Published in Interface. Vol. 2, No. 2, May 1994

University of South Alabama

by J.D. Becker

The research mission at the University of South Alabama (USA) includes an ongoing commitment to utilize faculty expertise to benefit the state and region. Benefits resulting from faculty research provide extraordinary dividends to society through both the creation of new knowledge and the application of that new knowledge. Research, as a mission focus along with teaching and service, is considered by USA to be integral to the success of a strong instructional program.

Computational research is broadly dispersed across four colleges and one school across campus including Arts and Sciences, Engineering, Business and Management Studies, Medicine, and the School of Computer and Information Sciences. Faculty members frequently seek to enhance the studies of undergraduates and graduates through including these students as active participants in their computational research projects. Resources of the Alabama Supercomputer Network are used to facilitate USA research efforts in medicine, mathematics, statistics, engineering, economics, psychology, genetics, and high-energy physics.

Current research efforts in the College of Engineering are focused primarily on computational fluid dynamics (CFD) and heat transfer and the simulation of breaking water waves. Supported by the NASA JOVE program and NASA Langley Research Center, one project concerns turbulence modeling for strongly swirling flows such as aircraft trailing wing-tip vortices. Under the sponsorship of local industry and the Alabama/Tennessee Valley Research Consortium, CFD simulations of the flow patterns within a gas turbine combustor have recently been completed.

USA researchers working under a grant from Cray Research Inc., have developed a boundary element method (BEM) computer system for the simulation of breaking water waves. The BEM system accurately models the highly nonlinear, periodic water waves in the physical space, including the development of plunging breakers, without numerical instability. The BEM system uses the innovative Overhauser elements to eliminate discontinuities of slope on the water surface. To model the water wave as it moves through time, the BEM method is used to solve for the potential gradients on the wave surface. These gradients are then used with an Adams-Bashford-Moulton time stepping algorithm to calculate the location of the water surface at the next time step. This process is repeated until the wave breaks, the surface "folds" on itself, and the governing equations are no longer valid.

Researchers in the Chemistry Department are developing and applying computational techniques to a variety of problems in physical, organic, and biophysical chemistry. Some of the techniques being used to study problems in these fields are quantum chemistry, molecular mechanics, molecular dynamics, Monte Carlo, Poisson-Boltzmann electrostatics, crystal morphology, and Brownian dynamics.

One area of interest is in the application of Poisson-Boltzmann electrostatics, protein-dipole langevin-dipole (PDLD), and Brownian dynamics to study enzyme-substrate interactions. Of particular interest is understanding the interactions between sulfonamides and human carbonic anhydrase. This particular enzyme-substrate complex is of interest because of its relationship to a common eye-disorder known as glaucoma. Untreated glaucoma can eventually lead to blindness. The Cray is being used to compute enzyme-substrate interactions using the University of Houston Brownian Dynamics (UHBD) program.

Another area of interest is the study of the adsorption-inhibition mechanism of antifreeze peptides in contact with ice. This project uses CHARMM to perform energy minimizations and molecular dynamics as well as QUANTA 4.0 to visualize the system and CERIUS to construct the crystal structures. Figure 6 summarizes the results of calculations. Figure 6(a) is a side view of winter flounder D-isomer (foreground) and L-isomer (background) on the (201) ice surface. Figure 6(b) is a rotated view of Fig. 6(a) in which one is now looking down the c-axis. The D-isomer is on the left and the L-isomer is on the right. In this view, each peptide is represented as a helical backbone with the leucine, threonine, and asparagine side chains drawn explicitly.

A new and exciting area of research is the application of density functional methods to predict and understand organometallic chemistry. The Amsterdam Density Functional program (ADF) is being used on the Cray to calculate the reactivity of Vaska-like compounds containing rhodium.

Prediction of molecular properties for pteridine and folate substrates is another area of interest. Gaussian 92 is used to calculate the geometry and charges of these large substrates. The calculated properties are then visualized with Spartan on graphics workstations in the Chemistry Department. This work is being done in collaboration with scientists at the Medical School.

USA researchers are developing plans for the creation of two on-campus computational centers that will increase supercomputer usage, attract research, and promote interaction with local industry that has significant computational needs. One of the centers will be located in the College of Engineering and will be called the Center for Computational Mechanics. This facility will enable researchers from the four engineering departments to access a high-performance graphics workstation as well as the ASA Cray supercomputer.

The other center will be located in the Chemistry building and will be linked to two auxiliary sites located in the Life Sciences and the Medical buildings. This center will provide a computational facility for scientists in the departments of Biology, Chemistry, Geology, Marine Science, and Pharmacology.

The establishment of these two centers, combined with the recent upgrading of the USA local area network and the installation of high-resolution graphics workstations and software, will enable researchers at USA to have access to state-of-the-art visualization equipment that will facilitate and enhance usage of the ASA Cray. Along with the enhanced university research infrastructure, faculty opportunities in computational research are expected to substantially increase over the next several years.