Computing – Modeling COVID dynamics

To better understand the spread of SARS-CoV-2, the virus that causes COVID-19, Oak Ridge National Laboratory researchers have harnessed the power of supercomputers to accurately model the spike protein that binds the novel coronavirus to a human cell receptor.

These simulations also shed light on the ligand molecules that can inhibit such binding, pointing the way to potential drug therapies.

An ultrafast quantum chemical modeling method provides information about the critical electronic interactions between protein and ligand chemicals, going beyond the classical interaction models that are normally employed in computational drug discovery.

The findings will enable accurate predictions of the performance of currently available inhibitors and inform the future development of even more potent, novel inhibitor compounds, demonstrating the effectiveness of quantum chemical approaches in simulation for drug discovery.

“Quantum mechanics on supercomputers accelerates computational COVID-19 drug discovery by accurately describing inhibitor–virus protein interactions,” said ORNL’s Stephan Irle.


Caption: ORNL has modeled the spike protein that binds the novel coronavirus to a human cell for better understanding of the dynamics of COVID-19. Credit: Stephan Irle/ORNL, U.S. Dept. of Energy  


Climate – Permafrost lost

A study by Oak Ridge National Laboratory, the University of Copenhagen, the National Park Service and the U.S. Geological Survey showed that hotter summers and permafrost loss are causing colder water to flow into Arctic streams, which could impact sensitive fish and other wildlife.

To understand trends observed in 11 Alaskan streams, ORNL researchers modeled the flow of water through the semi-frozen landscape during summer months. Usually, permafrost forms an icy barrier that keeps groundwater flow to the topmost layer of soil, which allows the water to warm with summer air temperatures.

Researchers found that as thawing permafrost sinks lower beneath the surface, groundwater flows deeper underground and, therefore, stays colder.

“In this ecosystem, the lateral flow of water strongly influences stream levels and temperatures,” said ORNL’s Scott Painter, “but it is often neglected in models. Our Amanzi-ATS model provides a detailed representation of the physics that impact groundwater supplying Arctic streams.” 


Caption: ORNL researchers used the award-winning Amanzi-ATS model to simulate groundwater flow in Arctic ecosystems. As thawing permafrost sinks lower beneath the surface, groundwater flows deeper underground and, therefore, stays colder as it flow into streams. Credit: Michelle Lehman/ORNL, U.S. Dept. of Energy


Manufacturing – Taking the heat 

Oak Ridge National Laboratory researchers have demonstrated that a new class of superalloys made of cobalt and nickel remains crack-free and defect-resistant in extreme heat, making them conducive for use in metal-based 3D printing applications. 

Metal materials have proven to be cost-effective for manufacturing, and deploying them for use in additive processes could enable the production of innovative, complex designs with minimal material waste. However, these materials are primarily used in energy, space and nuclear applications that also produce extreme heat environments. 

In a study, researchers processed the cobalt and nickel class of superalloys and proved that they remained crack-free in electron-beam and laser-melting 3D printing processes. 

“The challenge has been producing alloys that don’t crack in the heat,” ORNL’s Mike Kirka said. “These superalloys have the material properties necessary for challenging environments, because they not only successfully withstood the heat but also retained strength when stretched.” 


Caption: A 3D printed turbine blade demonstrates the use of the new class of nickel-based superalloys that can withstand extreme heat environments without cracking or losing strength. Credit: ORNL/U.S. Dept. of Energy

Journal Link: Water Resources Research, Dec-2020 Journal Link: Nature Communications, Oct-2020