YEAR IN REVIEW - 2020
TABLE OF CONTENTS
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A WORD FROM THE DIRECTOR
UNIVERSITY OF MICHIGANâ&#x20AC;&#x2122;S PH.D. IN SCIENTIFIC COMPUTING: A HISTORY OF SUPPORTING RESEARCH THROUGH EDUCATION
RESEARCH SPOTLIGHT: COVID-19 & COMPUTATIONAL SCIENCE
COMPUTATIONAL SCIENTISTS AROUND THE WORLD HELP CITIES OPTIMIZE RESPONSE TO HAZARDOUS EVENTS
MOOC IN PROBLEM SOLVING USING COMPUTATIONAL THINKING
MICDE BY THE NUMBERS
THE MICDE TEAM
new clarity in the public sphere.
A fourth round of funding was awarded through MICDE’s Catalyst Grant program. In this cohort, totaling $240,000, interdisciplinary research teams from across U-M are seeking to catalyze advances in fields ranging from drug discovery and bacterial colonies through complex, turbulent flows, all the way to the origins of galaxies.
A WORD FROM THE DIRECTOR
At the Michigan Institute for Computational Discovery and Engineering we are committed to being the University of Michigan’s primary hub for computational science — widely recognized as the third pillar of scientific inquiry, along with theory and physical experimentation. The Institute brings together researchers from a wide range of disciplines in science and engineering to collaborate on the use of increasingly powerful computational approaches, spurring advances in areas ranging from neuroscience to climate science to cosmology. The past ten months, defined by the COVID-19 pandemic, have presented challenges to the Institute, just as it has to every activity that we engage in as individuals and communities. Nevertheless, MICDE’s core mission and vision remain just as relevant and, as we have seen in regard to the pandemic, the role of computation in navigating the present and charting the future has gained
MICDE’s depth and breadth of innovation in computational science are reflected in our affiliated faculty’s discoveries, groundbreaking ideas and achievements. Our three research centers, focused on Data-Driven Computational Physics, Network-Enabled Computational Science and Scientific Software, drive novel computational frameworks that accelerate and expand scientific discovery while highlighting the breadth and depth of activity in these areas at U-M. The Institute’s faculty, aligned with these centers, continue to attract significant federally funded projects.
intensive research and development in both academia and industry. To date, more than 150 students have graduated from the joint Ph.D. program in Scientific Computing. This program has experienced an explosion of interest, with its enrollment growing by 70% to 137 students within the last year. Separately, nearly 90 students have completed the graduate certificate in Computational Discovery and Engineering. In the past year, MICDE partnered with the U-M Center for Academic Innovation to launch Problem Solving using Computational Thinking, a Massively Open Online Course (MOOC). Targeted at high school and early college students, this MOOC has already drawn more than 1,200 worldwide learners. Computational Discovery is key to understanding the deepest mysteries of our world. In the coming year, MICDE will continue to develop new computational paradigms, with the unique UM brand, that will accelerate and expand scientific discovery and innovative research underlying progress in all aspects of society.
At MICDE, we understand that expertise in computational research methods is crucial to success in a wide range of fields. MICDE offers three MICDE Director, Professor of Mechanical Engineering graduate-level programs and Mathematics aimed at preparing students to MICDE YEAR IN REVIEW 2020 | PAGE excel in computationally
UNIVERSITY OF MICHIGAN’S PH.D. IN SCIENTIFIC COMPUTING: A HISTORY OF SUPPORTING RESEARCH THROUGH EDUCATION Last fall, the University of Michigan’s joint Ph.D. program in Scientific Computing achieved a record enrollment of 137 students. Between 2015, when 15 students were enrolled- mainly from the Colleges of Engineering and Literature, Science and the Arts- and today, the program has witnessed an explosive growth of interest on the part of U-M students. The program now has students enrolled from over 30 departments spanning different schools and colleges.
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Over 130 students graduated from the program in the last 31 years, including 17 students in 2020. This recent popularity is a direct outcome of the dominant role that computation plays in the world today. However, like all exceptionally successful undertakings, it owes a great deal to its past. We reached back more than three decades to piece together the history of the Ph.D. in Scientific Computing at U-M. Read More.
