CPLC second summer school a big success

Jaya Yodh
7/26/2010

The Center for the Physics of Living Cells (CPLC), an NSF Physics Frontier Center that includes Illinois researchers from physics, chemistry, biochemistry, microbiology, and electrical engineering, as well as faculty from Baylor University and The University of Notre Dame, held its 2nd annual ‘Physics of Living Cells Summer School’ from July 19-24, 2010, in Urbana.

Participating faculty included CPLC Co-Directors Taekjip Ha and Klaus Schulten, Paul Selvin, Yann Chemla, Aleksei Aksimentiev, and Nigel Goldenfeld, all from the Department of Physics, Zan Luthey-Schulten and Martin Gruebele from the Department of Chemistry, and Ido Golding and Anna Sokac from Baylor University College of Medicine, Department of Biochemistry and Molecular Biology. 

These researchers are pioneering the creation of synergies between different approaches, such as single-molecule and live-cell experimental techniques and biological computation and theory, to investigate biological problems such as dynamics of protein folding and gene expression in live cells, mechanics of protein-DNA interactions during replication and recombination, and structural and functional dynamics of the ribosome translational apparatus.

The Summer School, coordinated by Jaya Yodh, CPLC Director of Education and Outreach, is targeted at senior undergraduates, graduate students, postdoctoral fellows, and researchers in the chemical and life sciences, biophysics, physics and engineering who are looking to expand their research skills in these fields. This year's Summer School included 28 graduate students, 7 post-doctoral fellows, and 1 assistant professor, with 36 percent coming from International institutions and 22 percent of the US students coming from Midwest institutions. This year, nine of the international students are also currently participating in a ‘Junior Nanotech Network’ student exchange program between the CPLC/University of Illinois and the University of Münich.

The weeklong Summer School program included two-plus days of "basic training" elements for all participating students including lectures by CPLC faculty, a CPLC poster session, and introductory mini-courses taught by CPLC graduate students and postdocs on optics, software (Matlab, Labview), and Visual Molecular Dynamics (VMD).  A subsequent four-day "advanced module," also taught by CPLC graduate students and postdocs, offered intensive training in one of the following eleven topics based on faculty areas of expertise: 1) single-molecule FRET (Taekjip Ha); 2) single-molecule FIONA (Paul Selvin); 3) single-molecule force and optical trapping: (Yann Chemla); 4) super-resolution fluorescence microscopy (PALM/STORM) (Taekjip Ha), 5) single-event detection in living cells—bacterial swimming (Ido Golding and Yann Chemla); 6) single-event detection in living cells—phage infection (Ido Golding); 7) tracking cell surface growth in living fruit fly embryos (Anna Sokac) 8) Fast Relaxation Imaging (FReI): protein folding dynamics in living cells (Martin Gruebele); and three computational biophysics modules—9) molecular dynamics simulations of single-molecule motors (Klaus Schulten); 10) dynamical networks in protein: RNA assemblies (Zan Luthey-Schulten); and 11) observing biomolecular interactions with atomic resolution (Alek Aksimentiev).

One of the unique aspects of the CPLC Summer School is that the Center’s focus— physical quantification of processes in living cells—makes it possible to offer hands-on, on-site training. "We have a critical mass of experimentalists, computational physicists, and theorists in the Center, which also allows for integrative training in a diverse range of experimental and computational techniques," said Summer School organizer Jaya Yodh. .

Another significant impact the Summer School provides is an excellent opportunity for the Center’s own graduate students and post-doctoral fellows—a total of 25 this year—to gain valuable teaching experience to their peers. This interaction serves as an excellent foundation for knowledge transfer and networking between the next generation of scientists interested in the physics of living systems.

The value of the Summer School can be summed up in this testimonial by Ruby May Sullan, a student from University of Toronto, “...Talk about comprehensive learning, hands-on instrumentation on state-of-the-art equipment, stimulating discussions with leading fellows in their field, great interaction with fellow graduate students, nice UIUC environment, fun, fun, fun—all in a week’s time—that's CPLC summer school! One of the best weeks I’ve had!”

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The most intriguing and relevant science happens at the highest levels of scientific pursuit-at major research universities and laboratories, far above and beyond typical high-school science curriculum. But this summer, 12 rising high school sophomores, juniors, and seniors-eight from Centennial and four from Central High Schools, both in Champaign-had the rare opportunity to partake in cutting-edge scientific research at a leading research institution.

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Imagine planting a single seed and, with great precision, being able to predict the exact height of the tree that grows from it. Now imagine traveling to the future and snapping photographic proof that you were right.

If you think of the seed as the early universe, and the tree as the universe the way it looks now, you have an idea of what the Dark Energy Survey (DES) collaboration has just done. In a presentation today at the American Physical Society Division of Particles and Fields meeting at the U.S. Department of Energy’s (DOE) Fermi National Accelerator Laboratory, DES scientists will unveil the most accurate measurement ever made of the present large-scale structure of the universe.

These measurements of the amount and “clumpiness” (or distribution) of dark matter in the present-day cosmos were made with a precision that, for the first time, rivals that of inferences from the early universe by the European Space Agency’s orbiting Planck observatory. The new DES result (the tree, in the above metaphor) is close to “forecasts” made from the Planck measurements of the distant past (the seed), allowing scientists to understand more about the ways the universe has evolved over 14 billion years.

“This result is beyond exciting,” said Scott Dodelson of Fermilab, one of the lead scientists on this result. “For the first time, we’re able to see the current structure of the universe with the same clarity that we can see its infancy, and we can follow the threads from one to the other, confirming many predictions along the way.”

It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle.

The findings are reported in the journal Nature Communications.