SDSC Summer Interns Gain Valuable Research Experience

xploration of distant galaxies and solar systems has been a long-time dream for UCLA undergraduate student Patricia Bakkers, who was able to experience astrophysics research first-hand this summer at SDSC. Participating in the SDSC summer intern program, Bakkers gained knowledge that was literally scintillating, as she worked on an astrophysics project with UC San Diego researcher Bernie Jackson. Bakkers was one of several students who participated in the summer program, supported by the UC Leadership Excellence through Advanced Degrees (UC LEADS), the California Alliance for Minority Participation in Science, Mathematics, Engineering, and Technology (CAMP), NSF's Research Experiences for Undergraduates (REU), and NPACI.

BROADENING HORIZONS IN COMPUTATIONAL CHEMISTRY

MODELING AIR FLOW IN THE VOCAL TRACT

FURTHERING EDUCATIONAL OUTREACH

UC San Diego undergraduate intern Sharokina Shahbaz studied the interfaces in about 175 protein-protein complexes. One such computation is shown in an illustration, by post-doctoral researcher Julie Mitchell, which depicts the shape of the interface between fasciculin, a component of snake venom (light gray), and the neurotransmitter acetylcholinesterase (dark gray). Red spheres denote points on the interface that suggest the docking of a protrusion into a crevice, while yellow and green spheres indicate the docking of flat surfaces. Mutations to areas with highly complementary shapes produce significant changes in the inhibitory, and hence toxic, activity of fasciculin.

Renee Link, a summer intern working with SDSC computational chemist Kim Baldridge, incorporated visualizations into the ElemNet Web site, which will include a section relating to the history of chemistry. This image created by Link is used as an image map, or clickable menu, in a section of the ElemNet site regarding the molecular aspect of chemistry history.

BROADENING HORIZONS IN COMPUTATIONAL CHEMISTRY

Other SDSC summer interns included Sharokina Shahbaz and Renee Link, both UC San Diego students. Shahbaz was mentored by Lynn Ten Eyck, SDSC associate director of computational science research, and Julie Mitchell, a postdoctoral researcher supported by the La Jolla Interfaces in Science program, while Link was mentored by SDSC senior scientist Kim Baldridge. Both Shahbaz and Link worked on projects that provided them with a better understanding of molecules, depicting them via both models and computer simulations.

Shahbaz's research project focused on describing the shape of proteins using the Fast Atomic Density Evaluation method, which finds indentations on a molecule's surface and depicts a global characterization of the molecular geometry. She worked closely with Mitchell on the analysis of docked complexes (Figure 1). One such complex analyzed by Shahbaz included fasciculin, a potent nerve toxin found in snake venom, bound with acetylcholinesterase, an enzyme essential for transmitting nerve impulses.

Link's project also consisted of computational modeling work, allowing her to study the details of molecular structure and properties. To accomplish her research, she used a combination of tools such as GAMESS, a quantum mechanical program co-authored by Baldridge, and QMView, a visualization tool authored by Baldridge and SDSC chemist Jerry Greenberg. "The tools allow us to get a visual conception of the molecules in three dimensions," Link said. "I have also been able to incorporate some of my visualizations into a Web site that we're working on regarding the history of chemistry."

The chemistry history project is part of an ongoing effort in Baldridge's lab known as ElemNet (Figure 2), a Web site that contains a number of chemistry tutorials, activities, and additional resources for primary, secondary, and college students. "The history of chemistry portion will specifically focus on biographical information on scientists and historical developments in chemistry," Baldridge said. "It's great for our interns to work on this project, as they know first-hand what students are most interested in learning and can use that insight to present the material in a manner that makes learning about chemistry fun for other students."

Arnaldo Rodríguez, a student from the University of Puerto Rico, and Elisa Toulson from UC San Diego were also interns in Baldridge's SDSC lab this summer. While Rodriguez worked with Link on 3-D models in QMView and GAMESS, Toulson concentrated on C programming and Web development. "I took a class at UC San Diego that taught me the basics of C programming, and this summer I wrote a script to put a simulation of a potassium ion channel on the Web," Toulson said. "This experience will help me with future class work by improving my programming skills, and I learned a lot about fundamental research in Dr. Baldridge's lab."

Christy Zales, a UC San Diego chemistry undergraduate student, was another SDSC summer intern working in the field of organic chemistry. Zales, who was mentored by Jay Siegel, conducted research on the synthesis of fluorescent organic molecules that bind metal ions selectively. Zales studied the relationship between the structures of these molecules and their fluorescent properties. In conjunction with Baldridge's lab, the research interfaces with ab initio quantum mechanical calculations, which can provide insight to rationalize and predict these fluorescent properties.

MODELING AIR FLOW IN THE VOCAL TRACT

Voice production occurs when air flows through a person's vocal folds and then past the lips. While the larynx is responsible for this sound production, the vocal tract acts as a filter--modifying the sound that produces speech. Extending from the vocal folds to lips, an adult's vocal tract measures approximately 17 centimeters in length and its shape changes with the movement of the tongue, jaw, palate, and lips. This summer, Caitlin Smythe, a UC San Diego sophomore in aerospace engineering, was able to closely examine the airflow in the vocal tract and gain a better understanding of fundamental fluid phenomena.

Mentored by SDSC researcher Richard Charles, Smythe gained a basic understanding of fluid dynamics, as well as insight about Charles' research regarding the various ways to model airflow over stylized vocal tracts. Smythe specifically focused on studying three methods of modeling airflow in cases with a straight pipe, a straight pipe with small constriction, and a straight pipe with a larger constriction.

Smythe also gained experience in reading and understanding scientific literature, as well as honing her research paper skills. Over the summer internship period, she wrote a paper that discussed accurate modeling of fluid flow in stylized vocal tracts, including the various uses of computational fluid dynamics tools to complete this task.

FURTHERING EDUCATIONAL OUTREACH

UC San Diego student Nicole Batchelor worked with the SDSC External Relations group this summer on the center's Education, Outreach, and Training (EOT) efforts. Batchelor wrote press releases and articles for Online, the biweekly newsletter for NPACI and SDSC, worked with the group's Web developers, and assisted the staff with a wide array of additional EOT activities. As a writing/literature major, Batchelor was excited to have the opportunity to focus on science writing. "This internship provided me with a chance to realize the importance of being able to write about science and computing," Batchelor said. "I learned so much from both the External Relations staff and the researchers at SDSC, and I am now considering a career in science writing after I finish my degree."

Another UC San Diego student intern working in the educational outreach arena at SDSC this summer was Daniel Lander, who worked with SDSC visualization researcher Mike Bailey. Lander helped develop a ripple simulation that is being used within the center's new EnVision, Explore, Engage project--an interactive version of enVision aimed at secondary students. Lander's task involved developing for middle school students a lesson plan about crystallography. He created a C++ program that presents students with pictures of ripples in various shapes; the students then determine what object (a box, triangle, or octagon) was dropped to form the effect.

"This project helped me gain a better understanding of simulations and I really liked working with Dr. Bailey's group," Lander said. "I'm still exploring all of my opportunities through classes and research like this, but I feel that I am heading towards graduate studies in computer engineering." --KMB *