uring Winter and Spring Quarters, the Supercomputing Institute sponsored an Undergraduate Internship Program for eleven University of Minnesota undergraduates. These interns were chosen from twenty-three applicants to work ten-week appointments with faculty investigators from the University of Minnesota. The program allowed the students to perform research in close collaboration with these faculty investigators and their research groups and to discuss research with faculty members, post-doctoral associates, graduate students, and other interns with similar interests.
The program helps promote undergraduate involvement in ongoing and new research in scientific computing, digital technology, and visualization in the physical, medical, and social sciences and engineering. New software development efforts for scientific computing and graphics support for such research are also supported with the main goal being to carry out useful and interesting research. Overall, this program provides an opportunity for challenging and enriching educational experiences for undergraduate students interested in pursuing graduate or professional education and research in scientific computing and graphics.
Project Descriptions
Stefan Debbert worked with Professor Christopher Cramer of the Chemistry
Department during Winter Quarter on didehydroarenes, long known as reactive
intermediates. Hydrogen-abstracting propensities of didehydroarenes are closely
tied to the separation between their singlet and triplet spin states. Relative
energies for these states can be influenced by geometry and incorporation of
heteroatoms into the aromatic ring. Properties of the benzynes, pyridynes, and
pyridynium cations were compared and contrasted. Singlet-triplet splittings
in the pyridynium cations and 1H hyperfine couplings in the protonated pyridyl radicals were found to be well correlated.
David Dermer worked with Professor J. Ilja Siepmann of the Chemistry Department during Winter Quarter. They studied Monte Carlo calculations for perfluoroalkanes and their mixtures with alkanes and semifluorinated alkanes. Vapor-liquid coexistence curves of normal perfluoroalkanes with two to eight carbon atoms were calculated using configurational-bias Monte Carlo calculations in the Gibbs ensemble. A new set of united-atom Lennard-Jones interaction parameters for normal perfluoroalkanes were derived from fitting to saturated liquid densities and critical temperatures. The influence of semifluorinated alkane surfactants on the solubility of alkanes in perfluoroalkanes was also investigated.
Daniel Dittmer worked with Professor Alon McCormick of the Chemical Engineering and Materials Science Department during Spring Quarter on simulating the adsorption of xylene in zeolites. Zeolites are highly crystalline alumino-silicate frameworks whose pore sizes can be modified for use as molecular sieves. Cation effects can also be introduced by changing the silicon to aluminum ratio. Xylene is a colorless, oily, liquid aromatic hydrocarbon that can be obtained from petroleum. Separation of the isomers in xylene is difficult using standard distillation techniques. Finding a zeolite that would selectively absorb a particular isomer of xylene is then beneficial. The simulation of adsorption of xylene in zeolites was accomplished using several FORTRAN programs developed and run on IBM SP supercomputers. Analysis of the resulting data was performed using software on SGI workstations.
Derek Dolney worked with Professors Donald Truhlar and Christopher Cramer of the Chemistry Department as an intern during Spring Quarter. Their work presented three new parameterized solvation models in which the electrostatic part of the calculation is based on the conductor-like screening model (COSMO) parameterized for use with semiempirical Hamiltonians. Convergence of the calculated polarization free energies with respect to the numerical parameters of the model was examined. Accuracy and precision of the calculated values were improved by adjusting two parameters that control segmentation. Accuracy was further improved by adopting an optimized set of empirical electrostatic atomic radii. COSMO was then combined with SM5 surface tension functionals to compute the non-electrostatic portions of the solvation free energy.
David Dreytser worked with Professor David Thomas of the Biochemistry, Molecular Biology, and Biophysics Department during Winter and Spring Quarter on modifying the three-dimensional, atomic model of phospholamban, a 52 amino acid integral membrane protein of the sarcoplasmic reticulum, using molecular simulation software. This involved a search to find favorable packing arrangements for pentameric forms of phospholamban and modeling of its mutants. Their relative stabilities were then measured, and a suitable spacer was found. This required comparing the viability of different spacers with each other using molecular dynamics programs with an applied force between the bonding sites in order to force the spacer and phospholamban together. Results were consistent with laboratory experiments and provided a good structural model of the pentameric transmembrane domain of phospholamban.
Michael Enz worked with Professor David Thomas of the Biochemistry, Molecular Biology, and Biophysics Department during Winter and Spring Quarter on simulating random motion of spin labels attached to myosin molecules. Simulations and analysis were done on five different regulatory domain, myosin mutants. All mutants had previously been created in the wet-lab, so order parameter data was compared with simulations. A strong correlation was found between the simulated and experimental order parameters for the mutants investigated. Continued work was done to find a lower energy starting structure. Overall, the orientation of the spin label was found to be highly dependent on the initial structure.
Zack Greskowiak worked with Professors Douglas Ohlendorf of the Biochemistry, Molecular Biology, and Biophysics Department during Spring Quarter. Zackšs project was designed to find out which sites or portions of the TSST need to be mutated in order to bind to class I MHCs. The TSST is known to bind to class II MHCs and their structures have been solved. Zack worked on comparing and contrasting the known class II MHCs and all relevant binding TSST data to the class I MHCs to find similarities between them.
Justin Hietala worked with Professor J. Woods Halley of the Physics Department during Winter and Spring Quarter on modeling evaporation of helium atoms by sending a pulse through a metal film adjacent to a film of helium. The absorption of these atoms by a bolometer was also studied. Justin varied the kapitza resistances and temperature dependence in the specific heat calculation to see what effects differences in these would have on the overall temperature versus time dependence. He then made the number of atoms in the source dynamic by changing the thickness of the film as atoms were evaporated off. The code was then rewritten for the calculation of the power the atoms carry as they reach the bolometer after being evaporated.
Justin Sytsma worked with Professor George Wilcox of the Pharmacology Department during Winter and Spring Quarter on mathematical modeling of different pain fiber geometries and their affect of action potential generation and propagation. Justin started with a simple single compartment model for an unmyelinated axon at a single point in space that used a sodium current to produce the initial depolarization of the action potential. A leak current was used for the repolarization. This model was extended to include multiple points along the length of the axon. Work was then done on displaying the information from the simulations in an easily readable, graphical form.
Matthew Young worked with Professor Dennis Hejhal of the Mathematics Department during Spring Quarter on studying Lacunary Fourier Series. Matthew coded a C program that computes the distribution function and first to tenth moments of Lacunary Fourier Series. The program was run for typical examples and was tracked on how quickly the distribution converges to the normal distribution. In addition, investigations were made to see if the moments converged to normal distribution moments. The numerical data indicates that the moments do converge.
Chun-Hung Yu worked with Professor L.E. Scriven of the Chemical Engineering and Materials Science Department during Winter and Spring Quarter on the basic design of a slot coating die. The uniformity of the flow delivered by the often chosen two-chamber-and-two-slot design was compared with the simpler one-chamber-and-one-slot design by models in which chamber flow is approximated by variable Poiseuille flow in a circular tube. In the simpler case, the model lead to a linear, second-order ordinary differential equation (ODE); in the two-chamber-and-two-slot case, the model lead to a linear fourth-order ODE solved here for the first time.
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