• Modeling the injection of CO₂-N₂ in gas hydrates to recover methane using CMG STARS

      Oza, Shruti; Patil, Shirish; Dandekar, Abhijit; Khataniar, Santanu; Zhang, Yin (2015-08)
      The objective of this project was to develop a reservoir simulation model using CMG STARS for gas hydrates to simulate the Ignik Sikumi#1 field trial performed by ConocoPhillips at the North Slope, Alaska in 2013. The modeling efforts were focused exclusively on the injection of CO₂-N₂ in gas hydrate deposits to recover methane after an endothermic reaction. The model was history matched with the available production data from the field trial. Sensitivity analysis on hydrate saturation, intrinsic permeability, relative permeability curves, and hydrate zone size was done to determine the impact on the production. This was followed by checking the technical feasibility of the reservoir model for a long-term production of 360 days. This study describes the details of the reservoir simulation modeling concepts for gas hydrate reservoirs using CMG STARS, the impact on the long term production profile, and challenges and development schemes for future work. The results show that appropriate gas mixture can be successfully injected into hydrate bearing reservoir. The reservoir heat exchange was favorable, mitigating concerns for well bore freezing. It can be stated that CO₂-CH₄ exchange can be accomplished in hydrate reservoir although the extent is not yet known since the production declined for long term production period during forecasting study.
    • Modeling the interaction between hydraulic and natural fractures using three dimensional finite element analysis

      Nikam, Aditya Balasaheb; Awoleke, Obadare; Ahmadi, Mohabbat; Dandekar, Abhijit; Chen, Gang; Ahn, Il Sang (2016-08)
      Natural fractures are present in almost every formation and their size and density definitely affect the hydraulic fracturing job. Some of the analysis done in the past shed light on hydraulic fracture (HF) and natural fracture (NF) geometries. The interaction of the HF with existing NF in a formation results in a denser fracture network. The volume of rock covering this fracture network is called the stimulated reservoir volume (SRV). This SRV governs the hydrocarbon production and the ultimate revenue generation. Moreover, past studies show that a microseismic interpreted SRV can be different than the actual SRV. Additionally, there is always limited subsurface access, which makes it imperative to understand the HF – NF interaction to plan and execute a successful hydraulic fracturing job. A three layered, three dimensional complex geomechanical model is built using commercially available finite element analysis (FEA) software. A propagating HF approaching mainly orthogonal NF is studied and analyzed. Cohesive pore pressure elements in FEA software capable of modeling fluid continuity at HF – NF intersection are used to model the HF – NF interaction. Furthermore, a detailed sensitivity analysis considering the effect of stress contrast, job design parameters, NF properties, and properties of the formation is conducted. The sensitivity analysis of properties such as principal horizontal stress contrast, job design parameters, NF properties and properties of target formation reveals a broad variation in the impact of the sensitivity parameters on the HF, NF, and HF-NF geometry and interaction. The observations and the corresponding conclusions were based on broadly classified sensitivity parameters. The most important parameters solely for HF resultant geometry are observed to be a high stress contrast with stress reversal, highest injection rate, and farther NF distance from the injection point. The least important parameter is observed to be the scenario with almost equal horizontal stresses. However, the most important parameter solely for resulting NF geometry is only the high stress contrast with stress reversal. Conversely, for the considered sensitivity cases, the least important parameters are the injection rate, lower injection viscosity (10 cP), higher NF leak-off coefficient, target formation thickness, Young’s modulus, and lowest value of target formation Poisson’s ratio. Collective conclusions for considering HF-NF are also obtained.
    • Modeling the natural freezeback of piles using COMSOL Multiphysics®

      Clausen, Elliot D.; Peterson, Rorik; Shur, Yuri; Perkins, Robert (2017-05)
      Slurried pile foundations installed in predrilled holes are one of the most common foundations for building major structures on permafrost. This installation method relies on the cold permafrost to freeze the backfilled slurry around the piles to provide the strength required to support loads of a structure. Nearly all evaluations of freezeback time to date stems from the work of Frederick Crory presented to the First International Conference on Permafrost in 1963 and published in 1966. Crory never published field data but he provided an equation to determine freezeback time. This work was later expanded upon by G.H. Johnston in 1981 however Johnston gives no explanation for how or why he varied from what Crory had done. The purpose of this research is to check the results predicted by both Crory and Johnston with a contemporary computer modeling using COMSOL ® Multiphysics. Due to the advancement in technology and the power of COMSOL as a program more variables and situations will be able to be examined than what was available to Crory or Johnston at the times of their publications. This will be the first research in over 50 years to revise the work first published by Crory and show that his equation produces results that are significantly shorter than what the model calculates.
    • Modeling the Thermal Balance Between Groundwater Springs and River Ice

