Development of an Ultra-Cold Atom Atomic Clock

This thesis presents work on the development of an atomic clock using bosonic potassium (39K and 87Rb) in order to study the role of inter-atom interactions on an atomic time standard. The project designed and constructed an RF circuit and RF antenna to manipulate the internal hyper fine states of the ultra-cold atoms. We developed an optical trap to trap these atoms in a vacuum cell, and performed several tests to check their behavior and measure their temperature. We performed experiments to observe Rabi flopping between the hyper ne states of the atoms. The eventual goal of this project is to create an operational atomic clock and observe the effects of inter-atom interactions

The Atmospheric Impact of Energy and Food Production

Fossil fuel extraction and modern industrial agricultural practices both emit greenhouse gases and pollutants, including methane (CH4), nitrous oxide (N2O), ethane (C2H6), and black carbon (BC). Our understanding of emissions magnitudes, processes that control these emissions, and expected future emissions behavior from these sources and of these important atmospheric compounds have large uncertainty. Accurate, precise measurements made from aircraft can provide essential insights into emissions and their impact on climate and air quality. This thesis presents airborne observations using high-precision spectroscopy of atmospheric greenhouse gases and pollutants to quantify emissions. First, with airborne measurements we assess natural gas flaring efficiency of CH4, C2H6, and BC in the Bakken Shale region of North Dakota. We discover emissions from flares exhibit a heavy-tailed distribution and superemitter behavior with a small number of inefficient flares dominating the total source. This skewed distribution translates to total flaring emissions of CH4 and C2H6 that are 2.5 times higher than if standard flare efficiency is assumed. While we observe a skewed distribution for BC, emissions are lower than previous estimates and there is no significant correlation with CH4 emissions. Next, we describe the development and evaluation of an airborne system using an N2O, CO2, CO, and H2O laser spectrometer. Ambient pressure-related artifacts in the instrument are corrected for with a mass flow-controlled frequent calibration technique to achieve an 88% duty cycle with high precision and accuracy. The resultant flight system represents the current state-of-the-art airborne N2O system. Finally, with this new system and a series of flights, emissions from agricultural activity and fertilizer production are evaluated in the Lower Mississippi River Basin. The quantification of emission rates from two productive fertilizer plants finds good agreement with reported emissions of N2O and CO2, but a large underestimation in CH4, suggesting significant natural gas leakage. We calculate N2O emissions fluxes from cropland using the airborne mass balance technique, a first application of this method for N2O. The impact on emissions by associated factors—crop type, fertilizer application, soil moisture, and soil temperature—is investigated. We find the strongest predictors in a multiple linear regression are soil moisture and crop type. An average early-growing season N2O flux of 1.8 ± 1.4 g N2O-N ha^-1 hr^-1 is quantified for the region. The results demonstrate the ability to evaluate N2O emissions at regional scales from sources with large environmental heterogeneity using airborne observations. This thesis highlights the utility of aircraft measurements for investigating emissions of greenhouse gases and pollutants at varying spatial scales and from diverse sources associated with energy and food production supply chains.PHDApplied PhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/149817/1/agvak_1.pd

Evaluating Cropland N2O Emissions and Fertilizer Plant Greenhouse Gas Emissions With Airborne Observations

Agricultural activity is a significant source of greenhouse gas emissions. The fertilizer production process emits N2O, CO2, and CH4, and fertilized croplands emit N2O. We present continuous airborne observations of these trace gases in the Lower Mississippi River Basin to quantify emissions from both fertilizer plants and croplands during the early growing season. Observed hourly emission rates from two fertilizer plants are compared with reported inventory values, showing agreement for N2O and CO2 emissions but large underestimation in reported CH4 emissions by up to a factor of 100. These CH4 emissions are consistent with loss rates of 0.6–1.2%. We quantify regional emission fluxes (100 km) of N2O using the airborne mass balance technique, a first application for N2O, and explore linkages to controlling processes. Finally, we demonstrate the ability to use airborne measurements to distinguish N2O emission differences between neighboring fields, determining we can distinguish different emission behaviors of regions on the order of 2.5 km2 with emissions differences of approximately 0.026 μmol m−2 s−1. This suggests airborne approaches such as outlined here could be used to evaluate the impact of different agricultural practices at critical field‐size spatial scales.Key PointsReported N2O and CO2 emissions from fertilizer plants agree with observations, but CH4 is underestimated by orders of magnitudeWe demonstrate mass balance quantification of N2O emissions from agriculture at 10–100 km scalesAirborne measurements can observe and quantify N2O emission differences between agricultural fields of ∼2.5 km2Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156438/3/jgrd56401.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156438/2/jgrd5640-sup-0001-Figure_SI-S01.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156438/1/jgrd56401_am.pd

