A UO-led team of researchers spanning physics, neuroscience, molecular biology, ecology and evolution will use a new $325,000 grant to examine aquatic symbioses — the interactions between different animal species living together.
The project is funded by a 30-month award from the Gordon and Betty Moore Foundation and involves the study of zebrafish in controlled ecosystems.
The team will leverage decades’ worth of pioneering research at the UO involving zebrafish and explorations of the gut microbiome, in which vast numbers of microbes contribute to both health and disease in their hosts. UO has been a leader in zebrafish research since the 1960s, when the late biologist George Streisinger established zebrafish as an ideal model for studying human development and disease.
“We aim to develop new tools for studying these symbioses throughout the entire lifespan of zebrafish, which serves as a model aquatic animal and a model for phenomena relevant to all vertebrates, including humans,” said Raghuveer Parthasarathy, an Alec and Kay Keith Professor in the Department of Physics, a member of the UO’s Institute of Molecular Biology and Materials Science Institute, and the principal investigator on the award.
You can read the full Around-the-O article here.
UO physicist Jim Schombert’s research highlighted in Around-the-O
“The distance scale problem, as it is known, is incredibly difficult because the distances to galaxies are vast and the signposts for their distances are faint and hard to calibrate,” he said.
Schombert and colleagues used a new approach, recalibrating a distance-measuring tool known as the baryonic Tully-Fisher relation independently of the Hubble constant. They took the distances of 50 galaxies, as determined in part with help from the Spitzer Space Telescope, and used that hard data to estimate the distances of 95 other galaxies.
For more information, and to get an answer to that question, click here.
We would like to congratulate the following recipients for being selected for the distinguished 2020 Weiser awards:
Senior Teaching Assistant Awards:
First Year Teaching Assistant Awards:
Peer Learning Assistant Award:
Physics Project Class Prize:
Undergraduate Research Prizes:
Doctoral Thesis Prizes:
Weiser Leadership Awards:
You are invited to the
UO Department of Physics
to help celebrate in the achievements
of our graduating class of 2020.
Saturday, June 20th, 2020
Order of events:
10:30am: Physics Department Ceremony
Refer to: https://commencement.uoregon.edu/
Zoom meeting ID: 961 544 1031 https://uoregon.zoom.us/j/9615441031
Due to COVID 19, all events will be held remotely using on-line platforms.
More information and links can be found at https://commencement.uoregon.edu/
We are thrilled to see so many of our Physics students presenting at this year’s Undergraduate Research Symposium.
Mark your calendars: The Symposium YouTube channel will host live-streaming oral and poster presentations beginning at 10 a.m. on May 21.
Time-SPIDER: Characterizing the Electric Field of Pulsed LASERs: Jeremy Guenza-Marcus—Physics and MathFaculty Mentor(s): Brian Smith Session 1: It’s a Science ThingQuantifying precise measurements is critical in any field . Our research focuses on advancing quantum optical methods in the study of metrology . SPIDER is an interferometric approach to characterizing (mathematically describing) ultrashort laser pulses in the frequency domain . Our research aims to develop a sister method to the accepted SPIDER approach, dubbed Time-SPIDER . Its purpose is to use the same approach as SPIDER, but rather in the temporal domain . The procedure is to first develop the theoretical framework, and then set up the experiment . At the moment, our work approaches the issue from a purely theoretical perspective . We find that the Time-SPIDER method is useful as a direct measurement technique for non-ultrashort pulses . Many industry-standard interferometers require an iterative approach to pulse characterization, which may not be well-calibrated if the pulse is not ultrashort . Time-SPIDER solves both of these issues . If we are able to move past the theory and create a working Time-SPIDER, it would be possible to continue with other projects in the lab that may require such set-up . In the grand scheme, Time-SPIDER is a step towards continuing the study of metrology, along with quantum optics itself
Simulation of Bacterial Motion in Sterically Complex Environments: Matthew Kafker—Physics, MathematicsFaculty Mentor(s): Tristan Ursell Session: Prerecorded Poster PresentationMany species of bacteria navigate complex and heterogeneous environments to search for metabolic resources and avoid toxins . Common among such complexities is steric structure—solid objects whose surface curvature alters bacterial trajectories upon impact . In previous experiments, we characterized scattering of bacteria from vertical pillars of different radii, which provides the basis for understanding how impact with a solid, curved object alters bacterial motion . However, it remains poorly understood how multiple interactions affect bacterial trajectories and whether distinct object curvatures or length-scales of separation between steric objects have qualitatively distinct effects on bacterial motion . We address this question using agent-based computer simulations of cells moving within 2D environments . Each environment presents simulated cells with steric objects (i .e .circular pillars) of radius 8 .3μm and a controlled separation between pillars of L μm, where L is a parameter of the simulation . Cells then diffuse through this environment, scattering with pillars they encounter . By measuring the mean squared displacement (MSD) of the ensemble of trajectories in time for different values of L, we are able to quantify precisely how the length-scales of separation between steric structures affect bacterial trajectories . These MSD measurements will also allow us to compare our results with future experimental work . Ultimately, we hope that our results may contribute to a more realistic model of the behavior of motile cells in natural environments such as soils or a mammalian gut.
