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Journal of the Pennsylvania Governor's School for the Sciences Journal of the Pennsylvania Governor’s School for the Sciences Class of 2007 Volume 26, 2008 Mellon College of Science Carnegie Mellon University, Pittsburgh, PA 15213 Journal of the Pennsylvania Governor's School for the Sciences Class of 2007 Volume 26, 2008 Copyright (c) 2008, by The Pennsylvania Governor's School for the Sciences and Carnegie Mellon University Permission is granted to quote from this journal with the customary acknowledgement of the source. To reprint a figure, table or other excerpt, requires, in addition, the consent of one of the original authors and notification of the PGSS. Journal of the PGSS Page iii Table of Contents Preface ..................................................................................................................................................1 Biology Team Projects Detection and Identification of Genetically Modified Soy (Glycine max) in Assorted Chocolate Food Products Bhaskar, Hanzok, Kedar, Lu, Oniskey, Punati, Qin, Reddy, Shoemaker, Singh, Viswanathan, Young .............................................................................................................................................5 Determination of the Midpoint of Adolescent Myelin Maturation as Measured by Change in Radial Diffusivity in Diffusion Tensor Imaging Baybars, Chang, Jiang, Onofrey, Ponnappa, Ponte, Ramgopal, Shen, Trevisan, Sheng, .........35 Biophysics Team Projects The Isotope Effects of Deuterium on the Enzyme Kinetics of Alcohol Dehydrogenase Alla, Bharathan, Comerci, Desai, Field, Gillis-Buck, Hsu, Jain, Kessler, Kim, Kozminsky, Magge, Negrin, Owunna, Rogi, Tadavarthy, Vin, Wang, Wu, Zimmerman ..............................................69 Chemistry Team Projects Computational Predictions of Chromatographic Selectivity of Stationary Phases Badgley, Carpenter, Rastogi, Widenor, Zhang.............................................................................95 Effects on Resistance and Lattice Structure Using Substitution-Based Superconductors Cockerham, Frey, Herrold, Johnson, Ko, Lucas, Phan, Rosario, Ru.........................................117 Computer Science Team Projects LexerEvolution Bruggeman, Chu, Jiang, McGuier, Shotter, Triano ....................................................................159 Project LPX: A Functional Web Design Language in SML Elfont, Guenin, Kamani, McDowell, Ruberg ...............................................................................169 Mathematics Team Projects Isomorphisms of Three-Dimensional Lie Algebras Chan, Falk, Radomy, Wang, Warner..........................................................................................181 Journal of the PGSS Page iv Physics Team Projects Gambling for the Truth: A Monte Carlo Simulation of Magnetic Phase Transitions Helbers, Jordan, Petkun .............................................................................................................199 An Investigation of Chaos in One and Two Dimensions Das, Goyal, Manolache, Morris, Paul, Sampath.........................................................................225 A Verification of Wave-Particle Duality in Light Alexakos, Harder, Kapelewski, Long, Manolache, Miller, Rahman, Rastogi, Reichardt, Rhinehart ....................................................................................................................................................241 Wil-ber-force Be With You: An Analysis of the Wilberforce Pendulum Cook, Han, Jin, Menendez, Nataraj, Stein, Strom, Sunday, Yang .............................................283 Appendix The Students, Faculty, Teaching Assistants/Counselors of the Pennsylvania Governor's School for the Sciences for 2007................................................325 Journal of the PGSS Page 1 Preface The Pennsylvania Governor's School for the Sciences (PGSS) is a five-week residential summer program held on the campus of Carnegie Mellon University for talented Pennsylvania high school students. The PGSS was initiated and is supported by the Pennsylvania Department of Education (PDE). It has been continuously operating since 1982. The 2007 class consisted of 100 students, 56 male students and 44 female students. The PGSS was in session from June 24 to July 28. The program is very intense; students take formal courses in biotechnology of HIV and AIDS, organic chemistry, concepts of modern physics, discrete mathematics and computer science. They also have the opportunity to take a number of elective courses and a laboratory course in biology, chemistry, computer science or physics. A major objective of the PGSS is to provide an opportunity for students to participate in college-level courses, laboratories and research experiences designed to enrich their