Biophysics and engineering students from Johns Hopkins University and The Ohio State University (OSU) successfully used distance learning technology to participate in a short course, Molecular Modeling of Biological Interactions. Lectures culminated on March 31with two classes – one at the Ohio Supercomputer Center (OSC) and one at Hopkins more than 400 miles away. The classes studied how high performance computing (HPC) can advance scientific discovery in the biological sciences.
Taking science education beyond traditional textbook and theoretical approaches, Jim Giuliani, OSC’s Science and Technology Support Manager, presented an introduction to parallel computing. He demonstrated how parallel computing works, how it allows entirely new approaches to describing biological interactions, and brought to life parallel programming models in the context of biological systems. Giuliani focused on the software package, NAMD2, and how this molecular dynamics code runs on multiple processors.
Students then applied what they had learned about parallel computing to modeling molecular recognition in human immune system response. Students used classroom accounts to run the experiments on OSC’s 512-processor Pentium IV Xeon cluster.
The collaboration began as part of a request by Dr. Michael Paulaitis, Ohio Eminent Scholar Professor at OSU and Director of the Institute in Multiscale Modeling of Biological Interactions at Johns Hopkins. He recognized that the collaboration between OSU, OSC, and Johns Hopkins would facilitate interdisciplinary interactions among researchers and educators in the biological sciences, computation, and biotechnology areas.
“This collaboration represents a unique integration of expertise at OSU, OSC, and Johns Hopkins in the fields of advanced scientific computing, biophysics, and engineering,” said Paulaitis. “This effort will serve as a paradigm for interdisciplinary research and education in the biological sciences and bioengineering in the future.”
Dr. Paulaitis’ lab at OSU adopts an integrated approach to research in applying chemical engineering analytical and computational skills to address one of the most challenging problem in molecular biology and biotechnology -- organizing and interpreting vast amounts of data generated in the field today. Dr. Paulaitis’ specific research goals are to understand the inherently complex hierarchical relationships of biological organization, and develop novel approaches to data assimilation and handling.
For more information about using OSC’s machines or applying for an account, go to http://www.osc.edu/supercomputing/.
OSC is Ohio's high performance computing, networking, and research center. The Center provides scientific computing, networking, educational outreach, and information technology resources to state and national high performance computing and networking groups. OSC empowers its academic, industrial, and government partners to make Ohio the education and technology state of the future. More information about OSC can be found at www.osc.edu.