Visualizing Topocluster Algorithms for the Global Trigger: Sylvia Mason—PhysicsFaculty Mentor(s): Stephanie Majewski Session 5: To the Moon and Back—Relativity MattersThere is a Standard Model of particles and forces that explain the fundamental components of matter . However, this model is incomplete, seeing as we currently understand only about 5% of our universe . The Large Hadron Collider (LHC) is a particle accelerator that collides protons in the hopes of discovering new particles or forces, so that we can learn more about the other 95% of the universe . The LHC will undergo an upgrade in 2026 that will increase its luminosity, meaning there will be anÂ increased number of collisions per second (up to 200 collisions every 25 nanoseconds) .After this upgrade, the ATLAS trigger system will need to reduce the data by a factor of 40 within 10 microseconds, so we will need to sort out the interesting events very fast . Our group is designing an algorithm for implementation in firmware in the “Global Trigger” system for ATLAS to help select these interesting events . My research focuses on creating accurate 3-D visualizations of potential algorithms that cluster energies from particle showers in the ATLAS Calorimeters, and investigation splitting criteria for these clusters . These visualizations will help us understand the details of the performance of these algorithms, which can significantly help us reject background .
Supersymmetric Long Lived Particle Search Using Proton-Proton Collision Data and Simulations from the ATLAS Experiment: Laura Nosler—PhysicsFaculty Mentor(s): Laura Jeanty Session 5: To the Moon and Back—Relativity MattersDespite the wealth of information gained by high energy physics over the past few decades, there are still several fundamental gaps in our understanding of the universe . One theory that may provide answers to some of these questions is supersymmetry, which predicts the existence of new particles .In many variations of supersymmetry, some of these particles are expected to have comparatively longer lifetimes . Our research attempts to optimize searches for long lived particles by studying the properties of their signatures and comparing two different methods of reconstructing the energy missing after a collision, with the goal of understanding how the reconstruction algorithms behave for these new particles . To do this, we compare simulated data from proton-proton collisions detected by the ATLAS experiment at the Large Hadron Collider at CERN reconstructed with these two different algorithms and perform analyses that reveal their differences . The results we have found so far have displayed the differences in the efficiencies of these reconstruction methods in our search, revealing the impact these algorithms will have on our final results and allowing us to improve our sensitivity by tuning our selection routines . The final goal of our experiment is to gain a more comprehensive understanding of how to accurately identify these particles in real data, at which point we will extend our experiment to include non-simulated collision data from the ATLAS experiment.
Characterizing the relationship between bacterial motility and range expansion: Noah Pettinari—PhysicsFaculty Mentor(s): Raghuveer Parthasarathy Session 5: To the Moon and Back—Relativity MattersSelf-propelled organisms were first observed under the microscope over 300 years ago . Since then, great strides have been made in characterizing the mechanisms behind motile behavior in bacteria, but current models relating cellular motility to bulk range expansion have not been rigorously tested . To better characterize the relationship between these micro- and macroscale patterns, our research is focused on the analysis of images collected via light sheet fluorescence microscopy of bacterial cells and macroscopic imaging of range expansion . Preliminary results have suggested disagreements between predicted rates of range expansion and cellular motility . Further data and analysis is needed to confirm these results . These findings may highlight the need for the consideration of spatial structure or the possibility of unknown mechanisms in current models .
