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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Meteorological Conditions in Urban Sites in Knoxville, USA. 2025

This 2025 dataset, which contains five csv files, reports hourly air temperature, wind speed, solar radiation, incident short wave, reflected short wave, incident long wave, emitted long wave, net radiation, and photosynthetically active radiation (PAR) data measured in urban parks in Knoxville, Tennessee, USA. The sites include Cumberland Estates Park (CEP), Socially Equal Energy Efficient Development (SEEED), West Hills Park (WHP), West View Park (WVP), and Victor Ashe Park (VAP). Air temperature, wind speed, and solar radiation data were obtained from a METER ATMOS 41 All-in-One Weather Station (Pullman, Washington, USA). Incident and emitted radiation (shortwave and longwave) measurements were made using an Apogee (Logan, Utah, USA) net radiometer (Model SN-500-SS). The SQ-521 Full-Spectrum Quantum sensor (Apogee Instruments, Inc) recorded the PAR. The measurement data for all the sites started on January 1, 2025. and all measurement ended on December 31, 2025. This work is a part of a larger study which investigates the impact of soil moisture and plant evapotranspiration on ambient temperature and relative humidity in several city parks in Knoxville, Tennessee.

Salvador, Christian [ORNL] (ORCID:0000000283287777↗
DOE OSTI2024

A ligand discovery toolbox for the WWE domain family of human E3 ligases

The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, 15 N-NMR-based binding affinity assays and 19 F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso -ADP-ribose ( iso -ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Rapid organic carbon spiraling in a headwater stream linked with streamflow, biogeochemistry, and canopy phenology

Headwater streams are abundant worldwide and important to global biogeochemical cycles, serving as critical processors and transporters of C. C spiraling is a useful way to understand the retention and mineralization of organic C (OC) in streams. However, analyses of seasonal and interannual variability in OC spiraling are currently limited. In this study, we aimed to understand the temporal patterns and driving mechanisms of OC spiraling, which will inform our understanding of future OC changes under climate change. We used 7 y of daily data in a small headwater stream (Walker Branch, Tennessee, USA) to assess seasonal and interannual variability in OC spiraling length (S OC ) and mineralization velocity (v fOC ), as well as their potential related variables. On average, S OC in Walker Branch was ~10× shorter than in previously studied small streams, indicating strong connections between the water column and the benthic environment where OC mineralization mostly takes place. OC spiraling was faster during the more biologically active periods of spring and autumn compared with more elongated OC spiraling in summer and winter, when OC retention was lower and downstream transport was higher. Gross primary production (GPP) was most strongly related to S OC and v fOC . Photosynthetically active radiation (PAR) and NO 3 − were also positively and negatively related to v fOC , respectively. Trends toward earlier and longer canopy cover and reduced GPP and PAR may result in longer S OC and slower v fOC , reducing localized instream processing of OC and potentially shunting more OC downstream. However, long-term observations indicate reduced NO 3 − at Walker Branch, suggesting opposing effects to those of GPP and PAR, leading to faster v fOC and greater OC retention. Time-series analyses of OC spiraling in streams can enhance our understanding of current and future responses of OC processing and downstream transport to climate change, as well as implications for downstream OC dynamics.

biological activity↗
DOE OSTI2024

Beyond the visible: Accounting for ultraviolet and far‐red radiation in vegetation productivity and surface energy budgets

Photosynthetically active radiation (PAR) is typically defined as light with a wavelength within 400–700 nm. However, ultra-violet (UV) radiation within 280–400 nm and far-red (FR) radiation within 700–750 nm can also excite photosystems, though not as efficiently as PAR. Vegetation and land surface models (LSMs) typically do not explicitly account for UV's contribution to energy budgets or photosynthesis, nor FR's contribution to photosynthesis. However, whether neglecting UV and FR has significant impacts remains unknown. Here, we explored how canopy radiative transfer (RT) and photosynthesis are impacted when explicitly implementing UV in the canopy RT model and accounting for UV and FR in the photosynthesis models within a next-generation LSM that can simulate hyperspectral canopy RT. We validated our improvements using photosynthesis measurements from plants under different light sources and intensities and surface reflection from an eddy-covariance tower. Our model simulations suggested that at the whole plant level, after accounting for UV and FR explicitly, chlorophyll content, leaf area index (LAI), clumping index, and solar radiation all impact the modeling of gross primary productivity (GPP). At the global scale, mean annual GPP within a grid would increase by up to 7.3% and the increase is proportional to LAI; globally integrated GPP increases by 4.6 PgC year −1 (3.8% of the GPP without accounting for UV + FR). Further, using PAR to proxy UV could overestimate surface albedo by more than 0.1, particularly in the boreal forests. Our results highlight the importance of improving UV and FR in canopy RT and photosynthesis modeling and the necessity to implement hyperspectral or multispectral canopy RT schemes in future vegetation and LSMs.