Exceptional Alumni The Ph.D. in Scientific Computing has produced many exceptional alumni. The first student graduated from the program in 1992. A notable achievement within a time when gender balance was barely recognized in the field, two of the first four graduates were women. A majority of the program graduates went on to positions in academia or the National Laboratories, while others transitioned to varied fields in industry or government. These outstanding alumni include Suzanne Weekes, U-M 1995 (Mathematics and Scientific Computing), currently the Associate Dean of Undergraduate Studies, ad interim, and Professor of Mathematical Sciences at Worcester Polytechnic Institute. Prof. Weekes has recently been named SIAM executive director, and started her new role on January 1, 2021. Another alumna, Rona Oran, U-M 2014 (Space Science and Scientific Computing), is a computational plasma physicist at MIT and a member of the NASA team that is designing and planning a mission to the metal asteroid Psyche to be launched in 2022.
Rona Oran, U-M 2014 (Atmospheric, Oceanic and Space Sciences and Scientific Computing), is a computational plasma physicist at MIT and a member of the NASA team that is designing and planning a mission to the metal asteroid Psyche to be launched in 2020.
MICDE is premiering a winter webinar series featuring research talks by students in the Ph.D. in Scientific Computing. The webinars will run on Thursdays from 4-5 pm ET on Zoom. View the full schedule
Suzanne Weekes, U-M 1995 (Mathematics and Scientific Computing), Associate Dean of Undergraduate Studies, ad interim, and Professor of Mathematical Sciences at Worcester Polytechnic Institute.
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27 "Computational science has played a preeminent role in the broad scientific response to the COVID-19 pandemic. The use of modeling and simulations, and the power of high performance computing have delivered solutions faster than ever before." - Mariana Carrasco-Teja MICDE Associate Director, Assistant Research Scientist
COVID-19 & COMPUTATIONAL SCIENCE The COVID-19 pandemic has produced massive amounts of information that require accurate analyses to predict outcomes and design solutions rapidly. It also has required experts from many different backgrounds to rally together in the quest for rapid answers in the race to save lives. Many of the most prominent of these researchers are from U-M, and a significant number of them are computational scientists who addressed questions such as: What measures should be taken to minimize contagion? Is it safe to ride a bus? How are supply and demand chains being affected?
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U-M modeling epidemiologists helping navigate the COVID-19 pandemic The department of Epidemiology at U-M's School of Public Health has a very strong cohort of researchers who work on mathematical modeling of infectious disease dynamics, the analysis of these models, and large scale computer simulations â&#x20AC;&#x201D; all to understand the spread and mitigation of pandemics. Their long-standing experience and deep expertise has ideally positioned them at the leading edge of the scientific response to the COVID-19 pandemic, aiding public authorities in making informed decisions, and the media in producing accurate reports for the general public. Read more
Modeling the transmission of infectious aerosols Inhalation of micron-sized droplets represents the dominant transmission mechanism for influenza and rhinovirus, and recent research shows that it is likely also the case for the novel coronavirus. Improved predictive modeling capabilities for effectively tracking the aerosol paths are key to understanding its transmission. Dr. Aaron M. Lattanzi and Prof. Jesse Capecelatro, from Mechanical Engineering, are tackling this problem by focusing on mathematical modeling of aerosol dispersion. Prof. Capecelatro's research group develops physics-based models Jesse Capecelatro (left) Aaron Lattanzi (right)
and numerical algorithms to leverage supercomputers for prediction and optimization of the complex flows relevant to energy and the environment. This expertise has driven them to help design physics-informed guidelines to minimize the spread of this virus. Read more
Prof. Marisa Eisenberg (left) Prof. Jon Zelner (right)
A testing framework to make informed decisions to fight the COVID-19 pandemic Throughout the COVID-19 pandemic, testing has been central to an integrated, global community response. Accurate, effective and efficient testing leads to early detection and prompts an agile response by public health authorities. Since the early stages of the pandemic, Siqian Shen, Associate Professor of Industrial & Operations Engineering, and MICDE Associate Director, has used her expertise to design pivotal operations research and industrial engineering tools to optimize distribution of resources, including testing kits and facilities. Siqian Shen
Advancement of in-silico methods of drug discovery
Professor Rudy J. Richardson, Dow Professor Emeritus of Toxicology, Professor Emeritus of Environmental Health Sciences, and Associate Professor Emeritus of Neurology is working on in-silico models to identify compounds that bind to human proteins that facilitate entry and/or replication of the SARS-CoV-2 virus. Read more @UM_MICDE
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Beyond COVID-19, the breadth and reach of computational science research in 2020 was visible in every corner of the scientific enterprise. At U-M, our researchers made strides toward simulation-based solutions on multiple fronts.
