Theses and Dissertations at Montana State University (MSU)
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Item Modeling the effects of flare energy release and transport through chromospheric condensation and ultraviolet coronal emission(Montana State University - Bozeman, College of Letters & Science, 2022) Ashfield, William Henry, IV; Chairperson, Graduate Committee: Dana W. Longcope; This is a manuscript style paper that includes co-authored chapters.Solar flares arise from the release of magnetic free energy through reconnection. A fraction of this energy travels from the corona to the lower solar atmosphere, heating the plasma and driving downflows -- chromospheric condensations -- critical to our understanding of flare energetics. While flare models with impulsive energy injections have successfully reproduced observed chromospheric responses, they typically focus on heating via electron beam deposition, neglecting other modes of energy transport. Observations of long-duration coronal emission in the extreme ultraviolet have further indicated a two-phase energy release process: impulsive energy deposition followed by persistent low-rate heating. As flare energy release and transport are measured by the indirect signatures of condensation and coronal emissions, flare models must account for these phenomena' behavior to infer the characteristics of reconnection. We first investigated the chromospheric response to a constant flare energy flux using a thermal flare model driven by in-situ coronal heating. An analytical expression for the condensation velocity was developed and found to be well described by the observed characteristic properties, allowing condensation to serve as a diagnostic for both the energy flux at the reconnection site and the pre-flare density scale height of the chromosphere. These results were tested on condensations observed in Si IV 1403 ?A spectral line redshifts. A Gaussian heating profile, inferred from footpoint UV emission corresponding to the measured downflows, was used to drive a one-dimensional simulation from which Si IV spectra were synthesized. Although the synthetic velocity evolution agreed reasonably well with observation, thus providing evidence for our model's validity, the condensation's timescale was found to be independent of the time scale of the energy release. To address coronal EUV emission signatures, long-duration flare heating was modeled through the slow dissipation of turbulent Alfven waves. Motivated by observations of supra-arcade downflows, the waves were initiated by retracting newly-reconnected flux tubes through a current sheet and dissipated through their non-linear interaction. EUV lightcurves synthesized from simulation results reproduced emissions that decayed in 40 minutes. This model, created self-consistently from reconnection-powered flare energy release, offers a possible explanation for the outstanding problem of persistent flare emission.Item Stigmatic spectroscopy of the solar atmosphere in the vacuum-ultraviolet(Montana State University - Bozeman, College of Letters & Science, 2020) Courrier, Hans Thomas; Chairperson, Graduate Committee: Charles C. Kankelborg; Charles C. Kankelborg was a co-author of the article, 'Using local correlation tracking to recover solar spectral information from a slitless spectrograph' in the journal 'Journal of astronomical telescopes and imaging systems, SPIE' which is contained within this dissertation.; Charles C. Kankelborg, Bart De Pontieu and Jean-Pierre Wulser were co-authors of the article, 'An on orbit determination of point spread functions for the interface region imaging spectrograph' in the journal 'Solar physics' which is contained within this dissertation.; Charles C. Kankelborg, Amy R. Winebarger, Ken Kobayashi, Brent Beabout, Dyana Beabout, Ben Carroll, Jonathan W. Cirtain, James A. Duffy, Carlos Gomez, Eric M. Gullikson, Micah Johnson, Jacob D.Parker, Laurel A. Rachmeler, Roy T. Smart, Larry Springer and David L. Windt were co-authors of the article, 'The EUV snapshot imaging spectrograph (ESIS)' which is contained within this dissertation.The solar atmosphere presents a complicated observing target since tremendous variability exists in solar features over a wide range of spatial, spectral, and temporal scales. Stigmatic spectrographs are indispensable tools that provide simultaneous access to spatial context and spectroscopy, enabling the diagnosis of solar events that cannot be accomplished by imaging or spectroscopy alone. In this dissertation I develop and apply a novel technique for on orbit spectrograph calibration, recover co-temporal Doppler shifts of widely spaced solar features, and describe a new design for a slitless solar spectrograph. The Interface Region Imaging Spectrograph, (IRIS) is currently the highest spatial and spectral resolution, space based, solar spectrograph. Ongoing calibration is important to maintaining the quality of IRIS data. Using a Mercury transit against the backdrop of