Friday, December 4, 2009

Getting the word out

Dr. Mardis recently published a review article with her Argonne National Laboratory colleague, David Tiede, in the journal Photosynthesis Research.  The paper describes their use of the Advanced Photon Source at ANL to perform X-ray scattering experiments in solution.  Like X-ray crystallography, the technique is used to determine molecular structure.  The figure below, taken from their paper, provides an overview of the experiment.

High energy X-rays from the APS are directed towards a molecule in solution.  In the review, Dr. Mardis and co-authors focus on biological molecules like proteins and DNA.  X-rays "bounce" off the dissolved molecules, forming a 2D diffraction pattern.  That data can be further processed into a 1D spectrum of intensity versus frequency.

As if focusing high brilliance, high energy photons from a synchrotron source onto a temperature-controlled solution of biological material weren't difficult enough, the data from the experiment, at first glance, don't mean a whole heck of a lot.  That's where Dr. Mardis comes in.

Dr. Mardis is the computational chemist at CSU and she performs molecular dynamics simulations on a rather high-powered computer cluster.  [Note: I've been asking her for months now to host a Call of Duty 4 tournament, but she claims the NIH would not buy the argument that gaming would increase productivity.]  Molecular dynamics is the study of how molecules move, and Dr. Mardis' computational simulations of molecular motion can be used to explain experimental observations.

In X-ray crystallography, the diffraction pattern can be converted into a single structure of a molecule.  However in solution, a molecule is moving, stretching, vibrating, and spinning; and each orientation contributes differently to the 1D pattern of the X-Ray scattering experiment.  With molecular dynamics, Dr. Mardis determines a whole bunch (say, 1000) of structures that a molecule can exist in and then predicts the X-ray scattering pattern for each structure.  After averaging all those patterns together, she gets a final graph that looks pretty darn close to what her experimental colleagues find in the lab.

Dr. Mardis recently spoke about this publication at a departmental seminar.  Spending the summer at a national lab (and the hope of playing video games at break-neck speeds) is just one of the advantages of working in her research group.  If you'd like to read the article, you can find it here if you have access to the journal or contact Dr. Mardis for a copy (this link sends you to the CSU Chemistry and Physics faculty contact info).

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