Principles of Intelligent Behavior in Biological and Social Systems (PIBBSS) Fellowship

By | News, Research, SC2 jobs, Uncategorized

Summer fellowship for researchers, primarily for PhD students and postdocs with experience studying complex and intelligent behavior in biological and social systems. Fellows will work on selected projects at the intersection between the fellow’s field of expertise and AI alignment and/or governance in close collaboration with a mentor.

Date: June – August, 2023

Place: Europe (most likely one in near Oxford and one in near Prague)

Stipend: 3,000 USD/month

Deadline to apply: February 15, 2023

Application materials:

  • CV/résumé
  • Personal statement : A 600-800 word statement discussing a) your research background and interests, and b) why you are motivated to participate in the fellowship.
  • Past work (optional) : We are interested in examples representative of your research interests, expertise, and/or scientific writing style.

More information.

MICDE’s InfoReady portal logging in issue

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We are working on resolving a bug when logging in into the MICDE InfoReady portal using U-M’s SSO. While we fix it, if you are getting the following screen:

please follow these steps:

  • Go to https://micde.infoready4.com/#login.
  • Scroll down to the Login for Other Users, and click Forgot your password.
  • Enter your umich email address and then click Reset Password. An email will be sent to that address with instructions for resetting your password.
  • Follow the instructions, and you will be redirected to the site and logged in automatically.

You can use the Login for Other Users instead of the Single Sign On as long as necessary; the password will not change unless you change it in your User Profile.

We apologize for any inconvenience.

Prof. Monica Valluri Joins MICDE Leadership Team

By | News, Uncategorized
Portrait of Monica Valluri

Monica Valluri, Astronomy

This month, MICDE welcomed Monica Valluri, Research Professor of Astronomy, as an Associate Director. Prof. Valluri’s research is on the theoretical framework of Galactic Dynamics. Dr. Valluri uses galactic dynamics to interpret and model motions of stars observed with state-of-the-art telescopes using new and powerful numerical methods. Her work has led to important insights into how these dark components influence the structure and evolution of galaxies. In 2016, she won the University of Michigan Research Faculty Achievement Award for her or her outstanding research and teaching career in theoretical galaxy dynamics. In 2019, Prof. Valluri and a team of international collaborators were awarded an MICDE Catalyst Grant, “Determining the 3D Shape of Milky Way’s Dark Matter Halo” that has lead to several federally funded grants.

Annette Ostling - Portrait

Annette Ostling, Ecology and Evolutionary Biology

Prof. Valluri’s appointment succeeds former Associate Director Annette Ostling, Associate Professor of Ecology and Evolutionary Biology. We thank Prof. Ostling for her service to MICDE. Her contributions to the growth and resiliency of MICDE have been numerous over the last five years. 

Across six continents, scientists use computation to optimize cities’ responses to hazardous events

By | Events, Research, Uncategorized

“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.”

Sherif El-Tawil
Antoine E. Naaman Collegiate Professor,
Department of Civil and Environmental Engineering

The combination of natural hazards, climate change, and the COVID-19 pandemic has demonstrated the importance of community resilience. 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. Although achieving resilience is technically challenging and expensive, communities must strive to accomplish the highest level of resilience attainable with the engineering and financial resources available.

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 pathways. However, as computational models are well established in each discipline, computation is 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. 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 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 Centers’ or research groups’ capabilities and contributions, then reconvened for a panel discussion to address questions from the audience of nearly 250 participants from 30 countries, across six continents. The event also included a hands-on workshop that highlighted the Simple Run-Time Infrastructure software toolkit (SRTI). The SRTI is a free, open-source solution developed at the University of Michigan. It enables researchers to connect computer programs and simulators written in different languages, share data during execution, and design hybrid systems using disparate simulator modules, with a primary goal of being user friendly. The applications within this workshop demonstrated how one tool can be used to bring together multiple computational dialects to create a single language in the context of natural hazards research. The SRTI software toolkit is a result of the work of Dr. Sherif El-Tawil’s research group at the University of Michigan, supported by the National Science Foundation’s Office of Advanced Cyberinfrastructure (OAC) under grant CRISP TYPE II – 1638186. (icor.engin.umich.edu).

The range of techniques and principles that were detailed at this workshop can be applied to the current COVID-19 crisis. The pandemic is a perfect example that demonstrates that investing in mitigating risk reduces the cost, both human and material, of a hazard, and that even hazards with such a low probability of occurrence require enough investment to make ourselves resilient to it. The pandemic also illustrates that computational hazards research is a rich field with many opportunities at the intersection of the various disciplines. One of the most interesting ideas there is to explore is how to fuse sensor data – from the field – with simulations data, to achieve models that can help predict in real time the effect of a natural hazard.

