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How do scientists uncover phenomena and explain their connections? How do engineers design machines, methods and infrastructure? At omega tau, experts give detailed answers. Over the last ten years, we have produced over 350 episodes in which we dug deeper, until we ran out of questions. Join us on our journey through the world of science and engineering: the closer you look and listen, the more interesting things get.

https://omegataupodcast.net

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episode 355: Supercomputing for COVID-19


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.

Introduction 00:03:14

Andrew Emerson | Cineca Supercomputer Center | Exscalate4Cov Project | Computer Aided Drug Design | Simulation | Modelling | Synthesize | Side Effects | Active Ingredient | COVID-19 | SARS-CoV-2 | Virus | Drug Repurposing/Drug Repositioning | Toxicology | Virtual Screening | Protein | Enzyme | Cell | Replication | Inhibit | DNA | Cell Membranes | Amino Acid | RNA | Gene | Gene Expression | Genome | Lock and Key Model | Screening | Virtual Screening | Dompé | Parallel Process | Abstraction (PDB - Protein Data Bank)  | Bonding | Experimental data (Proteins - accurate 3d data | Drug molecules - basic data)  | X-Ray Diffraction | NMR | Cryogenic Electron Microscopy | Electromagnetic Force | Van der Waals Force | Electrostatic Interaction | LiGen | Molecular Docking | Toxicology | Few seconds per molecule for virtual screening

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

Results 01:20:24

Raloxifene | Clinical Trials | Dimer | Protease | Physical Chemistry | Computational Chemistry | Vector (Biology) | Vector (Mathematics)

Bradykinin Storm Analysis 01:30:59

Dan Jacobson | Computational Systems Biologist | Oak Ridge National Laboratory (OLCF - Oak Ridge Leadership Computing Facility)  | Evolution | Pathogenicity | 3D Structure | Human pathogenesis | Demographic factors | Bradykinin Storm Paper | 17000 samples across 57 different tissues | Regulatory circuits | Bronchoalveolar Lavage fluid | Bronchoscope | Terminal Bronchioles | Luminal surface | Gas Exchange | Pathways (RAS - Renin-Angiotensin System)  | Blood Pressure | Inflaitory RResponses | ACE2 | Cell Entry | ACE | Proteolytic Enzyme | Proteolytic cleavage | Peptide | Hypertensive | Upregulated (Ang-(1-9) - Angiotensin (1-9))  | AGTR2 receptor | Receptor | Bind | Kallikrein Kinin Pathway | C1-Inhibitor Protein | Biosynthesis | Vasodilation | Hyperpermeability | Plasma | Capillaries | Immune Cells | Transcription | Hyaluronic Acid | Hydrogel | Tropism | Renin | Vitamin D | Catabolise | Metabolite | Expression | Calcifediol | Icatibant | Dexamethasone | Phospholipase A2 | Arachidonic Acid | Cascade | Chemotaxis | Combinatorial Therapies

Computational Tools 01:56:58

Machine Learning | Functional Inference | Explainable AI | Data Analytics | ChIPseek | Transcription Factors | Traits | Phenotypes | Combinatorial Space | P-Values | Permutation Tests | Neural Network | Black Box | Classification Problem (IRF - Iterative Random Forests)  | Decision Tree | Iterative Approach | Summit Supercomputer | Flash Memory | Gordon Bell Prize 2018 | Tensor Cores | Matrix Multiplication | Exascale Barrier | Hyperparameter Sweeps | Monte Carlo Simulation | R | Python | Parsers


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 2020-10-29  2h28m