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.
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.
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.
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.
When the novel coronavirus pandemic hit, the Physics Department, like the rest of Oregon State University, scrambled to get its course offerings ready for remote learning in a few days. Professor David Roundy and his teaching team scrambled as hard as anyone – and incorporated some beginning epidemic modeling into the computational physics class so that the students would begin to acquire the skills that will serve them well as members of the technological community of which they are now junior members.
About the class:
PH366 – Computational Physics – is a course in which students learn how to solve mathematical equations in real-world, complex situations where analytical, “pencil-and-paper” solutions are far too difficult. For example, it’s easy for a student in Introductory Physics to solve a simple differential equation to find a solution in the form of an equation that describes how a ball falls towards the earth under the influence of gravity, a constant force near the earth’s surface. But add extra forces that describe real conditions like air resistance, wind and the earth’s rotation, and a simple equation to describe position as a function of time is impossible. The computer solves the problem numerically, chopping it up into very small time slices and finding a position and velocity for each of the times based on what is was at the previous time. In the PH36x Computational Physics series, students learn techniques to find numerical solutions to many differential equations and they can explore very complex, real-world situations. Roundy has chosen the Python programming language for this class, but the lessons are applicable to any language. In real physics research, few problems are already worked out in a textbook and numerical methods to solve them improve all the time, so the best information is often distributed all over the internet. Physics students must learn to navigate the body of existing literature and identify what information they need to solve a problem.
Another view of the solution shows the difference between displaying results on a linear plot and a logarithmic plot. The logarithmic plot (below) highlights the infection and recovery numbers, which are a small fraction of the overall population and we’d be tempted to ignore the fact that there are hundreds of thousands of sick people if we saw only the linear plot (above).
An example that David Roundy chose for the Spring 2020 Computational Physics course was about the spread of an epidemic, like covid-19. It was all everyone was talking about, and he wanted the students to learn how their new computational skills are at the heart of epidemiological modeling that gives us the information to understand and mitigate the spread of the coronavirus. This isn’t an accurate model, Roundy stresses, but it has valuable elements – start with a simple model, probably unrealistic, test it, make sure it works as expected. Add some complexity, test that, and then proceed. In his easy-to-read description at the PH366 course website, Roundy shows students how to model exponential growth – the increase in number of covid-19 cases is proportional to the number of cases: dI/dt = RI. Then you have to add in the real-world fact that the population is finite (with a doubling time of 1 day, the world human population would be infected in a little over a month). Some people recover and have immunity (we hope), so that must be factored into a more realistic model. More complexity comes in when you consider how long infected people are contagious, and whether there is a period of immunity following recovery.
Actually, the problem is not too hard to set up – it’s the solution that becomes tedious. That’s the beauty of computers is that they don’t care about tedium. They swiftly toil through tedious calculations without becoming bored or tired and their error rate is effectively zero! The humans have to set up the problem correctly, though, otherwise the results are meaningless. And this is the skill that Roundy teaches his students. The screenshots below show an example of the students’ work in PH366, with the by-now-familiar plot of an exponential rise in infections at the start, with a peak and fall. We see the basic recovery and death trends, too.
Screenshot of a student’s model of infections, recoveries and deaths due to an infectious disease
Another view of the solution shows the difference between displaying results on a linear plot and a logarithmic plot. The logarithmic plot (below) highlights the infection and recovery numbers, which are a small fraction of the overall population and we’d be tempted to ignore the fact that there are hundreds of thousands of sick people if we saw only the linear plot (above).
Linear and log plots emphasize different details
Julian Wulf, one of the Physics majors currently in PH 366 commented, “My favorite part of the class is how it allowed me to model physical situations that were too complex to picture, or model by hand. I have found it quite rewarding to finish coding something and have it modeled in front of me, a model that is often easy to adjust to new circumstances.” It’s easy to see how Julian would relish the challenge of modeling a much more complicated solution that factored in even more complexity such as social contact and real transmission rates.
