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At least 343 records · Page 19

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DOE OSTI2024

Unlocking the unfolded structure of ubiquitin: Combining time-resolved x-ray solution scattering and molecular dynamics to generate unfolded ensembles

The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.

Chemistry↗

DOE OSTI2021

Numerical investigation of active control of tearing mode by magnetic coils and the role of Δ'

Magnetic feedback stabilization of the tearing mode (TM) is numerically investigated, utilizing the MARS-F code (Liu et al 2000 Phys. Plasmas 7 3681) for toroidal tokamak equilibria. With control coil configurations assumed in this study, magnetic feedback partially or fully stabilizes the TM, with either vanishing or finite equilibrium pressure. The best control is achieved by the combination of internal active coils and internal poloidal sensors. The internal and external tearing indices are evaluated for the close-loop system, based on the MARS-F computed mode eigenvalue and eigenfunction, respectively. In the absence of the favorable curvature effect, these two indices are real-valued and quantitatively agree well with each other. For the equilibrium with finite pressure gradient at the mode rational surface, the favorable average curvature effect becomes important and the close-loop tearing index also becomes complex-valued, partly due to interaction of the feedback system with the dissipative wall eddy current response. Isolating the inner layer and outer region response to magnetic feedback, with either proportional or proportional-derivative actions, allows to establish that feedback stabilization of the TM occurs mainly due to modification of the behavior of the external ideal solution, further confirming the analytic result reported in He et al 2021 Phys. Plasmas 28 012504.

Physics↗

DOE OSTI2024

Evidence of the h c → K S 0 K + π − + c . c . decay

Based on ( 2.712 ± 0.014 ) × 10 9 ψ ( 3686 ) events collected by the BESIII Collaboration, evidence of the hadronic decay h c → K S 0 K + π − + c . c . is found with a significance of 4.3 σ in the ψ ( 3686 ) → π 0 h c process. The branching fraction of h c → K S 0 K + π − + c . c . is measured to be ( 7.3 ± 1.8 ± 0.8 ) × 10 − 4 , where the first and second uncertainties are statistical and systematic, respectively. Combining with the exclusive decay width of η c → K K ¯ π , our result indicates inconsistencies with both pQCD and NRQCD predictions. Published by the American Physical Society 2024

Ablikim, M.↗

DOE OSTI2025

Multi-phase Wireless Power Transfer with High Power Density Inductive Coils for Electric Drone Charging

Wireless charging of unmanned ground vehi-cles and aircraft has been proposed to increase charging reliability and security, allow for autonomous functionality, and either reduce battery size or increase continuous flight time. This paper proposes a three-phase Litz wire primary and a two-phase PCB secondary for high secondary-side power density considering misalignment tolerances, surface and volumetric power density, and coil sizing. Elec-tromagnetic 3D finite element analysis (FEA) simulations are conducted to study variation in mutual inductance and coupling coefficient with different secondary coil sizes and number of turns, horizontal and vertical misalignment between the primary and secondary, and a combination of both for a set of designs with the same rated power. Results indicate that receiver coils of reduced size relative to the primary can deliver rated power for increased power density and higher tolerance to misalignment.

Gastineau, Lucas [University of Kentucky]↗

DOE OSTI2021

Makah Tribe Climate Assessment, Adaptation, and Resilience Planning

Our aim was to develop a Climate Adaptation and Resilience Plan through gathering community input through personal interviews and individual surveys, building from our Climate Impacts Assessment work completed in 2018. This project has collected traditional, cultural, and local knowledge to support the ongoing multi-departmental environmental planning processes of the Makah Tribe. This information was then used to identify specific human wellbeing indicators to inform and enhance Makah tribal policy, management, and decision-making processes. Combined our tribal environmental planning to include the work of the Tribal Resilience Work Group (TRWG) and Oil Spill Work Group (OSWG), which relied on publicly available Western science-based data. While this information provided a strong basis for tribal environmental planning, it does not capture the unique traditional, cultural needs, and local knowledge and tribal voices of the Makah community.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Spatial heterogeneity effects on land surface modeling of water and energy partitioning

