Synergistic Voyage

XSEDE ECSS Expert at PSC Helps Simulate Microrobots

While shrinking doctors to the size of microbes to carry out miniature surgery inside a patient remains science fiction, scientists have made the first steps in designing microrobots that can carry out simple tasks. An XSEDE Extended Collaborative Support Service expert at PSC has helped them improve and speed simulations that will allow them to accelerate testing of new designs.

Why it’s important:

Since the science fiction novel Fantastic Voyage—and before—people have been fascinated with the idea of shrinking our tools so that we could carry out miniature tasks with extreme precision. Operating on a blood vessel in a person’s brain, as in the novel, without a single incision. Microrobots programmed to deliver a drug to the exact site of a disease, strengthening the drug’s effectiveness and eliminating side effects. Re-attaching nerve-cell connections to reverse stroke or Alzheimer’s disease. While none of these things are possible yet with today’s technology, the ability to make smaller and smaller tools with ever more control are putting us on the road to such miracles.

Metin Sitti, a professor at Carnegie Mellon University and director of the Max Planck Institute for Intelligent Sytems: Physical Intelligence, and his research group have been designing spinning magnetic microrobots that can do simple tasks such as creating localized current flows in a liquid and picking up and dropping microscopic objects. Most of their work had concentrated on creating microrobots and testing them under a microscope. But they had also begun simulating their robots on a computer, to enable them to accelerate testing of new designs and how to use them in an efficient way. However, the “finite-element method” computational approach they were using was taking days of calculations to do even a simple simulation on the computer in their lab.

“The boundary-element method cut simulation times from days to minutes, even on their lab machine. With the supercomputer, they can do simulations with ultra-high-resolution or of complex systems.”
—Anirban Jana, Pittsburgh Supercomputing Center

How PSC and XSEDE’s ECSS helped:

To speed their simulations, the scientists turned to Anirban Jana, an XSEDE Extended Collaborative Support Service (ECSS) expert at the Pittsburgh Supercomputing Center (PSC). Jana looked at their computational approach and realized that a different method, called the “boundary-element method,” could greatly simplify their calculations and provide more accuracy in addition. By happy coincidence, Carlos Rosales-Fernandez at the Texas Advanced Computing Center had years earlier written an open-source code for a very similar boundary-element simulation. Jana rewrote the code to simulate fluid flows generated by spinning bodies in a more general cavity. He also helped Sitti’s graduate students, Zhou Ye and Mehmet Yigit, develop workflows to make the calculations run smoothly. Finally, he “parallelized” the code to make it run on a supercomputer. He also helped them write an XSEDE proposal to get computational time on PSC’s Blacklight system.

The change to the boundary-element method allowed the computations to run in minutes rather than days, even on the scientists’ own computer. When they tested the new code on Blacklight, the program ran successfully in an environment that will allow them to simulate vastly more complicated—and more realistic—systems and environments. A paper on their initial work is now in review in a peer-reviewed scientific journal, with Jana a co-author.