In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions.

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

The empirical rules for the prediction of solid solution formation proposed so far in the literature usually have very compromised predictability. Some rules with seemingly good predictability were, however, tested using small data sets. Based on an unprecedented large dataset containing 1252 multicomponent alloys, machine-learning methods showed that the formation of solid solutions can be very accurately predicted (93%). The machine-learning results help identify the most important features, such as molar volume, bulk modulus, and melting temperature. As such a new thermodynamics-based rule was developed to predict solid–solution alloys. The new rule is nonetheless slightly less accurate (73%) but has roots in the physical nature of the problem. The new rule is employed to predict solid solutions existing in the three blocks, each of which consists of 9 elements. The predictions encompass face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal closest packed (HCP) structures in a high throughput manner. The validity of the prediction is further confirmed by CALculations of PHAse Diagram (CALPHAD) calculations with high consistency (94%). Since the new thermodynamics-based rule employs only elemental properties, applicability in screening for solid solution high-entropy alloys is straightforward and efficient.