      Jones, Chas; Kielland, Knut; Hinzman, Larry (2012-12)
      We modeled the thermal balance between groundwater discharge and ice-free areas in the Tanana River near Fairbanks, Alaska, a region that is characterized by discontinuous permafrost. Under degrading permafrost conditions, these areas have been hypothesized to have increased winter discharge due to increasing contributions from groundwater flow. In the winter, interior Alaskan rivers are fed almost entirely by groundwater, which also serves as an external source of heat energy to the system. Several reaches of the river fed by groundwater springs remain ice-free or have dangerously thin ice throughout the winter despite air temperatures that dip below -40° C. These areas are dangerous for winter travelers who regularly use Alaskan rivers for wintertime travel. Our model allows us to explore the relationship between seasonal groundwater flows and ice thickness under changing atmospheric conditions. Our model results explore how local and regional changes in groundwater flow can affect ice thickness by addressing two primary research questions: 1) What physical factors influence seasonal ice dynamics on the Tanana River? 2) How is the thermal balance maintained between changing groundwater flow and cold air temperatures?
    • Modeling volcanic ash and sulfur dioxide with the Weather Research Forecasting with Chemistry (WRF-Chem) model

      Egan, Sean D.; Cahill, Catherine; Stuefer, Martin; Webley, Peter; Lopez, Taryn; Simpson, William (2019-12)
      The Weather Research Forecasting with Chemistry (WRF-Chem) model is capable of modeling volcanic emissions of ash, sulfur dioxide and water vapor. Here, it is applied to eruptions from three volcanoes: the 2008 eruption of Kasatochi Volcano in Alaska, the 2010 eruption of Eyjafjallajökull in Iceland and the 2019 eruption of Raikoke in the Kurile Islands. WRF-Chem's ability to model volcanic emissions dispersion is validated through comparison of model output to remote sensing, in situ and field measurements. A sensitivity of the model to modeled plume height is discussed. This work also modifies the base WRF-Chem code in three ways and studies the effects of these modifications. First, volcanic ash aggregation parameterizations are added covering three modes of particle collisions through Brownian motion, differential settling and shear. Second, water vapor emissions from volcanic eruptions are added and coupled to the new aggregation scheme. The effects of these changes are assessed and found to produce volcanic ash concentrations in agreement with in situ measurements of plume concentrations and field measurements of tephra fallout. Third, the model is adapted to include multiple model initializations such that each is perturbed by selecting between two volcanic ash particle sizes and five initial plume heights. This modified WRF-Chem is nested in an application program interface that enables a new, automated, near real-time capability. This capability is assessed and the feasibility of its use as an augmenting tool to current operational VATD models is commented upon.
    • Modeling winter severity and harvest of moose: impacts of nutrition and predation

      Carroll, Cameron Jewett; Doak, Patricia; Kielland, Knut; Seaton, Kalin A. K.; Chapin, F. Stuart (2013-12)
      Climate change is expected to have both positive and negative impacts on northern ungulate populations. Moose (Alces alces) will likely benefit from an increase in the growing season length and frequency of wildfire. However, increases in extreme weather events may result in moose population declines, particularly for nutritionally stressed moose populations. Management strategies to reduce the nutritional stress of populations may become increasingly important. We used stage-structured population models to examine the impact of deep-snow events on moose population trajectories and evaluated female harvest strategies designed to mitigate nutritional stress by decreasing intraspecific competition. Population trajectories were primarily influenced by young adult and prime adult survival. Populations held at low density by predation are likely buffered against the effects of severe weather events, whereas nutritionally stressed populations are vulnerable to population declines from the same environmental conditions. Harvest of cow-calf pairs may be an effective way to maximize harvestable yield and maintain population resilience when nutritional condition is poor. Moose population abundance over the long-term may become more variable due to the effects of climate change. Future modeling needs to incorporate alternative harvest and climate scenarios to help us better understand how we can promote moose population resilience.
    • Modelling investigation of interaction between Arctic sea ice and storms: insights from case studies and climatological hindcast simulations

