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Description
Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving

Reductive dechlorination by members of the bacterial genus Dehalococcoides is a common and cost-effective avenue for in situ bioremediation of sites contaminated with the chlorinated solvents, trichloroethene (TCE) and perchloroethene (PCE). The overarching goal of my research was to address some of the challenges associated with bioremediation timeframes by improving the rates of reductive dechlorination and the growth of Dehalococcoides in mixed communities. Biostimulation of contaminated sites or microcosms with electron donor fails to consistently promote dechlorination of PCE/TCE beyond cis-dichloroethene (cis-DCE), even when the presence of Dehalococcoides is confirmed. Supported by data from microcosm experiments, I showed that the stalling at cis-DCE is due a H2 competition in which components of the soil or sediment serve as electron acceptors for competing microorganisms. However, once competition was minimized by providing selective enrichment techniques, I illustrated how to obtain both fast rates and high-density Dehalococcoides using three distinct enrichment cultures. Having achieved a heightened awareness of the fierce competition for electron donor, I then identified bicarbonate (HCO3-) as a potential H2 sink for reductive dechlorination. HCO3- is the natural buffer in groundwater but also the electron acceptor for hydrogenotrophic methanogens and homoacetogens, two microbial groups commonly encountered with Dehalococcoides. By testing a range of concentrations in batch experiments, I showed that methanogens are favored at low HCO3 and homoacetogens at high HCO3-. The high HCO3- concentrations increased the H2 demand which negatively affected the rates and extent of dechlorination. By applying the gained knowledge on microbial community management, I ran the first successful continuous stirred-tank reactor (CSTR) at a 3-d hydraulic retention time for cultivation of dechlorinating cultures. I demonstrated that using carefully selected conditions in a CSTR, cultivation of Dehalococcoides at short retention times is feasible, resulting in robust cultures capable of fast dechlorination. Lastly, I provide a systematic insight into the effect of high ammonia on communities involved in dechlorination of chloroethenes. This work documents the potential use of landfill leachate as a substrate for dechlorination and an increased tolerance of Dehalococcoides to high ammonia concentrations (2 g L-1 NH4+-N) without loss of the ability to dechlorinate TCE to ethene.
ContributorsDelgado, Anca Georgiana (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Halden, Rolf U. (Committee member) / Rittmann, Bruce E. (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2013
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Description
This work examines star formation in the debris associated with collisions of dwarf and spiral galaxies. While the spectacular displays of major mergers are famous (e.g., NGC 4038/9, ``The Antennae''), equal mass galaxy mergers are relatively rare compared to minor mergers (mass ratio <0.3) Minor mergers are less energetic than

This work examines star formation in the debris associated with collisions of dwarf and spiral galaxies. While the spectacular displays of major mergers are famous (e.g., NGC 4038/9, ``The Antennae''), equal mass galaxy mergers are relatively rare compared to minor mergers (mass ratio <0.3) Minor mergers are less energetic than major mergers, but more common in the observable universe and, thus, likely played a pivotal role in the formation of most large galaxies. Centers of mergers host vigorous star formation from high gas density and turbulence and are surveyed over cosmological distances. However, the tidal debris resulting from these mergers have not been well studied. Such regions have large reservoirs of gaseous material that can be used as fuel for subsequent star formation but also have lower gas density. Tracers of star formation at the local and global scale have been examined for three tidal tails in two minor merger systems. These tracers include young star cluster populations, H-alpha, and [CII] emission. The rate of apparent star formation derived from these tracers is compared to the gas available to estimate the star formation efficiency (SFE). The Western tail of NGC 2782 formed isolated star clusters while massive star cluster complexes are found in the UGC 10214 (``The Tadpole'') and Eastern tail of NGC 2782. Due to the lack of both observable CO and [CII] emission, the observed star formation in the Western tail of NGC 2782 may have a low carbon abundance and represent only the first round of local star formation. While the Western tail has a normal SFE, the Eastern tail in the same galaxy has an low observed SFE. In contrast, the Tadpole tidal tail has a high observed star formation rate and a corresponding high SFE. The low SFE observed in the Eastern tail of NGC 2782 may be due to its origin as a splash region where localized gas heating is important. However, the other tails may be tidally formed regions where gravitational compression likely dominates and enhances the local star formation.
ContributorsKnierman, Karen A (Author) / Scowen, Paul (Thesis advisor) / Groppi, Christopher (Thesis advisor) / Mauskopf, Philip (Committee member) / Windhorst, Rogier (Committee member) / Jansen, Rolf (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle:

Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands.

Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function.
ContributorsChapman, Eric (Author) / Childers, Daniel L. (Thesis advisor) / Cadillo-Quiroz, Hinsby (Committee member) / Hall, Sharon J (Committee member) / Turetsky, Merritt (Committee member) / Arizona State University (Publisher)
Created2015
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Description
The design, fabrication and testing of a novel full waveguide band ortho-mode transducer (OMT) for operation from 750-1150 GHz is presented in this dissertation. OMT is a device that separates orthogonal polarizations within the same frequency band. At millimeter and sub millimeter wavelengths, OMTs can achieve precise characterization of the

The design, fabrication and testing of a novel full waveguide band ortho-mode transducer (OMT) for operation from 750-1150 GHz is presented in this dissertation. OMT is a device that separates orthogonal polarizations within the same frequency band. At millimeter and sub millimeter wavelengths, OMTs can achieve precise characterization of the amplitude, spectrum and polarization of electromagnetic radiation by increasing spectral coverage and sensitivity while reducing aperture size, optical spill and instrumental polarization offsets. A fully planar design is implemented with the use of Robinson OMT model along with a planar finline circuit. CST Microwave Studio is used to design and simulate OMT. Existing finline circuits which were fabricated using photolithographic techniques on a thin dielectric substrate were employed. The finline chips are fabricated on a thin (1 µm) SOI substrate with thick (5 µm) gold finline metallization and gold beam leads for chip grounding. The OMT is designed with H plane splits in the through arm and E plane splits in the side arm to comply with the existing machining tools and technique. Computer Numerical Controlled (CNC) machining is used to fabricate the OMT split block. The OMT is tested at Jet Propulsion Laboratory (JPL) using Agilent PNA-X VNA and VDI WR1.0 extension heads. In the future, this OMT design could be a part of a fully integrated dual polarization mixer block, with the input horn, OMT and both mixers fabricated in a single flangeless split block. In Radio Astronomy, integrated dual polarization mixers of this type will increase the signal processing speed by 40%. This type of OMT can also be used for terahertz RADAR and communication purposes.
ContributorsSirsi, Siddhartha (Author) / Groppi, Christopher (Thesis advisor) / Aberle, James T., 1961- (Thesis advisor) / Mauskopf, Philip (Committee member) / Arizona State University (Publisher)
Created2014
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Description
The Milky Way galaxy is a powerful dynamic system that is highly efficient at recycling material. Stars are born out of intergalactic gas and dust, fuse light elements into heavier elements in their cores, then upon stellar death spread material throughout the galaxy, either by diffusion of planetary nebula or

The Milky Way galaxy is a powerful dynamic system that is highly efficient at recycling material. Stars are born out of intergalactic gas and dust, fuse light elements into heavier elements in their cores, then upon stellar death spread material throughout the galaxy, either by diffusion of planetary nebula or by explosive events for high mass stars, and that gas must cool and condense to form stellar nurseries. Though the stellar lifecycle has been studied in detail, relatively little is known about the processes by which hot, diffuse gas ejected by dying stars cools and conglomerates in the interstellar medium (ISM). Much of this mystery arises because only recently have instruments with sufficient spatial and spectral resolution, sensitivity, and bandwidth become available in the terahertz (THz) frequency spectrum where these clouds peak in either thermal or line emission. In this dissertation, I will demonstrate technology advancement of instruments in this frequency regime with new characterization techniques, machining strategies, and scientific models of the spectral behavior of gas species targeted by these instruments.

