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DOE OSTI2023

AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection

Protein-ligand docking is a computational method for identifying drug leads. The method is capable of narrowing a vast library of compounds down to a tractable size for downstream simulation or experimental testing and is widely used in drug discovery. While there has been progress in accelerating scoring of compounds with artificial intelligence, few works have bridged these successes back to the virtual screening community in terms of utility and forward-looking development. We demonstrate the power of high-speed ML models by scoring 1 billion molecules in under a day (50 k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate AI-based models as a pre-filter to a standard docking workflow. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01% of detecting the underlying best scoring 0.1% of compounds. Our analysis of the speedup explains that another order of magnitude speedup must come from model accuracy rather than computing speed. In order to drive another order of magnitude of acceleration, we share a benchmark dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million “in-stock” molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100 × or even 1000 × faster than current techniques and reduce missing top hits. The technique outlined aims to be a fast drop-in replacement for docking for screening billion-scale molecular libraries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

SmileyLlama: modifying large language models for directed chemical space exploration

Here we show that large language models (LLMs) can be transformed via supervised fine-tuning of engineered prompts into SmileyLlama for exploring the chemical space of drug molecules. We benchmark SmileyLlama against pretrained LLMs and chemical language models trained from scratch for generating valid and novel drug-like molecules, and use direct preference optimization to both improve SmileyLlama’s adherence to a prompt and as part of the iMiner reinforcement learning framework to predict molecules with optimized three-dimensional conformations and high binding affinity to drug targets. By training an LLM to speak directly as a chemical language model, while retaining most of its natural language capabilities, we show that SmileyLlama can reliably generate molecules with user-specified properties rather than acting only as a chatbot with knowledge of chemistry or as a virtual assistant. While SmileyLlama is geared toward drug discovery, the supervised fine-tuning/direct preference optimization/LLM framework can be extended to other chemical, biological and materials applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Electrochemistry of PUREX: R is for Reduction and Ion Transfer

The PUREX (Plutonium, Uranium, Reduction, EXtraction) process is the foundation of all industrial activities that involve the recycling of plutonium and uranium from used nuclear fuel. With over 70 years of research, engineering, and operations, it can be argued that little opportunity is left for further discovery and new fundamental understandings regarding PUREX, in general, and tri-n-butyl phosphate (TBP), in particular. Through use of an advanced electroanalytical approach, molecular-level insights regarding the back-extraction of Pu(IV) by reductive separation is reported. Studies of model PUREX systems, with lanthanide ions extracted into 20 % TBP in n-dodecane, are used to demonstrate the approach. These studies reveal knowledge pertinent to mass transfer aspects of the biphasic reductive stripping reaction central to the separation of U and Pu in PUREX. Two lanthanide ions—Ce(IV) and Yb(III)—were extracted from their concentrated solutions in aqueous 3 M HNO 3 to expressly provide electrically conducting third phases to facilitate electrochemical data acquisition. To simplify the diabolically-complicated reductive separation aspects of PUREX, the controlled polarization of electrode surfaces was used to reduce Ce(IV) and Yb(III) in place of chemical reductants. Electroanalyses of the biphasic systems with Ce(IV) and Yb(III) using three-phase electrode differential pulse voltammetry demonstrate the effects of mass transfer across water-oil interfaces on the electrode potentials for the reduction to Ce(III) and Yb(II). These reductions trigger nitrate transfer out of the oil phase for Ce and proton transfer into the organic phase for Yb. This is in correlation with the transfer of the charge-neutral ion pairs Ce·3NO 3 and Yb·2NO 3 out of the oil phases. Here, the differences in ion transfer steps reflect significant variations in the equilibrium speciation of multinuclear Ce(IV) and mononuclear Yb(III) solvates of TBP in the oil phases and the loading of the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1984

Impact phenomena as factors in the evolution of the Earth

It is estimated that 30 to 200 large impact basins could have been formed on the early Earth. These large impacts may have resulted in extensive volcanism and enhanced endogenic geologic activity over large areas. Initial modelling of the thermal and subsidence history of large terrestrial basins indicates that they created geologic and thermal anomalies which lasted for geologically significant times. The role of large-scale impact in the biological evolution of the Earth has been highlighted by the discovery of siderophile anomalies at the Cretaceous-Tertiary boundary and associated with North American microtektites. Although in neither case has an associated crater been identified, the observations are consistent with the deposition of projectile-contaminated high-speed ejecta from major impact events. Consideration of impact processes reveals a number of mechanisms by which large-scale impact may induce extinctions.