      Semenov, Alexander; Zhang, Xiangdong; Bhatt, Uma; Hutchings, Jennifer; Mölders, Nicole (2019-05)
      The goal of this study is to improve understanding of atmosphere, sea ice, and ocean interactions in the context of Arctic storm activities. The reduction of Arctic sea ice extent, increase in ocean water temperatures, and changes of atmospheric circulation have been manifested in the Arctic Ocean along with the large surface air temperature increase during recent decades. All of these changes may change the way in which atmosphere, sea ice, and ocean interact, which may in turn feedback to Arctic surface air warming. To achieve the goal, we employed an integrative approach including analysis of modeling simulation results and conducting specifically designed model sensitivity experiments. The novelty of this study is linking synoptic scale storms to large-scale changes in sea ice and atmospheric circulation. The models were used in this study range from the regional fully coupled Arctic climate model HIRHAM-NAOSIM to the ocean-sea ice component model of the Community Earth System Model CESM and the Weather Research and Forecasting (WRF) model. Analysis of HIRHAM-NAOSIM simulation outputs shows regionally dependent variability of storm count with a higher number of storms over the Atlantic side than over the Pacific side. High-resolution simulations also reproduce higher number of storms than lower resolution reanalysis dataset. This is because the high-resolution model may capture more shallow and small size storms. As an integrated consequence, the composite analysis shows that more numerous intense storms produce low-pressure systems centered over the Barents-Kara-Laptev seas and the Chukchi-East Siberian seas, leading to anomalous cyclonic circulation over the Atlantic Arctic Ocean and Pacific Arctic Ocean. Correspondingly, anomalous sea ice transport occurs, enhancing sea ice outflow out of the Barents-Kara-Laptev sea ice and weakening sea ice inflow into the Chukchi-Beaufort seas from the thick ice area north of the Canadian Archipelago. This change in sea ice transport causes a decrease in sea ice concentration and thickness in these two areas. However, energy budget analysis exhibits a decrease in downward net sea ice heat fluxes, reducing sea ice melt, when more numerous intense storms occur. This decrease could be attributed to increased cloudiness and destabilized atmospheric boundary layer associated with intense storms, which can result in a decrease in downward shortwave radiation and an increase in upward turbulent heat fluxes. The sea ice-ocean component CICE-POP of Community Earth System Model (CESM) was used to conduct sensitivity experiment to examine impacts of two selected storms on sea ice. CICE-POP is generally able to simulate the observed spatial distribution of the Arctic sea-ice concentration, thickness, and motion, and interannual variability of the Arctic sea ice area for the period 1979 to 2011. However, some biases still exit, including overestimated sea-ice drift speeds, particularly in the Transpolar Drift Stream, and overestimated sea-ice concentration in the Atlantic Arctic but slightly underestimated sea ice concentration in the Pacific Arctic. Analysis of CICE-POP sensitivity experiments suggests that dynamic forcing associated with the storms plays more important driving role in causing sea ice changes than thermodynamics does in the case of storm in March 2011, while both thermodynamic and dynamic forcings have comparable impacts on sea ice decrease in the case of the August 2012. In case of March 2011 storm, increased surface winds caused the reduction of sea ice area in the Barents and Kara Seas by forcing sea ice to move eastward. Sea ice reduction was primarily driven by mechanical processes rather than ice melting. On the contrary, the case study of August 2012 storm, that occurred during the Arctic summer, exemplified the case of equal contribution of mechanical sea ice redistribution of sea ice in the Chukchi - East Siberian - Beaufort seas and melt in sea ice reduction. To understand the impacts of the changed Arctic environment on storm dynamics, we carried out WRF model simulations for a selected Arctic storm that occurred in March 2011. Model output highlight the importance of both increased surface turbulent heat fluxes due to sea ice retreat and self-enhanced warm and moist air advection from the North Atlantic into the Arctic. These external forcing factor and internal dynamic process sustain and even strengthen atmospheric baroclinicity, supporting the storm to develop and intensify. Additional sensitivity experiments further suggest that latent heat release resulting from condensation/precipitation within the storm enhances baroclinicity aloft and, in turn, causes a re-intensification of the storm from its decaying phase.
    • Moderators of bicultural self-efficacy and mental health among Asian Americans