Quantifying the spatial morphology of organic films through polarization-dependent imaging: Madelyn Scott—Chemistry, PhysicsFaculty Mentor(s): Kelly Wilson, Cathy WongSession 2: Cells R UsOrganic semiconducting materials are appealing, green alternatives to conventional semiconductors because they can be solution-processed into flexible films . However, solution-processing fabrication methods can be prone to morphological disorder, meaning that crystalline structures in the film exhibit a variety of sizes and shapes . A large degree of morphological disorder inhibits the electronic functionality of a film for use in technological devices . Examining how film morphology varies with different deposition conditions allows us to connect the physical properties of organic semiconducting films to macroscopic perturbations in their formation environments . In this work, we used a homebuilt microscope to image the polarization-dependent absorption of organic films, and developed an image analysis software package to characterize their spatial morphology . A series of pictures are collected of the sample, rotating the polarizer between each image . For every pixel in the image, the absorption signal as a function of polarization angle is fit to a sinusoidal curve . These fits are employed to assign pixels in the image to discrete aggregate domains within the film . Quantitative domain metrics are computed to describe the morphology of the film . Several organic films are produced under different deposition conditions and their resulting morphologies are compared . By better understanding the relationship between deposition conditions and film formation, existing solution-processing techniques can be further controlled and refined to achieve target physical properties in organic semiconducting materials.
Equilibrium Solutions for 2-Dimensional Nonaxisymmetric Disks: Daniel Sellers—PhysicsFaculty Mentor(s): James Imamura Session 5: To the Moon and Back—Relativity MattersIn this study we seek equilibrium solutions for compressible, self-gravitating, 2-dimensional nonaxisymmetric disks . Such structures arise in binary star systems and other systems where tidal forces arise such as in the Earth-moon system . These disks are governed by a Scalar Momentum Equation (SME) and a partial differential equation describing hydrodynamic flow within the disk (Stream Function Equation) . We solve these equations using a self-consistent field approach . At each iterative step, the Stream Function and gravitational potential are approximated at all grid points using Guass-Seidel iteration . These quantities, taken with the SME and appropriate boundary conditions are used to find an updated guess for the density distribution .Guass-Seidel algorithms are applied to the relevant partial differential equations which have been discretized using a finite central-differencing technique . These solvers are implemented in python and verified using analytical solutions for simple cases, such as axisymmetric disks with uniform density . We find that our solvers converge to the analytical solutions over many iterations .Parameters for the overall equilibrium solutions are taken from Andalib’s 1998 Dissertation focused on 2-D self-gravitating systems . Present work is focused on reproducing some of the presented solutions as both a check on our equilibrium solutions and as a starting point for further research .
Vacuum Airship Design With Finite Element Analysis: Daniel Sellers—PhysicsFaculty Mentor(s): Ben McMorran Session: Prerecorded Poster PresentationThe ultimate expression of Archimedes’ principle of buoyancy would be to enclose a vacuum with some structure of less mass than the air displaced by that structure . So far such a craft has never been realized in prototype due to the daunting material and engineering challenges . We propose a novel design for such an airship, using inflatable supports and an Aramid fabric shell, and examine the physical constraints and material requirements using both SolidWorks (SW) Simulation Finite Element Analysis and principles of structural statics .We develop a dynamic simulator (in python) to approximate the shapes formed by thin fabric shell sections under unbalanced pressure loads . The resulting geometries are converted to thin shell SolidWorks models and analyzed . Attempts are made to verify the results, including mesh independence and comparison to empirical stress/strain results performed on similar materials and configurations .Deflection of thin shell sections using material properties of Kevlar Aramid fiber are found to agree qualitatively with the theoretical results of Timeshemko, though actual deflection predicted by SW is marginally smaller than predicted by theory, which in turn only very roughly agrees with the experimental results considered . The tensile stress within the shell models is found to be well within acceptable limits for typical Aramid fibers . Some models for the inflatable support structure currently under development are presented, without results . The advantages and challenges of the Finite Element Method for novel design concepts are briefly discussed .
