CUDA IN ACTION

CUDA + Research

Dramatically Accelerating Virus Simulation

		Viruses, the cause of many diseases, are the smallest natural organisms known. Because of their simplicity and small size, computational biologists selected a virus for their first attempt to simulate an entire life form using a computer, choosing one of the tiniest, the satellite tobacco mosaic virus. Researchers simulated the virus in a drop of salt water using a program called NAMD (Nanoscale Molecular Dynamics) from the University of Illinois at Urbana-Champaign.
Overview of STMV, showing the protective capsid enclosing the viral genome.	Icosahedral layout of the STMV capsid.

NAMD has been accelerated to run up to 12 times faster with CUDA™, achieving dramatic speedups of up to 330X vs. a single CPU core, when runing on a GPU-accelerated cluster at the National Center for Supercomputing Applications (NCSA). Researchers are optimistic that this step will assist modern medicine in efforts to better understand and treat viral illnesses.

For more information, please visit: www.ks.uiuc.edu/Research/namd/

Sites of ions binding the viral genome, located using a CUDA-accelerated program

Sites of ions (orange) binding the viral genome, located using a CUDA-accelerated program.