Sept. 29, 2021

Oregon State Physics is leading a Department of Energy Office of Science funded project to design computing and software infrastructure for the DUNE experiment.   DUNE is a future neutrino experiment that will aim a neutrino beam from Fermilab, in Batavia Illinois, at a very large detector in the Homestake mine in Lead, South Dakota.  The experiment is currently under construction with a 5% prototype running at CERN in 2018 and 2022 and the full detector expected in 2029. These experiments generate data at rates of 1-2 GB/sec, or 30 PB/year which must be stored, processed and distributed to over 1,000 scientists worldwide.

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The LBNF neutrino beam traveling (right to left) from Fermilab in Illinois to the Sanford Lab in South Dakota

The project “Essential Computing and Software Development for the DUNE experiment” is funded for 3M$ over 3 years, shared among 4 Universities (Oregon State, Colorado State, Minnesota and Wichita State) and three national laboratories (Argonne National Laboratory, Fermi National Laboratory and Brookhaven National Laboratory). The collaborators will work with colleagues worldwide on advanced data storage systems, high performance computing and databases in support of the DUNE physics mission.  See https://www.dunescience.org/ for more information on the experiment.

PI Heidi Schellman (Oregon State Physics) leads the DUNE computing and software consortium which is responsible for the international DUNE computing project. Physics graduate student Noah Vaughan helps oversee the global grid processing systems that DUNE uses for data reconstruction and simulation and recent graduate Amit Bashyal helped design the DUNE/LBNF beamline.  Graduate student Sean Gilligan is performing a statistical analysis of data transfer patterns to help optimize the design of the worldwide data network.  Postdoc Jake Calcutt recently joined us from Michigan State University and is designing improved methods for producing data analysis samples for the ProtoDUNE experiment at CERN.

One of the major thrusts of the Oregon State project is the design of robust data storage and delivery systems optimized for data integrity and reproducibility.  30 PB/year of data will be distributed worldwide and processed through a complex chain of algorithms. End users need to know the exact provenance of their data –  how was it produced, how was it processed, was any data lost – to ensure scientific reproducibility over the decades that the experiments will run.  Preliminary versions of the data systems have already led to results from the protoDUNE prototype experiments at CERN which are described in https://doi.org/10.1088/1748-0221/15/12/P12004 and https://doi.org/10.1051/epjconf/202024511002.

As an example of this work, three Oregon State Computer Science Majors (Lydia Brynmoor, Zach Lee and Luke Penner) worked with Fermilab scientist Steven Timm on a global monitor for the Rucio storage system shown below. This illustrates test data transfers between compute sites in the US, Brazil and Europe. The dots indicate compute sites in the DUNE compute grid while the lines illustrate test transfers. 

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Data transfer diagram for DUNE data.

Other projects will be a Data Dispatcher which optimizes the delivery of data to CPU’s across the DUNE compute systems and monitoring of data streaming between sites.

Physics students and faculty are well-represented in the College of Science 2020 Summer Undergraduate Research Experience (SURE) Awards. These awards provide 11-week employment in the summer for students, though this year, because of closures during the covid-19 pandemic, the research may have to be stretched out over the academic year.

This year’s physics student awardees are:
Hunter Nelson advised by Tuan Pham (Mathematics)
Rohal Kakepoto advised by Janet Tate
Alan Schultz advised by Hoe Woon Kim (Mathematics)
Alexander van Balderen advised by Liz Gire
Jessica Waymire advised by Matt Graham
Ryan Wong advised by Bo Sun

Students from other departments working with Physics faculty are:
Emily Gemmill, (Biochemistry & Biophysics), advised by Weihong Qiu
Ruben Lopez (BioHealth Sciences) advised by Bo Sun

Congratulations all!

Physics professor Weihong Qiu with Haelyn Epp, a BioHealth Sciences SURE awardee in 2019, in Prof Qiu’s biophysics laboratory at OSU (image from the CoS SURE website).

Three OSU Physics alums are among 2,046 graduate students nationwide to receive the NSF Graduate Research Fellowships Program award that pays stipend and partial tuition for 3 years. Congratulations to all three! See the Impact article from the College of Science for some more details about other College of Science GRFP recipients.

Head shot of Mirek Brandt at Oregon State
Mirek Brandt in 2017

Mirek Brandt (BS in Physics & Mathematics 2018) worked in the Graham group while at Oregon State. His thesis was on The Impact of Crystal Morphology on the Opto-Electronic Properties of Amorphous and Organic Crystalline Materials. He won a Goldwater Scholarship as an undergraduate and then moved on to the University of California at Santa Barbara where he is doing his doctorate in Astrophysics.

Katelyn Chase (BS in Physics 2018) worked in Bo Sun’s biophysics laboratory during her time at OSU and wrote her thesis on Synchronized Cellular Mechanosensing due to External Periodic Driving. She is now a Ph. D. candidate at the Lewis-Sigler Institute for Integrative Genomics at Princeton University, conducting research in the Gitai bacterial biology laboratory, studying cytoskeletal proteins. She is interested in proteins involved in bacterial cell shape formation and maintenance. Her photo shows her in Iceland in January.