Grieve, R. A. F.↗

NASA NTRS1985

Solar cycle variations of the anomalous cosmic ray component

The intensity of the anomalous cosmic ray component, consisting of He, N, O, and Ne, has long been known to be especially sensitive to the effects of solar modulation. Following its discovery in 1972, this component dominated the quiet-time flux of cosmic ray nuclei below approximately 30 MeV/nucleon during the 1972 to 1978 solar minimum, but then became essentially unobservable at 1 AU with the approach of solar maximum conditions. One recent theoretical model predicts substantial differences in the intensity of the anomalous fluxes from one solar minimum period to the next because of the reversal of the solar magnetic field. Using data from the Caltech experiments on IMP-8 and ICE (ISEE-3), the intensity of anomalous O and He at 1 AU during the years 1972 to 1985 is reported. We hope to determine whether the anomalous fluxes will return to their 1972 to 1978 levels, as predicted by spherically symmetric modulation models, or whether they will fail to return to 1 AU, as suggested by modulation models in which gradient and curvature drifts dominate.

Mewaldt, R. A.↗

NASA NTRS1988

The phase reversal phenomenon at flow separation and reattachment

Tests were conducted on two different airfoils, one of them in a low-turbulence tunnel, to detect laminar separation and turbulent reattachment locations. A 'nonintrusive' multielement sensor consisting of a large number of closely spaced individual nickel films was vacuum deposited on a thin substrate and bonded to the airfoil model surface. Each sensor element was a part of an independent constant temperature anemometer system. Time history as well as spectral analysis of signals from surface film gauges were used to determine the surface shear flow characteristics. A major breakthrough was achieved with the discovery of phase reversal in low-frequency dynamic shear stress signals across regions of flow separation and reattachment.

Stack, J. Pete↗

NASA NTRS1990

The extragalactic radiation field and sharp edges to HI disks in galaxies

Observations of neutral hydrogen (HI) are widely used as a probe of the interstellar medium in galaxies and of galactic kinematics and dynamics. The 21-cm line can be used to determine galactic rotation curves far beyond the optical disk, and is one of the prime sources of evidence for the existence of dark haloes in spiral galaxies. However, a recent attempt to measure the 21-cm emission from NGC 3198 to very low column densities (N sub H approx. equals 5 times 10 to the 18th power) found that the HI disk is very sharply truncated at a column density of a few times 10 to the 19th power (Sancisi 1989, private communication). This discovery reinforces the earlier suggestion (Briggs et al. 1980) that extended, low-column density envelopes of neutral hydrogen are not common around galaxies. Here the author suggests that the sharp edge seen in the HI disk in NGC 3198 is consistent with a model in which a self-gravitating neutral HI disk is photoionized by the extragalactic radiation field. The possibility that the extragalactic background would produce sharp edges to HI disks was first suggested by Silk and Sunyaev (1976).

