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• 1. [Article] High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models

  The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters ...

  Citation × Citation Citation Abstract Copy Title: High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models Author: Ozog, David Year: 2017 The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods in high performance computing (HPC). However, such massively parallel simulations increasingly require more complicated software to achieve good performance across the vastly diverse ecosystem of modern heterogeneous computer systems. Furthermore, advanced “multi-resolution” methods for modeling atoms and molecules continue to evolve, and scientific software developers struggle to keep up with the hardships involved with building, scaling, and maintaining these coupled code systems. This dissertation describes these challenges facing the computational chemistry community in detail, along with recent solutions and techniques that circumvent some primary obstacles. In particular, I describe several projects and classify them by the 3 primary models used to simulate atoms and molecules: quantum mechanics (QM), molecular mechanics (MM), and coarse-grained (CG) models. Initially, the projects investigate methods for scaling simulations to larger and more relevant chemical applications within the same resolution model of either QM, MM, or CG. However, the grand challenge lies in effectively bridging these scales, both spatially and temporally, to study richer chemical models that go beyond single-scale physics and toward hybrid QM/MM/CG models. This dissertation concludes with an analysis of the state of the art in multiscale computational chemistry, with an eye toward improving developer productivity on upcoming computer architectures, in which we require productive software environments, enhanced support for coupled scientific workflows, useful abstractions to aid with data transfer, adaptive runtime systems, and extreme scalability. This dissertation includes previously published and co-authored material, as well as unpublished co-authored material. Title: High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models Author: Ozog, David Year: 2017 The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods in high performance computing (HPC). However, such massively parallel simulations increasingly require more complicated software to achieve good performance across the vastly diverse ecosystem of modern heterogeneous computer systems. Furthermore, advanced “multi-resolution” methods for modeling atoms and molecules continue to evolve, and scientific software developers struggle to keep up with the hardships involved with building, scaling, and maintaining these coupled code systems. This dissertation describes these challenges facing the computational chemistry community in detail, along with recent solutions and techniques that circumvent some primary obstacles. In particular, I describe several projects and classify them by the 3 primary models used to simulate atoms and molecules: quantum mechanics (QM), molecular mechanics (MM), and coarse-grained (CG) models. Initially, the projects investigate methods for scaling simulations to larger and more relevant chemical applications within the same resolution model of either QM, MM, or CG. However, the grand challenge lies in effectively bridging these scales, both spatially and temporally, to study richer chemical models that go beyond single-scale physics and toward hybrid QM/MM/CG models. This dissertation concludes with an analysis of the state of the art in multiscale computational chemistry, with an eye toward improving developer productivity on upcoming computer architectures, in which we require productive software environments, enhanced support for coupled scientific workflows, useful abstractions to aid with data transfer, adaptive runtime systems, and extreme scalability. This dissertation includes previously published and co-authored material, as well as unpublished co-authored material. Close

• 2. [Article] Enhancing the effectiveness of conservation easements through trust building, partner coordination, and cooperation

  2 pages

  Citation × Citation Citation Abstract Copy Title: Enhancing the effectiveness of conservation easements through trust building, partner coordination, and cooperation Author: University of Oregon. Ecosystem Workforce Program Year: 2016, 2013 2 pages Title: Enhancing the effectiveness of conservation easements through trust building, partner coordination, and cooperation Author: University of Oregon. Ecosystem Workforce Program Year: 2016, 2013 2 pages Close

• 3. [Article] Measuring socioeconomic outcomes of forest and watershed restoration : state of the field

  2 pages

  Citation × Citation Citation Abstract Copy Title: Measuring socioeconomic outcomes of forest and watershed restoration : state of the field Author: Davis, Emily Jane, Moseley, Cassandra, Medley-Daniel, Michelle Year: 2015, 2012 2 pages Title: Measuring socioeconomic outcomes of forest and watershed restoration : state of the field Author: Davis, Emily Jane, Moseley, Cassandra, Medley-Daniel, Michelle Year: 2015, 2012 2 pages Close

• 4. [Article] Cross-trained local capacity for integrated wildfire managment

  2 pages

  Citation × Citation Citation Abstract Copy Title: Cross-trained local capacity for integrated wildfire managment Author: Huber-Stearns, Heidi, Ellison, Autumn, Moseley, Cassandra Year: 2016 2 pages Title: Cross-trained local capacity for integrated wildfire managment Author: Huber-Stearns, Heidi, Ellison, Autumn, Moseley, Cassandra Year: 2016 2 pages Close

• 5. [Article] The Politics of Fire and the Social Impacts of Fire Exclusion on the Klamath

  25 pages

  Citation × Citation Citation Abstract Copy Title: The Politics of Fire and the Social Impacts of Fire Exclusion on the Klamath Author: Norgaard, Kari Year: 2016, 2014 25 pages Title: The Politics of Fire and the Social Impacts of Fire Exclusion on the Klamath Author: Norgaard, Kari Year: 2016, 2014 25 pages Close