The SETI Scouts Project: Developing Scientifically Literate Young Women through an Astronomy Destination Camp at Pine Mountain Observatory: Maggie Thompson—PhysicsFaculty Mentor(s): Scott Fisher Session 5: To the Moon and Back—Relativity MattersPine Mountain Observatory (PMO) and the University of Oregon are partnered with the SETI Institute and the Girl Scouts to provide a week-long summer destination camp where 10 Girl Scouts from the US come together to engage in cohort building, outdoor adventuring, and an immersion in STEM programming related to astronomy . This program combines several of the main goals of PMO: undergraduate astronomical research, scientific outreach to public and educational partners, and the development of science literacy in STEM interested groups . The Destination Camp welcomes high-school age Girl Scouts from across the United States to the Observatory, where they learn about astronomy and astronomical research through interactive lessons and close peer mentoring from University of Oregon students . This program has not only educated and inspires the Girl Scouts to continue their interest in STEM careers, but it also provides an opportunity for undergraduate physics students to develop science communication skills through mentoring . Over the two years of the program, PMO has proven to be a great resource for astronomy outreach and research with many of the smaller projects introduced during the camp being replicated by the scout alumni of the program back with their home troops . Additionally, many of these programs can be adapted to other observatories to instill a greater passion for science in the general public.
Confirming the 3-dimensional shape of Asteroid 283 Emma from Observations at Pine Mountain Observatory: Maggie Thompson—PhysicsFaculty Mentor(s): Scott Fisher Session: Prerecorded Poster Presentation To determine the shape of asteroid 283 Emma, we obtained time-resolved photometry of the asteroid on August 28, 2019 from 07:44:24 to 09:27:39 UTC at Pine Mountain Observatory (PMO) . The observations were carried out using the 0 .35m Robbins telescope and a large format CCD camera with a Sloan g filter . The brightness of 283 Emma was calibrated using three standard stars removing the influence of airmass . We found that the brightness changed from mag(g) = 12 .5 to 12 .8 . The light curve (time variation of the brightness) we obtained was consistent with the previous research which determined that the shape of 283 Emma is an ellipsoid . Through the process of data analysis, information on the atmospheric extinction coefficient in the Sloan g-band at the PMO was also obtained, which is useful for other observations at the observatory . The results of our observations give us confidence that we can obtain research-grade data with PMO and that this data can be analyzed by undergraduate students.
Quantification of Point Defects in Perovskite Solar Cells: Nicole Wales—Chemistry and Physics Faculty Mentor(s): Mark Lonergan, Zack CrawfordSession 5: The Bonds that Make UsIn order to improve perovskite solar cell efficiency, it is necessary to minimize defects within the perovskite absorber layer, which may include crystallographic point defects . By understanding how these defects form and contribute to the material’s electronic structure, we will gain insight into routes of Shockley-Read-Hall recombination and associated efficiency loss . Theoretical studies have credited some point defects with the production of energy trap states within the bandgap .As such, we aim to measure and describe the nature and formation of traps in real materials .External quantum efficiency measurements are used to describe a gaussian distribution of traps .Additionally, capacitance techniques are applied with the added advantage of increased sensitivity to the absorber layer . However, capacitance techniques are complicated by the hysteretic perovskite system, which is discussed . The samples used in this study include methylenediammonium dichloride-stabilized alpha-formamidinium lead triiodide, a perovskite with interstitially incorporated chloride .External quantum efficiency measurements showed lower defect densities compared to devices of different compositions, however, one sample did show a small signal with a defect transition energy of 1 .08 ± 0 .01 eV . Findings may point to material suppression of sub-gap defects associated with methylenediammonium dichloride-stabilization compared to alternative compositions . It will be interesting to determine if methylenediammonium dichloride is the source of defect suppression in these samples . To understand how the composition might affect defect states, it will also be necessary to take measurements of other stabilizing agents with different compositions .
