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• 11. [Article] Application of Paleoenvironmental Data for Testing Climate Models and Understanding Past and Future Climate Variations

  Paleo data-model comparison is the process of comparing output from model simulations of past periods with paleoenvironmental data. It enables us to understand both the paleoclimate mechanism and responses ...

  Citation × Citation Citation Abstract Copy Title: Application of Paleoenvironmental Data for Testing Climate Models and Understanding Past and Future Climate Variations Author: Izumi, Kenji Year: 2014 Paleo data-model comparison is the process of comparing output from model simulations of past periods with paleoenvironmental data. It enables us to understand both the paleoclimate mechanism and responses of the earth environment to the climate and to evaluate how models work. This dissertation has two parts that each involve the development and application of approaches for data-model comparisons. In part 1, which is focused on the understanding of both past and future climatic changes/variations, I compare paleoclimate and historical simulations with future climate projections exploiting the fact that climate-model configurations are exactly the same in the paleo and future simulations in the Coupled Model Intercomparison Project Phase 5. In practice, I investigated large-scale temperature responses (land-ocean contrast, high-latitude amplification, and change in temperature seasonality) in paleo and future simulations, found broadly consistent relationships across the climate states, and validated the responses using modern observations and paleoclimate reconstructions. Furthermore, I examined the possibility that a small set of common mechanisms controls the large-scale temperature responses using a simple energy-balance model to decompose the temperature changes shown in warm and cold climate simulations and found that the clear-sky longwave downward radiation is a key control of the robust responses. In part 2, I applied the equilibrium terrestrial biosphere models, BIOME4 and BIOME5 (developed from BIOME4 herein), for reconstructing paleoclimate. I applied inverse modeling through the iterative forward-modeling (IMIFM) approach that uses the North American vegetation data to infer the mid-Holocene (MH, 6000 years ago) and the Last Glacial Maximum (LGM, 21,000 years ago) climates that control vegetation distributions. The IMIFM approach has the potential to provide more accurate quantitative climate estimates from pollen records than statistical approaches. Reconstructed North American MH and LGM climate anomaly patterns are coherent and consistent between variables and between BIOME4 and BIOME5, and these patterns are also consistent with previous data synthesis. This dissertation includes previously published and unpublished coauthored material. Title: Application of Paleoenvironmental Data for Testing Climate Models and Understanding Past and Future Climate Variations Author: Izumi, Kenji Year: 2014 Paleo data-model comparison is the process of comparing output from model simulations of past periods with paleoenvironmental data. It enables us to understand both the paleoclimate mechanism and responses of the earth environment to the climate and to evaluate how models work. This dissertation has two parts that each involve the development and application of approaches for data-model comparisons. In part 1, which is focused on the understanding of both past and future climatic changes/variations, I compare paleoclimate and historical simulations with future climate projections exploiting the fact that climate-model configurations are exactly the same in the paleo and future simulations in the Coupled Model Intercomparison Project Phase 5. In practice, I investigated large-scale temperature responses (land-ocean contrast, high-latitude amplification, and change in temperature seasonality) in paleo and future simulations, found broadly consistent relationships across the climate states, and validated the responses using modern observations and paleoclimate reconstructions. Furthermore, I examined the possibility that a small set of common mechanisms controls the large-scale temperature responses using a simple energy-balance model to decompose the temperature changes shown in warm and cold climate simulations and found that the clear-sky longwave downward radiation is a key control of the robust responses. In part 2, I applied the equilibrium terrestrial biosphere models, BIOME4 and BIOME5 (developed from BIOME4 herein), for reconstructing paleoclimate. I applied inverse modeling through the iterative forward-modeling (IMIFM) approach that uses the North American vegetation data to infer the mid-Holocene (MH, 6000 years ago) and the Last Glacial Maximum (LGM, 21,000 years ago) climates that control vegetation distributions. The IMIFM approach has the potential to provide more accurate quantitative climate estimates from pollen records than statistical approaches. Reconstructed North American MH and LGM climate anomaly patterns are coherent and consistent between variables and between BIOME4 and BIOME5, and these patterns are also consistent with previous data synthesis. This dissertation includes previously published and unpublished coauthored material. Close

• 12. [Article] Synthesis, Characterization, and Electrical Properties of ([SnSe]1+δ)m(NbSe2)3 Ferecrystalline Compounds

  29 pages. A thesis presented to the Department of Chemistry and Biochemistry, and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor ...

