We welcome 15 students to the 2020-21 class of MICDE graduate fellows

By | Educational, News

MICDE is proud to announce the recipients of the 2020 MICDE graduate fellowships. The fellows’ research projects involve the use and advancement of scientific computing techniques and practices. From political science, psychology, physics, and applied and interdisciplinary mathematics within the College of Literature, Science & the Arts to aerospace engineering, mechanical engineering, materials science engineering, industrial & operations engineering, and civil & environmental engineering within the College of Engineering, the 2020 MICDE fellows epitomize the reach of computation in diverse scientific disciplines.

For the past six years, MICDE has awarded fellowships to over 120 graduate students from our large community of computational scientists. The MICDE graduate student top-off fellowship provides students with a stipend to use for supplies, technology, and other materials that will further their education and research. Among other things, awards have helped many to travel to conferences and meetings around the world to share the rich and diverse research in computational science being carried out at U-M.

The awardees are:

Eytan Adler, Aerospace Engineering
Hessa Al-Thani,
Industrial and Operations Engineering
Zijie Chen,
Mechanical Engineering
Alexander Coppeans
, Aerospace Engineering
Xinyang Dong, Physics
Karthik Ganesan,
Psychology
Iman Javaheri, Aerospace Engineering
Huiwen Jia, Industrial and Operations Engineering
Daeho Kim, Civil and Environmental Engineering
Yudan Liu,
Chemistry
Emily Oliphant
, Materials Science and Engineering
Ryan Sandberg, Applied and Interdisciplinary Mathematics
Patrick Wu, Political Science
Zhucong Xi, Materials Science and Engineering
Yi Zhu, Civil and Environmental Engineering

Learn more about the fellows and the MICDE Fellowship program

Graduate Research Assistantships for Fall 2020 Term in Computational Multiphase/Multi-Physics Projects

By | News, SC2 jobs

Professor Jesse Capecelatro’s Computational Multiphase/Multi-Physics Flow Lab is seeking Three Graduate Students

 

Professor Jesse Capecelatro is a faculty member within the College of Engineering’s Mechanical and Aerospace Engineering departments. Prof. Capecelatro’s lab group is seeking current or recently graduated Master’s or Ph.D. students for paid Research Assistant positions starting in the Fall 2020 term. Read more about Prof. Capecelatro’s research group here.

Research Assistants will be working on one of three projects.

PROJECT #1: MODELING TURBULENT FLOWS WITH FINITE SIZE PARTICLES ON HETEROGENEOUS ARCHITECTURES

Description: The objective of this project is to develop a highly scalable direct numerical simulation (DNS) code that leverages new algorithmic advances in (a) turbulence simulation using a pseudo-spectral approach on heterogeneous architectures and (b) efficient scaling of particle dynamics with number of particles, to perform massive-scale simulations with a mixture of CPUs and GPUs. The student will work with Prof. Capecelatro at UM and collaborators at Iowa State and Georgia Tech. The majority of the code will be written in Fortran 90 and C.

This position is expected to last 1 year in duration with the possibility of extension, and work will be performed remotely. Compensation for this position will be based on experience and qualifications.

Desired Qualifications:

  • Major in Mechanical Engineering, Computer Science, or similar
  • Strong background in fluid mechanics
  • Good knowledge in turbulence
  • Excellent programming skills in a high-performance language like C, Fortran, Python
  • Familiar with parallel computing

PROJECT #2: MULTI-STEP EFFECTIVENESS FACTORS FOR NON-SPHERICAL CATALYSTS

Description: Prof. Capecelatro and his postdoc Aaron Lattanzi will provide support to the graduate student on development of new models for diffusion limited reaction schemes that will be delivered to the National Renewable Energy Laboratory (NREL). The multi-step effectiveness vector (MEV) previously derived by CO-PI Lattanzi will be expanded to account for cylindrical and infinite slab catalyst geometries. Reactant concentration profiles and volume-averaged reaction rates predicted by the new MEV will be directly compared to high-fidelity simulations conducted by NREL to verify the model.

This position is expected to last 9 months in duration with the possibility of extension, and work will be performed remotely. Compensation for this position will be based on experience and qualifications.

