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DOE OSTI2024

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Understanding Photocarrier and Gas Dynamics to Rationally Design Heterostructured Nanocatalysts for Efficient Solar CO 2 Conversion

Recent research in CO 2 photocatalysis has largely focused on exploring new catalysts; however, details of the relationship between charge carrier dynamics and gas dynamics on the surface of nanomaterials often remain unclear. Knowledge of these processes will allow one to rationally design highly efficient catalysts for solar CO 2 conversion. This project aimed to develop state-of-the-art techniques and establish new capabilities in SRNL to enable the study of photocatalysts and other materials in detail. In FY21, we developed two new in situ techniques that are unique to SRNL, allowing the study of reaction intermediates and adsorbed gases during photocatalysis at various wavelengths of excitation. We also established a new in-house capability for catalyst synthesis and product evaluation which enables a deep understanding of how catalyst preparation methodologies impact product generation. In FY22, we gained in-house expertise and knowledge on the newly constructed a physical vapor deposition device, i.e. glancing angle deposition (GLAD) system, and constructed a flow photoreactor system for CO 2 photoconversion and other photocatalytic studies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Texas A&M University Mobile Facility Measurements during TRACER (Field Campaign Report)

One of the main goals of the U.S Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Tracking Aerosol Convection Interactions Experiment (TRACER) near Houston, Texas is to improve understanding of how meteorology and aerosols impact storm dynamical and microphysical processes in deep convection to better constrain and improve their model representation. The Houston area is strongly influenced by sea- and bay-breeze circulations that generate convergence and help to initiate and organize deep convection. To properly isolate and understand the roles of varied meteorological conditions and cloud condensation nuclei (CCN) and ice nucleation particles (INP) distributions in different air masses, co-located thermodynamic, kinematic, and aerosol vertical profile observations are needed. The focus of this campaign was to provide key measurements in air masses both in front of and behind sea/bay breeze fronts moving through the greater Houston area to sample the airmass heterogeneity. The overarching scientific goal of this campaign is to understand how the vertical distributions of both CCN and INP correspond to the inflow layer of deep convection in maritime, background continental, and polluted continental air masses, and how these variations influence deep convection. To fully sample the heterogeneity in both meteorological conditions and aerosols across the sea-breeze front (SBF), Texas A&M University (TAMU) deployed a InterMet 3050A 403 MHz mobile unit launching iMet-4 radiosondes and the new Rapid Onsite Atmospheric Measurement Van (ROAM-V) for aerosol sampling during the TRACER intensive operational period (IOP) from June to September 2022. The suite of instruments deployed on ROAM-V included a condensation particle counter (CPC; GRIMM Model 5.403 CPC), scanning mobility particle sizer (SMPS; TSI 3750 detector, TSI 3082 classifier, TSI 3088 neutralizer, TSI 3081A differential mobility analyzer), cloud condensation nuclei counter (Droplet Measurement Technologies CCN counter), micropulse lidar (Droplet Measurement Technologies micropulse lidar [miniMPL]), and a Davis Rotating Uniform size-cut Monitor (DRUM; DRUMAir 4-DRUM). Before sampling at each location, the latitude and longitude were recorded using the Global Positioning System (GPS) on the phone application “My Altitude”. The DRUM data were collected as part of a closely related ARM field campaign and also supported by DOE Atmospheric System Research grant DE-SC0021047. The TAMU team sampled these airmass heterogeneities by strategically choosing deployment sites in a different airmass than the ARM fixed sites in La Porte and Guy, Texas. On days when the sea/bay breeze boundary was pushing inland, the TAMU team would usually sample the airmass on the maritime side of the SBF at a coastal site in Galveston, Texas in the early afternoon (1730-1900 UTC) and then move inland ahead of the SBF to sample the airmass on the continental side during late afternoon (2030-2230). Figure 1 shows the Galveston maritime site and the array of sites for the late afternoon continental measurements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Electric Transportation and Distribution Infrastructure: A Heavy-Duty Vehicle Deep Dive

This presentation is a deep dive into charging behavior and grid impacts of short-haul electric Class 8 semi trucks.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

