355 – Supercomputing for COVID-19

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Guests: Andrew Emerson, Daniel Jacobson
Host: Markus Voelter   Shownoter: Andy Joiner

In this episode we look at how supercomputers are used to help with managing the pandemic. It’s a double-header with two guests. We start with Cineca‘s Andrew Emerson. As part of the EXSCALATE 4 COV EU-funded research project, he works of virtual screening of existing drugs regarding their potential efficacy against SARS-CoV-2. In part two we talk with Dan Jacobson of the Oak Ridge National Laboratory. He and his team used a big data analysis to understand how the virus “works”, and they figured out very interesting mechanisms and pathways.

Molecular Dynamics Simulation

00:31:06

Molecular Dynamics Simulation | Thermal effects | Stable State | Statistical techniques | Numerical Simulation | Newton's Laws of Motion | Bond vibration | Coulomb's law | Multi-Body Problem | Unfold | Molecular dynamics simulation can take about a week | Clustering | Degrees of Freedom | Energy Surface | Boltzmann Distribution | Virtual screening filtered ~400,000 possible drugs to ~7000 to go to the laboratory | Vaccine | Immune Response | ~100 of ~7000 screened molecules were interesting | In Vitro Tests | 40 effective molecules limited virus replication | Antiviral | Cortisone

Computer Software and Hardware

01:09:44

GROMACS | Open Source | GPU | Homology Model | C++ | CUDA | Marconi 100 | Galileo Linux Cluster | Eni | HPC5 | Nvidia V100 | Scheduling