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Physicist Lands Supercomputer Time Fund for SJU

Wednesday, November 2, 2016

Md Rejwan Ali, Ph.D., assistant professor in the Department of Physics and an expert in experimental and computational biophysics research with applications in protein target and drug design, has just made St. John’s University one of the recipient institutions in supercomputing time at the undergraduate level. He was awarded a supercomputer resources allocation from the National Science Foundation (NSF) for approximately $25,307 in high-end computational resources, visualization, and storage. The allocation initially covers one year, from October 2016 to October 2017, and can be renewed under NSF advanced computing infrastructure program policies.

The allocation makes use of the Extreme Science and Engineering Discovery Environment (XSEDE), a virtual system for scientists to share computing resources, data, and expertise. Through XSEDE, the SJU physics department will now be able to use the Stampede supercomputer from the Texas Advanced Computing Center (TACC), along with 500 GB of archival storage. The technology will enable SJU students and faculty to perform molecular simulations of protein and ligand complex system to pinpoint how a drug targets and binds to certain proteins. The technology also aids researchers in designing drugs for many lethal diseases like Alzheimer’s, Parkinson’s, and cancer.

“It’s amazing that so many chemical reactions and molecular recognition processes are simultaneously taking place in one living cell. We just simulate one at a time, and it takes a supercomputer 24 computational hours to capture a few nanoseconds of a single process in a real-time scale,” said Ali. “Biology is an incredibly complex system to understand via physics-based equations and models. Our chair, Professor Mostafa Sadoqi, has been very auspicious and supportive of these new directions in computational biophysics research,” said Ali.  

Ali looks forward not only to the research advances facilitated by the supercomputer resources, but also to the training opportunities it will make available to undergraduate students at St. John’s. Unlike most personal computers, supercomputers use the Linux operating system, and SJU undergraduates will gain valuable first-hand experience using this technology. “New York City has many excellent graduate programs for computational and experimental biophysics,” said Ali. “My goal is to provide adequate undergraduate exposure to supercomputing and the Linux operating system for our students to get into those programs. This kind of technological environment usually isn’t available in a smaller laboratory setting – as TACC is now the most powerful supercomputer in academia and the twelfth fastest supercomputer in the world.”  

“Dr. Ali’s NSF grant will offer our students a novel opportunity for learning and expanding their undergraduate experience,” said Professor and Chair of physics Mostafa Sadoqi, Ph.D. “They will be introduced to the exciting and innovative areas of computational biophysics, quantum chemistry, computational drug design, and bioinformatics. Also, the grant will expose them to the high-performance computing system for learning computational techniques in biophysics or other fields and will provide them with adequate preparation for graduate programs in this rapidly growing field. We extend our congratulations to him for this grant.”