DOE OSTI2022

Impacts, processes and projections of the quasi-biennial oscillation

In the tropical stratosphere, deep layers of eastward and westward winds encircle the globe and descend regularly from the upper stratosphere to the tropical tropopause. With a complete cycle typically lasting almost 2.5 years, this quasi-biennial oscillation (QBO) is arguably the most predictable mode of atmospheric variability that is not linked to the changing seasons. Here, the QBO affects climate phenomena outside the tropical stratosphere, including ozone transport, the North Atlantic Oscillation and the Madden–Julian Oscillation, and its high predictability could enable better forecasts of these phenomena if models can accurately represent the coupling processes. Climate and forecasting models are increasingly able to simulate stratospheric oscillations resembling the QBO, but exhibit common systematic errors such as weak amplitude in the lowermost tropical stratosphere. Uncertainties about the waves that force the oscillation, particularly the momentum fluxes from small-scale gravity waves excited by deep convection, make its simulation challenging. Improved representation of the processes governing the QBO is expected to lead to better forecasts of the oscillation and its impacts, increased understanding of unusual events such as the two QBO disruptions observed since 2016, and more reliable future projections of QBO behaviour under climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Summary Data for paper titled: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Summary Data

Naasko, Katherine I↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Sequence Data

Naasko, Katherine I↗

DOE OSTI2021

Impact of galactic cosmic ray simulation on nutritional content of foods

Foods packaged for future deep-space exploration missions may be prepositioned ahead of astronaut arrival, and will be exposed to galactic cosmic rays (GCRs) and solar radiation in deep space at higher levels and different spectrums than those found in low-Earth orbit (LEO). In this study, we have evaluated the impact of a GCR simulation (approximately 0.5 and 5 Gy doses) at the NASA Space Radiation Laboratory (NSRL) on two retort thermostabilized food products that are good sources of radiation labile nutrients (thiamin, vitamin E, or unsaturated fats). No trends or nutritional differences were found between the radiation-treated samples and the control immediately after treatment or one-year after treatment. Small changes in a few nutrients were measured following one-year of storage. Further studies are needed to confirm these results, as the foods in this study were heterogeneous, and this may have masked meaningful changes due to pouch-to-pouch variations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Science Plan for the Deployment of the Third ARM Mobile Facility to the Southeastern United States at the Bankhead National Forest, Alabama (AMF3 BNF)

In 2018, the U.S. Department of Energy (DOE) held a workshop for the Atmospheric Radiation Measurement (ARM) (Mather and Voyles 2013) user facility to discuss critical climate challenges and locations where key ARM Mobile Facility (AMF) observational assets could impact Earth system modeling (ESM). As an outcome, the southeast United States (SE U.S.) was identified as a high-priority region to target climate-process studies that promote a deeper understanding of the climate system and bolster ARM interactions with the community to drive ESM advancement. The DOE ARM user facility is a globally recognized leader in deploying and operating strategically located observation sites around the world for studying the properties of aerosols and clouds and their interaction with radiation, precipitation, and the Earth’s surface. In partnering with the DOE Atmospheric System Research (ASR) program, ARM solicited a multi-agency Site Science Team approach to provide input and close interaction with ARM management towards a successful SE U.S. deployment of the ARM third Mobile Facility (AMF3) (Miller et al. 2016). These efforts included identifying key locations, science drivers and instruments, and measurement strategies to address the wider climate-process needs and ESM improvement. Community input served a vital role in establishing, refining, and informing the relevant drivers and decisions regarding this AMF3 deployment. The team has identified Northern Alabama (N. AL) as regionally representative to unlock the key opportunities that will improve our understanding and model representation of aerosol, cloud, and land surface processes and their couplings in the SE U.S. A defining aspect of the AMF3 deployment is its commitment to long-term (anticipated five-year) observations to mitigate potential seasonal-to-annual variability that often limits appropriate attribution of phenomena to local or larger-scale processes. The proposed location may leverage nearby surface networks and multi-agency and partner assets to enrich this multi-year deployment. One motivation is to understand the role of spatiotemporal variability (thermodynamic, land-surface) across aspects of the climate system, with our AMF3 team anticipating future demands on characterizing the relationships between local-to-regional cloud development and surface processes across a diverse patchwork of natural, managed, and urban landscapes as found throughout the N. AL regions. The main site targets an intact, representative, forested region – the Bankhead National Forest (BNF) – underscoring further team commitment to regionally important land atmosphere two-way interactive studies “from the canopy to the clouds”, with enhanced tower instrumentation augmenting traditional ARM capabilities adjacent to this site. Multiple supplemental sites will also be distributed across this region, prioritizing added needs for biodiversity. Anticipated high-priority cloud science themes will target N. AL as a regional SE U.S. hotbed for high-impact weather, convective cloud onset, and shallow to-deep cloud transitioning. Anticipated aerosol drivers will focus on chemical processes that control the evolution of organic aerosol, the seasonality and spatial distribution of water vapor and particle-phase water, and its role on aerosol optical properties. Anticipated land atmosphere drivers consider the two-way feedbacks between surface influence on aerosols, clouds, and precipitation properties and the associated radiative impacts on plant physiology and canopy-scale fluxes. Emphasis will include the study of the impact of surface processes on aerosols via precursor emission, and on clouds via moisture flux and thermal development.