Teaching in the age of coronavirus:
To deliver PH366, David Roundy goes into Weniger Hall by himself every Tuesday and Thursday and turns on some 20 computers with separate Zoom sessions running (see the panorama view below). The 40 students and the 4 TAs (teaching assistants) log in from their remote locations. The students implement Roundy’s “pair programming” strategy where they decide how to solve the problem and code in pairs, each providing the crucial check on the other to ensure that the steps make sense. They constantly question their results, and look up techniques to improve their code and to interpret the results. It’s a real-world programmer situation! Roundy and the teaching assistants hop between the Zoom breakout rooms to discuss with each pair of students how to troubleshoot and debug their code. It wasn’t easy for the instructors to change their mode of operation from in-person to remote learning. TA Elena Wennstrom comments, “At the beginning, our TA meetings were devoted to brainstorming possible class formats, testing the limits of our Zoom powers, and discussing issues and possible improvements to the class we had the day before. Now we are more able to focus on the content, and trying out the assignments ourselves (like usual). I’m really proud of the system we’ve developed. Classes go surprisingly smoothly, and the time flies.” Wennstrom adds that she gets more and better questions from the students in the remote mode. Roundy remarks that he will offer this new mode of teaching to students with seasonal influenza in “normal” times to help curb the spread of that particular virus.
A panoramic view of the computers in the PH366 classroom in Weniger Hall
The students’ response:
The students agree. Julian Wulf says, “I think the transition to remote learning has mostly gone smoothly. There has been a rapid increase in how well things are being communicated remotely, as well as an increasing ability of the teaching assistants and professor to respond to difficulties we encounter while programming. I find myself looking forward to the continued improvement as each class has run more smoothly than the last, with the teaching assistants and Professor Roundy being increasingly able to react to difficulties people encounter by jumping in and out of Zoom breakout rooms to help.”
As “newbie programmer”, Wulf feels that the pair programming method helped him get over an initial fear of programming, and that he has learned to appreciate how quickly he learns to solve new problems. He found the disease and epidemic modeling project interesting, intellectually stimulating and fun.
Wulf says that the coding skills he is developing will be useful in the future, and that they have already entirely changed his perspective. He now routinely plots equations in Mathematica to visualize a physical situation, and his new skills make the task “pain-free” and fun rather than being as a dreaded chore.
Former Physics major John Waczak, now a graduate student in Physics at the University of Texas at Dallas, offers similar observations about the Computational Physics series. He says that Computational Physics is an incredibly powerful tool for building physics understanding and to tackle problems that are otherwise unsolvable. It also enables him to create detailed visualizations of just about anything, and those visualizations don’t have to be static! Computers makes it possible to manipulate 2-, 3-, and even 4-dimensional data and create animations. “I have been using this skill a lot lately to visualize results in my [graduate] classes,” he says. Waczak further appreciates that PH36x made him an autodidact. “Dr. Roundy encouraged us to become familiar with the documentation and common programming forums like Stack Exchange. Instead of giving us working code to start with, we had to learn how to diagnose bugs and navigate the wide variety of (often incorrect) answers that exist online.” This meant that he became better programmer (and physicist). “I certainly do not know all of the tools and features that exist in the python programming language. What I do understand is how to evaluate the credibility of a resource and how to extract what’s important from the large body of existing information.”
David Roundy is an Associate Professor of Physics at Oregon State University, and has been teaching and researching at OSU since 2006. His work in computational physics spans exotic superconductors, metal-organic frameworks, classical and quantum density functional theory, biological motor proteins and many other topics. He invented the Darcs version control software. He is a member of the Paradigms in Physics team with significant funding from the National Science Foundation for education-related research focusing on thermal physics and computational physics.
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.
Undergraduate volunteers from the Department of Physics presented kid-friendly demonstrations last week at the 2020 Family Science Night at Franklin School, Corvallis.
The activities and demonstrations focused on mechanical phenomena: Marbles racing down tracks, carts on a frictionless rail, a chain fountain, and weight lifting with pulleys and double pulleys. In addition to mechanics, there were some new demos related to the physics of air included a curve-ball demonstration with paper cups, and a cloud in bottle.
Many thanks to our undergraduate volunteers Steve Nieman, Ryan French, Stephanie Keyes, and Genevieve Connolly, and faculty mentors Weihong Qiu and Ethan Minot.
Physics will attend several more Family Science Nights at local schools in the upcoming weeks.