  Citation × Citation Citation Abstract Copy Title: Synthesis, Characterization, and Electrical Properties of ([SnSe]1+δ)m(NbSe2)3 Ferecrystalline Compounds Author: Ta, Phuong Kim Year: 2015 29 pages. A thesis presented to the Department of Chemistry and Biochemistry, and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Title: Synthesis, Characterization, and Electrical Properties of ([SnSe]1+δ)m(NbSe2)3 Ferecrystalline Compounds Author: Ta, Phuong Kim Year: 2015 29 pages. A thesis presented to the Department of Chemistry and Biochemistry, and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2015. Close

• 13. [Article] DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION

  36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION Author: McIntosh, Hanna Year: 2016 36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Title: DROSOPHILA SUZUKII DEVELOPMENT & ATTRACTION Author: McIntosh, Hanna Year: 2016 36 pages. A thesis presented to the Department of Environmental Science and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Close

• 14. [Article] Electron spin resonance and molecular motion of the RCH2CHCOOR' radicals in X‑irradiated ester‑urea inclusion compounds

  13 pages

  Citation × Citation Citation Abstract Copy Title: Electron spin resonance and molecular motion of the RCH2CHCOOR' radicals in X‑irradiated ester‑urea inclusion compounds Author: Griffith, O. H. Year: 2016, 1964 13 pages Title: Electron spin resonance and molecular motion of the RCH2CHCOOR' radicals in X‑irradiated ester‑urea inclusion compounds Author: Griffith, O. H. Year: 2016, 1964 13 pages Close

• 15. [Article] The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary

  133 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring ...

  Citation × Citation Citation Abstract Copy Title: The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary Author: Dorning, Sandra Lynn Year: 2017 133 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Title: The Ecology and Demography of the Invasive Ascidian Botrylloides violaceus in the Coos Estuary Author: Dorning, Sandra Lynn Year: 2017 133 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Close

• 16. [Article] Soil-Climate Feedbacks: Understanding the Controls and Ecosystem Responses of the Carbon Cycle Under a Changing Climate

  Soil organic matter (SOM) decomposition and formation is an important climate feedback, with the potential to amplify or offset climate forcing. To understand the fate of soil carbon (C) stores and fluxes ...

  Citation × Citation Citation Abstract Copy Title: Soil-Climate Feedbacks: Understanding the Controls and Ecosystem Responses of the Carbon Cycle Under a Changing Climate Author: Reynolds, Lorien Year: 2016 Soil organic matter (SOM) decomposition and formation is an important climate feedback, with the potential to amplify or offset climate forcing. To understand the fate of soil carbon (C) stores and fluxes (i.e., soil respiration) under future climate it is necessary to investigate responses across spatial and temporal scales, from the ecosystem to the molecular level, from diurnal to decadal trends. Moreover, it is important to question the assumptions and paradigms that underlie apparently paradoxical evidence to reveal the true nature of soil-climate feedbacks. My dissertation includes research into the response of soil respiration in Pacific Northwest prairies to warming and wetting along a natural regional climate gradient (Chapter II), and then delves deeper into the mechanisms underlying SOM decomposition and formation, examining the temperature sensitivity of SOM decomposition of prairie soils that were experimentally warmed for ~2 yr, and a forest soil in which litter-inputs were manipulation for 20 yr (Chapter III), and finally testing soil C cycling dynamics, including mineral-associated C pools, decomposition dynamics, and the molecular nature of SOM itself, under litter-manipulation in order to understand the controls on SOM formation and mineralization (Chapter IV). This dissertation includes previously published and unpublished coauthored material; see the individual chapters for a list of co-authors, and description of contributions. Title: Soil-Climate Feedbacks: Understanding the Controls and Ecosystem Responses of the Carbon Cycle Under a Changing Climate Author: Reynolds, Lorien Year: 2016 Soil organic matter (SOM) decomposition and formation is an important climate feedback, with the potential to amplify or offset climate forcing. To understand the fate of soil carbon (C) stores and fluxes (i.e., soil respiration) under future climate it is necessary to investigate responses across spatial and temporal scales, from the ecosystem to the molecular level, from diurnal to decadal trends. Moreover, it is important to question the assumptions and paradigms that underlie apparently paradoxical evidence to reveal the true nature of soil-climate feedbacks. My dissertation includes research into the response of soil respiration in Pacific Northwest prairies to warming and wetting along a natural regional climate gradient (Chapter II), and then delves deeper into the mechanisms underlying SOM decomposition and formation, examining the temperature sensitivity of SOM decomposition of prairie soils that were experimentally warmed for ~2 yr, and a forest soil in which litter-inputs were manipulation for 20 yr (Chapter III), and finally testing soil C cycling dynamics, including mineral-associated C pools, decomposition dynamics, and the molecular nature of SOM itself, under litter-manipulation in order to understand the controls on SOM formation and mineralization (Chapter IV). This dissertation includes previously published and unpublished coauthored material; see the individual chapters for a list of co-authors, and description of contributions. Close

