The purpose of this study is to determine structure-solvent property relationships in organic photovoltaic polymers, with the overarching goal of increasing the efficiency of organic solar cells (OPVs). OPVs are of great interest due to their flexibility, low environmental impact, and modest cost. Additionally, OPVs can be dissolved in organic solvents and printed using roll-to-roll, high-throughput processing – a feature that lends them a large advantage in the photovoltaic industry. Unfortunately, OPVs fall short within the realm of efficiency; the ~10% efficiency of OPVs can hardly rival the ~40% efficiency of inorganic photovoltaic technology. Improving the efficiency of OPVs is an important obstacle in producing low-area, economically viable solar cells. This project aims to use computational models to study the role of organic solvents in mediating the self-assembly of polythiophenes, a commonly studied class of OPV polymers. These models are generated in GROMACS, a program that uses an empirical potential energy function for the polymer, solvent, and polymer-solvent interactions to predict the molecule’s time-dependent behavior with classical molecular dynamics. In particular, these simulations can predict how physical properties such as the free energy of the polymers change as the torsional angles between monomers are varied throughout the simulation. Moreover, changes in the preferred conformations of the polymer are primarily signified by the lowest free-energy states. If we do discover changes in the preferred conformations of the polymer, simulations can be used to test whether these changes are predominantly due to the solvent or the structure of the polymer. This yields information about the equilibrium and self-assembly of the polymer, which can eventually improve the efficiency of OPVs by allowing more control over the polymer nanostructure during high throughput manufacturing processes such as roll-to-roll printing.

Breaking waves dissipate energy in the form of turbulence and bubbles, and are important to many fundamental processes at the air-sea interface. Breaking waves are also a hazard to safe operations at sea and to the survivability of coastal structures. Recent buoys developed at the Applied Physics Lab are designed to study the dynamics of a breaking wave. The buoys are mounted with a number of instruments, including a camera pointed down at the surface of the water. Until now, there has been no useful, automated method to correlate these images with underwater measurements. Using MATLAB, I have produced an algorithm that analyzes the images taken by SWIFT drifters during deployment. Images with breaking waves and breaking rates during each deployment are outputted. I accomplish this through a ‘scoring’ system combining three image-processing techniques. The images go through brightness detection, searching for the signature white color encountered when a wave breaks, as well as through texture analysis. If the images pass certain thresholds for these analyses, points are awarded to their score. The images then pass through glare detection algorithms that remove points from their score if certain thresholds are met. This provides a method for identifying images, with various levels of certainty, which contain breaking waves. This method of scoring and a system of manual checks minimizes the number of false positives, increasing the algorithm accuracy. This algorithm is starting to be put to use on data sets, adding valuable information to current research at the APL. Much of the current area of study is the mouth of the Columbia River, on the Washington-Oregon border, but these devices have been deployed worldwide, including a study this summer in the Arctic Circle. Studying these breaking waves adds a wealth of information to coastal engineering applications and study of air-sea interactions.

From 1951 to 1981, the Canadian weathership program collected nearly continuous wind and wave observations at Station Papa, a common reference site in the North Pacific. The length of this time series makes it a valuable tool in determining long-term trends and statistics of North Pacific wind and waves. Due to the uncertain quality and poor documentation of the data, extensive cross-referencing and quality control of disparate data sources was performed, leading to the development of a single, high-quality dataset. To verify the accuracy and consistency of the weathership measurements, histograms of wind speed, wave height, and wave period were compared with those from modern wave buoy measurements at Station Papa, taken since 2010. While the wind measurements aligned well with the newer data, the wave observations showed notable biases. These biases are likely due to the outdated method of visually observing waves from the weatherships. A time-series model with an annual oscillation and autoregressive component was fit to the wind measurements. Such a model accurately represents both the seasonal weather cycle and short-term storm pattern at Station Papa. In addition, it was found that the wind and wave statistics were significantly correlated on interannual timescales with the El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO). Quantifying the impacts of these trends has practical implications for predicting future changes in wind and wave climate.

The Society for Ecological Restoration, University of Washington Student Chapter (SER-UW), has for the past several years been restoring a forested site near the North Campus Residence Halls. After years of hard work clearing the area of invasive species, SER-UW has begun an effort to share the site and their ideas of habitat and biodiversity revitalization with the community at the University of Washington. The big question for the group now is, can we turn the restored forest into a community space for use and recreation? As the Design Intern for the group, I am utilizing my background as a Landscape Architecture student to create a design that will activate "new" space, as it was inaccessible prior to invasive species removal, and allow for an exciting interaction with, and interpretation of, a Northwest Forest experience. I have performed as a mediator for SER UW, to turn their ideas and desires for the site into design. I set to work discovering how to establish the site as an interpreted and useable site for the community. I developed drawings, diagrams, a prototype sign, and a site plan, then held a work shop with SER UW to discuss the preliminary design. From there, and through a meeting with the Campus Landscape Architect, I created a fourteen page report including details and guidelines of the site design. The design focuses on programs of community gathering and art, as well as elements implemented to influence interaction with the site. Through our design, SER UW will create a legacy at the Whitman Walk Restoration Site. The site will be sustainable from the active involvement and care of the Whitman Walk through students who grow to appreciate the site and find a sense of belonging there. Whitman Walk will grow a greater understanding of the significance of ecology in its visitors for many years to come.