Modeling and simulation for lung cancer prevention and treatment Lung cancer remains the leading cause of cancer-related mortality in the U.S., and globally, accounting for 1.8 million deaths annually. Many of these deaths are avoidable by the implementation of prevention strategies, including tobacco control policies and lung cancer screening recommendations, and by improvements in lung cancer treatment. In the U.S., these policies have generally been implemented based on the analyses and outcomes of the population as a whole, although data analyses have shown that smoking and lung cancer rates, and access to healthcare and interventions vary significantly by education level, income, race and ethnicity. The Cancer Intervention and Surveillance Modeling Network (CISNET) Lung Working Group (LWG), led by Rafael Meza, Associate Professor of Epidemiology in the School of Public Health, investigate the synergistic impacts of tobacco control policies, lung cancer screening and treatment interventions in the U.S. and in middle-income nations. Read more
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Mathematics and computation flip the script on cancer Mathematics Professor, Trachette Jackson, brings mathematics and computation to the battle against cancer. Working with her colleagues at Michigan Medicine and
Illustrations and animation by Ravi Teja Bandaru, linked article by Anna Megdell
at the University of Chicago, Professor Jackson creates mathematical models for targeted molecular therapeutics. This form of precision medical therapy hones in on the factors that drive the spectrum of disease paths that may develop in individual patients. Prof. Jackson's newly awarded NIH grant, which aims to develop predictive methods for optimizing immunotherapy and targeted molecular therapies, will propel a robust understanding of the mechanisms by which different cancer targeting drugs interact. Ultimately, this research could lead to techniques that combine promising anticancer agents for clinical trials. Read more
Computation powers greenhouse gas mitigation strategies Consistent methods are required to fairly assess a regionâ&#x20AC;&#x2122;s impact on climate change. Two leading reasons for the existence of different accounting systems are the political pressures, and the actual costs of climate change mitigation to local governments. Consensus has grown at the international level, and now, global, environmentally extended multi-regional input-output (EE-MRIO) models have been constructed that capture the interdependence of regional emissions and their environmental impacts. However in China, with the largest greenhouse gas emissions of any country, this information is sporadic and inconsistent. This is notwithstanding expertsâ&#x20AC;&#x2122; judgment that accurate interregional trade-related emission accounts are critical in developing mitigation strategies and monitoring progress at the regional level in that country. Prof. Ming Xu from the School of Environment and Sustainability, and his research group, has analyzed the available data from China dating back to 2012. Read more
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Since 2017, the Michigan Institute for Computational Discovery and Engineering Catalyst Grants program has funded a wide spectrum of cutting-edge research that combines natural science, engineering, mathematics and computer science. This year the program funded four new projects that continue this tradition. Prof. Aaron Towne's (Mechanical Engineering) project is advancing the modeling of complex, turbulent flows and other large-scale systems in engineering science. His research will enable orders of magnitude of acceleration in the computation of extremely large scale flows in a number of engineering systems.
Prof. Oleg Gnedin (Astronomy) is developing novel techniques to tailor the mathematical initial conditions from which to simulate chosen regions of the universe. The resulting insights will help uncover the origins of our own galaxy, the Milky Way.
â&#x20AC;&#x153;These four projects have the potential to catalyze and reorient the directions of their research fields by developing and harnessing powerful paradigms of computational scienceâ&#x20AC;? -Krishna Garikipati, MICDE Director, Professor of Mechanical Engineering, and Mathematics
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“MICDE’s mission is to lead advances in computational science research by bringing together interdisciplinary teams at U-M, and these projects embody that vision.” - Krishna Garikipati, MICDE Director
Prof. Marisa Eisenberg (Epidemiology, Mathematics, and Complex Systems) and Prof. Alexander Rickard’s (Epidemiology) groups are developing novel computational techniques to study biofilm architectures. Biofilms are complex assemblages of microbial cells that form on almost any natural and man-made surface. They cause several debilitating diseases, and can even damage machinery and equipment, elevating the understanding of their behaviour to a critical need. Prof. Aaron Frank (Chemistry) and his group are spearheading efficient strategies to rapidly develop treatments for emerging diseases– a need made more compelling by the current COVID-19 Pandemic. Their approach combines generative artificial intelligence models and molecular docking to rapidly explore the space of chemical structures and generate target-specific virtual libraries for drug discovery.
