Elizabeth Villa
TBCG / Beckman Institute
405 N. Mathews
Urbana, IL 61801 USA
Telephone: +1 (217) 244 7403
e-mail: villa@ks.uiuc.edu
Ribosome and me, Cape Cod 2007
Home Department:
Center for
Biophysics
and Computational Biology
University of Illinois at Urbana-Champaign
156 Davenport Hall
607 South Mathews Avenue
Urbana, IL 61801
Research Projects
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| Multiscale modeling of protein-DNA complexes | Flexible Fitting of Atomic Structures into EM maps | Structure and Dynamics of the Ribosome |
Publications
Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Kirby Vandivort, James C. Phillips, Elizabeth Villa, Peter L. Freddolino, James Gumbart, Leonardo G. Trabuco, Danielle E. Chandler, Jen Hsin, Christopher B. Harrison, Laxmikant Kale, and Klaus Schulten. Proceedings of the 2008 TeraGrid Conference, 2008.
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16:673-683, 2008.
Molecular mechanisms of cellular mechanics. Mu Gao, Marcos Sotomayor, Elizabeth Villa, Eric Lee, and Klaus Schulten. Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.
Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005.
Structural dynamics of the Lac repressor-DNA complex revealed by a multiscale simulation. Elizabeth Villa, Alexander Balaeff, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 102:6783-6788, 2005.
Multi-scale method for simulating protein-DNA complexes. Elizabeth Villa, Alexander Balaeff, L. Mahadevan, and Klaus Schulten. Multiscale Modeling and Simulation, 2:527-553, 2004.
Teaching
Summer School on
Theoretical and Computational Biophysics. Urbana, 2003.
A great source for tutorials on Molecular Graphics, Molecular Dynamics,
Bioinformatics,
and other theoretical areas of Biophysics.
Winter School on
Theoretical and Computational Biophysics. Perth, Australia,2004.This time we went to Australia, in the first of a series of new schools. Updated tutorials, and fun pics.
Computational
Biophysics Workshop. San Francisco, California, 2005.We have now established a series of workshops in which twenty students learn all the material out of 15" powerbooks. This one happened to be in a great location. All the tutorials are available online on all platforms!