      Shah, Dhara; David, E.J.R.; Lopez, Ellen; Campbell, Kendra; Buckingham, Sarah (2019-08)
      The relationship between acculturation and mental health among Asian Americans has been established. For example, the integration strategy, often associated with bicultural competence, has been shown to positively predict well-being and self-esteem, and negatively predict various indicators of distress (Nguyen, Messe, & Stollak, 1999; Oh, Koeske, & Sales, 2002; Yoon, Lee, & Goh, 2008). Further, biculturalism (Chen, Benet-Martinez, & Bond, 2008) and bicultural self-efficacy (David, Okazaki, & Saw, 2009) have been associated with positive mental health outcomes among Asian Americans. That is, perceiving oneself as capable of navigating various domains (e.g., values, behaviors) within two cultures is associated with better mental health. Little is known, however, regarding the factors that may influence the strength of this relationship. Thus, the present study aimed to identify some moderating factors of the relationship between bicultural self-efficacy and mental health among Asian Americans. Considering previous research examining the factors associated with acculturation and mental health (Berry, 1980; Nguyen & Benet-Martinez, 2007; Padilla, 2006), it was hypothesized that bicultural identity integration, cognitive flexibility, psychological flexibility, and resilience would each moderate the relationship between bicultural self-efficacy and satisfaction with life, and between bicultural self-efficacy and psychological distress. Results indicated that bicultural identity integration approached significance, indicating that of all the hypotheses presented in this study, it may be the only moderator of the relationship between bicultural self-efficacy and life satisfaction. Thus, viewing two cultures as compatible may act as a protective factor, or buffer, against the negative effects of low bicultural self-efficacy on some aspects of mental health. Further, the null findings suggest that the relationships between the measured variables may be more complex than simple moderation. It is recommended that future research continue to explore and test moderation and mediation models, while considering alternative measures and specific subscales. Recommended service implications for Asian Americans include interventions geared to increase one's level of bicultural identity integration or bicultural selfefficacy, as well as to encourage systems or communities to provide the appropriate resources needed to do so.
    • MODIS Satellite vegetation indices over partially vegetated pixels on the Arctic Coastal Plain of Alaska

      Macander, Matt (2005-08)
      The performance and response of the MODIS Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) were evaluated over the Arctic coastal plain of Alaska. At the 250-l000-m resolution of moderate resolution sensors, a substantial portion of this landscape is a mixture of vegetated and non-vegetated cover types. Single-date MODIS swath scenes were used because of the higher geolocation accuracy, lack of radiometric artifacts, and temporal specificity. A higher resolution earth cover classification was used to sample pixels with a mixture of vegetation, water, and barren ground. The MODIS NDVI and EVI were compared to aggregated Landsat ETM+ NDVI. The subpixel ETM+ NDVI was a good predictor of the MODIS EVI in all mixed pixels, and of the MODIS NDVI in mixed vegetation and barren ground pixels. In these cases a simple linear relationship between subpixel ETM+ NDVI and the MODIS vegetation indices was observed. In the mixed pixels with vegetation and water, the MODIS NDVI had a curvilinear response to the ETM+ NDVI and the performance decreased as the subpixel water fraction increased. Spectral mixture modeling was then applied to synthesize mixed pixel spectral values and plot the response of the MODIS vegetation indices to subpixel non-vegetated fractions. The MODIS NDVI had a highly variable response to subpixel fractions of different non-vegetated backgrounds, while the MODIS EVI was fairly insensitive to background type. The models also suggest that large changes in observed NDVI values could occur due to changes in the spectral characteristics of the non-vegetated portion of a pixel-in particular, the conversion of ice to water in subpixel water fractions.
    • A modular LoRaWAN inspired Internet of Things approach to collecting sensor data via Software Defined Radio

      Van Cise, Tristan; Genetti, Jon; Lawlor, Orion; Metzgar, Jonathan (2020-05)
      The emergence of simple Internet of Things (IoT) devices has habituated the ability to efficiently collect data and communicate information between devices with ease. Similarly, Software Defined Radio (SDR) has compacted radio communication into a USB dongle capable of receiving radio signals from most radio transmitters. In this approach, the ease of IoT device communication and versatility of SDR data collection and transmission techniques is combined to monitor building thermal decay. The system developed to collect thermal decay data is adapted from the Long Range Wide Area Network (LoRaWAN) IoT architecture and is designed to facilitate variable size collection environments and real-time data visualization. This paper will outline the implementation and capabilities of the collection system and highlight alternate applications and hardware implementations of the underlying framework.
    • Modulating neuronal aging: insights from insulin signaling genes and Alaskan nutraceuticals

