Home Department: Physics 

Email: gumbart@ks.uiuc.edu

Telephone: 217-244-4361

Fax: 217-244-6078

Theoretical and Computational Biophysics Group
Beckman Institute, Room 3161
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

I am currently investigating the transport properties of the membrane channel SecY. SecY is part of a three-protein complex that serves to allow proteins to cross membranes or insert into them. This task is so important that a form of the Sec system exists in each domain of life! More information about this dynamic and multi-functional protein can be found at our Protein Translocation website.

Another interesting problem is how Gram-negative bacteria (those possessing two membranes surrounding them) import large nutrients across the outer membrane. Since they cannot generate energy at the outer membrane, they possess an inner membrane protein, TonB, that couples across the periplasm to an outer membrane transporter in order to import large molecules, such as vitamin B12. The mechanisms of this interaction and how it causes transport are still open questions in the field of microbiology.

Photosynthesis is an elemental process of nature and occurs not just in plants, but also in some bacteria as well. In these bacteria, membrane-bound pseudo-organelles known as chromatophores contain the proteins necessary to turn sunlight into chemical energy. These chromatophores come in different shapes depending on the organism but no one knows how they self-assemble into spheres or sheets, one question we now hope to answer.

(Talk) Regulation of the Protein-conducting Channel by a Bound Ribosome. James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Eduard Schreiner, Christopher B. Harrison, and Klaus Schulten. Biophysical Society Meeting, 2009. Boston, MA.

(Poster) Coupling of Ca2+ and Substrate Binding in the Outer Membrane Transporter BtuB. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Society Meeting, 2009. Boston, MA.

(Talk) Membrane Protein Insertion in the Translocon. James Gumbart and Klaus Schulten. CECAM Workshop on Membrane Protein Assembly: Theory and Experiment, 2008. Lausanne, Switzerland.

(Poster) The Roles of the Pore Ring and the Plug in the SecY Protein-conducting Channel. James Gumbart and Klaus Schulten. Biophysical Society Meeting, 2008. Long Beach, CA.

(Poster) Computational Studies of Substrate-dependent Behavior of the E. coli Cobalamin Transporter BtuB. James Gumbart, Christian Banchs, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Society Meeting, 2008. Long Beach, CA.

(Talk) Mechanics of force propagation in TonB-dependent outer membrane transporters. James Gumbart, Michael Wiener, and Emad Tajkhorshid. Biophysical Society Meeting, 2007. Baltimore, MD.

(Poster) Opening of the Lateral Gate of the Translocon SecY. James Gumbart and Klaus Schulten. Biophysical Society Meeting, 2007. Baltimore, MD.

(Poster) Dynamics of the Translocon SecY Investigated Through MD. James Gumbart and Klaus Schulten. Biophysical Society Meeting, 2006. Salt Lake City, UT.

(Talk) Modeling Magnetic Fields with FEMM 3.1. James Gumbart and James Rabchuk. American Physical Society Meeting, 2003. Austin, TX.

(Poster) Optimal perturbations of a finite-width mixing layer near the trailing edge. James Gumbart and James Rabchuk. American Physical Society Meeting, 2002. Indianapolis, IN.

Physics 550, Molecular Biophysics. Spring, 2006, 2008, 2009.
A course on biophysics for graduate students in physics. I was a teaching assistant which involved communicating with students, preparing solutions, and grading homeworks.

Physics 598NSM, Non-equilibrium Statistical Mechanics, Fall 2007.
I was the teaching assistant for this graduate level course for physics students. It was an excellent way to learn the material better than when I took the course myself!

Computational Biophysics Workshop. NIH, Bethesda, MD, Nov. 2007.
For this workshop, we went to the source of the Resource, the National Institutes of Health (NIH).

Computational Biophysics Workshop. Pittsburgh, Pennsylvania, Nov. 2006.
Another workshop in a fixed computer lab, this one was provided for students in the Department of Structural Biology at the University of Pittsburgh.

Computational Biophysics Workshop. Frankfurt, Germany, Mar. 2006.
This workshop served as the ultimate test of the training material; we allowed participants, students at the Max Planck Institute in Frankfurt, to use their own laptops. The material was up to the task however, working on any platform and operating system.

Computational Biophysics Workshop. Pittsburgh, Pennsylvania, Nov. 2005.
Here, we tried a new idea, in conjuction with the Pittsburgh Supercomputing Center: working on computers prepared on site instead of the usual laptops. It was a successful test of the portability of the training material.

Computational Biophysics Workshop. Lake Tahoe, California, May 2005.
This time, we took the laptops to the beautiful Sierra Nevada mountains. We had a great group of participants, including one bear!

Computational Biophysics Workshop. Boston, Massachusetts, Dec. 2004.
One of the early workshops. We took 20 laptops to a hotel in Boston and taught students from around the world.

Physics 112 (now 212). Fall, 2003.
An introductory calculus-based EM course for those in engineering and science. I led four discussion sections of approximately 20-25 students each.