energy budget↗
DOE OSTI2022

Scoping Analysis of MACCS Modeling Improvements for the Study of Protective Action Recommendations

In late 2004, the U.S. Nuclear Regulatory Commission (NRC) initiated a project to analyze the relative efficacy of alternative protective action strategies in reducing consequences to the public from a spectrum of nuclear power plant core melt accidents. The study is documented in NUREG/CR-6953, “Review of NUREG-0654, Supplement 3, ‘Criteria for Protective Action Recommendations for Severe Accidents,’” Volumes 1, 2, and 3. The Protective Action Recommendations (PAR) study provided a technical basis for enhancing the protective action guidance contained in Supplement 3, “Guidance for Protective Action Strategies,” to NUREG-0654/FEMA-REP-1, Rev. 1, “Criteria for Preparation and Evaluation of Radiological Emergency Response Plans and Preparedness in Support of Nuclear Power Plants, ” dated November 2011. In the time since, a number of important changes and additions have been made to the MACCS code suite, the nuclear accident consequence analysis code used to perform the study. The purpose of this analysis is to determine whether the MACCS results used in the PAR study would be different given recent changes to the MACCS code suite and input parameter guidance. Updated parameters that were analyzed include cohorts, keyhole evacuation, shielding and exposure parameters, compass sector resolution, and a range of source terms from rapidly progressing accidents. Results indicate that using updated modeling assumptions and capabilities may lead to a decrease in predicted health consequences for those within the emergency planning zone compared to the original PAR study.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

SLOPE daily and 250 m gross primary productivity (GPP) for the CONUS, 2000-2019, Carbon Monitoring System (CMS)

The SatelLite Only Photosynthesis Estimation (SLOPE) GPP product is a daily, 250 m GPP dataset covering the Contiguous United States (CONUS) from 2000 to present with 1 day latency. Gross primary productivity (GPP) quantifies the amount of carbon dioxide (CO2) fixed by plants through photosynthesis. Although as a key quantity of terrestrial ecosystems, there is a lack of high-spatial-and-temporal-resolution, real-time, and observation-based GPP products. This product has been developed to address this critical gap, leveraging a number of MODIS land and atmosphere products. There are three distinct features of the SLOPE GPP production algorithm. (1) SLOPE couples machine learning models with MODIS atmosphere and land products to accurately estimate PAR. (2) SLOPE couples highly efficient and pragmatic gap-filling and filtering algorithms with surface reflectance acquired by both Terra and Aqua MODIS satellites to derive a soil-adjusted NIRv (SANIRv) dataset. (3) SLOPE couples a temporal pattern recognition approach with a long-term Crop Data Layer (CDL) product to predict dynamic C4 crop fraction. PAR, SANIRv and C4 fraction are used to drive a parsimonious model with only two slope parameters to estimate GPP along with a quantitative uncertainty on a per-pixel and daily basis. The slope GPP product has a R2 = 0.84 and a root-mean-square error (RMSE) of 1.65 gC m-2 d-1, evaluated against from 50 AmeriFlux eddy covariance sites (332 site-years). Archived data from 2000 to 2019 are publicly available at the NASA's Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC). Data from 2020 are available from the authors upon request. All data are projected in the standard MODIS Land Integerized Sinusoidal tile map projection. Each processing tile is in size of 4800 pixels by 4800 pixels, representing approximately 1200 km by 1200 km land region. In addition to the GPP product, SLOPE PAR, SANIRV, and C4 fraction, along with their uncertainties, are also released.