The purpose of this study is to improve biomass processes that utilize renewable feedstock to produce value added chemicals. While much research has been conducted into biomass processing over the last decade, the conversion to small molecules for production of fuels and value-added chemicals is not economically viable and must be improved. Chemical processing is hindered by the robust structure, composed of cellulose and lignin and its resistance to breakdown, which results in expensive treatment methods. In the last several years, ionic liquids have shown by experiment to dissolve recalcitrant biomass allowing for more efficient chemical conversion. Ionic liquids are a class of solvents composed of ions that are liquid at near room temperature. There are a countless number of solvents considered ionic liquids and many have potential to improve biomass processing. The optimal ionic liquid is unknown, and the determination of one is not inspired by molecular scale design principles. My project focuses on providing fundamental knowledge to understand the dissolution of biomass in ionic liquids by using molecular dynamics (MD) in combination with enhanced sampling techniques. Enhanced sampling allows the efficient exploration of the free energy landscape of a system by modifying MD algorithms and without such methods, MD cannot reasonably make conclusions about the effect of ionic liquids. The enhanced sampling method that I employed in this work is Parallel Tempering Metadynamics which is used to explore the conformational free energy of cellulose oligomers. The conformational free energy of short cellulose chains can provide insight to the mechanism of dissolution and eventually optimize biomass processing.

Forests in the Appalachian Mountains are downwind from coal-fired power plants and other industrial sources in the Midwest, thus forests are exposed to relatively high concentrations of metal pollutants. Despite heightened public concern and tighter regulations to reduce anthropogenic pollutants, spruce-fir forests in the Appalachian Mountains are declining. In previous work at our study site, elevated phytochelatins were correlated with red spruce (Picea rubens) forest decline by altitude. Phytochelatins are metal-binding peptides synthesized from glutathione, from the precursor cysteine. Phytochelatins provide a sensitive and direct indication of metals stress at the cellular level. Metal analysis in soils can reflect historical metals deposition, while lichens can reflect recent deposition. In previous research, we studied metal stress and phytochelatin production in P. rubens from six mountains in the Appalachian Mountains. We found that patterns of foliar uptake and PC production are complex, but appear consistent with induction by Zn and Cd in organic soil. Our current purpose was to collect data along an elevational gradient on Whiteface Mountain, New York to supplement the east-west transect data collected previously and to characterize mycorrhizal fungus communities on sapling and mature tree roots. In recent work, we i) explored elevation patterns in the dominance of mycorrhizal species using PCR, DNA sequencing, and BLAST search; ii) measured Cd, Cu, Hg, Pb, and Zn in organic soil, mineral soil and metals uptake in P. rubens foliage and lichens; and iii) assessed P. rubens phytochelatin, glutathione, and cysteine production in order to monitor ongoing changes in red spruce response to metals deposition. While there was a consistent trend of increasing Pb and Zn with elevation in mineral soils, reflecting historic deposition patterns, there was no evidence for any systematic variation in metals content of foliage with elevation. Phytochelatin and mycorrhizal analyses are ongoing.

Over half of the world’s population lives in urban areas. With that percentage increasing each year, enormous stress is put on the ecological health of freshwater lakes. Moreover, the urban poor are reliant on these resources for recreation and nutrition, while at the same time their health is increasingly threatened by harmful algal blooms caused by cultural eutrophication. Basic water quality monitoring data is sparse for many small lakes in Washington, despite heavy use by the public. Data collected on urban lakes using standard water quality tests are key to understanding how lakes across the country affected by anthropogenic pollution can be restored for public use. This study uses basic water quality monitoring data to determine trophic status of Wapato Lake in Tacoma, Washington. The lake has historic problems with toxic algae blooms, a result of anthropogenic nutrient input. Water samples were collected at various depths using a Niskin bottle for determination of total phosphorus and to visually identify important plankton species, both toxic and beneficial. Other water quality parameters were measured in situ, including Secchi depth and vertical profiles of temperature, specific conductivity, dissolved oxygen, pH, and chlorophyll using a multiparameter water quality probe (HydroLab MS5 or Quanta). Aquatic birds were also counted each visit, as waterfowl were shown to contribute significant nutrients to the lake in a previous study. This year-long study is still in progress. Preliminary results indicate Wapato Lake is a non-stratified lake due to shallow depth, and a very productive lake, with Secchi depth between 1.25 and 2 meters for the duration of the study. In comparison with previous years, data show an increase in maximum total phosphorus concentrations, unchanged productivity as measured by Secchi depth, and a dramatic decrease in waterfowl present around the lake. Recommendations for improvements in water quality will be presented.