2021 REQUEST FOR PRE-PROPOSALS Due March 5, 2021
The 2021 Request for Catalyst Grants Pre-proposals is seeking to advance the following research areas: Artificial Intelligence for physically-based biomedicine Quantum computing Convergence of natural hazards (hurricanes, earthquakes, pandemics, slowly evolving climate change) with economic dislocation Computation integrating across levels of organization and disciplines in biology However, all aspects of computational science remain of broad interest. To learn more please visit micde.umich.edu/catalyst MICDE YEAR IN REVIEW 2020 | PAGE 11
Across six continents, scientists use computation to optimize cities' responses to hazardous events
Sherif El-Tawil Antoine E. Naaman Collegiate Professor, Department of Civil and Environmental Engineering, organizer of the workshop in Resilient Cities through Computation
"Community resilience is a manifestation of the human trait of adaptation. A resilient community is able to withstand and recover from hazardous events with minimal disruption to its way of life."
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Community resilience is a manifestation of the human trait of adaptation. A resilient community is able to withstand and recover from hazardous events with minimal disruption to its way of life. As humans, we seek to use our ability to engineer to adapt to the threat of natural hazards. The science behind resilience engineering involves many disciplines, each dedicated to a subset of the overall problem. Complex issues lie at the intersection of these subsets, but interdisciplinary research is difficult to achieve because researchers in various disciplines frame problems and perform research from different perspectives and along distinct paths. However, computational models are well established in each discipline, and provide a natural language that links the disciplines together.
Last fall, the Michigan Institute for Computational Discovery and Engineering and the department of Civil and Environmental Engineering brought together established leaders, and some of the most innovative rising scholars in the computational hazards research, to present and discuss different computational approaches used in modeling, assessing, and defining standards for community resilience.
address questions from the audience of nearly 250 realtime participants from 30 countries, across 6 continents.
"The applications discussed in this workshop demonstrated how a single tool can bring together multiple computational dialects to create a single language."
The speakers included representatives from leading research centers in the field: keynote speaker, Terri McAllister, from the National Institute of Standards and Technology (NIST); John van de Lindt (Colorado State University) co-director of the NIST-funded Center of Excellence (CoE) for Risk-Based Community Resilience Planning; Gregory Deierlein (Stanford University) from the
The range of techniques and principles that were detailed at this workshop can also be applied to the COVID-19 crisis. The pandemic illustrates that investing in risk mitigation strategies reduces both the human and material cost of a hazard, and that even hazards with a low probability of occurrence require significant investment of resources to achieve resilience. The pandemic also illustrates that computational hazards research is a rich field with many opportunities at the intersection of the various disciplines.
SimCenter, which represents a consortium of universities on the U.S. West Coast; Sherif El-Tawil (University of Michigan) from ICoR, and Wael El-Dakhakhni (McMaster University) from INTERFACE. They were joined by other leaders in the fields including Tasos Sextos from Bristol University, UK, Xinzheng Lu, head of the Institute of Disaster Prevention and Mitigation of Tsinghua University; Hiba Baroud from Vanderbilt University, and Seth Guikema from the University of Michigan. The speakers highlighted their Centersâ&#x20AC;&#x2122; or research groupsâ&#x20AC;&#x2122; capabilities and contributions, then reconvened for a panel discussion to @UM_MICDE
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LEARNER QUOTES “For the final project, I am assuming the role of a member of the team responsible to combat COVID-19 from India and I have to decide on what should be our strategy to fight coronavirus in India, be it the extension of a lockdown or any other important decision related to this pandemic.”
“Fantastic, loved it!”