Jiang, Chongya↗
DOE OSTI2021

The response of the Amazon ecosystem to the photosynthetically active radiation fields: integrating impacts of biomass burning aerosol and clouds in the NASA GEOS Earth system model

The Amazon experiences fires every year, and the resulting biomass burning aerosols, together with cloud particles, influence the penetration of sunlight through the atmosphere, increasing the ratio of diffuse to direct photosynthetically active radiation (PAR) reaching the vegetation canopy and thereby potentially increasing ecosystem productivity. In this study, we use the NASA Goddard Earth Observing System (GEOS) model with coupled aerosol, cloud, radiation, and ecosystem modules to investigate the impact of Amazon biomass burning aerosols on ecosystem productivity, as well as the role of the Amazon's clouds in tempering this impact. The study focuses on a 7-year period (2010–2016) during which the Amazon experienced a variety of dynamic environments (e.g., La Niña, normal years, and El Niño). The direct radiative impact of biomass burning aerosols on ecosystem productivity – called here the aerosol diffuse radiation fertilization effect – is found to increase Amazonian gross primary production (GPP) by 2.6 % via a 3.8 % increase in diffuse PAR (DFPAR) despite a 5.4 % decrease in direct PAR (DRPAR) on multiyear average during burning seasons. On a monthly basis, this increase in GPP can be as large as 9.9 % (occurring in August 2010). Consequently, the net primary production (NPP) in the Amazon is increased by 1.5 %, or ~92 Tg C yr -1 – equivalent to ~37 % of the average carbon lost due to Amazon fires over the 7 years considered. Clouds, however, strongly regulate the effectiveness of the aerosol diffuse radiation fertilization effect. The efficiency of this fertilization effect is the highest in cloud-free conditions and linearly decreases with increasing cloud amount until the cloud fraction reaches ~0.8, at which point the aerosol-influenced light changes from being a stimulator to an inhibitor of plant growth. Nevertheless, interannual changes in the overall strength of the aerosol diffuse radiation fertilization effect are primarily controlled by the large interannual changes in biomass burning aerosols rather than by changes in cloudiness during the studied period.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evaluating integration and performance of containerized climate applications on a Hewlett Packard Enterprise Cray system

Containers have taken over large swaths of cloud computing as the most convenient way of packaging and deploying applications. The features that containers offer for packaging and deploying applications translate to high performance computing (HPC) as well. At The National Oceanic and Atmospheric Administration, containers provide an easy way to build and distribute complex HPC applications, allowing faster collaboration, portability, and experiment computer environment reproducibility amongst the scientific community. The challenge arises when applications rely on message passing interface (MPI). This necessitates investigation into how to properly run these applications with their own unique requirements and produce performance on par with native runs. We investigate the MPI performance for benchmarks and containerized climate models for various containers covering selection of compiler and MPI library combinations from the Cray provided programming environments on the Cray XC supercomputer GAEA. Performance from the benchmarks and the climate models shows that for the most part containerized applications perform on par with the natively built applications when the system optimized Cray MPICH libraries are bound into the container, and the hybrid model containers have poor performance in comparison. We also describe several challenges and our solutions in running these containers, particularly challenges with heterogeneous jobs for the containerized model runs.

Abraham, Subil↗
DOE OSTI2021

Pigment modulation in response to irradiance intensity in the fast-growing alga Picochlorum celeri

Picochlorum celeri has among the fastest photoautotrophic growth rates (~2 h doubling time in optimal conditions) reported to date for a marine alga. This study comprehensively analyzes the levels of Picochlorum celeri photosynthetic pigments, which can reach up to ~13% of the total particulate organic carbon (POC) under light-limiting conditions. The main Picochlorum celeri pigments identified include: chlorophyll a, chlorophyll b, lutein, β-carotene, canthaxanthin, violaxanthin, neoxanthin, zeaxanthin and antheraxanthin. The ketocarotenoid canthaxanthin can accumulate up to 120 mg L -1 in Picochlorum celeri liquid culture; ~12% of it was found in an extracellular polysaccharide matrix. Using a solar-simulating automated photobioreactor, we monitor the photoacclimation of cultures maintained in unshaded conditions (<0.5 μg mL -1 of total chlorophyll) through transitions from high irradiance (1000 μmoles photosynthetically active radiation (PAR) m -2 s -1 ) to low irradiance (60 μmoles PAR m -2 s -1 ), and conversely from low to high irradiance. Canthaxanthin and zeaxanthin accumulation are among the most rapid modulation responses when cultures are shifted from low to high irradiance. The violaxanthin, antherazanthin, and zeaxanthin (VAZ) pool is ~3-fold higher in high-light cultures, suggesting that the VAZ cycle combined with a dramatic reduction in chlorophyll levels are among the major mechanisms used in Picochlorum celeri to efficiently acclimate to high-irradiance levels. Responsive pigment modulation was also observed in denser cultures (~0.65 g L –1 ) grown under a diel cycle (pond-mimicking conditions). Furthermore, this research provides unique insights into the dynamics of pigment modulation and photoacclimation in response to changing irradiance in a biotechnologically promising alga and will inform future pigment engineering strategies to further improve light capture and biomass accumulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Design, dynamic modeling and wave basin verification of a Hybrid Wave–Current Energy Converter