Desired Qualifications:

  • Major in Chemical Engineering, Mechanical Engineering, or similar
  • Excellent programming skills in a high-performance language like C, Fortran, Python
  • Strong background in fluid mechanics
  • Familiarity with chemical kinetics (CHE 344. Reaction Engineering and Design or similar class)

PROJECT #3: SENSITIVITY AND UNCERTAINTY QUANTIFICATION OF MODELING PARAMETERS FOR SIMULATING HIGH-SPEED MULTIPHASE FLOWS

Description: The student will perform a literature review on the state-of-the-art in modeling compressible particle-laden flows. Simulations will be performed of shock waves interacting with solid particles using our in-house high-speed multiphase flow solver (Fortran 90). A sensitivity analysis will be performed to quantify the effect of particle statistics on modeling parameters.

This position is expected to last 9 months in duration with the possibility of extension, and work will be performed remotely. Compensation for this position will be based on experience and qualifications.

Desired Qualifications:

  • Major in Aerospace Engineering, Mechanical Engineering, or similar
  • Excellent programming skills in a high-performance language like C, Fortran, Python
  • Familiar with uncertainty quantification, tools for sensitivity analyses
  • Strong background in fluid mechanics
  • United States citizenship

APPLY  TODAY!
Please send your CV, transcript, and a brief statement about your interests and background relative to the projects listed above to Professor Jesse Capecelatro jcaps@umich.edu with subject, “Fall 2020 Research Assistantship”.

Graduate Research Assistantships for Fall 2020 Term in Physics-based Data-driven Modeling Projects

By | News, SC2 jobs

Professor Julie Young’s Lab Seeking Two Engineering-focused Grad Students to Assist in Modeling Research

Professor Julie Young is a faculty member within the College of Engineering’s Naval Architecture and Marine Engineering, Mechanical Engineering, and Aerospace Engineering departments. Professor Young’s lab group is seeking graduate students (current or recently graduated master’s or Ph.D.’s) for paid Research Assistant positions starting in the Fall 2020 term. The expected time commitment for these positions is 20 hours per week.

Students will be working on one of two projects:

Project #1 Description: Development of a physics-based data-driven model for system identification and control of lifting surfaces in multiphase flow.

Project #1 Desired Qualifications:

  • Excellent programming skills
  • Good knowledge of system identification
  • Familiarity with data-driven models, control methods
  • Familiarity with experimental modeling and data analysis
  • Good knowledge of nonlinear fluid and structural dynamics
  • Engineering major or extensive coursework in engineering-related field
  • United States citizenship

Project #2 Description: Development of physics-based data-driven model for marine ship-propulsion system.

Project #2 Desired Qualifications:

  • Excellent programming skills
  • Good knowledge of system identification and data-driven models
  • Familiarity with experimental modeling and data analysis
  • Good knowledge of propulsion systems
  • Engineering major or extensive coursework in engineering-related field
  • United States citizenship

Compensation:
Compensation for these positions will be commensurate with experience and qualifications.

Apply Today!
Please send your CV, transcript, and a brief statement about your interests and background relative to the projects listed above to Professor Julie Young at ylyoung@umich.edu with subject, “Fall 2020 Research Assistantship”.

Alternatives Research & Development Foundation to Support Research on COVID-19, Aiming for Advancement in Non-animal Methods of Drug Discovery

By | News, Research

Pharmaceutical companies across the globe are racing to introduce clinically tested and approved therapeutic drugs that fight COVID-19 virus to market. As is typical in drug discovery research, animals have played a critical role in the development and testing of COVID-19 therapeutics. A proposal by U-M Professor Rudy J. Richardson, Dow Professor Emeritus of Toxicology, Professor Emeritus of Environmental Health Sciences, and Associate Professor Emeritus of Neurology at the University of Michigan, titled “Discovering host factor inhibitors in silico for SARS-CoV-2 entry and replication” has been awarded funding to identify compounds that bind to human proteins that facilitate entry and/or replication of the SARS-CoV-2 virus. Awarded, in part, because of its potential to develop alternative methods to advance science and replace or reduce animal use, this research will employ in silico ligand protein docking to discover existing drugs (repurposing) and/or new drug candidates capable of inhibiting host proteins involved in infection pathways for the COVID-19 virus, SARS-CoV-2.

Protein docking targets include four serine hydrolases. Using these targets, researchers will reversibly dock approximately 40,000 ligands from the Binding Database comprising FDA-approved drugs along with serine protease and PLA2 inhibitors, including organoboron compounds. Then, covalent docking will be conducted on a ligand subset containing pharmacophores capable of covalently binding serine hydrolases. Consensus ranking from four docking programs will be used to generate a penultimate list of candidate compounds. Those showing high predicted potency against off-target serine hydrolases will be excluded. The final list of compounds will be made publicly available for further evaluation in bioassays.