MOOC INSTRUCTORS Darin Stockdill Instructional and Program Design Coordinator and Lecturer I in Teach Education, School of Education Rafael Meza Associate Professor of Epidemiology, School of Public Health Christopher Quintana Associate Professor of Education, School of Education Mariana Carrasco-Teja MICDE Associate Director and Assistant Research Scientist, University of Michigan Office of Research MICDE YEAR IN REVIEW 2020 | PAGE 14
U-M DRAWS GLOBAL ATTENTION FOR MOOC IN PROBLEM SOLVING USING COMPUTATIONAL THINKING Problem Solving using Computational Thinking, a Massive Open Online Course (MOOC) launched by the University of Michigan in November of 2019, has already drawn more than 1,200 learners from around the globe. MICDE and the Center for Academic Innovation partnered to create this course. The idea for this MOOC arose from the team’s recognition of the ubiquity of computation. However, the developers were equally keen to highlight how broader computational thinking also makes its presence felt in somewhat unexpected domains. The MOOC is organized in a series of real-world examples that include how, using computational thinking, it is possible to help plan and prepare for a flu season, track human rights violations, or monitor the safety of crowds. Across the board, the MOOC has received tremendously positive reviews, and the projects done by learners within the MOOC provide shots of inspiration in troubled times. For their final project, learners have applied the computational thinking strategies discussed throughout the MOOC to a wide array of social problems with hopes of finding cogent solutions. Not surprisingly, several projects have aimed to address challenges related to COVID 19. Learners addressing today’s most pressing societal concerns, such as COVID-19, exemplifies the transformative potential of open-access, digital, and distance education made possible by a MOOC.
Chanese is a Ph.D. candidate in Environmental Health Sciences and Scientific Computing. She uses big data analyses and predictive modeling to study the link between environmental toxins and the development of cancer.
Jessica is a Clare Boothe Luce Fellow, and Ph.D. Chanese pre-candidate in Applied & Interdisciplinary Forte Mathematics and Scientific Computing, studying inverse problems in mathematical epidemiology, particularly focused on using computational and mathematical methods to gain useful insight into public health problems. Fifteen students were awarded MICDE Top-off Fellowships in the 2020-2021 academic year. Fellows' research projects involve the use and advancement of scientific computing techniques and practices.
MICDE Graduate Fellowships
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MICDE by the Numbers
STUDENTS ENROLLED IN MICDE GRADUATE CERTIFICATE AND JOINT PH.D. PROGRAMS
CATALYST GRANTS AWARDED
STUDENT FELLOWSHIPS AWARDED
The Michigan Institute for Computational Discovery and Engineering (MICDE) is the focal point for the wide spectrum of research in computational science and engineering at the University of Michigan. This includes the development and deployment of sophisticated models in every field of science and engineering on high-performance computers (HPC) to support basic and applied research. Computational Discovery and Engineering (CDE) is an enabling discipline with computation widely accepted as the third mode of scientific discovery on par with theory and physical experimentation. MICDE YEAR IN REVIEW 2020 | PAGE 16
The MICDE Team
Krishna Garikipati MICDE Director, Professor of Mechanical Engineering, and Mathematics
Mariana Carrasco-Teja MICDE Associate Director, Assistant Research Scientist
Karthik Duraisamy MICDE Associate Director, Associate Professor of Aerospace Engineering
Annette Ostling MICDE Associate Director, Associate Professor of Ecology and Evolutionary Biology
Siqian Shen MICDE Associate Director, Associate Professor of Industrial & Operations Engineering, and Civil and Environmental Engineering
Heidi Bennett Ph.D. Program Coordinator Jennifer Henry Sr. Administrative Assistant
External Advisory Board
Marsha Berger, New York University
Victoria Booth Sherif El-Tawil C. Alberto Figueroa Vikram Gavini Emanuel Gull Christiane Jablonowski Eric Johnsen Robert Krasny Shawn McKee Barzan Mozafari Paul Zimmerman
Omar Ahmed Brendan Kochunas Kenneth Powell Chris Quintana Quentin Stout Shravan Veerapaneni
Jacqueline Chen, Sandia National Laboratories Margot Gerritsen, Stanford University Christopher Johnson, Scientific Computing and Imaging Institute, University of Utah Tinsley Oden & Karen Willcox Oden Institute for Computational Engineering and Sciences, University of Texas Austin @UM_MICDE
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The Michigan Institute for Computational Discovery & Engineering is the focal point for the wide spectrum of research in computational science and engineering at the University of Michigan
Michigan Institute for Computational Discovery & Engineering Weiser Hall, 500 Church Street, Suite 600 Ann Arbor, MI 48109 micde.umich.edu ÂŠ 2021 by the Regents of the University of Michigan: Jordan B. Acker, Michael J. Behm, Mark J. Bernstein, Paul W. Brown, Sarah Hubbard, Denise Ilitch, Ron Weiser, Katherine E. White Mark S. Schlissel, ex officio A Non-discriminatory, Affirmative Action Employer