Massive and high-density Marine and Hydrokinetic (MHK) energy is contained in the ocean, including waves, tidal streams, and ocean currents. Traditional MHK energy converters harvest energy from only a single MHK energy source, which does not fully exploit the energy potential that co-exists in multiple forms of MHK energy in the ocean. This paper presents the design and dynamics of a Hybrid Wave–Current Energy Converter (HWCEC) that can simultaneously convert both wave and current energy to electricity with a single Power Take-off (PTO) through the engagement and disengagement of the three one-way clutches. The critical design parameters are analyzed through modeling and simulation, including the transmission ratios, the electrical impedance, and the turbine-heave plate distance. Water basin tests in a wave–current tank were conducted, which shows the prototyped HWCEC can improve the electric power output by 38%–71% for regular waves and 79% for irregular waves, while providing a 70% reduction of the Peak to Average Ratio (PAR) of power compared to the baseline Wave Energy Converter (WEC). Here we further analyze the occurring percentages of the instant power of both WEC and HWCEC in irregular wave tests, shedding new insight on how HWCEC reduces the PAR.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

A late glacial paleoenvironmental and climate record from the Sierra de Juarez, Baja California

Ciénegas are desert wetlands that are strongly correlated with the stability of the hydrologic cycle in arid landscapes. However, these environments are particularly vulnerable to climate change, drought, water diversion, and fire suppression which all have contributed to the degradation of ciénegas along the U.S.-Mexican borderlands. Therefore, identifying the timing of precipitation patterns in this region is of particular interest because of its relationship to many ecological responses of the landscape such as groundwater recharge and fire. Here, we present the first-ever fire paleoenvironmental record from Ciénega Chimeneas, a ciénega complex in the Sierra de Juárez of Baja California. We explore how changes in the amount and seasonality of moisture affected ciénega complexes and fire activity from across the southwestern North American region over the past 45,000 years. Further, our record suggests that during the late glacial period, 41,000–21,000 cal yr BP, the increase of Larrea and Quercus indicate an increase in summer precipitation. Subsequently, when summer precipitation increased, pollen preservation and pollen accumulation rates (PAR) also increased. Increased vegetation allowed for increased fire activity during the late glacial period. Regionally, most of the comparison sites also indicated wet conditions during the full glacial period. However, around 21,000 cal yr BP, effective moisture decreased resulting in a dramatic change in the vegetation assemblage. Specifically, the summer wet taxa disappeared, while pollen preservation and PAR decreased, suggesting a dry period until ~14,000 cal yr BP. Little fire activity is recorded after 21,000 cal yr BP, likely due to the absence of fuels. At ~14,000 cal yr BP, Larrea and Quercus reappear suggesting increased summer precipitation. However, the appearance of Cyperaceae and increases in grasses suggest increased winter precipitation. We suggest that the combination of summer wet and winterwet taxa ~14,000 cal yr BP represents an increase in ENSO conditions, while the summer moisture controls remained relatively constant.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Down-regulation of A3AR signaling by IL-6-induced GRK2 activation contributes to Th17 cell differentiation