Professor Richardson’s grant, awarded by the Alternatives Research & Development Foundation, is a part of the ARDF’s 2020 Open Grants program, funding research projects that develop alternate methods to advance science and replace or reduce animal use. Although the immediate goal of this computational study supports the identification or development of a COVID-19 vaccine, the long-range vision is to advance computational and in vitro approaches to eliminate animal use from drug discovery for humans and other species. 

MICDE Affiliated Faculty member Rudy J. Richardson is a Dow Professor Emeritus of Toxicology and Professor Emeritus of Environmental Health Sciences within the School of Public Health, and Associate Professor Emeritus of Neurology within the Medical School at the University of Michigan.

1-3 Year Postdoc Opportunities with the Center for Exascale Monte Carlo Neutron Transport

By | News, SC2 jobs

Positions in Computational Science Research, Code Development, and Student Mentoring Support at Oregon State University and the University of Notre Dame

The Center for Exascale Monte Carlo Neutron Transport (CEMeNT) is recruiting for two postdoctoral scholars to provide computational science research, code development, and student mentoring support. These positions are full-time, 12-month Postdoctoral Scholar positions: one located in Corvallis, Oregon, working within the School of Nuclear Science and Engineering at Oregon State University, and one located in South Bend, Indiana, working within the Department of Aerospace and Mechanical Engineering at the University of Notre Dame. Funding for these positions is expected to exist for three years; however, contracts are annual and are eligible for extension based on satisfactory performance and mutual agreement.

CEMeNT is a competitively designated National Nuclear Security Administration funded Focused Investigatory Center as part of the Predictive Science Academic Alliance Program (PSAAP – https://share-ng.sandia.gov/psaapIII/). Within CEMeNT, researchers from Oregon State University, the University of Notre Dame, and North Carolina State University work to develop the mathematics, computational physics, and computer science required to scale time-dependent Monte Carlo neutron transport simulations to exascale-class computers. Our work has high visibility in the US National Laboratories and the computational science community.

The universities participating in CEMeNT commit to inclusive excellence by advancing equity and diversity in all that we do. We are Affirmative Action/Equal Opportunity employers, and particularly encourage applications from members of historically underrepresented racial/ethnic groups, women, individuals with disabilities, veterans, LGBTQ community members, and others who demonstrate the ability to help us achieve our shared vision of a diverse and inclusive community.

Responsibilities:

  • Collaborate with the CEMeNT Leadership and CEMeNT-affiliated faculty to conduct cutting edge research in computational and develop software for solving neutron transport problems on world-leading architectures.
  • Advance the state-of-the-art in Monte Carlo particle transport, hybrid methods, uncertainty quantification, and/or machine-learning enhanced physics simulation.
  • Work alongside colleagues at US National Laboratories to further the impact of the research and development at CEMeNT.
  • Mentor and direct the research work of graduate students.

Required Qualifications:

  • Ph.D. in nuclear engineering, mechanical engineering, computational physics, applied mathematics or scientific computing disciplines.
  • Proven track-record of independent research, critical thinking, and successful academic publications.
  • Excellent written and verbal communication skills.
  • Experience in developing software for high performance computing
  • applications using Python and C++.
  • A demonstrable commitment to promoting and enhancing diversity.

Preferred Qualifications:

  • Ph.D. in nuclear engineering, mechanical engineering, computational physics, applied mathematics or scientific computing disciplines.
  • Proven track-record of independent research, critical thinking, and successful academic publications.
  • Excellent written and verbal communication skills.
  • Experience in developing software for high performance computing
  • applications using Python and C++.
  • A demonstrable commitment to promoting and enhancing diversity.

Position available: August 14, 2020 (open until filled) U.S. citizens and residents will be prioritized.

Stipend and benefits conform with postdoctoral scholar standards at Oregon State University and Notre Dame University. More information about postdoctoral scholar appointments can be found at the Office of Postdoctoral Scholars at ​Oregon State University​ and the ​University of Notre Dame​.

Apply Today!

For full consideration, apply by August 7, 2020. Applicants must send the following documents in a single PDF file (Word documents will not be opened) to ​both contacts​ listed below:

  • A detailed CV and academic transcript
  • A one-page statement describing your background and how you fit the
  • advertised position. Please specifically reference the required and preferred qualifications.
  • Contact information for three references
  • The subject line of your email should contain the following text: “CEMeNT Post-doctoral Scholar – (your last name).” Please note that only candidates that meet the required skills and expertise will be contacted.