      Scerbak, Courtney; Taylor, Barbara; Podlutsky, Andrej; Harris, Michael; Dunlap, Kriya; Driscoll, Monica; Vayndorf, Elena (2016-05)
      While aging impacts most, if not all, living organisms, the molecular mechanisms behind this phenomenon are not completely understood. Here, I aimed to further describe the intricate relationship between genetics and diet in aging, focusing on touch receptor neuron aging processes in the model nematode, Caenorhabditis elegans. I specifically tested the hypotheses that (1) age-related touch receptor neuron morphological changes are associated with whole organism health, (2) intrinsic (i.e. genetic) and extrinsic (i.e. nutritional) factors can influence these morphological changes, and (3) specific cellular signaling processes underlie these morphological changes. To this end, this dissertation has three components: (1) the impact of insulin signaling disruption on neuron morphology and protein aggregation in a model of Huntington’s Disease; (2) establishment of Alaskan nutraceutical treatments that extend lifespan and offset age-related decline in neuron and whole organism health; and (3) description of mechanisms driving Alaskan nutraceutical treatment effects using RNA sequencing to target subsequent experiments. In all three of these components, I measured markers of whole organism health (e.g. lifespan, motility, endogenous reactive oxygen species) and markers of touch receptor neuron health (e.g. neuron morphology, mechanosensation). Together, this dissertation demonstrated that lifespan-extending interventions (e.g. decreased insulin signaling, Alaskan nutraceutical treatments) improved mechanosensation and, interestingly, differentially modulated development of age-related neuron morphological changes. That beneficial treatments increased the occurrence of posterior neuron process branching and/or decreased the occurrence of several anterior cell soma morphologies (e.g. soma outgrowths) suggests that some morphologies are representative of successful defense of the cell against age-related deterioration, while others are markers of cellular dysfunction. These results support the idea that multiple cellular signaling pathways are involved in aging of touch receptor neurons, and thus, there are multiple mechanisms for promoting health with age at the cellular level.
    • Modulation of ischemia- reperfusion injury in mammalian hibernators and non-hibernators: a comparative study

      Bhowmick, Saurav; Drew, Kelly L.; Kuhn, Thomas B.; Duffy, Lawrence K.; Oliver, Scott R. (2017-12)
      Events characterized by ischemia/reperfusion (I/R), such as stroke and cardiac arrest, are among the most frequent causes of debilitating neurological injury and death worldwide. During ischemia, the brain experiences oxygen and nutrition deprivation due to lack of blood flow, and tissue damage ensues. Arctic ground squirrel (AGS; Urocitellus parryii), a hibernating species has the innate ability to survive profound decreases in blood flow (ischemia) during torpor and return of blood flow (reperfusion) during intermittent euthermic periods without any neurological deficit. However, the mechanisms by which AGS tolerate the extreme fluctuations in blood flow remain unclear. The main focus of this thesis is to investigate the modulation of I/R injury in mammalian hibernators and non-hibernators. The first study validates the microperfusion approach for studying in vitro I/R injury (oxygen glucose deprivation, OGD) modeled in acute hippocampal slices and investigates the complex interactions of glutamate-mediated excitotoxicity with acidosis-mediated acidotoxicity to understand the role of acid-sensing ion channels (ASIC1a) and pH in mediating cellular injury during OGD. Using an ischemic tolerant animal model, AGS, the second and third studies explore if hibernation season or state influences tolerance to I/R injury and tests hypotheses regarding mechanisms involving nitric oxide and superoxide radicals in mediating cellular damage during cerebral I/R. Together, this dissertation demonstrates that when OGD is combined with acidosis as occurs in vivo, acidotoxicity mediated via ASIC1a occurs but low pH abolishes NMDAR mediated excitotoxicity. This dissertation also presents evidence that AGS tolerate OGD injury independent of hibernation season and state. At the tissue level, when tissue temperature is normalized to 36°C despite ATP depletion, ionic derangement, tissue acidosis, and excitatory neurotransmitter efflux, AGS hippocampus resists OGD injury. Finally, the dissertation shows that AGS resist brain injury caused by ONOO- generated from NO or O2•− during OGD while rat brain tissue succumbs to this mechanism of injury.
    • Modulation of nicotinic receptors by an allosteric ligand assessed using fast jumps in acetylcholine