background in science and to encourage them to pursue technological careers. One of the many student activities during the PGSS is the participation in a team research project in biology, chemistry, computer science, mathematics or physics. Team research projects involve the investigation of an original problem or the solution of a problem by techniques original to the investigators. The students choose the area of science for their project and faculty suggest specific possible topics in these areas. Interested students form teams. While faculty is available for initial direction and advice, most of the accomplishments come from the students' own initiative. The Journal of the Pennsylvania Governor's School for the Sciences reports the results of the students' efforts and is the official record of these team research projects. Each team investigated their chosen problem using resources and techniques appropriate for that topic. The following reports were written by the student team members. The faculty in each respective area reviewed the final reports and made necessary minor corrections. This journal was edited by Maria Wilkin, who assumed the responsibility of converting all the reports to a similar format, reproducing figures, and dealing with other publication issues. Otherwise, the original character of the student-authored papers was maintained to the maximum feasible extent. The PGSS gratefully acknowledges the continuing support of the Mellon College of Science at Carnegie Mellon University and generous contributions from the parents and guardians of the PGSS Class of 2007. Barry B. Luokkala, Ph.D. University Director of the Pennsylvania Governor's School for the Sciences April 2008 BIOLOGY TEAM PROJECTS Detection and Identification of Genetically Modified Soy (Glycine max) in Assorted Chocolate Food Products Ashok Bhaskar, Jackie Hanzok, Vijay Kedar, Louis Lu, Taylor Oniskey, Ramya Punati, Frank Qin, Varun Reddy, Katie Shoemaker, Rohini Singh, Varun Viswanathan, Matthew Young Abstract Soybean (Glycine max) is a major commercial GM crop found in many products including various chocolate products (Theobroma cacao derivatives) and was detected and identified through the utilization of techniques in DNA and protein isolation, PCR analysis, and ELISA. The purpose of the experiment was to detect GM soy in assorted chocolates, to determine whether products corroborate or conflict with the “organic”/“non-GMO” claim made on product labels, and to compare the prevalence of genetic modification in small samples of American and European chocolates. The PCR analysis yielded inconclusive results for most samples; there was some evidence for GM in a few samples, but the sequences could not be conclusively linked to soy. A kanamycin selectable marker was identified, but further studies are required for a definitive conclusion. In the ELISA analysis, five chocolate samples tested slightly positive for Roundup Ready® protein indicating the possible presence of CP4-EPSPS. Improving DNA extraction is necessary for further work. I. Background A. An Introduction to Genetically Modified Organisms A gene is a section of DNA that encodes for a specific inherited trait. Whereas genes can be altered through natural mutations, scientists can also create a genetically modified organism (GMO) by experimental means such as by inserting a gene from one species into another species, inducing the organism to express traits that it would not usually have1. Scientists have several methods of making recombinant DNA. One method is using a transformed bacterium as a vector to transform other organisms2. A second commonly-used method is to insert DNA-coated particles via a gene gun into a cell that will uptake the foreign DNA and incorporate it into its chromosome. A third method involves cross-breeding GM plants through cross-pollination, encouraging a certain phenotype to be acquired by more organisms1. In general, genetic modification can be useful in developing organisms that overcome the obstacles they face in the environment. Introducing herbicide-resistant genes into plants, for example, enable farmers to use herbicides more liberally with less damage to crops and to plant more crops per acre3. Pest-resistant plants reduce the need to spray pesticides, decreasing side effects on non-target insects. As a result, crop yield may improve. Page 6 Bhaskar, Hanzok, Kedar, Lu, Oniskey, Punati, Qin, Reddy, Shoemaker, Singh, Viswanathan, Young Alternatively, the taste, hardiness, and nutritional value of certain foods can be improved via genetic modification3. For example, introducing pectin into tomatoes increases water retention, making the tomatoes plumper and juicier4. Golden rice is healthier rice that has been genetically engineered to produce beta-carotene, a precursor
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