First Atom-by-Atom Simulation of a Life Form


3/1/2006

The computing horsepower of one of the world’s most powerful supercomputers has been harnessed by Swanlund Professor of Physics Klaus Schulten and his research group to visualize the behavior of a complete life form, the satellite tobacco mosaic virus. "This is just a first glimpse of a moving virus,” Schulten said, “but it looks gorgeous.”

According to the researchers, their simulation is the first to capture an entire biological organism in atom-by-atom detail. The simulation was done at the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign.

A better understanding of viral structures and mechanisms is an essential step in allowing scientists to develop improved methods of combatting viral infections in plants, animals, and eventually, humans.

Schulten’s group, which includes Peter Freddolino, a graduate student in biophysics and computational biology, and Anton Arkhipov, a graduate student in physics, collaborated with crystallographers at the University of California, Irvine—Alexander McPherson, a professor of molecular biology and biochemistry, and research specialist Steven Larson. The group’s results were published in the March issue of Structure (P.L. Freddolino, et al., Structure 14, 1767–1777 [2006]).

The researchers visualized the dynamic atomic structure of the virus in a saline solution by calculating, in femtosecond time steps, how each of its »1 million atoms moved.

The simulation utilized the latest version of NAMD, a software program developed by Schulten and his colleagues over the last decade to model the molecular dynamics of biological molecules. The program allowed the supercomputer’s five hundred processors to work in parallel on the same problem. Even so, the simulation took about 50 days to generate 50 ns of virus activity.

“Such a task would take a desktop computer around 35 years," according to Schulten.

“The simulations followed the life of the satellite tobacco mosaic virus, but only for a very brief time,” added Freddolino and Arkhipov. “Nevertheless, they allowed us to discover key physical properties of the viral particle, as well as providing crucial information on its assembly.”

In the brief simulation, the virus looks spherical but expands and contracts asymmetrically, as if it were “breathing.” The model also shows that the virus coat collapses without its genetic material, suggesting that when reproducing, the virus builds its coat around the genetic material, rather than inserting it into a pre-existing coat as was commonly assumed. “We saw something that is truly revolutionary,” Schulten said.

Ultimately, computational biophysicists will generate longer simulations of larger biological macromolecules, but that development will wait on the next generation of supercomputers, the so-called “petascale high-performance computing systems.”

“It may take still a long time to simulate a dog wagging its tail with a computer,” said Schulten. “But a big first step has been taken to ‘test fly’ living organisms. Naturally, this step will assist modern medicine as we continue to learn more about how viruses live.”

This work was supported by the National Institutes of Health and by allotments of computing time from the National Center for Supercomputing Applications through its National Science Foundation funding. The conclusions presented are those of the authors and not necessarily those of the funding agencies.

Recent News

  • Research
  • Condensed Matter Physics
  • Condensed Matter Experiment
  • Condensed Matter Theory

One of the greatest mysteries in condensed matter physics is the exact relationship between charge order and superconductivity in cuprate superconductors. In superconductors, electrons move freely through the material—there is zero resistance when it’s cooled below its critical temperature. However, the cuprates simultaneously exhibit superconductivity and charge order in patterns of alternating stripes. This is paradoxical in that charge order describes areas of confined electrons. How can superconductivity and charge order coexist?  

Now researchers at the University of Illinois at Urbana-Champaign, collaborating with scientists at the SLAC National Accelerator Laboratory, have shed new light on how these disparate states can exist adjacent to one another. Illinois Physics post-doctoral researcher Matteo Mitrano, Professor Peter Abbamonte, and their team applied a new x-ray scattering technique, time-resolved resonant soft x-ray scattering, taking advantage of the state-of-the-art equipment at SLAC. This method enabled the scientists to probe the striped charge order phase with an unprecedented energy resolution. This is the first time this has been done at an energy scale relevant to superconductivity.

  • Alumni News
  • In the Media

Will Hubin was one of those kids whose wallpaper and bed sheets were covered in airplanes and who loved building model airplanes. By the time he took his first flight in the late 1940s, he was hooked.

Now, he shares his passion for planes with children by taking them for their first flight, at no charge, in his four-seat 2008 Diamond DA-40 aircraft through the local Experimental Aircraft Association’s Young Eagles program.

“It’s a lot of fun and pretty rewarding. Anyone who loves flying likes to introduce others to it. It’s true of anything, any hobbyist. Some will talk constantly but they’re ecstatic,” said Hubin, a retired Kent State University physics professor.

Hubin learned to fly in 1962 when he was earning a doctorate in physics at the University of Illinois and has been flying ever since, adding commercial, instrument, instructor, multi-engine and seaplane ratings.

  • Research
  • Theoretical Biological Physics
  • Biological Physics
  • Biophysics

While watching the production of porous membranes used for DNA sorting and sequencing, University of Illinois researchers wondered how tiny steplike defects formed during fabrication could be used to improve molecule transport. They found that the defects – formed by overlapping layers of membrane – make a big difference in how molecules move along a membrane surface. Instead of trying to fix these flaws, the team set out to use them to help direct molecules into the membrane pores.

Their findings are published in the journal Nature Nanotechnology.

Nanopore membranes have generated interest in biomedical research because they help researchers investigate individual molecules – atom by atom – by pulling them through pores for physical and chemical characterization. This technology could ultimately lead to devices that can quickly sequence DNA, RNA or proteins for personalized medicine.

  • In Memoriam

We are saddened to report that John Robert Schrieffer, Nobel laureate and alumnus of the Department of Physics at the University of Illinois at Urbana-Champaign, passed away on July 27, 2019, in Tallahassee, Florida. He was 88 years old.

Schrieffer was the “S” in the famous BCS theory of superconductivity, one of the towering achievements of 20th century theoretical physics, which he co-developed with his Ph.D advisor Professor John Bardeen and postdoctoral colleague Dr. Leon N. Cooper. At the time that Schrieffer began working with Bardeen and Cooper, superconductivity was regarded as one of the major challenges in physics. Since the discovery of the hallmark feature of superconductivity in 1911—the zero resistance apparently experienced by a current in a metal at temperatures near absolute zero—a long list of famous theoretical physicists had attempted to understand the phenomenon, including Albert Einstein, Niels Bohr, Richard Feynman, Lev Landau, Felix Bloch, Werner Heisenberg and John Bardeen himself (who was awarded the Nobel Prize for his co-invention of the transistor at around the time that Schrieffer began working with him in 1956).