Highlights: • Cyclic AMP-PKA signaling is involved in Th17 cell differentiation. • IL-6 stimulation triggers the internalization of A{sub 3}AR and promotes cAMP production in T cells. • IL-6 induces A{sub 3}AR internalization in a GRK2 dependent manner. • GRK2 is a potential therapeutic target for treating Th17 driving immune diseases. IL-6-triggered Th17 cell expansion is responsible for the pathogenesis of many immune diseases including rheumatoid arthritis (RA). Traditionally, IL-6 induces Th17 cell differentiation through JAK-STAT3 signaling. In the present work, PKA inhibition reduces in vitro induction of Th17 cells, while IL-6 stimulation of T cells facilitates the internalization of A{sub 3}AR and increased cAMP production in a GRK2 dependent manner. Inhibition of GRK2 by paroxetine (PAR) or genetic depletion of GRK2 restored A{sub 3}AR distribution and prevented Th17 cell differentiation. Furthermore, in vivo PAR treatment effectively reduced the splenic Th17 cell proportion in a rat model of collagen-induced arthritis (CIA) which was accompanied by a significant improvement in clinical manifestations. These results indicate that IL-6-induced Th17 cell differentiation not only occurs through JAK-STAT3-RORγt but is also mediated through GRK2-A{sub 3}AR-cAMP-PKA-CREB/ICER-RORγt. This elucidates the significance of GRK2-controlled cAMP signaling in the differentiation of Th17 cells and its potential application in treating Th17-driven immune diseases such as RA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Impact of Sr-Containing Secondary Phases on Oxide Conductivity in Solid-Oxide Electrolyzer Cells

Solid-oxide electrolyzer cells (SOECs) based on a yttria-stabilized zirconia (YSZ) oxide electrolyte produce hydrogen from water with the assistance of excess thermal energy; however, Sr diffusion within the Gd-doped CeO 2 (GDC) barrier layer during processing or operation can lead to the formation of unwanted secondary phases such as SrO and SrZrO 3 . Here, to establish and compare the degree of impact of these phases on SOEC performance, we conduct first-principles calculations to study their bulk oxide conductivities and compare them to that of the YSZ electrolyte. We find that SrO has a low conductivity arising from the poor mobility and low concentration of mobile oxygen vacancies, and its presence in SOECs should therefore be avoided. SrZrO 3 also has a lower oxide conductivity than YSZ; however, this discrepancy is primarily due to lower vacancy concentrations rather than low mobility. We find that sufficient levels of Y-doping on the Zr site can increase oxygen vacancy concentrations in SrZrO 3 to achieve an oxide ionic conductivity on par with that of YSZ, thereby mitigating any potential deleterious effect on transport performance. Energy-dispersive X-ray spectroscopy confirms that Y is the most common minority element present in SrZrO 3 forming near the GDC–YSZ interface, alleviating concerns regarding the impact of SrZrO 3 on device performance. These results from our combined computational–experimental analysis can inform future engineering strategies designed to limit the detrimental effects of Sr-induced secondary phase formation on SOEC performance.

08 HYDROGEN↗
DOE OSTI2025

DeSelenator: A Se-Removal Process for Environmental Decontamination of Wastewaters from Coal-Burning Power Plants

Selenium may become a toxic contaminant of freshwater systems when released into the environment through industrial wastewaters from mining, coal-burning power plants, or oil refining. Efficient and cost-effective Se-removal technologies are therefore necessary to reduce Se concentrations in these wastewaters to below the regulatory discharge limits. In this study, we have demonstrated an effective process that removes Se, mostly as selenate anions, from wastewaters generated by coal-burning power plants. This process, dubbed DeSelenator, leverages the high concentration of sulfate relative to selenate in the wastewater and the propensity of these oxyanions to cocrystallize with benzene-bis-iminoguanidinium (BBIG) cations into extremely insoluble salts (on par with BaSO 4 ). The SO 4 2− /SeO 4 2− cocrystallization with BBIG removes over 90% of S and Se from the wastewater. Following removal of the precipitate by filtration, the filtrate is passed over an anion-exchange resin that further reduces selenium concentration to 5 ppb, the EPA’s regulatory limit for freshwater systems. Finally, the effluent is passed over an activated carbon column, which removes 99.8% of the residual BBIG ligand remaining after crystallization, allowing for the safe discharge of the treated water into the environment. The Se-removal process was first optimized in the lab at the bench scale and then tested in the field at the Tennessee Valley Authority’s Bull Run coal-burning power plant. A technoeconomic assessment found the cost of water treatment with DeSelenator is on par with that of the active biological method, which is currently considered a state-of-the-art Se-removal technology.