the dynamic solar atmosphere, I characterize the spatial point spread functions of the spectrograph with a unique, iterative, blind, deconvolution algorithm. An associated deconvolution routine improves the ability of IRIS to resolve spatially compact solar features. This technique is made freely available to the community for use with past and future IRIS observations. The Multi-Order Extreme Ultraviolet Spectrograph (MOSES) is a slitless spectrograph that collects co-temporal, but overlapping spatial and spectral images of solar spectral lines. Untangling these images presents an ill-posed inversion problem. I develop a fast, automated method that returns Doppler shifts of compact solar objects over the entire MOSES field of view with a minimum of effort and interpretation bias. The Extreme ultraviolet Snapshot Imaging Spectrograph (ESIS) is a slitless spectrograph that extends the MOSES concept. I describe this new instrument, which is far more complex and distinct as compared to MOSES, and the contributions I made in the form of optical design and optimization. ESIS will improve the quality of spatial and spectral information obtained from compact and extended solar features, and represents the next step in solar slitless spectroscopy. Taken together, these contributions advance the field by supporting existing instrumentation and by developing new instrumentation and techniques for future observations of the solar atmosphere.Item Excited-state dynamics of biological molecules in solution: photoinduced charge transfer in oxidatively damaged DNA and deactivation of violacein in viscous solvents(Montana State University - Bozeman, College of Letters & Science, 2017) Beckstead, Ashley Ann; Chairperson, Graduate Committee: Robert WalkerUV radiation from the sun is strongly absorbed by DNA, and the resulting electronic excited states can lead to the formation of mutagenic photoproducts. Decades of research have brought to light the excited-state dynamics of single RNA and DNA nucleobases, but questions remain about the nature of excited states accessed in DNA strands. In this thesis, I present ultrafast spectroscopic observations of photoinduced electron transfer from the oxidatively damaged bases, 8-oxo-7,8-dihydro-2'-deoxyguanosine, 5-hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine, to adenine in three dinucleotides. The results reveal that charge transfer states are formed on a timescale faster than our instrumental resolution (<0.5 ps), and back electron transfer efficiently returns the excited-state population to the ground state on timescales from tens to hundreds of ps. In addition to recent spectroscopic observations of charge transfer state species in DNA by other groups, our results have augmented understanding of the long-lived transient signals observed in DNA strands. The observation of photoinduced electron transfer in these oxidatively damaged nucleobases also supports a recent proposal regarding the role of oxidative products in pre-RNA catalysis. I discuss these observations in the contexts of fundamental DNA excited-state dynamics and prebiotic chemical evolution. In this thesis, I also present the first ultrafast spectroscopic investigation of violacein, a pigment isolated from Antarctic bacteria. Despite claims for the photoprotective role of this pigment, there has never been a spectroscopic analysis of excited-state deactivation in violacein. Emission spectra, fluorescence quantum yields and excited-state lifetimes of violacein in various solvents were measured for the first time. Both the fluorescence quantum yield and excited-state lifetime of violacein increase in increasingly viscous solvents, suggesting a large-scale motion mediates excited-state deactivation. I compare these results to similar observations of viscosity-dependent excited-state decay rates in other molecules. I also consider the relevance of violacein's excited-state properties to the hypothesized sunscreening role of violacein. Overall, the studies presented in this dissertation illustrate how ultrafast spectroscopic techniques can be used to unravel complex biomolecular excited-state dynamics in solution.Item Ultrafast photochemistry of aqueous iron(III) complexes(Montana State University - Bozeman, College of Letters & Science, 2017) Danforth, Rebecca Ann; Chairperson, Graduate Committee: Erik Grumstrup; Bern Kohler was a co-author of the article, 'Ultrafast photochemical dynamics of hexaaqua iron(III) ion' in the journal 'Chemical physics letters' which is contained within this thesis.The ultrafast photochemical dynamics of aqueous iron(III) solutions were measured utilizing ultrafast pump probe spectroscopy. Aqueous solutions of iron(III) were prepared at low pH (<4.5) and low iron(III) concentration (<5 mM) to allow for small aquairon(III) complexes and ferrihydrite to be studied. Small monomeric and dimeric aquairon(III) complexes were studied to elucidate the mechanisms involved in the formation of OH ° after UV excitation which