      Hirt, Spencer L.; Edmonds, Brian; Duffy, Lawrence; Drew, Kelly (2016-05)
      Properties of ligand-gated ion channels such as α4β2 nicotinic acetylcholine receptors (nAChRs) and their interactions with various pharmacologic compounds have been studied using voltage clamping techniques for decades. The peak current amplitude, measured in whole-cell experiments, gives us an idea of how receptors will respond to a ligand in situ. Some ligands have the potential to potentiate the peak amplitude, by various mechanisms such as destabilization of receptor desensitized states. The ability of a ligand to increase the peak amplitude of α4β2 nAChRs has the potential to treat a variety of neuronal disorders; however unique properties of these receptors such as fast activation and long-lived desensitized states create significant challenges in determining the extent of modulation of the peak current using these techniques. To correctly assess the peak amplitude, the experiment must achieve synchronous activation of all surface receptors by optimizing solution exchange rates. Failure to do so leads to blunted peak-amplitude measurements in acetylcholine (ACh). This study found that previous reports of the modulating effects of desformylflustrabromine (dFBr), a positive allosteric modulator (PAM) of α4β2 nAChRs, neglected to account for the large surface area of Xenopus oocytes and slow solution exchange rates, leading to an artificially large potentiation of the peak current in dFBr. This study utilized cell lines with a relatively small surface area and a high-speed perfusion system to achieve fast solution exchange rates, and found the potentiation of the peak current by dFBr to be ~1.5-fold. Further studies involving PAMs of α4β2 nAChRs should take necessary steps to optimize solution exchange rates to improve accuracy and reproducibility of their results. In addition, analysis of the whole-cell responses of α4β2 nAChRs to dFBr and Ach have lead to new insights on their effect on not only the peak amplitude, but also on the time-to peak, and the steady-state current. On average, we found that dFBr decreased the time-to peak by 38% and increased the steady-state current ~1.5-fold. Further studies should also consider modulation of the steady-state current to be just as, if not more important than the peak amplitude, as this feature may be a better predictor of the therapeutic benefit of PAMs of α4β2 nAChRs.
    • Moisture-Temperature Realtionships in a Sand Due to Outward, Radial Freezing

      Juel, Erling A. (1989-05)
      A "clean" sand is commonly specified as backfill around the evaporator section of thermosyphons designed to maintain the thermal regime of pernnially, frozen, thaw-unstable soils. A series of laboratory tests were performed to determine the magnitude of moisture migration. The test results indicate the moisture migration can result due to outward radial freezing in a nonfrost susceptible sand possessing a low to moderate degree of saturation. Moisture did not migrate when the sand was saturated prior to freezing. The redistribution of moisture changes the thermal properties of the soil system which effects the maximum radius of freezing by desiccating soil at the outermost radius of influence and increasing the degree of saturation around the evaporator. The desiccated soil region will experience an accelerated rate of thaw due to a lower volumetric latent heat of fusion. In addition, the radius of freezing is reduced as moisture migrates towards the evaporator section. These effects warrant additional considerations that must be addressed when designing refrigerated foundations with thermosyphons.
    • Molar size and shape in the estimation of biological affinity: a comparison of relative cusp locations using geometric morphometrics and interlandmark distances

      Kenyhercz, Michael W.; Irish, Joel D.; Druckenmiller, Patrick S.; Hoover, Kara C. (2014-12)
      The study of teeth has been a central tenet in biological anthropology since the inception of the field. Teeth have been previously shown to have a high genetic component. The high heritability of teeth has allowed researchers to use them to answer a myriad of anthropological questions ranging from human origins to modern variation due to microevolution. Traditionally, teeth have been studied either morphologically, through the assignment of nonmetric character states, or metrically, through mesiodistal and buccolingual crown measures. Increasingly, geometric morphometric techniques are being used to answer anthropological questions, especially dentally. However, regardless of analytical technique utilized, the biological affinity of modern U.S. individuals has often been limited to examination under a forensic lens (classification of either American Asian, black, Hispanic, or white) without consideration of parent populations. The current study uses geometric morphometric techniques on human molars for two main goals: 1) to examine biological affinity of each of the four largest population groups in regard to population history; and 2) examine the variation within and among the four modern groups as a means of classification. A total of 1,225 dentitions were digitized. Each of the four modern U.S. groups was compared to possible parental groups via discriminant function analysis (DFA). Additionally affinity was examined using Mahalanobis generalized distances (D²) wherein significance of distances between groups was calculated via permutation tests. Furthermore, the D² values were subjected to principal coordinate analysis, or classical multidimensional scaling, to visualize group similarity and dissimilarity. Each group demonstrated affinity with potential parental groups and geographically similar groups as expected given population histories; however, each was also significantly unique from the comparison groups. The four modern U.S. groups were then compared to one another using the same statistical tests. Total among-group correct classifications ranged from 33.9-55.5%, indicating a greater classification than random chance (25%). These classifications were negatively correlated with the reported intermarriage rates for each group: American whites and blacks have the lowest intermarriage rates, which resulted in the highest correct classifications. Conversely, American Asians and Hispanics have the highest intermarriage rates, which resulted in the lowest total correct classifications. Still, the DFA model created from the modern U.S. sample was able to accurately classify a holdout sample. Lastly, a comparison of the three most abundant groups in the U.S. (black, Hispanic, and white), achieved a total correct classification of 72.3%, which is comparable to other studies focusing on the same populations. Restricted gene flow through sociologically constructed barriers and positive assortative mating are the likely factors in the observed variation.
    • Molecular and morphological perspectives on post-glacial colonization of Clethrionomys rutilus and Clethrionomys gapperi in Southeast Alaska