With departmental funding and an SPS travel grant, undergraduate student Acacia Patterson attended PhysCon, the 2019 Physics Congress, in Providence, Rhode Island 11/14-11/16. Over 1000 people attended the conference, which is hosted by the jointly by Sigma Pi Sigma and the Society of Physics Students and has occurred every 4 years since 1928. A group of OSU students attended the last conference in San Francisco, California.
Acacia Patterson at PhysCon 2019
The 2019 Congress began with tours at Harvard, MIT, and Brown physics departments and at Optikos Corporation, Woods Hole Oceanographic Institute, Naval Submarine Base New London, and Rhode Island Hospital. The conference included speeches on the work of Einstein and Eddington from Dame S. Jocelyn Bell-Burnett and on the projects of GoogleX and how physics majors can prepare for a career in industry from Sandeep Giri. In addition, there were talks on the use of disruptive technology to mitigate climate change from Ellen Williams, on intellectual property rights from Jami Valentine Miller, and on the Big Bang and the future of astronomy from John Mather. Finally, Jim Gates shared a talk on how to use physics to become like Indiana Jones. A Congress workshop was held in which students brainstormed solutions to the issues that they and their organizations face.
The most important issues which the conference identified were imposter syndrome, mental health, and inclusiveness in physics. Two breakout sessions were offered with topics including science policy and communication, physics careers, physics and astronomy outreach, inclusivity, climate change, and graduate student panels.
Acacia, who is a member of Janet Tate’s research group, was among the 150 students who presented their research during two poster and art exhibit sessions. Other activities included a lunch with scientists, a demo show at Brown and a tour at the LADD Observatory, a game night with Brown’s SPS chapter, and career and graduate school fairs. Acacia is grateful for this rewarding experience and looks forward to bringing what she learned to OSU.
Physics research isn’t just for Physics majors. Biophysicist Weihong Qiu hosts students from BioHealth Sciences and Biochemistry in his lab as well.
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:
In January 2019, undergraduate students McKenzie Meyer, Austin Mullins, Acacia Patterson, Elena Wennstrom and Kasey Yoke, accompanied by graduate students Mackenzie Lenz and Nicole Quist, participated in the Conference for Undergraduate Women in Physics (CUWiP) at the University of Washington. The conference is a venue for students to share their research, to hear from successful women in physics, to learn about graduate school and employment, and to meet other physicists. The participants heard from keynote speaker Dr. Fabiola Gianotti of CERN, and others who discussed their careers and addressed the barriers to the success of women and minorities in STEM. The group also toured condensed matter labs in UW’s physics department and labs at the Center for Experimental Nuclear Physics and Astrophysics, which are interested in dark matter, accelerator physics, nuclear physics, and gravity. During the “Physics Slam,” faculty members competed to deliver the most entertaining presentation of their research, and one of the many attendees to present posters was OSU’s Kasey Yoke who authored “Validation of Anti-Neutrino Data from the MINERvA Experiment at Fermilab” co-authored by physics department head Dr. Heidi Schellman. The group also heard from a career panel highlighting the diverse employment opportunities for physicists, and they had the opportunity to meet with representatives of employers in small groups. The participants attended sessions including those on impostor syndrome, applying and succeeding in graduate school, participating in undergraduate research, applying to jobs in the industry, and writing in science. This annual conference is open to all undergraduate physics majors and proved to be an invaluable experience for the attendees. There are several venues around the country where the CUWiP conferences are held simultaneously. OSU hosted the Pacific Northwest CUWiP conference in 2016 and in 2020, the Pacific Northwest CUWiP will be at Washington State University.
Undergraduate volunteers from the Department of Physics presented kid-friendly demonstrations at the annual Family Science Night at Franklin School, Corvallis, on January 24th.
The hands-on demonstrations focused on the electromagnetic spectrum, from invisible infra-red wavelengths to ultra-violet wavelengths, and everything in between. With an infra-red camera, kids could see through black plastic bags and discover warm hand prints on the table, and show their parents the heat leaks in a model house. At the other end of the spectrum, kids played with fluorescent markers and brought their artwork to life in a UV light box.
Many thanks to our undergraduate volunteers Rosemary Williams, Garrett Jepson, Christian Wood and Hunter Nelson.
Physics will attend several more Family Science Nights at local schools in the upcoming weeks.