• 17. [Article] EFFECTS OF ACUTE PASSIVE HEAT EXPOSURE

  42 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, ...

  Citation × Citation Citation Abstract Copy Title: EFFECTS OF ACUTE PASSIVE HEAT EXPOSURE Author: Harris, Sarianne Year: 2016 42 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Title: EFFECTS OF ACUTE PASSIVE HEAT EXPOSURE Author: Harris, Sarianne Year: 2016 42 pages. A thesis presented to the Department of Human Physiology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2016. Close

• 18. [Article] Fractal Electrodes for Interfacing Neurons to Retinal Implants

  With life expectancy on the rise, age-related ailments are a significant strain on the welfare of individuals and the economy. Progress is being made towards combating the leading cause of unavoidable ...

  Citation × Citation Citation Abstract Copy Title: Fractal Electrodes for Interfacing Neurons to Retinal Implants Author: Montgomery, Rick Year: 2015 With life expectancy on the rise, age-related ailments are a significant strain on the welfare of individuals and the economy. Progress is being made towards combating the leading cause of unavoidable blindness, age-related macular degeneration (AMD). AMD affects ten million Americans and costs the world economy $343 billion annually. Retinal implants promise to restore sight by replacing the eye's damaged photoreceptors with electronic photodiodes. Clinical trials succeed at restoring some vision, but are limited by the stimulating electrodes. We study the electrode-neuron interface with a focus on the geometrical dependence of the electrode. The functionality of neurons is intimately connected to their branching and curving shape, described by fractal geometry. We examine the morphology of neurons using fractal analysis. The results inform our electrode designs, which are fabricated using top-down lithographic and bottom-up self-assembly techniques. A novel technique for fabricating a fractal electrode is presented. Heating and cooling a film of poly(methyl methacrylate) on a SiO2 substrate causes fractal structures to form on the surface. The geometry of the structures is temperature dependent, producing crystalline branches at lower temperatures and diffusion-limited aggregates at higher temperatures. Subsequent deposition of antimony nanoclusters shows preferred diffusion to the fractal surface features. The dependence of a photodiode's performance on its top contact geometry is explored using modified nodal analysis. The results reinforce the need to balance a low mean semiconductor-metal separation distance with an adequate contact width for low resistance, all while maximizing light input. Future designs will benefit from the spatial voltage maps produced by the simulation. The electric field emanating from an electrode is also dependent on the geometry of the electrode. The Faraday cage effect is exploited to achieve similar electric field responses to traditional electrode shapes. A preliminary study of neural adhesion to SU-8 fractal electrodes is promising. The neuron grows along the electrode even at 90° turns. The role the fractal geometry plays in neuron and electrode functionality is shown to be significant. Continued study of, and experimentation with, new electrode designs is sure to produce exciting possibilities in the future. This dissertation includes previously unpublished co-authored material. Title: Fractal Electrodes for Interfacing Neurons to Retinal Implants Author: Montgomery, Rick Year: 2015 With life expectancy on the rise, age-related ailments are a significant strain on the welfare of individuals and the economy. Progress is being made towards combating the leading cause of unavoidable blindness, age-related macular degeneration (AMD). AMD affects ten million Americans and costs the world economy $343 billion annually. Retinal implants promise to restore sight by replacing the eye's damaged photoreceptors with electronic photodiodes. Clinical trials succeed at restoring some vision, but are limited by the stimulating electrodes. We study the electrode-neuron interface with a focus on the geometrical dependence of the electrode. The functionality of neurons is intimately connected to their branching and curving shape, described by fractal geometry. We examine the morphology of neurons using fractal analysis. The results inform our electrode designs, which are fabricated using top-down lithographic and bottom-up self-assembly techniques. A novel technique for fabricating a fractal electrode is presented. Heating and cooling a film of poly(methyl methacrylate) on a SiO2 substrate causes fractal structures to form on the surface. The geometry of the structures is temperature dependent, producing crystalline branches at lower temperatures and diffusion-limited aggregates at higher temperatures. Subsequent deposition of antimony nanoclusters shows preferred diffusion to the fractal surface features. The dependence of a photodiode's performance on its top contact geometry is explored using modified nodal analysis. The results reinforce the need to balance a low mean semiconductor-metal separation distance with an adequate contact width for low resistance, all while maximizing light input. Future designs will benefit from the spatial voltage maps produced by the simulation. The electric field emanating from an electrode is also dependent on the geometry of the electrode. The Faraday cage effect is exploited to achieve similar electric field responses to traditional electrode shapes. A preliminary study of neural adhesion to SU-8 fractal electrodes is promising. The neuron grows along the electrode even at 90° turns. The role the fractal geometry plays in neuron and electrode functionality is shown to be significant. Continued study of, and experimentation with, new electrode designs is sure to produce exciting possibilities in the future. This dissertation includes previously unpublished co-authored material. Close