• 6. [Article] Promoting fire-adapted communities : the importance of social diversity in the wildland urban interface

  2 pages

  Citation × Citation Citation Abstract Copy Title: Promoting fire-adapted communities : the importance of social diversity in the wildland urban interface Author: Paveglio, Travis, Ellison, Autumn, Abrams, Jesse, Moseley, Cassandra, Carroll, Matthew S. (Matthew Stephen) Year: 2015, 2014 2 pages Title: Promoting fire-adapted communities : the importance of social diversity in the wildland urban interface Author: Paveglio, Travis, Ellison, Autumn, Abrams, Jesse, Moseley, Cassandra, Carroll, Matthew S. (Matthew Stephen) Year: 2015, 2014 2 pages Close

• 7. [Article] Microbial Biodiversity of the Atmosphere

  Microorganisms are critical to the functioning of terrestrial and aquatic ecosystems and may also play a role in the functioning of the atmosphere. However, little is known about the diversity and function ...

  Citation × Citation Citation Abstract Copy Title: Microbial Biodiversity of the Atmosphere Author: Klein, Ann Year: 2016 Microorganisms are critical to the functioning of terrestrial and aquatic ecosystems and may also play a role in the functioning of the atmosphere. However, little is known about the diversity and function of microorganisms in the atmosphere. To investigate the forces driving the assembly of bacterial microbial communities in the atmosphere, I measured temporal variation in bacterial diversity and composition over diurnal and inter-day time scales. Results suggest that bacterial communities in the atmosphere markedly vary over diurnal time scales and are likely structured by inputs from both local terrestrial and long-distance sources. To assess the potential functions of bacteria and fungi in the atmosphere, I characterized total and potentially active communities using both RNA- and DNA-based data. Results suggest there are metabolically active microorganisms in the atmosphere that may affect atmospheric functions including precipitation development and carbon cycling. This dissertation includes previously published and unpublished co-authored material. Title: Microbial Biodiversity of the Atmosphere Author: Klein, Ann Year: 2016 Microorganisms are critical to the functioning of terrestrial and aquatic ecosystems and may also play a role in the functioning of the atmosphere. However, little is known about the diversity and function of microorganisms in the atmosphere. To investigate the forces driving the assembly of bacterial microbial communities in the atmosphere, I measured temporal variation in bacterial diversity and composition over diurnal and inter-day time scales. Results suggest that bacterial communities in the atmosphere markedly vary over diurnal time scales and are likely structured by inputs from both local terrestrial and long-distance sources. To assess the potential functions of bacteria and fungi in the atmosphere, I characterized total and potentially active communities using both RNA- and DNA-based data. Results suggest there are metabolically active microorganisms in the atmosphere that may affect atmospheric functions including precipitation development and carbon cycling. This dissertation includes previously published and unpublished co-authored material. Close

• 8. [Article] A quick guide for incorporating collaboration into the Watershed Condition Framework

  4 pages

  Citation × Citation Citation Abstract Copy Title: A quick guide for incorporating collaboration into the Watershed Condition Framework Author: Moseley, Cassandra, Medley-Daniel, Michelle, Davis, Emily Jane Year: 2016, 2012 4 pages Title: A quick guide for incorporating collaboration into the Watershed Condition Framework Author: Moseley, Cassandra, Medley-Daniel, Michelle, Davis, Emily Jane Year: 2016, 2012 4 pages Close

• 9. [Article] Fire science needs in the Pacific Northwest

  12 pages

  Citation × Citation Citation Abstract Copy Title: Fire science needs in the Pacific Northwest Author: Abrams, Jesse, Creighton, Janean H., Moseley, Cassandra, Olsen, Christine S., Davis, Emily Jane, Pomeroy, Alaina, Hamman, Sarah, Bruce, Josh, Perleberg, Andrew B., DeMeo, Thomas, Evers, Louisa, Fitzgerald, Stephen Arthur Year: 2015, 2011 12 pages Title: Fire science needs in the Pacific Northwest Author: Abrams, Jesse, Creighton, Janean H., Moseley, Cassandra, Olsen, Christine S., Davis, Emily Jane, Pomeroy, Alaina, Hamman, Sarah, Bruce, Josh, Perleberg, Andrew B., DeMeo, Thomas, Evers, Louisa, Fitzgerald, Stephen Arthur Year: 2015, 2011 12 pages Close

• 10. [Article] Forest and watershed restoration in Linn County, Oregon : economic impacts, trends, and recommendations

  28 pages

  Citation × Citation Citation Abstract Copy Title: Forest and watershed restoration in Linn County, Oregon : economic impacts, trends, and recommendations Author: Davis, Emily Jane, White, Eric M., Rishel, Branden, Moseley, Cassandra Year: 2015, 2013 28 pages Title: Forest and watershed restoration in Linn County, Oregon : economic impacts, trends, and recommendations Author: Davis, Emily Jane, White, Eric M., Rishel, Branden, Moseley, Cassandra Year: 2015, 2013 28 pages Close