Link to event information and recordings

Stephen Timoshenko Distinguished Postdoctoral Fellowship at Stanford University

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Stephen Timoshenko Distinguished Postdoctoral Fellowship at Stanford University

The Mechanics and Computation Group (Department of Mechanical Engineering) at Stanford University is seeking applicants for the “Stephen Timoshenko Distinguished Postdoctoral Fellowship.” This appointment is for a term of two years, beginning in September 2018.

The Stephen Timoshenko Distinguished Postdoctoral Fellow will be given the opportunity to pursue independent research in the general area of solid mechanics, as well as to contribute to ongoing research in the Mechanics and Computation Group. Research activities should be in the field of solid mechanics interpreted broadly. The candidate should be aligned with interests in the group, which include additive manufacturing, micro- and nano-mechanics, and bio-mechanics, with an interest in machine learning as it applies to the field of computational mechanics. Candidates will be given opportunities to develop their teaching experience by designing and teaching a class in the mechanics curriculum. This position might be of particular interest to candidates who are seeking an academic career.

Candidates are expected to show outstanding promise in research, as well as strong interest and ability in teaching. They must have received a Ph.D. prior to the start of the appointment, but not before 2018. Applicants should send a cover letter (one page); a curriculum vitae; a list of publications; brief statements of proposed research (up to three pages) and teaching (one page); the names and contact information of three recommendation letter writers. For full consideration, applications must be completed no later than 11PM PST, Sunday December 15, 2019.

Please send your application by email to:
Kelly Chu, kchu22@stanford.edu
Email subject: Stephen Timoshenko Distinguished Postdoctoral Fellow search All documents attached to the email should be PDF (Portable Document Format).

MICDE Director, Krishna Garikipati, wins USACM Fellow award

By | News, Uncategorized

Krishna Garikipati, professor of Mechanical Engineering and of Mathematics, and director of MICDE, has been granted a 2019 United States Association for Computational Mechanics (USACM) Fellows award for his work in developing numerical methods applied to strongly nonlinear problems in living and nonliving material systems.

The Fellows Award recognizes individuals with a distinguished record of research, accomplishment and publication in areas of computational mechanics and demonstrated support of the USACM through membership and participation in the Association, its meetings and activities. All recipients shall be members in good standing of USACM. Multiple awards may be given at two-year intervals.

The 2018 MICDE Symposium: Summary by Bradley Dice, Ph.D student in Physics and Computational Science

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This piece was first published in LinkedIn by Bradley Dice, U-M Ph.D student in Physics and Computational Science.

MICDE Symposium 2018: Computation, A Pillar of Science and a Lens to the Future

High-performance computing (HPC) is becoming an increasingly powerful tool in the hands of scientists, driving new discoveries in physical sciences, life sciences, and social sciences. The development of new (frequently domain-specific) approaches to machine learning and faster, smarter processing of sets of Big Data allows us to explore questions that were previously impossible to study. Yesterday, I presented a poster at the Michigan Institute for Computational Discovery & Engineering (MICDE) annual Symposium and attended a number of talks by researchers working at the intersection of high-performance computing and their domain science. The theme for the symposium was “Computation: A Pillar of Science and a Lens to the Future.”

Collaborative Computational Science with signac

My scientific work, and the work of my colleagues in the Glotzer lab, has been made vastly more efficient through the use of tools for collaborative science, particularly the signac framework. I presented a poster about how the signac framework (composed of open-source Python packages signacsignac-flow, and signac-dashboard) enables scientists to rapidly simulate, model, and analyze data. The name comes from painter Paul Signac, who, along with Georges Seurat, founded the style of pointillism. This neo-impressionist style uses tiny dots of color instead of long brushstrokes, which collectively form a beautiful image when the viewer steps back. This metaphor fits the way that a lot of science works: given only points of data, scientists aim to see the whole picture and tell its story. Since our lab studies materials, our “points” of data fit into a multidimensional parameter space, where quantities like pressure and temperature, or even particles’ shapes, may vary. Using this data, our lab computationally designs novel materials from nanoparticles and studies the physics of complex crystalline structures.

The core signac package, which acts as a database on top of the file system, helps organize and manage scientific data and metadata. Its companion tool signac-flow enables users to quickly define “workflows” that run on supercomputing clusters, determining what operations to perform and submitting the jobs to the cluster for processing. Finally, signac-dashboard (which I develop) provides a web-based data visualization interface that allows users to quickly scan for interesting results and answer scientific questions. These tools include tutorials and documentation, to help users acquaint themselves and get on to doing science as quickly as possible. Importantly, the tools are not specific to materials science. Many scientific fields have similar questions, and the toolkit can easily be applied in fields where exploration or optimization within parameter spaces are common, ranging from fluid mechanics to machine learning.

During the symposium, I learned a lot about how others are using scientific computing in their own work. The symposium speakers came from a wide range of fields, including biology, mathematics, and fluid dynamics. Some of my favorite talks are described below.