anions↗
DOE OSTI2020

Systematic Assessment of Retrieval Methods for Canopy Far-Red Solar-Induced Chlorophyll Fluorescence Using High-Frequency Automated Field Spectroscopy

Remote sensing of solar-induced chlorophyll fluorescence (SIF) offers potential to infer photosynthesis across scales and biomes. Many retrieval methods have been developed to estimate top-of-canopy SIF using ground-based spectroscopy. However, inconsistencies among methods may confound interpretation of SIF dynamics, eco-physiological/environmental drivers, and its relationship with photosynthesis. Using high temporal- and spectral resolution ground-based spectroscopy, we aimed to (1) evaluate performance of SIF retrieval methods under diverse sky conditions using continuous field measurements; (2) assess method sensitivity to fluctuating light, reflectance, and fluorescence emission spectra; and (3) inform users for optimal ground-based SIF retrieval. Analysis included field measurements from bi-hemispherical and hemispherical-conical systems and synthetic upwelling radiance constructed from measured downwelling radiance, simulated reflectance, and simulated fluorescence for benchmarking. Fraunhofer-based differential optical absorption spectroscopy (DOAS) and singular vector decomposition (SVD) retrievals exhibit convergent SIF-PAR relationships and diurnal consistency across different sky conditions, while O2A-based spectral fitting method (SFM), SVD, and modified Fraunhofer line discrimination (3FLD) exhibit divergent SIF-PAR relationships across sky conditions. We find that such behavior holds across system configurations, though hemispherical-conical systems diverge less across sky conditions. O 2 A retrieval accuracy, influenced by atmospheric distortion, improves with a narrower fitting window and when training SVD with temporally local spectra. This may impact SIF-photosynthesis relationships interpreted by previous studies using O 2 A-based retrievals with standard (759–767.76 nm) fitting windows. Fraunhofer-based retrievals resist atmospheric impacts but are noisier and more sensitive to assumed SIF spectral shape than O 2 A-based retrievals. We recommend SVD or SFM using reduced fitting window (759.5–761.5 nm) for robust far-red SIF retrievals across sky conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

PCM1 coordinates centrosome asymmetry with polarized endosome dynamics to regulate daughter cell fate

Vertebrate radial glia progenitors (RGPs) balance self-renewal and differentiation through asymmetric cell division (ACD), which involves unequal centrosome inheritance. How centrosome asymmetry directs cell fate remains poorly understood. Here, we identify Pericentriolar material 1 (Pcm1) as a key player in this process. In zebrafish embryonic RGPs, Pcm1 is asymmetrically associated with Cep83, a mother centrosome marker. Using in vivo time-lapse imaging and nanoscale-resolution expansion microscopy, we detect Pcm1 on Notch ligand-containing endosomes, where it interacts–either directly or indirectly–with Par-3 and dynein. Loss of pcm1 disrupts endosome dynamics, increasing neuronal differentiation at the expense of RGP self-renewal. Mechanistically, Pcm1 facilitates the transition from Rab5b to Rab11a and promotes the assembly of Par-3 and dynein macromolecular complexes on recycling endosomes. Furthermore, we find conserved PARD3-PCM1-CEP83-RAB11 associations in human cortical brain organoids. Our findings uncover that Pcm1 links centrosome asymmetry to polarized endosome trafficking, thereby regulating RGP fate decisions.

Cell fate and cell lineage↗
DOE OSTI2021

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for an electronic structure that is designed as a drop-in replacement for groundstate density functional theory (DFT) energy calculations. The model is a message-passing graph neural network that uses symmetryadapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 × 10 6 DFT calculations on molecules and geometries. This dataset covers the most common elements in biochemistry and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, and I) and charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformer benchmark set, OrbNet Denali has a median correlation coefficient of R 2 = 0.90 compared to the reference DLPNO-CCSD(T) calculation and R 2 = 0.97 compared to the method used to generate the training data (ωB97X-D3/def2- TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for noncovalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of ωB97X-D3/def2-TZVP with an average mean absolute error of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