• 19. [Article] METAL-OXIDE THIN FILMS DEPOSITED FROM AQUEOUS SOLUTIONS: THE ROLE OF CATION/WATER INTERACTIONS

  Metal-oxide thin films are used in a wide variety of electronic devices. Although many techniques have been developed to deposit thin films of metal oxides, there is still a need for alternative cost- ...

  Citation × Citation Citation Abstract Copy Title: METAL-OXIDE THIN FILMS DEPOSITED FROM AQUEOUS SOLUTIONS: THE ROLE OF CATION/WATER INTERACTIONS Author: Plassmeyer, Paul Year: 2017 Metal-oxide thin films are used in a wide variety of electronic devices. Although many techniques have been developed to deposit thin films of metal oxides, there is still a need for alternative cost- and energy-effective deposition methods. Deposition of metal oxide thin films from aqueous solutions of all-inorganic metal salts is a viable method that meets these needs. Although many aqueous-deposited metal-oxide thin films have been successfully incorporated into functioning devices, many of the mechanisms that occur as precursors transition to metal oxides are not well understood. The work presented in this dissertation is primarily concerned with examining the processes that occur as metal oxide thin films form from spin-deposited aqueous precursor solutions with a particular focus on the role of H2O in these processes. Chapter I summarizes methods for thin film deposition, and describes the use of aqueous metal salt solutions as viable precursors for the deposition of metal oxide thin films. Chapter II investigates the precursor chemistry, film-formation processes and properties of LaAlO3 thin films deposited from aqueous precursors. This chapter also serves as general guide to the processes that occur as metal-oxide thin films form from spin-deposited aqueous precursors. Chapters III and IV focus on the effects of H2O(g) during spin-deposition of precursor thin films and during the annealing process in which precursors are converted to metal oxides, respectively. The presence of H2O(g) during spin-deposition has a striking effect on the thickness of the resulting thin films and also affects the elemental gradient and density profiles. During annealing, H2O(g) reduces the temperatures at which counterions are expelled and influences the metal-hydroxide framework formation and its condensation to a metal oxide. The data also indicate that H2O(g) enhances diffusion of gaseous byproducts from within the films. Chapter V focuses on precursor concentration and its impact on the thermal evolution of thin films. The processes involved in the conversion of precursors to metal oxide thin films occur at lower temperatures as precursor concentration decreases. Although this is likely in part due to thickness effects, concentration-dependent precursor speciation may also be involved in lowering the temperatures at which films densify. Title: METAL-OXIDE THIN FILMS DEPOSITED FROM AQUEOUS SOLUTIONS: THE ROLE OF CATION/WATER INTERACTIONS Author: Plassmeyer, Paul Year: 2017 Metal-oxide thin films are used in a wide variety of electronic devices. Although many techniques have been developed to deposit thin films of metal oxides, there is still a need for alternative cost- and energy-effective deposition methods. Deposition of metal oxide thin films from aqueous solutions of all-inorganic metal salts is a viable method that meets these needs. Although many aqueous-deposited metal-oxide thin films have been successfully incorporated into functioning devices, many of the mechanisms that occur as precursors transition to metal oxides are not well understood. The work presented in this dissertation is primarily concerned with examining the processes that occur as metal oxide thin films form from spin-deposited aqueous precursor solutions with a particular focus on the role of H2O in these processes. Chapter I summarizes methods for thin film deposition, and describes the use of aqueous metal salt solutions as viable