Contacts

Dr. Todd Palmer, CEMeNT Director (todd.palmer@oregonstate.edu); School of Nuclear Science and Engineering Oregon State University

Dr. Ryan McClarren, CEMeNT Deputy Director (rmcclarr@ndu.edu); Department of Aerospace and Mechanical Engineering University of Notre Dame

Computational Biologist Postdoc-level Opening in Bioinformatics

By | News, SC2 jobs

Air Force Research Labs Seeking Postdoc-level Computational Biologist for Bioinformatics Position

The Air Force Research Labs at the Wright-Patterson Air Force Base is seeking a Computational Biologist with experience in bioinformatics and machine learning. The Computational Biologist will have the opportunity to work on novel microbial degradation of perfluoroalkyl (PFAS) compounds using genomics, enzyme mining, and AI/ML. The successful candidate will use bioinformatics and AI/ML to identify biological PFAS degradation pathways and enzymes to aid in the generation of testable hypotheses for wet-lab experiments. This role requires effective teamwork and communication of results with colleagues from diverse backgrounds. 

Functions for this Role will also Include:

  • Bioinformatics on enriched and complex microbial communities generated from metagenomics including assembly, binning, annotation, enzyme mining, and phylogenetic analyses
  • Applying AI/ML for identifying optimized biological modes of PFAS degradation
  • Documentation and presentation of research progress in the forms of reports, publications, and oral presentations
  • Periodic travel to scientific reviews and conferences

Required Qualifications:

  • Ph.D. (or M.Sc. with 5+ years of relevant experience) in Computational Biology, Bioinformatics, or Microbial Genomics
  • Fluent in major scripting languages such as Python or Perl, and proficient in using the command line in Unix environments
  • Experience in applying machine learning algorithms or statistical methods to solving biological problems
  • Deep understanding of phylogenetic analyses and comparative genomics methods
  • Demonstrated understanding of relevant public metagenomic databases
  • Ability to work effectively in a multidisciplinary team, and communicate results clearly to non-computational scientists
  • Excellent organizational skills
  • This position is working on-site at a government facility and requires U.S. citizenship

Apply Today!

Apply via this link: https://ues.hrmdirect.com/employment/job-opening.php?req=1328011&&cust_sort1=-1&&nohd#job

If you have any questions, please email eric.harper.4@us.af.mil and vanessa.varaljay.1@us.af.mil.

Computational Biologist Postdoc-level Opening in Microbial Genomics

By | News, SC2 jobs

Air Force Research Labs Seeking Postdoc-level Computational Biologist for Microbial Genomics Position

 The Air Force Research Laboratory near Dayton, OH is seeking a Computational Biologist with experience in microbial genomics. The successful candidate will have the opportunity to work across multiple collaborative projects in the areas of microbial biofouling and corrosion, polymicrobial interactions of DoD relevant microbial communities, and mechanisms of polymer biodegradation. The selected candidate will use informatics to assemble, annotate, and perform comparative analyses of both bacteria and fungi to aid in generation of testable hypotheses. This role requires effective teamwork and communication of results with colleagues from diverse backgrounds.

Functions for this Role will also Include:

  • Transcriptomics of bacteria and fungi communities including differential expression analyses and identifying upregulated proteins
  • Analysis and interpretation of microbial community data using network analyses and visualization tools
  • Informatics on enriched and complex microbial communities generated from metagenomics and metatranscriptomics including assembly, binning, annotation, enzyme mining, and phylogenetic analyses
  • Documentation and presentation of research progress in the forms of reports, publications, and oral presentations
  • Travel to scientific reviews and conferences

Required Qualifications:

  • Ph.D. (or M.Sc. with 5+ years of relevant experience) in Computational Biology, Bioinformatics, or Microbial Genomics
  • Demonstrated success in applying open source software and in developing novel algorithms for the comparative analysis of genomes
  • Deep understanding of phylogenetic analyses and comparative genomics methods
  • Fluent in major scripting languages such as Python or Perl, and proficient in using the command line in Unix environments
  • Previous experience in comparative genomics or an understanding of secondary metabolite biosynthesis is highly desirable
  • Experience in applying machine learning algorithms or statistical methods to solving biological problems is desirable
  • Demonstrated understanding of relevant public genomic databases
  • Ability to work effectively in a multidisciplinary team, and communicate results clearly to non-computational scientists
  • Excellent organizational skills
  • This position is working on-site at a government facility and requires U.S. citizenship

Apply Today!