Patrick Flynn (BS in Physics and Mathematics, 2018) did his senior thesis project on Localized structures in a diffusive run and tumble model for M. xanthus, as part of the Complex Systems REU at the University of Minnesota with Arnd Scheel (Bo Sun was the local advisor).  Patrick also contributed to the linear solver code for the Monte-Carlo simulations performed in David Roundy’s research group in Physics.  Patrick is now a Ph. D. candidate in the Department of Applied Mathematics at Brown University. He is studying the Euler- and Vlasov-Poisson models appearing in plasma and astrophysics. His NSF GRFP proposal was about answering questions such as the existence and stability of solitary waves, or the existence of solutions containing many interacting solitary waves, for the Euler- and Vlasov-Posson equations.  Patrick says he is “very enthusiastic about being able to address questions that have been partially addressed by the physics community to discover new mathematics, and in turn inform scientific discovery. Of course, my time at Oregon State was very formative in this regard, and I still heavily rely on what I learned in the mathematics and physics programs there. After all, I first learned what a dispersion relation was from David Roundy!” The accompanying picture shows Patrick on the Brown Campus.

See the Impact article from the College of Science for some more details about College of Science GRFP recipients.

Prof. Bo Sun

In December 2019, Associate Prof. Bo Sun received the Richard T. Jones New Investigator Award from the Medical Research Foundation of Oregon for his work on the biophysics of collective behavior in cells.

For more details on the award see the MRF awards site and the longer College of Science IMPACT article about Bo’s work.

And check out his research group at https://sites.google.com/site/biophysicsbosun/ to read about the successes of the large number of graduate and undergraduate students working in his lab.

Congratulations Bo!

Dear Physics community,

The Physics Beavers are studying remotely this quarter.

Oregon State Physics is still operating, although our labs are in standby mode and our teaching is now all remote.   We’re using online channels like Zoom and Slack to maintain our tradition of student interaction in courses.  Students are still working together on problems and the Society of Physics Students  is launching an online game night.  We could not have done this without herculean efforts by faculty and students to create online labs, videos, and sophisticated live classes in 3 weeks.  Grad students are writing new labs and undergraduates are serving as learning assistants in the Virtual Wormhole.  See this video on vectors produced in our Lightboard studio to see what our students see.

On campus, research is on standby. Biophysicists Weihong Qiu and Bo Sun led the Physics effort to collect personal protective equipment (PPE) that Oregon State then donated to Oregon Emergency Management agencies.  https://today.oregonstate.edu/news/oregon-state-collects-nearly-200000-pairs-gloves-other-medical-supplies-covid-19-crisis  But, you can’t grow carbon nanotubes or cancer cell lines at home so on-campus research is now on hold.  In the short run, we can work on writing things up, doing the literature searches we never have time for and analyzing data, but we’re eager to get back to our labs. 

If you are interested in helping students financially in the short term, Oregon State has set up an emergency fund for students in need.  Many students (or their parents) have lost their jobs and are struggling with basics like books, rent,  food and the now vital internet connection. Please consider donating to the Beavers Care fund which is providing emergency funding to OSU students https://app.fundmetric.com/qvRUQF9u4 (You can designate the College of Science) or to the Human Services Resource Center (HSRC) https://studentlife.oregonstate.edu/hsrc which provides food boxes, loaner computers and other emergency supplies for students.  

We’ll be providing updates as things progress. 

Heidi Schellman

Physics research isn’t just for Physics majors. Biophysicist Weihong Qiu hosts students from BioHealth Sciences and Biochemistry in his lab as well.

Haelyn Epp and Weihong Qiu preparing motor protein samples in the lab.

BioHealth student Haelyn Epp used her #SUREScience scholarship to work in a biophysics lab on motor proteins. “My scholarship replaced one of my jobs, [and] allowed me to focus on research in a way I had not been able to,” says Haelyn. Read the full article at:

Prof. Bo Sun has received an NSF CAREER award for his biophysics research. Please look at the longer IMPACT article for details. (And he’s also the 2019 Richard T. Jones New Investigator Award for the Medical Research Foundation of Oregon, more details on that after the ceremony in Portland later this term.)

Jake Jacobs (far right) and his family.

Robert  “Jake” Jacobs has been awarded a NASA Future Investigators in NASA Earth and Space Science and Technology (FINESST) award for 2019 in the competitive Earth Science Division. With this award, he is developing a method to analyze latitudinal circulation utilizing satellite measurements of ocean surface vector winds measured by the QuickSCAT and ASCAT scatterometers. Our objectives are to improve understanding of climatological atmospheric circulation patterns and how surface winds in the tropical Pacific influence El Niño-Southern Oscillation (ENSO) events. Latitudinal circulation plays an important role in weather and climate variability as it shapes where precipitation falls and how heat moves from the equator to polar regions. Improved accuracy of the boundaries between large-scale atmospheric cells can advance our understanding of climate and weather models.