precursors for the deposition of metal oxide thin films. Chapter II investigates the precursor chemistry, film-formation processes and properties of LaAlO3 thin films deposited from aqueous precursors. This chapter also serves as general guide to the processes that occur as metal-oxide thin films form from spin-deposited aqueous precursors. Chapters III and IV focus on the effects of H2O(g) during spin-deposition of precursor thin films and during the annealing process in which precursors are converted to metal oxides, respectively. The presence of H2O(g) during spin-deposition has a striking effect on the thickness of the resulting thin films and also affects the elemental gradient and density profiles. During annealing, H2O(g) reduces the temperatures at which counterions are expelled and influences the metal-hydroxide framework formation and its condensation to a metal oxide. The data also indicate that H2O(g) enhances diffusion of gaseous byproducts from within the films. Chapter V focuses on precursor concentration and its impact on the thermal evolution of thin films. The processes involved in the conversion of precursors to metal oxide thin films occur at lower temperatures as precursor concentration decreases. Although this is likely in part due to thickness effects, concentration-dependent precursor speciation may also be involved in lowering the temperatures at which films densify. Close

• 20. [Article] Emergent thermodynamics in a system of macroscopic, chaotic surface waves

  The properties of conventional materials are inextricably linked with their molecular composition; to make water flow like wine would require changing its molecular identity. To circumvent this restriction, ...

  Citation × Citation Citation Abstract Copy Title: Emergent thermodynamics in a system of macroscopic, chaotic surface waves Author: Welch, Kyle Year: 2016 The properties of conventional materials are inextricably linked with their molecular composition; to make water flow like wine would require changing its molecular identity. To circumvent this restriction, I have contstructed and characterized a two-dimensional metafluid, so-called because its constitutive dynamics are derived not from atoms and molecules but from macroscopic, chaotic surface waves excited on a vertically agitated fluid. Unlike in conventional fluids, the viscosity and temperature of this metafluid are independantly tunable. Despite this unconventional property, our system is surprisingly consistent with equilibrium thermodynamics, despite being constructed from macroscopic, non-equilibrium elements. As a programmable material, our metafluid represents a new platform on which to study complex phenomena such as self-assembly and pattern formation. We demonstrate one such application in our study of short-chain polymer analogs embedded in our system. Title: Emergent thermodynamics in a system of macroscopic, chaotic surface waves Author: Welch, Kyle Year: 2016 The properties of conventional materials are inextricably linked with their molecular composition; to make water flow like wine would require changing its molecular identity. To circumvent this restriction, I have contstructed and characterized a two-dimensional metafluid, so-called because its constitutive dynamics are derived not from atoms and molecules but from macroscopic, chaotic surface waves excited on a vertically agitated fluid. Unlike in conventional fluids, the viscosity and temperature of this metafluid are independantly tunable. Despite this unconventional property, our system is surprisingly consistent with equilibrium thermodynamics, despite being constructed from macroscopic, non-equilibrium elements. As a programmable material, our metafluid represents a new platform on which to study complex phenomena such as self-assembly and pattern formation. We demonstrate one such application in our study of short-chain polymer analogs embedded in our system. Close