Doppler lidar, aerosols, convection↗

DOE OSTI2023

Science Plan for the Deployment of the Third ARM Mobile Facility to the Southeastern United States at the Bankhead National Forest, Alabama (AMF3 BNF)

In 2018, the U.S. Department of Energy (DOE) held a workshop for the Atmospheric Radiation Measurement (ARM) (Mather and Voyles 2013) user facility to discuss critical climate challenges and locations where key ARM Mobile Facility (AMF) observational assets could impact Earth system modeling (ESM). As an outcome, the southeast United States (SE U.S.) was identified as a high-priority region to target climate-process studies that promote a deeper understanding of the climate system and bolster ARM interactions with the community to drive ESM advancement. The DOE ARM user facility is a globally recognized leader in deploying and operating strategically located observation sites around the world for studying the properties of aerosols and clouds and their interaction with radiation, precipitation, and the Earth’s surface. In partnering with the DOE Atmospheric System Research (ASR) program, ARM solicited a multi-agency Site Science Team approach to provide input and close interaction with ARM management towards a successful SE U.S. deployment of the ARM third Mobile Facility (AMF3) (Miller et al. 2016). These efforts included identifying key locations, science drivers and instruments, and measurement strategies to address the wider climate-process needs and ESM improvement. Community input served a vital role in establishing, refining, and informing the relevant drivers and decisions regarding this AMF3 deployment. The team has identified Northern Alabama (N. AL) as regionally representative to unlock the key opportunities that will improve our understanding and model representation of aerosol, cloud, and land-surface processes and their couplings in the SE U.S. A defining aspect of the AMF3 deployment is its commitment to long-term (anticipated five-year) observations to mitigate potential seasonal-to-annual variability that often limits appropriate attribution of phenomena to local or larger-scale processes. The proposed location may leverage nearby surface networks and multi-agency and partner assets to enrich this multi-year deployment. One motivation is to understand the role of spatiotemporal variability (thermodynamic, land-surface) across aspects of the climate system, with our AMF3 team anticipating future demands on characterizing the relationships between local-to-regional cloud development and surface processes across a diverse patchwork of natural, managed, and urban landscapes as found throughout the N. AL regions. The main site targets an intact, representative, forested region – the Bankhead National Forest (BNF) – underscoring further team commitment to regionally important land-atmosphere two-way interactive studies “from the canopy to the clouds”, with enhanced tower instrumentation augmenting traditional ARM capabilities adjacent to this site. Multiple supplemental sites will also be distributed across this region, prioritizing added needs for biodiversity. Anticipated high-priority cloud science themes will target N. AL as a regional SE U.S. hotbed for high-impact weather, convective cloud onset, and shallow-to-deep cloud transitioning. Anticipated aerosol drivers will focus on chemical processes that control the evolution of organic aerosol, the seasonality and spatial distribution of water vapor and particle-phase water, and its role on aerosol optical properties. Anticipated land-atmosphere drivers consider the two-way feedbacks between surface influence on aerosols, clouds, and precipitation properties and the associated radiative impacts on plant physiology and canopy-scale fluxes. Emphasis will include the study of the impact of surface processes on aerosols via precursor emission, and on clouds via moisture flux and thermal development.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Insights from a coupled thermo-hydro-mechanical analysis of a layered high-temperature thermal energy storage reservoir