I begin this work with a description of radiation pattern measurements and their use in astronomical instrument characterization. I will introduce a novel technique to measure complex (phase-sensitive) field patterns using direct detectors. I successfully demonstrate the technique with a single pixel microwave inductance detectors (MKID) experiment. I expand that work by measuring the APEX MKID (A-MKID) focal plane array of 880 pixel detectors centered at 350 GHz. In both chapters I discuss the development of an analysis pipeline to take advantage of all information provided by complex field mapping. I then discuss the design, simulation, fabrication processes, and characterization of a circular-to-rectangular waveguide transformer module integrated into a circularly symmetric feedhorn block. I conclude with a summary of this work and how to advance these technologies for future ISM studies.
ContributorsDavis, Kristina (Author) / Groppi, Christopher E (Thesis advisor) / Bowman, Judd (Committee member) / Mauskopf, Philip (Committee member) / Jellema, Willem (Committee member) / Pan, George (Committee member) / Trichopoulos, Georgios (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The development of new Ultra-Violet/Visible/IR range (UV/Vis/IR) astronomical instrumentation that use novel approaches for imaging and increase the accessibility of observing time for more research groups is essential for rapid innovation within the community. Unique focal planes that are rapid-prototyped, low cost, and provide high resolution are key.

In this

The development of new Ultra-Violet/Visible/IR range (UV/Vis/IR) astronomical instrumentation that use novel approaches for imaging and increase the accessibility of observing time for more research groups is essential for rapid innovation within the community. Unique focal planes that are rapid-prototyped, low cost, and provide high resolution are key.

In this dissertation the emergent designs of three unique focal planes are discussed. These focal planes were each designed for a different astronomical platform: suborbital balloon, suborbital rocket, and ground-based observatory. The balloon-based payload is a hexapod-actuated focal plane that uses tip-tilt motion to increase angular resolution through the removal of jitter – known as the HExapod Resolution-Enhancement SYstem (HERESY), the suborbital rocket imaging payload is a Jet Propulsion Laboratory (JPL) delta-doped charge-coupled device (CCD) packaged to survive the rigors of launch and image far-ultra-violet (FUV) spectra, and the ground-based observatory payload is a star centroid tracking modification to the balloon version of HERESY for the tip-tilt correction of atmospheric turbulence.

The design, construction, verification, and validation of each focal plane payload is discussed in detail. For HERESY’s balloon implementation, pointing error data from the Stratospheric Terahertz Observatory (STO) Antarctic balloon mission was used to form an experimental lab test setup to demonstrate the hexapod can eliminate jitter in flight-like conditions. For the suborbital rocket focal plane, a harsh set of unit-level tests to ensure the payload could survive launch and space conditions, as well as the characterization and optimization of the JPL detector, are detailed. Finally, a modification of co-mounting a fast-read detector to the HERESY focal plane, for use on ground-based observatories, intended to reduce atmospherically induced tip-tilt error through the centroid tracking of bright natural guidestars, is described.
ContributorsMiller, Alexander Duke (Author) / Scowen, Paul (Thesis advisor) / Groppi, Christopher (Committee member) / Mauskopf, Philip (Committee member) / Jacobs, Daniel (Committee member) / Butler, Nathaniel (Committee member) / Arizona State University (Publisher)
Created2019
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Description
The universe since its formation 13.7 billion years ago has undergone many changes. It began with expanding and cooling down to a temperature low enough for formation of atoms of neutral Hydrogen and Helium gas. Stronger gravitational pull in certain regions caused some regions to be denser and hotter than

The universe since its formation 13.7 billion years ago has undergone many changes. It began with expanding and cooling down to a temperature low enough for formation of atoms of neutral Hydrogen and Helium gas. Stronger gravitational pull in certain regions caused some regions to be denser and hotter than others. These regions kept getting denser and hotter until they had centers hot enough to burn the hydrogen and form the first stars, which ended the Dark Ages. These stars did not live long and underwent violent explosions. These explosions and the photons from the stars caused the hydrogen gas around them to ionize. This went on until all the hydrogen gas in the universe was ionized. This period is known as Epoch Of Reionization. Studying the Epoch Of Reionization will help understand the formation of these early stars, the timeline of the reionization and the formation of the stars and galaxies as we know them today. Studying the radiations from the 21cm line in neutral hydrogen, redshifted to below 200MHz can help determine details such as velocity, density and temperature of these early stars and the media around them.