      Runck, Amy Marie (2001-05)
      Pleistocene events had a significant impact on the geographic distributions of high latitude organisms. Recently deglaciated, Southeast Alaska has been colonized by two species of red-backed voles, clethrionomys rutilus and C. gapperi. With distinct biogeographic histories, post-glacial colonization of C. rutilus and C. gapperi into this region would have occurred by different routes. Variation in the mitochondrial cytochrome b gene, the MYH2 nuclear intron, and the post palatal bridge were assessed to examine phylogeographic patterns of these two species, and a proposed contact zone in southeast Alaska. Low, but consistent, levels of sequence divergence of the cytochrome b gene were found among four endemic populations, which corresponded with the complex topography of southeast Alaska. Asymmetrical introgression of the mitochondrial genome diagnostic of C. rutilus was observed in C. gapperi. Post glacial contact resulting from the retreat of the Cordilleran and Laurentide ice sheets has apparently led to the formation of this hybrid zone.
    • The molecular basis of aerobic metabolic remodeling in threespine stickleback in response to cold acclimation

      Orczewska, Julieanna Inez (2011-05)
      Increases in mitochondrial density during cold acclimation have been documented in many fish species, however the mechanism regulating this process is not understood. The present study sought to characterize metabolic changes in response to cold acclimation and identify how these changes are regulated in oxidative muscle, glycolytic muscle and liver tissue of threespine stickleback, Gasterosteus aculeatus. Fish were warm (20°C) or cold (8°C) acclimated for 9 weeks and harvested during acclimation. Mitochondrial volume density was quantified using transmission electron microscopy and aerobic metabolic capacity assessed by measuring the maximal activity of citrate synthase and cytochrome c oxidase. The molecular mechanism mediating changes in aerobic metabolic capacity were assessed by quantifying transcript levels of aerobic metabolic genes and known regulators of mammalian mitochondrial biogenesis using quantitative real-time PCR. Our results indicate that while the maximal activity of aerobic metabolic enzymes increased in all tissues, mitochondrial biogenesis only occurred in oxidative muscle. Our results also suggest that the time course of metabolic remodeling is tissue specific. Lastly, we identified differences in the magnitude and timing of transcriptional and co-transcriptional activators driving metabolic remodeling between each tissue. These results suggest aerobic metabolic remodeling may be triggered by different stimuli in different tissues.
    • Molecular basis of mitochondrial form and function in the hearts of antarctic notothenioids that vary in the expression of hemoglobin and myoglobin

      Urschel, Matthew R. (2008-08)
      Antarctic icefish (suborder Notothenioidei, family Channichthyidae) do not express hemoglobin (Hb), and 6 of the 16 members of this family do not express myoglobin (Mb) in their cardiac muscle. The loss of Hb and Mb correlates with an increase in mitochondrial volume density, a decrease in the mitochondrial surface-to-volume ratio and a decrease in the surface density of inner mitochondria) membranes in the hearts of icefishes compared to red-blooded notothenioids. We sought to understand the molecular mechanisms that regulate differences in mitochondrial density and morphology among the hearts of the notothenioids Notothenia coriiceps (+Hb/+Mb), Gobionotothen gibberifrons (+Hb/+Mb), Chaenocephalus aceratus ( -Hb/-Mb) and Chionodraco rastrospinosus ( -Hb/+Mb). We also sought to determine if alterations in mitochonmdrial structure affect mitochondrial function. Our results indicate that high mitochondrial densities in icefish hearts may be maintained by a novel pathway of mitochondrial biogenesis leading to an increase in the size, rather than number of mitochondria. The expression of mitofilin, which regulates mitochondrial cristae morphology, correlates with differences in the architecture of inner mitochondrial membranes between C. aceratus and N. coriiceps. Moreover, differences in mitochondrial morphology among hearts of G. gibberifrons, C. rastrospinosus and C. aceratus are associated with differences in oxygen consumption rates of isolated mitochondria.
    • Molecular dynamics simulations to study the effect of fracturing on the efficiency of CH₄ - CO₂ replacement in hydrates