Coupled thermal-hydraulic-mechanical (THM) modeling is applied to investigate the performance of a seasonal high-temperature aquifer thermal energy storage operation based on data and conditions from current site investigations at the Geostorage Forsthaus pilot project in Bern (Switzerland). The model includes subhorizontal sand lenses of various lengths and dips that are embedded in a low permeability clay matrix. Thermal energy storage is simulated by seasonal injection and withdrawal of hot (up to 90 °C) water from a main well, with reservoir pressure regulated by two auxiliary wells at a distance of about 70 m from the main well. The results show how targeted injection into deeper permeable storage formations, along with active deep well pressure control, can effectively minimize geomechanical impact and the potential risk of damaging subsurface storage and sealing formations, or even surface facilities. With such pressure control, the subsurface mechanical responses are dominated by thermal strain and stress, which can be monitored with subsurface fiber optics. The study demonstrates how coupled THM modeling can be applied for the design of a safe and efficient thermal energy storage operation, and how subsurface fiber optic monitoring can be applied for performance confirmation, allowing for more confident operational forecasting.

Rutqvist, Jonny↗

DOE OSTI2025

Designing a repository in domal salt: The influence of design variants in different modelling environments

To understand the long-term environmental impact of disposing radioactive waste of in a deep geological repository and to optimise its design, performance assessments are used. In this study, four teams (COVRA, GRS, Quintessa, and DOE) modified the previously developed generic repository of DECOVALEX task F2 to identify commonalities and differences between the teams for specific changes in repository design. The teams tested six design modifications: (1) Replacing concrete abutments with run-of-mine salt; (2) Replacing the salt seal with a concrete abutment and using run-of-mine salt instead for the two concrete abutments in each drift seal; (3) Halving the size of the infrastructure area; (4) Using run-of-mine salt instead of gravel for backfilling the infrastructure area; (5) Disposal of spent nuclear fuel without the POLLUX-10 containers (6); Lower initial saturation of the spent nuclear fuel and vitrified waste disposal drifts. Despite different modelling strategies used, models agreed that a smaller infrastructure area has a limited effect on radionuclide transport. Responses to the absence of the two concrete abutments in each seal, the use of single large concrete abutments (200 m each), or the use of run-of-mine salt in the infrastructure area differ between teams due to differing modelling assumptions. Based on these results, the estimated efficacy of containment depends strongly on the model assumptions of each team. More specifically, it appears to depend on the compaction model used and therefore on the backfill material used in different areas of the repository. However, the drift seal appears to be a critical design element in all models, effectively limiting radionuclide transport by hydrologically disconnecting sections of the repository. Additional beneficial design choices include the use of dry salt in disposal drifts to limit radionuclide transport and reducing the infrastructure area costs and minimizing host rock damage.

DECOVALEX↗

DOE OSTI2023

Structure–Thermodynamic Relationship of a Polysaccharide Gel (Alginate) as a Function of Water Content and Counterion Type (Na vs Ca)

Biofilms are the predominant mode of microbial life on Earth, and so a deep understanding of microbial communities-and their impacts on environmental processes-requires a firm understanding of biofilm properties. Because of the importance of biofilms to their microbial inhabitants, microbes have evolved different ways of engineering and reconfiguring the matrix of extracellular polymeric substances (EPS) that constitute the main non-living component of biofilms. This ability makes it difficult to distinguish between the biotic and abiotic origins of biofilm properties. An important route toward establishing this distinction has been the study of simplified models of the EPS matrix. This study builds on such efforts by using atomistic simulations to predict the nanoscale (≤10 nm scale) structure of a model EPS matrix and the sensitivity of this structure to interpolymer interactions and water content. To accomplish this, we use replica exchange molecular dynamics (REMD) simulations to generate all-atom configurations of ten 3.4 kDa alginate polymers at a range of water contents and Ca–Na ratios. Simulated systems are solvated with explicitly modeled water molecules, which allows us to capture the discrete structure of the hydrating water and to examine the thermodynamic stability of water in the gels as they are progressively dehydrated. Our primary findings are that (i) the structure of the hydrogels is highly sensitive to the identity of the charge-compensating cations, (ii) the thermodynamics of water within the gels (specific enthalpy and free energy) are, surprisingly, only weakly sensitive to cation identity, and (iii) predictions of the differential enthalpy and free energy of hydration include a short-ranged enthalpic term that promotes hydration and a longer-ranged (presumably entropic) term that promotes dehydration, where short and long ranges refer to distances shorter or longer than ~0.6 nm between alginate strands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Machine Learning–Based Detection of Weather Fronts and Associated Extreme Precipitation in Historical and Future Climates