Abstract. Understanding the influence of land surface heterogeneity on surface water and energy fluxes is crucial for modeling earth system variability and change. This study investigates the effects of four dominant heterogeneity sources on land surface modeling, including atmospheric forcing (ATM), soil properties (SOIL), land use and land cover (LULC), and topography (TOPO). Our analysis focused on their impacts on the partitioning of precipitation (P) into evapotranspiration (ET) and runoff (R), partitioning of net radiation into sensible heat and latent heat, and corresponding water and energy fluxes. An initial set of 16 experiments were performed over the continental US (CONUS) using the E3SM land model (ELMv1) with different combinations of heterogeneous and homogeneous datasets. The Sobol' total and first-order sensitivity indices were utilized to quantify the relative importance of the four heterogeneity sources. Sobol' total sensitivity index measures the total heterogeneity effects induced by a given heterogeneity source, consisting of the contribution from its own heterogeneity (i.e., the first-order index) and its interactions with other heterogeneity sources. ATM and LULC are the most dominant heterogeneity sources in determining spatial variability of water and energy partitioning, mainly contributed by their own heterogeneity and slightly contributed by their interactions with other heterogeneity sources. Their heterogeneity effects are complementary, both spatially and temporally. The overall impacts of SOIL and TOPO are negligible, except TOPO dominates the spatial variability of R/P across the transitional climate zone between the arid western and humid eastern CONUS. Accounting for more heterogeneity sources improves the simulated spatial variability of water and energy fluxes when compared with ERA5-Land reanalysis dataset. An additional set of 13 experiments identified the most critical components within each heterogeneity source, which are precipitation, temperature, and longwave radiation for ATM, soil texture, and soil color for SOIL and maximum fractional saturated area parameter for TOPO.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Classical Optimizers for Noisy Intermediate-Scale Quantum Devices

We present a collection of optimizers tuned for usage on Noisy Inter-mediate-Scale Quantum (NISQ) devices. Optimizers have a range of applications in quantum computing, including the Variational Quantum Eigensolver (VQE) and Quantum Approximate Optimization (QAOA) algorithms. They have further uses in calibration, hyperparameter tuning, machine learning, etc. We employ the VQE algorithm as a case study. VQE is a hybrid algorithm, with a classical minimizer step driving the next evaluation on the quantum processor. While most results to date concentrated on tuning the quantum VQE circuit, our study indicates that in the presence of quantum noise the classical minimizer step is a weak link and a careful choice combined with tuning is required for correct results. We explore state-of-the-art gradient-free optimizers capable of handling noisy, black-box, cost functions and stress-test them using a quantum circuit simulation environment with noise injection capabilities on individual gates. Our results indicate that specifically tuned optimizers are crucial to obtaining valid science results on NISQ hardware, as well as projecting forward on fault tolerant circuits.

Lavrijsen, Wim↗

DOE OSTI2026

Cross-sectoral synergies for household energy savings: the role of electric vehicles, solar photovoltaics, and remote work

Over the past two decades, new technologies and behavioral shifts – such as electric vehicles, solar photovoltaics, and increased work-from-home practices – have reshaped residential electricity consumption and cost. However, their combined or synergistic impact on a household’s electricity cost remains unexplored. Leveraging data from the 2020 Residential Energy Consumption Survey, this study uses a structural equation model to unravel the extent to which the bundled adoption of EV-PV and stay-at-home decisions impact the total electricity cost of households. Results indicate that adopting both EVs and PV reduces electricity costs by 31% despite a 16% rise in consumption. When combined with stay-at-home practices, households still experience a 13% cost reduction, even with a 25% increase in electricity consumption. In conclusion, these findings suggest that financial savings are not merely a byproduct of adopting new technologies or behavioral changes but could serve as a key consideration for household contemplating engagement with multiple modern energy solutions simultaneously.