Stress reduction and improved solar electricity could someday come together in an unexpected package, and a University of Oregon study suggests that a new design of eye-pleasing, fractal-patterned rooftop solar panels could deliver the goods.
In an open-access study published in the journal PLOS ONE, an eight-member team led by UO physicist Richard Taylor and UO psychologist Margaret Sereno combined the psychology of aesthetics — in this case, the appreciation of beauty seen in nature — and the electrical engineering of solar panel designs.
“Our findings have the potential to address two major challenges of today’s society simultaneously: the critical need for increased clean energy production and the need to reduce escalating stress-induced illnesses,” Taylor said. “Stress currently costs the U.S. economy more than $300 billion annually.”
Taylor has drawn on nature’s fractal geometry for diverse applications, ranging from art authentication to a patented approach to create retinal implants to restore human vision. His collaboration with Sereno now suggests that fractal electrodes in solar panel photodiodes will surpass busbars aesthetically.
The studies drew from biophilia, defined in a hypothesis introduced in 1984 by Harvard University naturalist Edward O. Wilson as “the urge to affiliate with other forms of life.” The current work is the latest in a series of publications by Sereno and Taylor investigating fractal fluency.
You can read the full Around-the-O article here.
Researchers and labs from across the University of Oregon have donated thousands of masks, medical supplies and personal protective equipment items to help local medical providers respond to the COVID-19 pandemic.
The UO Incident Management Team coordinated the campus wide effort to help the Lane County Public Health Division build a stockpile of vital equipment for its COVID-19 (coronavirus) response, addressing local and nationwide concerns that the magnitude of the pandemic could cause shortages in critical medical supplies.
County officials will distribute the donated supplies throughout the region to medical professionals treating COVID-19 patients. Most of the equipment donated by the UO is expected to land at PeaceHealth Sacred Heart Medical Center at Riverbend and McKenzie-Willamette Medical Center.
You can read the full Around-the-O article here.
Given how abundant glass is, a surprising amount remains unknown about the material. One of physics’ great unsolved mysteries is why glass looks and behaves the way it does, which involves characteristics of both liquids and solids.
But a new study from UO physicists Eric Corwin and Andrew Hammond offers an important clue to help researchers crack the glass mystery.
Corwin’s lab conducted one of the first physical experiments to help explain the glass transition, the process when heat physically changes the material from something that is rock-hard to something soft and malleable. It’s a process that is incredibly useful for shaping and molding glass but a perplexing one for physicists, because on a molecular level glass looks like a liquid, but its mechanical properties resemble a solid.
You can read the full article here.
Prof. Richard Taylor’s research is mentioned in The Guardian article on why people should walk in nature in this time of crisis.
If you were in any doubt that it was OK to go outside, while keeping at least two metres away from others, the chief medical officer Chris Whitty told the BBC on Wednesday: “Being outside in the park is a very good thing to do.”
He would know. In the past decade, the scientific evidence that connection with nature has important therapeutic benefits for human mental health has mushroomed. Robust studies from disciplines across the world are demystifying what many intuitively know – that we often feel restored when we spend time in nature.
You can read the full article here.
Tristan Ursell at the University of Oregon, inspired by Kerr and Bohannan’s work, wanted to take it one step further. Although their study had shown that the distribution of organisms was key to the development of rock-paper-scissors, the environments in their experiments didn’t have physical barriers that would prevent the bacteria from moving about. The natural world is nothing like that: Whether a microbe is living on a plant’s roots or snuggled up somewhere in our intestines, its environment is filled with obstructions. Ursell, a biophysicist rather than a microbiologist, decided to create a series of computer models to see how physical obstacles could alter the rock-paper-scissors cycles.
Going into the project, Ursell expected that the obstacles might have minor consequences for the simulation. “I did not anticipate that it would in some cases completely flip over the stability,” he said.
Why Saving Single Species Isn’t Enough
Pitting two species against each other in an open space, for example, typically ended with one replacing the other. But if the landscape in Ursell’s computer model had barriers, both species could often coexist. Meanwhile, three species locked in a rock-paper-scissors game in an open space could coexist by cycling in and out of dominance. Introducing a barrier into their world often led to one species eliminating the others.
You can read the full article here.