      Akheramka, Aditaya O.; Dandekar, Abhijit; Patil, Shirish; Ahmadi, Mohabbat; Ismail, Ahmed E. (2018-05)
      Feasible techniques for long-term methane production from naturally occurring gas hydrates are being explored in both marine and permafrost geological formations around the world. Most of the deposits are found in low-permeability reservoirs and the economic and efficient exploitation of these is an important issue. One of the techniques gaining momentum in recent years is the replacement of CH₄-hydrates with CO₂-hydrates. Studies have been performed, at both laboratory and field based experimental and simulation scale, to evaluate the feasibility of the in situ mass transfer by injecting CO₂ in gaseous, liquid, supercritical and emulsion form. Although thermodynamically feasible, these processes are limited by reaction kinetics and diffusive transport mechanisms. Increasing the permeability and the available surface area can lead to increased heat, mass and pressure transfer across the reservoir. Fracturing technology has been perfected over the years to provide a solution in such low-permeability reservoirs for surface-dependent processes. This work attempts to understand the effects of fracturing technology on the efficiency of this CH₄-CO₂ replacement process. Simulations are performed at the molecular scale to understand the effect of temperature, initial CO₂ concentration and initial surface area on the amount of CH₄ hydrates dissociated. A fully saturated methane hydrate lattice is subjected to a uniaxial tensile loading to validate the elastic mechanical properties and create a fracture opening for CO₂ injection. The Isothermal Young's modulus was found to be very close to literature values and equal to 8.25 GPa at 270 K. Liquid CO₂ molecules were then injected into an artificial fracture cavity, of known surface area, and the system was equilibrated to reach conditions suitable for CH₄ hydrate dissociation and CO₂ hydrate formation. The author finds that as the simulation progresses, CH₄ molecules are released into the cavity and the presence of CO₂ molecules aids in the rapid formation of CH₄ nanobubbles. These nanobubbles formed in the vicinity of the hydrate/liquid interface and not near the mouth of the cavity. The CO₂ molecules were observed to diffuse into the liquid region and were not a part of the nanobubble. Dissolved gas and water molecules are found to accumulate near the mouth of the cavity in all cases, potentially leading to secondary hydrate formation at longer time scales. Temperatures studied in this work did not have a significant effect on the replacement process. Simulations with varying initial CO₂ concentration, keeping the fracture surface area constant, show that the number of methane molecules released is directly proportional to the initial CO₂ concentration. It was also seen that the number of methane molecules released increases with the increase in the initial surface area available for mass transfer. On comparing the positive effect of the two parameters, the initial CO₂ concentration proved to have greater positive impact on the number of methane molecules released as compared to the surface area. These results provide some insight into the mechanism of combining the two recovery techniques. They lay the groundwork for further work exploring the use of fracturing as a primary kick-off technique prior to CO₂ injection for methane production from hydrates.
    • Molecular evidence of epithelial cell damage caused by iqmik, an Alaska smokeless tobacco mixture

      Dwyer, Gaelen K.; Knall, Cindy; Ferrante, Andrea; McGill, Colin; Johnson, Rhonda; Dunlap, Kriya (2015-08)
      The percentage of Alaska Natives who use smokeless tobacco (SLT) is 4 times that of non-Native Alaskans and 45 times higher for Alaska Native women than non-Native women. The use of SLT is concentrated in Southwest Alaska where 32% of all adult Alaska Natives use SLT. Out of those users, 35% use only iqmik, a unique form of SLT in Alaska, which is a combination of tobacco leaf mixed with Phellinus igniarius (punk fungus). There is little evidence of the pathological effects of iqmik to assist in the development of an evidenced-based intervention regarding the harmful effects of iqmik. The current lack of evidence reinforces a belief that iqmik is less harmful than other tobacco alternatives. The overall objective of this thesis is to elucidate the effect of iqmik and iqmik-mediated metal exposure on oxidative stress and nuclear factor- κB (NF-κB) induced inflammation in human gingival epithelial cells. The central hypothesis of this thesis is that cadmium (Cd), cobalt (Co) and nickel (Ni) accumulate in human gingival epithelial cells from iqmik treatments, inducing oxidative stress and promoting an intracellular environment that alters NF-κB proinflammatory signaling targets. Our findings indicate that iqmik is a greater source of heavy metals, such as Cd, Co and Ni, than air-cured tobacco leaf. Human gingival epithelial cells accumulate more Cd, Co and Ni from the punk ash component of iqmik than from the air-cured tobacco. These metals have the capacity to accumulate in cells from iqmik treatments and generate and propagate the production of endogenous reactive oxygen species (ROS), which activates NF-κB significantly altering its signaling targets, more so than tobacco alone. The results of this thesis identify iqmik as a unique health hazard compared to other tobacco products and enhances our understanding of how iqmik may contribute to oral pathologies.