Maloney, Philip Richard↗

NASA NTRS1993

Collisions of small Spacewatch asteroids with the Earth

The discovery, with the Spacewatch Telescope, of 8 Earth-approaching objects smaller than 100 m in diameter has been reported. I have calculated the probability and velocity of collision with Earth for each of these objects. Using a code we have successfully employed to model the Tunguska and Revelstoke atmospheric explosions, I have simulated the entry of these objects into Earth's atmosphere, assuming iron, stony, carbonaceous, and cometary compositions. The smallest of these objects, with tens to hundreds of kilotons of kinetic energy, pose a substantial threat at the surface only if they are iron objects. An object is taken to 'pose a substantial threat' if it either craters the ground, or explodes in the atmosphere with sufficient energy at low enough altitude to create an overpressure at the surface capable of felling trees or destroying buildings. Larger objects, with energies greater than about a megaton, devastate the surface regardless of whether they are of iron, stony, or carbonaceous composition. Iron objects crater the ground, whereas stony and carbonaceous objects explode in the atmosphere low enough to fell trees and damage buildings over thousands of square kilometers. Spacewatch objects, if presumed to be of carbonaceous composition, are as dangerous as their stony counterparts, as the former objects' lower yield strengths (and hence, higher explosion altitudes) are roughly compensated by their larger masses (as derived from their lower albedos for a given observed magnitude). Although comets are intrinsically less dangerous than asteroids, the 90 m diameter Spacewatch objects would devastate hundreds of square kilometers at the surface, even if cometary.

Chyba, C. F.↗

NASA NTRS1994

Rare gases systematics and mantle structure

The following points are emphasized: one of the most important ones is certainly the first set of experimental data on the solubility of noble gases in metal phases at intermediate pressures, since the core was certainly not formed at ultra high pressures, as emphasized by Ahrens and confirmed by trace elements systematics Wanke. The experimental data clearly show that the core can not be a major reservoir for terrestrial rare gases; the second point is a more elaborate reconsideration of the (40)K-(40)Ar budget of the Earth. This shows that (40)Ar contained in continental crust plus upper mantle plus atmosphere is at maximum half of the (40)Ar inventory of the whole earth. This implies the existence of a two layered mantle; the third point is the discovery by the Australian noble gases group of the existence of high (20)Ne/(22)Ne and low (21)Ne/(22)Ne isotopic ratios in Loihi seamount samples. This results which are different to the MORB ratios confirm the idea of a two layered model, but suggest the existence of a primordial solar type Ne reservoir. Several possibilities about the origin of this (20)Ne excess in the mantle will be discussed; The high (40)Ar/(36)Ar, (129)Xe/(130)Xe and (134) Xe/(130)Xe, (136)Xe/(130)Xe are confirmed by new data. The corresponding ratios for the lower mantle will be discussed. (40)Ar/(36)Ar ratios up to 6000 can be accepted and will not modify the general model of the mantle. They confirm the atmosphere chronology, about 85 percent of the atmosphere was formed in the first 50 My and 15 percent later on.

Allegre, C. J.↗

NASA NTRS2010

Leading the Public Face of Space

The National Aeronautics and Space Administration (NASA) is fully committed to sharing the excitement of America's international space missions with its stakeholders, particularly the general public. In 2009, the Space Shuttle delivered astronauts to the Hubble Space Telescope to service that great observatory and to the International Space Station to install the observation platform on the Japanese Kibo laboratory. The Lunar Reconnaissance Orbiter is showing an unprecedented view of the Moon, confirming the presence of hardware left behind during the Apollo missions decades ago and helping scientists better understand Earth's natural satellite. These and numerous other exciting missions are fertile subjects for public education and outreach. NASA's core mission includes engaging the public face of space in many forms and forums. Agency goals include communicating with people across the United States and through international opportunities. NASA has created a culture where communication opportunities are valued avenues to deliver information about scientific findings and exploration possibilities. As this presentation will show, NASA's leaders act as ambassadors in the public arena and set expectations for involvement across their organizations. This presentation will focus on the qualities that NASA leaders cultivate to achieve challenging missions, to expand horizons and question "why". Leaders act with integrity and recognize the power of the team multiplier effect on delivering technical performance within budget and schedule, as well as through participation in education and outreach opportunities. Leaders are responsible for budgeting the resources needed to reach target audiences with compelling, relevant information and serve as role models, delivering key messages to various audiences. Examples that will be featured in this presentation include the Student Launch Projects and Great Moonbuggy race, which reach hundreds of students who are a promising pipeline for new scientists and engineers for a new generation of discovery. The popular Exploration Experience trailer is an interactive-exhibit environment that travels across the United States, conveying the innovation necessary for space travel and the wonder of discovery that comes from viewing our planet as part of the larger space-scape.