Large Fugitive Methane Emissions From Urban Centers Along the U.S. East Coast

Urban emissions remain an underexamined part of the methane budget. Here we present and interpret aircraft observations of six old and leak‐prone major cities along the East Coast of the United States. We use direct observations of methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), ethane (C2H6), and their correlations to quantify CH4 emissions and attribute to natural gas. We find the five largest cities emit 0.85 (0.63, 1.12) Tg CH4/year, of which 0.75 (0.49, 1.10) Tg CH4/year is attributed to natural gas. Our estimates, which include all thermogenic methane sources including end use, are more than twice that reported in the most recent gridded EPA inventory, which does not include end‐use emissions. These results highlight that current urban inventory estimates of natural gas emissions are substantially low, either due to underestimates of leakage, lack of inclusion of end‐use emissions, or some combination thereof.Plain Language SummaryRecent efforts to quantify fugitive methane associated with the oil and gas sector, with a particular focus on production, have resulted in significant revisions upward of emission estimates. In comparison, however, there has been limited focus on urban methane emissions. Given the volume of gas distributed and used in cities, urban losses can impact national‐level emissions. In this study we use aircraft observations of methane, carbon dioxide, carbon monoxide, and ethane to determine characteristic correlation slopes, enabling quantification of urban methane emissions and attribution to natural gas. We sample nearly 12% of the U.S. population and 4 of the 10 most populous cities, focusing on older, leak‐prone urban centers. Emission estimates are more than twice the total in the U.S. EPA inventory for these regions and are predominantly attributed to fugitive natural gas losses. Current estimates for methane emissions from the natural gas supply chain appear to require revision upward, in part possibly by including end‐use emissions, to account for these urban losses.Key PointsAircraft observations downwind of six major cities along the U.S. East Coast are used to estimate urban methane emissionsObserved urban methane estimates are about twice that reported in the Gridded EPA inventoryMethane emissions from natural gas (including end use) in five cities combined exceeds nationwide emissions estimate from local distributionPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151283/1/grl59329.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151283/2/grl59329_am.pd

Circadian deep sequencing reveals stress-response genes that adopt robust rhythmic expression during aging

Disruption of the circadian clock, which directs rhythmic expression of numerous output genes, accelerates aging. To enquire how the circadian system protects aging organisms, here we compare circadian transcriptomes in heads of young and old Drosophila melanogaster. The core clock and most output genes remained robustly rhythmic in old flies, while others lost rhythmicity with age, resulting in constitutive over- or under-expression. Unexpectedly, we identify a subset of genes that adopted increased or de novo rhythmicity during aging, enriched for stress-response functions. These genes, termed late-life cyclers, were also rhythmically induced in young flies by constant exposure to exogenous oxidative stress, and this upregulation is CLOCK-dependent. We also identify age-onset rhythmicity in several putative primary piRNA transcripts overlapping antisense transposons. Our results suggest that, as organisms age, the circadian system shifts greater regulatory priority to the mitigation of accumulating cellular stress

Fugitive emissions from the Bakken shale illustrate role of shale production in global ethane shift

Ethane is the second most abundant atmospheric hydrocarbon, exerts a strong influence on tropospheric ozone, and reduces the atmosphere’s oxidative capacity. Global observations showed declining ethane abundances from 1984 to 2010, while a regional measurement indicated increasing levels since 2009, with the reason for this subject to speculation. The Bakken shale is an oil and gas‐producing formation centered in North Dakota that experienced a rapid increase in production beginning in 2010. We use airborne data collected over the North Dakota portion of the Bakken shale in 2014 to calculate ethane emissions of 0.23 ± 0.07 (2σ) Tg/yr, equivalent to 1–3% of total global sources. Emissions of this magnitude impact air quality via concurrent increases in tropospheric ozone. This recently developed large ethane source from one location illustrates the key role of shale oil and gas production in rising global ethane levels.Key PointsThe Bakken shale in North Dakota accounted for 1–3% total global ethane emissions in 2014These findings highlight the importance of shale production in global atmospheric ethane shiftThese emissions impact air quality and influence interpretations of recent global methane changesPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142509/1/grl54333.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142509/2/grl54333-sup-0001-2016GL068703-SI.pd

Quantifying atmospheric methane emissions from oil and natural gas production in the Bakken shale region of North Dakota

We present in situ airborne measurements of methane (CH4) and ethane (C2H6) taken aboard a NOAA DHC‐6 Twin Otter research aircraft in May 2014 over the Williston Basin in northwestern North Dakota, a region of rapidly growing oil and natural gas production. The Williston Basin is best known for the Bakken shale formation, from which a significant increase in oil and gas extraction has occurred since 2009. We derive a CH4 emission rate from this region using airborne data by calculating the CH4 enhancement flux through the planetary boundary layer downwind of the region. We calculate CH4 emissions of (36 ± 13), (27 ± 13), (27 ± 12), (27 ± 12), and (25 ± 10) × 103 kg/h from five transects on 3 days in May 2014 downwind of the Bakken shale region of North Dakota. The average emission, (28 ± 5) × 103 kg/h, extrapolates to 0.25 ± 0.05 Tg/yr, which is significantly lower than a previous estimate of CH4 emissions from northwestern North Dakota and southeastern Saskatchewan using satellite remote sensing data. We attribute the majority of CH4 emissions in the region to oil and gas operations in the Bakken based on the similarity between atmospheric C2H6 to CH4 enhancement ratios and the composition of raw natural gas withdrawn from the region.Key PointsCH4 emissions from the Bakken region of North Dakota quantifiedFirst emission estimate using in situ CH4 measurementsCH4 sources dominated by oil‐ and gas‐related activitiesPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/122415/1/jgrd52986.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/122415/2/jgrd52986_am.pd

Reporter Proteins in Whole-Cell Optical Bioreporter Detection Systems, Biosensor Integrations, and Biosensing Applications

Whole-cell, genetically modified bioreporters are designed to emit detectable signals in response to a target analyte or related group of analytes. When integrated with a transducer capable of measuring those signals, a biosensor results that acts as a self-contained analytical system useful in basic and applied environmental, medical, pharmacological, and agricultural sciences. Historically, these devices have focused on signaling proteins such as green fluorescent protein, aequorin, firefly luciferase, and/or bacterial luciferase. The biochemistry and genetic development of these sensor systems as well as the advantages, challenges, and common applications of each one will be discussed