were previously known to generate OH ° in vastly different quantities. Upon excitation of Fe 3+, a proton is released from a coordinated water molecule to generate FeOH 2+ in less than 200 fs. The newly generated FeOH 2+ can then undergo numerous recombination pathways to regenerate the Fe 3+. Approximately 10% of the excited Fe 3+ undergoes photoreduction and subsequent release of OH ° and Fe 2+ within 20 ps. Exciting FeOH 2+, results in homolysis to form Fe 2+ and OH ° with a wavelength dependent yield with a lifetime of 20 ps. Fe 2(OH) 2 4+ does not appear to generate significant quantities of OH ° however, the dimer is photostable in comparison to Fe 3+ and FeOH 2+. To further the understanding of the primary kinetics of iron(III) in aqueous solutions, ferrihydrite nanoparticles were studied. Ferrihydrite exhibits similar dynamics to hematite in which electrons are excited into the conduction band of ferrihydrite. The electrons can then relax to the bottom of the conduction band within 390 fs before undergoing various recombination process. This limits the amount of iron(III) converted into iron(II) in ferrihydrite. All iron(III) systems studied show unique kinetics after excitation that elucidate the mechanisms behind the generation of OH °.Item Subnanosecond emission from model DNA oligomers characterized through time-correlated single-photon counting spectroscopy(Montana State University - Bozeman, College of Letters & Science, 2017) Skowron, David John; Chairperson, Graduate Committee: Robert Walker; Yuyuan Zhang, Ashley A. Beckstead, Jacob M. Remington, Madison Strawn and Bern Kohler were co-authors of the article, 'Subnanosecond emission dynamics of AT DNA oligonucleotides' in the journal 'Journal of chemical physics and physical chemistry' which is contained within this thesis.Exposure of DNA to UV radiation creates electronic excited states that can decay to mutagenic photoproducts. Excited states can return to the electron ground state through deactivation pathways, preventing photochemical damage. Understanding has significantly advanced over the last decade through the applications of time-resolved techniques capable of picosecond and femtosecond time-resolution. While significant strides have been made towards understanding monomeric deactivation pathways, unraveling the complex photophysics of base multimers still presents a significant challenge. This report uses time-resolved fluorescence and ultrafast transient absorbance to analyze model DNA oligomers to understand how fundamental interactions between monomeric constituents influences the dynamics of base multimers. Model single- and double-stranded DNA oligomers were investigated using the time correlated single photon counting technique to address the uncertainty over how to compare results from time-resolved fluorescent and transient absorption techniques. Emission lifetimes ranging from 50 to 200 ps quantitatively agree with lifetimes measured from transient absorption experiments indicating emission observed on timescales greater than a few picoseconds is the result of excimer or charge recombination luminescence. In attempts to further characterize the time-resolved emission from model oligomers adenine oligomers consisting of 2 and 18 base constituents were examined in aqueous water and heavy water solutions. Differences in dynamics between the two oligomers revealed the average number of bases present within a stacked domain influence the dynamics of these systems. Lifetimes of the emission decays were assigned excimer-like states with various degrees of charge-transfer character. Finally, to further demonstrate the importance of base stacking domain length on the dynamics of these systems, time-resolved emission and absorption of the adenine dinucleotide and 18-mer where examined at temperatures ranging from 7 °C - 80 °C. It was observed that the kinetics between the oligomers was noticeably different at lower temperatures, but not at higher temperatures. It was concluded the domain length of the 18-mer was similar to the domain length of the dinucleotide at high temperatures, but not at low temperatures, demonstrating the domain length significant impacts theS photophysics of DNA.Item Explosive events in the quiet Sun: extreme ultraviolet imaging spectroscopy instrumentation and observations(Montana State University - Bozeman, College of Letters & Science, 2017) Rust, Thomas Ludwell; Chairperson, Graduate Committee: Charles C. KankelborgExplosive event is the name given to slit spectrograph observations of high spectroscopic velocities in solar transition region spectral lines. Explosive events show much variety that cannot yet be explained by a single theory. It is commonly believed that explosive events are powered by magnetic reconnection. The evolution of the line core appears to be an important indicator of which particular reconnection process is at work. The Multi-Order Solar Extreme Ultraviolet Spectrograph (MOSES) is a novel slitless spectrograph