Robert “Jake” Jacobs has been awarded a NASA Future Investigators in NASA Earth and Space Science and Technology (FINESST) award for 2019 in the competitive Earth Science Division.  With this award, he is developing a method to analyze latitudinal circulation utilizing satellite measurements of ocean surface vector winds measured by the QuickSCAT and ASCAT scatterometers.  Our objectives are to improve understanding of climatological atmospheric circulation patterns and how surface winds in the tropical Pacific influence El Niño-Southern Oscillation (ENSO) events.  Latitudinal circulation plays an important role in weather and climate variability as it shapes where precipitation falls and how heat moves from the equator to polar regions.  Improved accuracy of the boundaries between large-scale atmospheric cells can advance our understanding of climate and weather models.

This type of work while exciting is not new, as astronautical projects have been a driving force in Jake’s life. His passion for space has taken him from an undergraduate degree in Aerospace Engineering, from Purdue University, to satellite remote sensing at Oregon State University (OSU) where he is completing a PhD in Physics. Before arriving at OSU, Jake obtained a master’s degree in physics from Eastern Michigan University (EMU). While there, he worked with funds from the NASA Space Grant to develop an ion source that would be used in sputtering experiments to model the solar wind.

Connecting with his advisor, Dr. Larry O’Neill at OSU, has created an excellent partnership, as they bring different strengths to the table.  Dr. O’Neill’s wealth of experience has helped Jake to greatly advance his knowledge of atmospheric and oceanic sciences.  While Jake’s physics and math background have assisted with advancing spatial derivative analysis techniques.  This newest project has combined Jake’s passion for physics and math with a novel astronautical venture. He greatly looks forward to continuing this project with the support of the FINESST Fellowship.

In his limited free time, Jake enjoys reading, hiking, swimming and playing disc golf with his two small children, wife and two dogs.  An extra joy in his life is watching his children grow to love the universe and all its boundless opportunities.  The family also enjoys star gazing, which can be difficult in Oregon, so they use a home star theater system to learn about space, stars and the world above.

Tyler Parsotan
Tyler Parsotan

Tyler Parsotan has been awarded a NASA Future Investigators in NASA Earth and Space Science and Technology (FINESST) award for 2019 in the extremely competitive Astrophysics category. His proposal, titled “Demystifying the Interplay between Explosion Dynamics and Electromagnetic Radiation in Gamma Ray Bursts”, was one of the 11% of selected proposals in this category.

Originally from NY, Tyler is a first generation student. His family is from the Caribbean island nation of Trinidad and Tobago. He acquired a BS in Space Physics from Embry-Riddle Aeronautical University and is now working on a PhD in Physics at Oregon State University.

Tyler is currently a fourth year graduate student working with Dr. Davide Lazzati on understanding the most powerful explosions in the Universe known as Gamma Ray Bursts. These events are so energetic that in the first few seconds of the explosion, they release more energy than our sun will emit in its entire lifetime. Understanding these events allows us to get a better handle on how matter behaves in extreme conditions and may eventually lead to using these Gamma Ray Bursts as tools that can uncover new cosmological truths.

Besides working on his research project, Tyler is the president and co-founder fo the OSU astronomy Club. The club is focused on fostering interest in astronomy at OSU and the community of Corvallis in general. Tyler, with the help of many other undergraduate and graduate students, has hosted the Astronomy Open House events where members fo the public are invited to Weniger Hall to learn about astronomy though interactive demos and rooftop observations. More information regarding OSU Astronomy can be found at: https://physics.oregonstate.edu/astronomy-club

Graduate Student Jihan Kim has won the 2018 Physics Department Graduate Research Award

Jihan Kim in the lab

Jihan Kim works with Prof. Bo Sun on biophysical problems. Jihan’s research focuses on the mechanics of cancer-extra-cellular medium (ECM) interactions, which is one of the major factors dictating the physiology of tumors. This is a particularly fertile ground for interdisciplinary research, as physicists are  trained to analyze forces in complex systems. Jihan takes advantage of his physics knowledge in understanding deep biological questions.

Jihan’s first project is to measure the force exerted by cancer cells in 3D collagen matrices, which simulate a realistic tissue environment. He quickly learned MATLAB programing, and wrote a sophisticated image analysis algorithm to enhance images, and to determine the 3D deformation field caused by cancer cells. After publishing his first paper in PLoS ONE, Jihan noticed that a pair of cancer cells can permanently remodel a collagen matrix by creating a bundle of concentrated collagen fibers between them. He talked to a friend during the APS meeting about the observation, which eventually evolved into a collaborative project published in Nature Communications.

Having studied the forces generated by cancer cells and how these forces modify the cells’ environment, Jihan is working on his latest project. In this project, he studies how the environment direct cancer migration. Once completed, his PhD thesis will have a completed loop indicating the feedback between cancer cells and their physical environment.