The EDGES program is one of the many programs that aim to study the Epoch of Reionization. It is a ground-based project deployed in Murchison Radio-Astronomy Observatory in Western Australia. At ground level the Radio Frequency Interference from the ionosphere and various man-made transmitters in the same frequency range as the EDGES receiver make measurements, receiver design and extraction of useful data from received signals difficult. Putting the receiver in space can help majorly escape the RFI. The EDGES In Space is a proposed project that aims at designing a receiver similar to the EDGES receiver but for a cubesat.

This thesis aims at designing a prototype receiver that is similar in architecture to the EDGES low band receiver (50-100MHz) but is significantly smaller in size (small enough to fit on a PCB for a cubesat) while keeping in mind different considerations that affect circuit performance in space.
ContributorsJambagi, Ashwini (Author) / Mauskopf, Philip (Thesis advisor) / Aberle, James T., 1961- (Thesis advisor) / Trichopoulos, Georgios (Committee member) / Arizona State University (Publisher)
Created2019
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Description
The Cosmic Microwave Background (CMB) has provided precise information on the evolution of the Universe and the current cosmological paradigm. The CMB has not yet provided definitive information on the origin and strength of any primordial magnetic fields or how they affect the presence of magnetic fields observed throughout the

The Cosmic Microwave Background (CMB) has provided precise information on the evolution of the Universe and the current cosmological paradigm. The CMB has not yet provided definitive information on the origin and strength of any primordial magnetic fields or how they affect the presence of magnetic fields observed throughout the cosmos. This work outlines an alternative method to investigating and identifying the presence of cosmic magnetic fields. This method searches for Faraday Rotation (FR) and specifically uses polarized CMB photons as back-light. I find that current generation CMB experiments may be not sensitive enough to detect FR but next generation experiments should be able to make highly significant detections. Identifying FR with the CMB will provide information on the component of magnetic fields along the line of sight of observation.

The 21cm emission from the hyperfine splitting of neutral Hydrogen in the early universe is predicted to provide precise information about the formation and evolution of cosmic structure, complementing the wealth of knowledge gained from the CMB.

21cm cosmology is a relatively new field, and precise measurements of the Epoch of Reionization (EoR) have not yet been achieved. In this work I present 2σ upper limits on the power spectrum of 21cm fluctuations (Δ²(k)) probed at the cosmological wave number k from the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) 64 element deployment. I find upper limits on Δ²(k) in the range 0.3 < k < 0.6 h/Mpc to be (650 mK)², (450 mK)², (390 mK)², (250 mK)², (280mK)², (250 mK)² at redshifts z = 10.87, 9.93, 8.91, 8.37, 8.13 and 7.48 respectively

Building on the power spectrum analysis, I identify a major limiting factor in detecting the 21cm power spectrum.

This work is concluded by outlining a metric to evaluate the predisposition of redshifted 21cm interferometers to foreground contamination in power spectrum estimation. This will help inform the construction of future arrays and enable high fidelity imaging and

cross-correlation analysis with other high redshift cosmic probes like the CMB and other upcoming all sky surveys. I find future

arrays with uniform (u,v) coverage and small spectral evolution of their response in the (u,v,f) cube can minimize foreground leakage while pursuing 21cm imaging.
ContributorsKolopanis, Matthew John (Author) / Bowman, Judd (Thesis advisor) / Mauskopf, Philip (Thesis advisor) / Lunardini, Cecilia (Committee member) / Chamberlin, Ralph (Committee member) / Vachaspati, Tanmay (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Peatlands represent 3% of the earth’s surface but have been estimated to contain up to 30% of all terrestrial soil organic carbon and release an estimated 40% of global atmospheric CH4 emissions. Contributors to the production of CH4 are methanogenic Archaea through a coupled metabolic dependency of end products released