Dumbacher, Daniel L.↗

NASA NTRS2009

Leading the Public Face of Space

Dumbacher, Daniel L.↗

NASA NTRS2012

Survival of Flux Transfer Event (FTE) Flux Ropes Far Along the Tail Magnetopause

During intervals of southward IMF, magnetic reconnection can result in the formation of flux transfer events (FTEs) on the dayside magnetopause which travel along the magnetopause in the anti-sunward direction. Of particular interest is their fate and the role they play transporting solar wind plasma into the magnetosphere. We present the discovery of FTEs far along the distant tail magnetopause (x = 67 Earth radii) using data from ARTEMIS on the dusk flank magnetopause under southward/duskward IMF conditions. The identification of several events is further supported by excellent fits to a force-free flux rope model. The axis of each structure is principally north-south, i.e., perpendicular to the Sun-Earth line. Simultaneous observations by THEMIS on the dayside magnetopause indicate that FTEs are being produced there, although perhaps 2-4 times smaller in size. The convection time from the dayside magnetopause to ARTEMIS is 30 min, and the FTEs have a flux content comparable to those typically observed on the dayside magnetopause, indicating that these features are in quasi-equilibrium as they are convected downtail. By considering the relative orientations of the FTEs observed by THEMIS and ARTEMIS, the magnetic field geometry is consistent with the FTEs being produced on the dayside magnetopause along an extended X-line in the presence of IMF By and bending as they are convected to the flanks.

ARTEMIS↗

NASA NTRS2024

A Fair, Economically-Efficient, Incentive-Aligned, Scalable Airspace Auction Mechanism for UAV Traffic Management

Unmanned Aerial Vehicles (UAVs) are increasingly used in a wide range of applications such as cinematography, package delivery, and surveying. As a result, regulators have become interested in developing UAV Traffic Management (UTM) systems to coordinate UAV traffic. One possible framework for UTM is a combinatorial auction. Under this framework, airspace is modeled as a grid of space-time cells. UAV operators bid on sets of cells which collectively form flight paths for their UAVs. An ideal airspace auction should: be fair, be incentive-aligned, be scalable, allocate airspace economically-efficiently, enable price discovery, and reduce the work required to participate where possible. In this paper, we propose the first auction mechanism for airspace allocation that meets the criteria above. Our mechanism: (a) is provably economically-efficient, fair and incentive-aligned, (b) shares pricing information with bidders and (c) has features which reduce the burden of participating. We evaluate our mechanism on scenarios based on a Japan Aerospace Exploration Agency (JAXA) case study and find that it can scale to 26,000 bids.

Robert Allan Morris↗

DOE OSTI2026

Scientific Discovery with Physics-Informed System Identification (Abbreviated Report)

My fellowship research focused on making physics-based simulations faster and more useful through machine learning. Many problems in science and engineering are governed by partial differential equations, but high-fidelity simulations are often too expensive to run repeatedly. I worked on improving Latent Space Dynamics Identification (LaSDI), a reduced-order modeling framework that compresses large simulation data sets into a smaller representation and then learns how that representation evolves over time. The motivation was to develop reduced models that remain accurate for more challenging systems, especially when predictions must remain reliable over long time intervals or when the underlying dynamics are more complicated than standard methods can easily handle. I also contributed to related work on Quandary, a high-performance software effort for simulation and control of open quantum systems, before focusing primarily on Latent Space Dynamics Identification methods. The main outcomes of the fellowship were two new algorithms (both of which were published), Rollout-LaSDI and Higher-Order LaSDI, together with supporting work on multi-stage Latent Space Dynamics Identification. Rollout-LaSDI improved long-term prediction by training the model to stay accurate over extended time horizons, and Higher-Order LaSDI broadened the method so it could model systems with higher-order time dynamics. My contributions to multistage Latent Space Dynamics Identification also helped show that its later training stages could be simplified without losing effectiveness, and that this behavior held across different model architectures and training strategies. Taken together, these advances improved the accuracy, flexibility, and practical value of reduced-order modeling tools for computational science.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1997

