A PhD Student’s Summer Research Experiences at ChemMatCARS

During August 2015, ChemMatCARS welcomed a PhD student, Travis Mitchell, from Prof. Jason Benedict’s group in University at Buffalo to participate in synchrotron x-ray scattering experiments in the Advanced Crystallography for his research training. 


Prof. Jason Benedict

This past summer, Dr. Yu-Sheng Chen invited my first year graduate student, Travis Mitchell, to spend one month training and performing experiments at the ChemMatCARS Beamline at the Advanced Photon Source at Argonne National Laboratory. During his stay, Travis received an invaluable educational experience that spanned the teaching of the fundamentals of crystallography to participating in cutting edge synchrotron-based experiments with world class researchers. When not performing hands-on duties at the beamline, Travis’s time was spent reading a wide-variety of materials related to X-ray diffraction provided by Dr. Chen. With respect to hands-on training, Travis is now experienced in every aspect of crystal structure determination including sample preparation, data collection and structure refinement. Prior to his stay at ChemMatCARS, Travis was a young PhD student discovering himself within my research group. Travis is now without a doubt a more confident, mature, and capable chemical researcher who has a much better grasp of ‘big-picture’ concepts in Chemistry and thinks well-beyond his PhD. I remain incredibly grateful to ChemMatCARS for providing my student with such a rich and rewarding life experience.


Travis Mitchell

Dr. Yu-Sheng Chen invited me to participate in an internship at the Advanced Photon Source in the ChemMatCARS division within the Argonne National Laboratory. The internship was a month long experience during which I had the opportunity to work with Dr. Chen and his peers as well as users performing X-Ray diffraction studies using synchrotron radiation at 15 ID-B.

Prior to this experience, I had some exposure to XRD instruments: a home source at SUNY UB and two previous trips to the APS with my research group. On the home source, I was mainly told the general procedures for setting up an experimental data collection and which buttons to click in order to process the data eventually leading to a solved crystal structure with structure refinement with only a rudimentary knowledge with respect to what I was doing. I spent my first two visits to the APS mainly observing the senior students in my research group run the experiments. I didn’t have the experience or confidence to do anything myself other than an occasional unit cell determination or an attempt at solving a structure in Olex2. Fortunately, that all changed throughout the past month while working under Dr. Chen.

My first week at the APS, Dr. Chen had me read Foundations of Crystallography with Computer Applications by Maureen M. Julian which I supplemented with a few online resources. Dr. Chen’s recommendation was well received, and I was able to better understand some of the fundamental concepts of crystallography. The book covered many different topics: lattices, space groups, point groups, properties of x-rays and metric matrices to name a few. After reading that book, I had a better appreciation for all of the math and theory involved in crystallography which helped me prepare for the next three weeks.

The second week started the cycle when users visited APS to perform experiments on beamline 15 ID-B. Dr. Chen wanted me to be able to assist users with their experiments, so he first made sure that I was familiar with how to fill the liquid nitrogen tank safely to ensure that the Cryojet was always supplied with liquid N2 for users that required lower temperatures for their experiments. I honed my skills on making fibers from capillary tubes to be used for mounting crystals for experiments to be ran in the hutch. Dr. Chen showed me how to properly turn on the beam, once the hutch was searched, and use attenuators if necessary. He also showed me how to use the command prompt to test for oversaturation during data collection on the CCD. I worked with a user who was performing charge density studies which really put my crystallography knowledge to the test. I now know how to set up a charge density study which required collecting experimental data at both high and low angles. Following data collection, I gained experience in properly integrating the data and learned the importance of updating the orientation matrix with each successive integration. I also learned how to go through the lst file and determine how good the collected data was. The remainder of my stay with Dr. Chen allowed me to have continuous exposure to ApexII and become more familiar with its uses.

During the middle of my internship, my research group, from SUNY UB, had beamtime for a week at 15 ID-B. This time around, I was able to be more involved with running experiments. I was confident enough to step up and was even able to run a couple of day shifts myself which made me even more confident with using the beamline. Following my group’s departure, I worked with a few more users. I was able to experience another charge density study followed by a search for phase transitions at liquid helium temperatures.

As a graduate student studying in a research group that does crystallography, this internship will have a profound impact on my future. I now have another path down which I can go as I make progress towards obtaining my PhD and eventually a postdoctoral position where I can see myself doing crystallography. This internship opened a whole new world of possibilities for career opportunities as well, one of which involves me working as a crystallographer solving crystal structures for pharmaceutical companies or other major industries as a part of a company or my own company. With more training, another possibility involves me running a beamline by myself at the APS as a career beamline scientist. I know that with the training I received from Dr. Chen and continuing to learn, I will have the opportunity to have a successful career as a crystallographer if I choose to take that path.

All-in-all, Dr. Chen is an amazing mentor. While Dr. Chen was tough with me, it was for the best; he wasn’t afraid to point out my mistakes which allowed me to learn from them which I greatly appreciate. After returning home, I’ve been participating in some crystallography challenges setup by the crystallographer in my research group, so I’m continuing to apply the knowledge I gained with Dr. Chen even after my internship. I’m eager to learn other techniques that require synchrotron radiation and hope that I will have that opportunity in the future. I’d like to thank Dr. Chen, his peers, users at 15 ID-B with whom I worked, Argonne National Laboratory and the University of Chicago for the opportunity.