utilizing two labeled beads and a functionalized glass micro-rod. The attachment chemistry reported here enables rapid capture of multiple DNA tethers in parallel, overcomes the difficulties associated with bead aspiration, and preserves the ability to perform differential extension measurements from the bead centroids. Combined with micro-injection pipettes, a new sample cell design, and a buffer exchange system, the components increase the ease-of-use and experimental throughput of the magnetic tweezers device. On the software side, several unique computational methods for interrogating single molecule data are described. First, a technique that uses the diffraction pattern of beads to perform sub-pixel, ~10 nm-level localization of the bead centroids is explained. Second, a novel method for automatically detecting steps in DNA extension data is presented. This algorithm is well-suited for analyzing experiments involving binding and force-induced unbinding of DNA-protein complexes, which produce flat extension regions - steps - corresponding to the times between individual protein association or dissociation events. Finally, a new algorithm for tracking densely-populated, fast spawning, indistinguishable objects moving unidirectionally at high-velocities is developed and its performance thoroughly characterized. Together, these results should improve single molecule micromanipulation techniques by providing a hardware and software combination that can be implemented and used relatively easily, while enabling near-Brownian-noise limit force and extension measurements on DNA and DNA-protein complexes.
-
- Dual Firing of Hydrogen and Heavy Hydrocarbon Fuels
- Degree Awarded: Ph.D. Mechanical Engineering. The Catholic University of America, Heavy hydrocarbon fuels are common logistics fuel, even for small, mobile systems. In this work, jet fuel is used as a representative heavy hydrocarbon fuel. At low power output (under 2 kilowatts), technologies such as Stirling engines, thermo-electric thermo-photovoltaic generators have the potential to compete with diesel engines, but require reliable jet fuel combustion. Hydrogen enrichment is presented as a control parameter to improve jet fuel combustion. Research in fuel reforming gives an opportunity for hydrogen production at the point of use. Hydrogen enriched combustion of jet fuel seeks to take advantage of the energy density of jet fuel and the combustibility of hydrogen. Experiments were conducted with atomized jet fuel in an open flame. Jet fuel is sprayed through an air atomizing nozzle. Hydrogen was added to either the atomizing air or to a concentric tube supplying the main combustion air. During hydrogen enrichment, jet fuel flow rate was reduced to maintain constant fuel energy input. Temperature is measured vertically and laterally through the flame. Gaseous pollutant emissions were measured above the visible flame. The use of hydrogen and gases other than air to control an air siphon nozzle is demonstrated. In these experiments, hydrogen represented up to 26% of the fuel energy contribution. Substantial changes to the combustion profile occur with small amounts of hydrogen enrichment. Hydrogen enrichment increased peak temperature and reduced standoff distance. It expanded lower flammability limit and reduced emission of unburned hydrocarbons and carbon monoxide. Numerical simulations expanded the results to examine an enclosed burner more suitable for power generation applications. Results showed that at lean conditions, dual firing of hydrogen or reformate with jet fuel provided improved fuel conversion, better flame stability and higher fuel burnout. The advantages provided by dual firing jet fuel and hydrogen represent opportunities for reduced combustor size, improved power system operational reliability and control and reduced pollutant emissions.