designed for imaging spectroscopy of solar extreme ultraviolet (EUV) spectral lines. The spectrograph design forgoes a slit and images instead at three spectral orders of a concave grating. The images are formed simultaneously so the resulting spatial and spectral information is co-temporal over the 20'x10' instrument field of view. This is an advantage over slit spectrographs which build a field of view one narrow slit at a time. The cost of co-temporal imaging spectroscopy with the MOSES is increased data complexity relative to slit spectrograph data. The MOSES data must undergo tomographic inversion for recovery of line profiles. I use the unique data from the MOSES to study transition region explosive events in the He II 304 A spectral line. I identify 41 examples of explosive events which include 5 blue shifted jets, 2 red shifted jets, and 10 bi-directional jets. Typical doppler speeds are approximately 100km s-1. I show the early development of one blue jet and one bi-directional jet and find no acceleration phase at the onset of the event. The bi-directional jets are interesting because they are predicted in models of Petschek reconnection in the transition region. I develop an inversion algorithm for the MOSES data and test it on synthetic observations of a bi-directional jet. The inversion is based on a multiplicative algebraic reconstruction technique (MART). The inversion successfully reproduces synthetic line profiles. I then use the inversion to study the time evolution of a bi-directional jet. The inverted line profiles show fast doppler shifted components and no measurable line core emission. The blue and red wings of the jet show increasing spatial separation with time.Item Design, fabrication, and implementation of an embedded flight computer in support of the ionospheric-thermospheric scanning photometer for ion-neutral studies CubeSat mission(Montana State University - Bozeman, College of Engineering, 2017) Handley, Matthew Lee; Chairperson, Graduate Committee: Brock LaMeresAs society increasingly relies on space-based assets for everything from GPS-based directions and global communications to human-driven research on the ISS, our understanding of space weather becomes vital. Timely predictions of a solar storm's impact on the ionosphere are imperative to safing these assets before damaging storms hit, while minimizing downtime during lighter storms. The topside transition region (TTR) is a global boundary where the concentration of O+ significantly decreases due to charge exchange with H+ and He+ from the thermosphere, as well as protons and neutral atomic oxygen from the plasmasphere. When high-energy electrons in the ionosphere intercept O+ ions, they combine and release photons at 135.6-nm. The Ionospheric-Thermospheric Scanning Photometer for Ion-Neutral Studies (IT-SPINS) mission will provide 135.6-nm nightglow measurements from a 3U CubeSat equipped with a high-sensitivity UV photometer. The CubeSat will spin about orbit normal, sweeping its photometer field of view through the ionosphere. Ground-based post processing will yield 2D altitude/in-track images of O+ density, providing weighting parameters for models of the TTR. This low-earth orbit (LEO) small satellite mission is a collaboration between the John Hopkins University Applied Physics Laboratory, SRI International, and Montana State University (MSU). This research describes the design, fabrication, and implementation of the space flight computer (SFC) hardware and software responsible for handling all commands, telemetry, and scientific data required by this National Science Foundation (NSF) funded mission. The SFC design balances requirements derived from the mission objectives while leveraging heritage hardware and software from MSU's many successful CubeSat missions (HRBE, FIREBIRD, FIREBIRD-II) and payloads (EPISEM) [1-3]. This low-power (100 mW) embedded computer features dual 16- bit PIC microcontrollers running at 16 MHz with only 96 kB of RAM and runs the microC/OS-II real-time operating system (RTOS). The SFC also includes a TCXO-driven mission elapsed time clock with plus or minus 2 ppm temperatures stability, a 1 GB NAND flash for data storage, and interfaces to all other subsystems in the satellite. The SFC has passed all standalone testing. It is currently being integrated and tested with the entire IT-SPINS spacecraft and is planned to fly in late 2018.Item Effects of ultraviolet irradiation of host and parasite on attachment of Bdellovibrio bacteriovorus to Escherichia coli(Montana State University - Bozeman, College of Agriculture, 1969) Castric, Kathleen ForsgrenItem Measurement of the variations in the reception of solar ultra-violet radiation at the earth's surface(Montana State University - Bozeman, College of Letters & Science, 1949) Kutzman, Nathaniel J.Item Coupling the photospheric and coronal magnetic fields : observations and analysis(Montana State University - Bozeman, College of Letters & Science, 1998) Handy, Brian Neal