Peatlands represent 3% of the earth’s surface but have been estimated to contain up to 30% of all terrestrial soil organic carbon and release an estimated 40% of global atmospheric CH4 emissions. Contributors to the production of CH4 are methanogenic Archaea through a coupled metabolic dependency of end products released by heterotrophic bacteria within the soil in the absence of O2. To better understand how neighboring bacterial communities can influence methanogenesis, the isolation and physiological characterization of two novel isolates, one Methanoarchaeal isolate and one Acidobacterium isolate identified as QU12MR and R28S, respectively, were targeted in this present study. Co-culture growth in varying temperatures of the QU12MR isolate paired with an isolated Clostridium species labeled R32Q and the R28S isolate were also investigated for possible influences in CH4 production. Phylogenetic analysis of strain QU12MR was observed as a member of genus Methanobacterium sharing 98% identity similar to M. arcticum strain M2 and 99% identity similar to M. uliginosum strain P2St. Phylogenetic analysis of strain R28S was associated with genus Acidicapsa from the phylum Acidobacteria, sharing 97% identity to A. acidisoli strain SK-11 and 96% identity similarity to Occallatibacter savannae strain A2-1c. Bacterial co-culture growth and archaeal CH4 production was present in the five temperature ranges tested. However, bacterial growth and archaeal CH4 production was less than what was observed in pure culture analysis after 21 days of incubation.
ContributorsRamirez, Zeni Elizia (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Roberson, Robert (Thesis advisor) / Wang, Xuan (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Measurements of the response of superconducting nanowire single photon detector (SNSPD) devices to changes in various forms of input power can be used for characterization of the devices and for probing device-level physics. Two niobium nitride (NbN) superconducting nanowires developed for use as SNSPD devices are embedded as the inductive

Measurements of the response of superconducting nanowire single photon detector (SNSPD) devices to changes in various forms of input power can be used for characterization of the devices and for probing device-level physics. Two niobium nitride (NbN) superconducting nanowires developed for use as SNSPD devices are embedded as the inductive (L) component in resonant inductor/capacitor (LC) circuits coupled to a microwave transmission line. The capacitors are low loss commercial chip capacitors which limit the internal quality factor of the resonators to approximately $Qi = 170$. The resonator quality factor, approximately $Qr = 23$, is dominated by the coupling to the feedline and limits the detection bandwidth to on the order of 1MHz. In our experiments with this first generation device, we measure the response of the SNSPD devices to changes in thermal and optical power in both the time domain and the frequency domain. Additionally, we explore the non-linear response of the devices to an applied bias current. For these nanowires, we find that the band-gap energy is $\Delta_0 \approx 1.1$meV and that the density of states at the Fermi energy is $N_0 \sim 10^{10}$/eV/$\mu$m$^3$.

We present the results of experimentation with a superconducting nanowire that can be operated in two detection modes: i) as a kinetic inductance detector (KID) or ii) as a single photon detector (SPD). When operated as a KID mode in linear mode, the detectors are AC-biased with tones at their resonant frequencies of 45.85 and 91.81MHz. When operated as an SPD in Geiger mode, the resonators are DC biased through cryogenic bias tees and each photon produces a sharp voltage step followed by a ringdown signal at the resonant frequency of the detector. We show that a high AC bias in KID mode is inferior for photon counting experiments compared to operation in a DC-biased SPD mode due to the small fraction of time spent near the critical current with an AC bias. We find a photon count rate of $\Gamma_{KID} = 150~$photons/s/mA in a critically biased KID mode and a photon count rate of $\Gamma_{SPD} = 10^6~$photons/s/mA in SPD mode.

This dissertation additionally presents simulations of a DC-biased, frequency-multiplexed readout of SNSPD devices in Advanced Design System (ADS), LTspice, and Sonnet. A multiplexing factor of 100 is achievable with a total count rate of $>5$MHz. This readout could enable a 10000-pixel array for astronomy or quantum communications. Finally, we present a prototype array design based on lumped element components. An early implementation of the array is presented with 16 pixels in the frequency range of 74.9 to 161MHz. We find good agreement between simulation and experimental data in both the time domain and the frequency domain and present modifications for future versions of the array.
ContributorsSchroeder, Edward, Ph.D (Author) / Mauskopf, Philip (Thesis advisor) / Chamberlin, Ralph (Committee member) / Lindsay, Stuart (Committee member) / Newman, Nathan (Committee member) / Easson, Damien (Committee member) / Arizona State University (Publisher)
Created2018