14 SOLAR ENERGY↗

DOE OSTI2023

Predicting fatal heat and humidity using the heat index model

A unique wet-bulb temperature of 35°C is often used as the threshold for human survivability, but recent experiments have shown that a person’s core temperature starts to rise at a wide range of critical wet-bulb temperatures. Here, it is shown that the model underlying the heat index correctly predicts those critical wet-bulb temperatures, explaining 95% of the variance in the values observed in laboratory heat-stress experiments. This is the first time the heat-index model has been validated against physiological data from laboratory experiments. For light and moderate exertion in an indoor setting, the heat index model predicts that the critical wet-bulb temperature ranges from 20 to 32°C, depending on the relative humidity, consistent with experimental results. Furthermore, for the same setting and exertion, the heat index model predicts fatal wet-bulb temperatures ranging from 24 to 37°C. Recent experiments have identified the critical combinations of heat and humidity, in an indoor setting, above which an individual is unable to maintain a standard core temperature, indicating severe heat stress. It is shown here why this state of severe heat stress cannot be predicted using the wet-bulb temperature. Instead, it is shown that the recently extended heat index model can explain nearly all of the variance in the observed critical combinations of temperature and humidity, and can be used to calculate fatal combinations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

L-H transition trigger physics in ITER-similar plasmas with applied n = 3 magnetic perturbations

The L–H transition power threshold PLH is observed to increase with applied n = 3 resonant magnetic perturbations (RMP) in ITER-similar-shape plasmas with balanced neutral beam torque injection in DIII-D. The increase is most pronounced with added electron–cyclotron heating: PLH increases with decreasing edge plasma collisionality as PLH/PLH-08 ~ (ν*)−0.5, where PLH-08 is the 2008 ITPA multi-machine power threshold scaling. This result raises concerns for H-mode access at low edge collisionality in ITER, where RMP may have to be applied before the L–H transition to safely suppress the first edge-localized mode. Non-axisymmetric modifications with RMP include a simultaneous reduction of the radial electric field (Er) well depth and E × B shear. This can be attributed to increasing edge toroidal co-current rotation, and is consistent with substantially increased local long-wavelength turbulence (measured via beam emission spectroscopy). At high RMP perturbation strength the edge electric field Er reverses sign locally (becomes positive), with changes in dominant turbulence modes. Edge magnetic stochasticity provides an attractive explanation of the observed modifications, and the observed changes in toroidal rotation and Er are consistent with a simple fluid model describing radial electron current flow along stochastic fieldlines. The observed collisionality dependence of the L-mode edge electric field with applied RMP is also qualitatively consistent with this model. Reflectometry data indicate a significant reduction of the normalized L-mode radial density gradient a/Ln at high RMP field with simultaneous increase in radial particle flux and electron thermal flux from power balance analysis. We conjecture that the increase of PLH with RMP results from the combined effects of reduced E × B flow shear (increasing turbulent transport levels) and toroidal/poloidal flow modulation due to edge stochasticity. Initial experiments indicate that non-resonant n = 3 magnetic perturbations lead only to relatively small changes in Er, E × B shear and fluctuation characteristics, and have less impact on the L–H transition power threshold. This motivates further exploration of the RMP spectrum dependence of PLH for possible mitigation of the observed threshold increase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Simulated effect of defect volume and location on very high cycle fatigue of laser beam powder bed fused AlSi10Mg

This study quantifies the interaction between volumetric defect location and size on the very high cycle fatigue (VHCF) of laser beam powder bed fused (LB-PBF) AlSi10Mg. Crystal plasticity finite element method (CPFEM) simulations were used to investigate the effects of defect location and size on the driving force for crack initiation. The CPFEM model was calibrated against uniaxial and cyclic experimental data of LB-PBF AlSi10Mg. Defect characteristics were informed by experimental data from the specimens produced in various geometries to create realistic representative volume elements (RVEs) with equivalent volume fractions of defects. By embedding defects of varying sizes and locations within the RVEs, fatigue indicator parameters (FIPs) were calculated to analyze the impact of defects’ characteristics on fatigue performance. Different combinations of defect volume and locations were generated for various microstructure instantiations, providing insight into extreme value fatigue responses. Larger defect volumes located on free surfaces consistently generated the highest FIPs, suggesting defect size and boundary proximity intensify stress concentration effects. RVEs with multiple smaller defects produced lower FIPs than those with single large critical defects. These findings underscore the critical role of defect characteristics on fatigue life, providing a foundation for future predictive modeling in fatigue-sensitive AM applications.