Extreme precipitation events, including those associated with weather fronts, have wide-ranging impacts across the world. Here we use a deep learning algorithm to identify weather fronts in high resolution Community Earth System Model (CESM) simulations over the contiguous United States (CONUS), and evaluate the results using observational and reanalysis products. We further compare results between CESM simulations using present-day and future climate forcing, to study how these features might change with climate change. We find that detected front frequencies in CESM have seasonally varying spatial patterns and responses to climate change and are found to be associated with modeled changes in large scale circulation such as the jet stream. We also associate the detected fronts with precipitation and find that total and extreme frontal precipitation mostly decreases with climate change, with some seasonal and regional differences. Here, decreases in Northern Hemisphere summer frontal precipitation are largely driven by changes in the frequency of different front types, especially cold and stationary fronts. On the other hand, Northern Hemisphere winter exhibits some regional increases in frontal precipitation that are largely driven by changes in frontal precipitation intensity. While CONUS mean and extreme precipitation generally increase during all seasons in these climate change simulations, the likelihood of frontal extreme precipitation decreases, demonstrating that extreme precipitation has seasonally varying sources and mechanisms that will continue to evolve with climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Deep Convection‐Driven Downward Transport of Trace Gases and Aerosols From the Free Troposphere to the Boundary Layer

Deep convective clouds regulate Earth's energy and moisture budgets, yet their impact on the atmospheric boundary layer (BL) composition remains underexplored. Using long-term observations from three mid-latitude sites, we show that deep convection (DC) consistently enhances nighttime surface ozone and is often accompanied by modest increases in ultrafine particle concentrations. Within the BL, the condensational growth of these transported ultrafine particles may contribute up to 60% of total cloud condensation nuclei (CCN). Mass flux calculations suggest that short-lived convective cores (∼30 min) account for ∼2% of total vertical air mass transport relative to steady entrainment, increasing to ∼13% when the trailing stratiform regions are included. These results show that DC provides an episodic but efficient pathway linking the free troposphere and BL, influencing oxidant budgets, CCN variability, and climate forcing. Accurately representing this process in climate models may help reduce uncertainties in climate projections, under both preindustrial and present-day conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Calcium dissolution in bridgmanite in the Earth’s deep mantle

Accurate knowledge of the mineralogy is essential for understanding the lower mantle, which represents more than half of Earth'svolume. CaSiO 3 perovskite is believed to be the third-most-abundant mineral throughout the lower mantle, following bridgmanite and ferropericlase. Here we experimentally show that the calcium solubility in bridgmanite increases steeply at about 2,300 kelvin and above 40 gigapascals to a level sufficient for a complete dissolution of all CaSiO 3 component in pyrolite into bridgmanite, resulting in the disappearance of CaSiO 3 perovskite at depths greater than about 1,800 kilometres along the geotherm. Hence we propose a change from a two-perovskite domain (TPD; bridgmanite plus CaSiO 3 perovskite) at the shallower lower mantle to a single-perovskite domain (SPD; calcium-rich bridgmanite) at the deeper lower mantle. Iron seems to have a key role in increasing the calcium solubility in bridgmanite. The temperature-driven nature can cause large lateral variations in the depth of the TPD-to-SPD change in response to temperature variations (by more than 500 kilometres). Furthermore, the SPD should have been thicker in the past when the mantle was warmer. Our finding requires revision of the deep-mantle mineralogy models and will have an impact on our understanding of the composition, structure, dynamics and evolution of the region.

58 GEOSCIENCES↗

DOE OSTI2022

Trends in surface equivalent potential temperature: A more comprehensive metric for global warming and weather extremes

Significance The Earth has warmed by 1.2 ± 0.1 °C since the preindustrial era. The most common metric to measure the ongoing global warming is surface air temperature since it has long and reliable observational records. However, surface air temperature alone does not fully describe the nature of global warming and its impact on climate and weather extremes. Here we show that surface equivalent potential temperature, which combines the surface air temperature and humidity, is a more comprehensive metric not only for the global warming but also for its impact on climate and weather extremes including tropical deep convection and extreme heat waves. We recommend that it should be used more widely in future climate change studies.

54 ENVIRONMENTAL SCIENCES↗