Discovery of Interstellar Hydrogen Fluoride

We report the first detection of interstellar hydrogen fluoride. Using the Long Wavelength Spectrometer of the Infrared Space Observatory (ISO), we have detected the 121.6973 micron J = 2-1 line of HF in absorption toward the far-infrared continuum source Sagittarius B2. The detection is statistically significant at the 13 sigma level. On the basis of our model for the excitation of HF in Sgr B2, the observed line equivalent width of 1.0 nm implies a hydrogen fluoride abundance of about 3 x 10 (exp -10) relative to H, If the elemental abundance of fluorine in Sgr B2 is the same as that in the solar system, then HF accounts for about 2% of the total number of fluorine nuclei. We expect hydrogen fluoride to be the dominant reservoir of gas-phase fluorine in Sgr B2, because it is formed rapidly in exothermic reactions of atomic fluorine with either water or molecular hydrogen; thus, the measured HF abundance suggests a substantial depletion of fluorine onto dust grains. Similar conclusions regarding depletion have previously been reached for the case of chlorine in dense interstellar clouds. We also find evidence at a lower level of statistical significance (about 5 sigma) for an emission feature at the expected position of the 4(sub 32)-4(sub 23) 121.7219 micron line of water. The emission-line equivalent width of 0.5 mm for the water feature is consistent with the water abundance of 5 x 10(exp -6) relative to H, that has been inferred previously from observations of the hot core of Sgr B2.

Neufeld, David A.↗

NASA NTRS1997

Discovery of Interstellar Hydrogen Fluoride

We report the first detection of interstellar hydrogen fluoride. Using the Long Wavelength Spectrometer of the Infrared Space Observatory (ISO), we have detected the 121.6973 micron J = 2-1 line of HF in absorption toward the far-infrared continuum source Sagittarius B2. The detection is statistically significant at the 13 sigma level. On the basis of our model for the excitation of HF in Sgr B2, the observed line equivalent width of 1.0 nm implies a hydrogen fluoride abundance of approximately 3 x 10(exp -10) relative to H2. If the elemental abundance of fluorine in Sgr B2 is the same as that in the solar system, then HF accounts for approximately 2% of the total number of fluorine nuclei. We expect hydrogen fluoride to be the dominant reservoir of gas-phase fluorine in Sgr B2, because it is formed rapidly in exothermic reactions of atomic fluorine with either water or molecular hydrogen; thus, the measured HF abundance suggests a substantial depletion of fluorine onto dust grains. Similar conclusions regarding depletion have previously been reached for the case of chlorine in dense interstellar clouds. We also find evidence at a lower level of statistical significance (approximately 5 sigma) for an emission feature at the expected position of the 4(sub 32)-4(sub 23) 121.7219 micron line of water. The emission-line equivalent width of 0.5 nm for the water feature is consistent with the water abundance of 5 x 10(exp -6) relative to H2 that has been inferred previously from observations of the hot core of Sgr B2.

Neufeld, David A.↗

DOE OSTI2025

Deep-learning atomistic semi-empirical pseudopotential model for nanomaterials

The semi-empirical pseudopotential method (SEPM) has been widely applied to provide computational insights into the electronic structure, photophysics, and charge carrier dynamics of nanoscale materials. We present “DeepPseudopot”, a machine-learned atomistic pseudopotential model that extends the SEPM framework by combining a flexible neural network representation of the local pseudopotential with parameterized non-local and spin-orbit coupling terms. Trained on bulk quasiparticle band structures and deformation potentials from GW calculations, the model captures many-body and relativistic effects with very high accuracy across diverse semiconducting materials, as illustrated for silicon and group III-V semiconductors. DeepPseudopot’s accuracy, efficiency, and transferability make it well-suited for data-driven in silico design and discovery of novel optoelectronic nanomaterials.

Lin, Kailai [University of California, Berkeley, C↗

DOE OSTI2024

An emerging multi-omic understanding of the genetics of opioid addiction

Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction–associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease.

60 APPLIED LIFE SCIENCES↗