NERSC & LCLS Team Up on SARS-CoV-2 Research

The Linear Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory is a NERSC Superfacility Partner

NERSC is working with scientists and staff at LCLS to enable real-time data analysis for two LCLS experiments examining the structure of the SARS-CoV-2 virus.

The first beam time (Aug 14-17) by Hasan DeMirci’s group at Koç Üniversitesi (with an international research team) studied two crystal forms of SARS-CoV-2 main protease (Mpro) at near-physiological-temperature which offers invaluable information for drug-repurposing studies. LCLS data systems division in partnership with SLAC scientific computing services, NERSC and CRD, built an SFX analysis pipeline to optimize for running on NERSC resources. Optimizations included improved communication, minimizing I/O, and seamless portability from LCLS to NERSC through a Docker/Shifter environment, and customized job submission to the batch queue system for optimized node sharing and memory allocation. NERSC and CRD staff assisted with the real-time data analysis.
The second beam time (Sept 18-21) studied the atomic structure, dynamics, and function of the SARS-CoV-2 main protease (Mpro) and the papain-like protease (PLpro) at room temperature. These two enzymes are critical to the life cycle of the virus in human cells. The goal of the international team (in collaboration with LCLS and NERSC staff) is to inhibit these two enzymes with chemical compounds contributed from the COVID-19 Moonshot initiative that may eventually lead to antiviral treatments in humans. The collaboration used LCLS to determine the time-resolved atomic structure from a slurry of microcrystals to which the drugs are added. The ability to process data in near to real time with access to resources at NERSC was essential for the team's decision making processes during the beamtime.

About NERSC and Berkeley Lab
The National Energy Research Scientific Computing Center (NERSC) is a U.S. Department of Energy Office of Science User Facility that serves as the primary high performance computing center for scientific research sponsored by the Office of Science. Located at Lawrence Berkeley National Laboratory, NERSC serves almost 10,000 scientists at national laboratories and universities researching a wide range of problems in climate, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a DOE national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. Department of Energy. »Learn more about computing sciences at Berkeley Lab.