Apply via this link: https://ues.hrmdirect.com/employment/job-opening.php?req=1328012&&cust_sort1=-1&&nohd#job

If you have any questions, please email eric.harper.4@us.af.mil and vanessa.varaljay.1@us.af.mil.

Air Force Research Labs Seeking Student Research Assistant for Bioinformatics and Machine Research Project

By | News, SC2 jobs

Research Assistant in Bioinformatics and Machine Research Opportunity for the Fall 20 – Winter 21 Academic Year + Possibility of Summer Extension

The Air Force Research Labs at the Wright-Patterson Air Force Base is seeking a Student Research Assistant to contribute to a project that combines bioinformatics and machine learning. Upper-level undergraduate students, Master’s students, and recent graduates are encouraged to apply.

Position Details: 

  • The expected time commitment for this position is ~10 hours/week for the Fall 2020 and Winter 2021 terms, with the opportunity to work full time in the summer of 2021.
  • This position will work remotely throughout the academic year, with the possibility of working on-site next summer at the Wright-Patterson Air Force base near Dayton, Ohio.
  • This position will be co-advised by two AFRL researchers.
  • Compensation will be commensurate with experience and education.

Required Qualifications:

  • Applicants for this position should have an interest and/or familiarity with biology or data analysis and machine learning, with an academic major or concentration in one of the following science or engineering fields:
    • Biology, Chemistry, Computer Science, Data Science, Information
    • Biomedical Engineering, Chemical Engineering, Materials Science & Engineering, Computer Science and Engineering, Electrical Engineering and Computer Science

Apply Today!

To apply for this position, please email eric.harper.4@us.af.mil and vanessa.varaljay.1@us.af.mil with a brief resume or CV.

MICDE funds wide-ranging computational discovery in galactic formation, drug discovery, bacterial biofilm colonies and turbulence simulations

By | News, Research

Since 2017 the Michigan Institute for Computational Discovery & Engineering (MICDE) Catalyst Grants program has funded a wide spectrum of cutting-edge research that combines science, engineering, mathematics and computer science. This year the program will fund four new projects that continue this tradition: Prof. Aaron Frank (Chemistry) and his group will spearhead 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. Prof. Marisa Eisenberg (Epidemiology, Mathematics, and Complex Systems) and Prof. Alexander Rickard’s (Epidemiology) groups will develop 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. Oleg Gnedin (Astronomy) will develop 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. Finally, Prof. Aaron Towne (Mechanical Engineering) will advance 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.

“These four projects have the potential to catalyze and  reorient the directions of their research fields by developing and harnessing powerful paradigms of computational science”, said Krishna Garikipati, Professor of Mechanical Engineering and of Mathematics, and MICDE’s Director. “MICDE’s mission is to lead the advances in computational science research by bringing together interdisciplinary teams at U of M, and these projects embody that vision.” 

More about MICDE’s catalyst grant program and the projects can be found at micde.umich.edu/catalyst.

Fabricio Vasselai wins the Irving Louis Horowitz Award from the Horowitz Foundation for Social Policy

By | News

Fabricio Vasselai, a dual Ph. D. candidate in Political Science and Scientific Computing is a recipient of this year’s Horowitz Foundation awards from the Horowitz Foundation for Social Policy. His proposal titled “Elections in the AI era: using Machine Learning and Multi-Agent Systems to detect and study menaces to election integrity” won the Irving Louis Horowitz Award, given to the overall most outstanding project of the year, as well as the Joshua Feigenbaum Award as the most outstanding project on Arts, Popular Culture and Mass Communication.

The proposal develops Artificial Intelligence tools to detect and to study threats to election integrity. First, novel Multi-agent simulations of elections (MASE) are derived and implemented to be the data-generating process of synthetic data. Then these data is used to train Supervised Machine Learning (SML) to detect fraud in real election result counts. He uses such ability to create simulated training data to properly bootstrap the SML classifications, allowing for the novel estimation of uncertainty around election fraud detection. He also uses MASE to perform virtual experiments on the spread of fake news, showing that biased misinformation is critical for political polarization to flourish in majoritarian elections.

Fabricio Vasselai is an MICDE Fellow (awarded on 2018), and he is currently a Researcher at U-M’s Center for Political Studies and Center for Complex Systems.

Established in 1998, the Horowitz Foundation awards grants to scholars to assist them in completing their dissertations. It is highly competitive, with less than 3 percent of applicants receiving an award this year.