The Past: Phylogeny and Uncovering Life’s Origins

High-performance computing is enabling scientists to look in all sorts of directions, including into the past. Stephen Smith, Assistant Professor of Ecology and Evolutionary Biology at the University of Michigan, talked about his lab’s research in detecting evolutionary patterns using genomic data. From the wealth of genetic data that scientists have collected, the Smith lab aims to improve our understanding of the “tree of life”: the overarching phylogenetic tree that can explain the progress of speciation over time. Projects like Open Tree of Life and PHLAWD, an open-source C++ project to process data from the National Center for Biotechnology Information’s GenBank data source, are just two of the ways that open science and big data are informing our understanding of life itself.

The Present: From Algebra to Autonomy

Cleve Moler, the original author of the MATLAB language and chief mathematician, chairman, and cofounder of MathWorks, spoke about his career and how the tools MATLAB has provided for numerical linear algebra (and many other computational tasks) have been important for the development of science and engineering over the last 34 years. MATLAB is taught to STEM students in many undergraduate curricula, and is used widely across industry to simulate and model the behavior of real systems. Features like the Automated System Driving Toolbox are poised to play a role in autonomous vehicles and the difficult computational tasks inherent in their operation.

The Future: Parallel-in-Time Predictions and Meteorology

A significant challenge in weather and climate modeling is that supercomputer architectures are highly parallel, while many simulations of fluids are inherently serial: each timestep must be computed before the next timestep can begin. Beth Wingate, Professor of Mathematics at the University of Exeter and published poet, is developing a powerful approach that may change the way that such models work. Called “parallel-in-time,” it separates the effects of slow dynamics and fast dynamics, enabling parallel architectures to take advantage of longer timesteps and separate the work across many processors.

Conclusions

Computational science is growing rapidly, improving our ability to address the most pressing questions and the mysteries of our world. As new supercomputing resources come online, such as Oak Ridge National Laboratories’ Summit, the promise of exascale computing is coming ever closer to reality. I look forward to what the next year of HPC will bring to our world.

Faculty search in Computational Science at U-M

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MICDE is pleased to bring to your attention a faculty search in Computational Science at University of Michigan. This position will be filled within the Mechanical Engineering Department, but the search will be carried out with the active engagement of MICDE. We expect that the successful candidate will be a highly visible affiliate of MICDE, and will leverage its resources.

We are interested in candidates of any rank, who can bring advances in computer science, data-driven modeling and/or mathematics to bear upon the most compelling questions in engineering science. MICDE strives to define future paradigms of computational science, in collaboration with traditional disciplines in engineering and science. This is the environment that a successful candidate will have to develop a career.

All applicants should submit, in PDF format:
(1) a detailed resume,
(2) a statement of research and teaching interests,
(3) up to three representative publications, and
(4) the names and contact information of at least three references.

Applications must be submitted electronically at http://me.engin.umich.edu/facultysearch.

The University of Michigan is a non-discriminatory/affirmative action employer and is responsive to the needs of dual career families.

For more information please visit https://me.engin.umich.edu/about/positions/faculty.

Computational Science around U-M: Ph.D. Candidate Shannon Moran (Chemical Engineering) has won an ACM SIGHPC Intel Fellowship

By | Happenings, HPC, Uncategorized

Moran_HighRes_SqShannon Moran, a Ph.D. Candidate in the department of Chemical Engineering, has won a 2017 SIGHPC Intel Fellowship. Shannon is a member of the Glotzer Group. They use computer simulation to discover the fundamental principles of how nanoscale systems of building blocks self-assemble, and to discover how to control the assembly process to engineer new materials.

ACM’s Special Interest Group on High Performance Computing is an international group with a major professional society that is devoted to the needs of students, faculty, researchers and practitioners in high performance computing. This year they awarded 12 fellowships around the country with the aim of increasing the diversity of students pursuing graduate degrees in data science and computational science, including women as well as students from racial/ethnic backgrounds that have been historically underrepresented in the computing field. The fellowship provides $15,000 annually for study anywhere in the world.

The fellowship is funded by Intel and is presented at the annual Super Computing conference that this year will take place in November 13-16 in Denver, Colorado.

MICDE sponsored miRcore Biotechnology Summer Camp for the second year in a row

By | Happenings, HPC, Uncategorized

miRcoreBioTec2017This year’s miRcore’s Biotechnology summer camp was a big success.  The participants had hands-on experience in a wet-lab, and with the UNIX command line while accessing U-M’s High Performance Computing cluster, Flux, in a research setting. For the second year in a row MICDE and ARC-ts sponsored the campers to access Flux as they learned the steps that are needed to run code in a computer cluster. The camp also combined theoretical thermodynamic practices that gave participants an overall research experience in nucleotide biotechnology.

miRcore’s camps are designed to expose high school students to career opportunities in biomedicine and to provide research opportunities beyond the classroom setting. For more information please visit http://www.mircore.org/summer-camps/.