AlSi10Mg↗

DOE OSTI2021

Identifying insects, clouds, and precipitation using vertically pointing polarimetric radar Doppler velocity spectra

Abstract. This study presents a method to identify and distinguish insects, clouds, and precipitation in 35 GHz (Ka-band) vertically pointing polarimetric radar Doppler velocity power spectra and then produce masks indicating the occurrence of hydrometeors (i.e., clouds or precipitation) and insects at each range gate. The polarimetric radar used in this study transmits a linear polarized wave and receives signals in collinear (CoPol) and cross-linear (XPol) polarized channels. The measured CoPol and XPol Doppler velocity spectra are used to calculate linear depolarization ratio (LDR) spectra. The insect–hydrometeor discrimination method uses CoPol and XPol spectral information in two separate algorithms with their spectral results merged and then filtered into single value products at each range gate. The first algorithm discriminates between insects and clouds in the CoPol Doppler velocity power spectra based on the spectra texture, or spectra roughness, which varies due to the scattering characteristics of insects vs. cloud particles. The second algorithm distinguishes insects from raindrops and ice particles by exploiting the larger Doppler velocity spectra LDR produced by asymmetric insects. Since XPol power return is always less than CoPol power return for the same target (i.e., insect or hydrometeor), fewer insects and hydrometeors are detected in the LDR algorithm than the CoPol algorithm, which drives the need for a CoPol based algorithm. After performing both CoPol and LDR detection algorithms, regions of insect and hydrometeor scattering from both algorithms are combined in the Doppler velocity spectra domain and then filtered to produce a binary hydrometeor mask indicating the occurrence of cloud, raindrops, or ice particles at each range gate. Forty-seven summertime days were processed with the insect–hydrometeor discrimination method using US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program Ka-band zenith pointing radar observations in northern Oklahoma, USA. For these 47 d, over 70 % of the hydrometeor mask column bottoms were within ±100 m of simultaneous ceilometer cloud base heights. All datasets and images are available to the public on the DOE ARM repository.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

Abstract Motivation Millions of protein sequences have been generated by numerous genome and transcriptome sequencing projects. However, experimentally determining the function of the proteins is still a time consuming, low-throughput, and expensive process, leading to a large protein sequence-function gap. Therefore, it is important to develop computational methods to accurately predict protein function to fill the gap. Even though many methods have been developed to use protein sequences as input to predict function, much fewer methods leverage protein structures in protein function prediction because there was lack of accurate protein structures for most proteins until recently. Results We developed TransFun—a method using a transformer-based protein language model and 3D-equivariant graph neural networks to distill information from both protein sequences and structures to predict protein function. It extracts feature embeddings from protein sequences using a pre-trained protein language model (ESM) via transfer learning and combines them with 3D structures of proteins predicted by AlphaFold2 through equivariant graph neural networks. Benchmarked on the CAFA3 test dataset and a new test dataset, TransFun outperforms several state-of-the-art methods, indicating that the language model and 3D-equivariant graph neural networks are effective methods to leverage protein sequences and structures to improve protein function prediction. Combining TransFun predictions and sequence similarity-based predictions can further increase prediction accuracy. Availability and implementation The source code of TransFun is available at https://github.com/jianlin-cheng/TransFun.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Safety and antiviral activity of triple combination broadly neutralizing monoclonal antibody therapy against HIV-1: a phase 1 clinical trial

HIV-1 therapy with single or dual broadly neutralizing antibodies (bNAbs) has shown viral escape, indicating that at least a triple bNAb therapy may be needed for robust suppression of viremia. We performed a two-part study consisting of a single-center, randomized, double-blind, dose-escalation, placebo-controlled first-in-human trial of the HIV-1 V2-glycan-specific antibody PGDM1400 alone or in combination with the V3-glycan-specific antibody PGT121 in 24 adults without HIV in part 1, as well as a multi-center, open-label trial of the combination of PGDM1400, PGT121 and the CD4-binding-site antibody VRC07-523LS in five viremic adults living with HIV not on antiretroviral therapy (ART) in part 2. The primary endpoints were safety, tolerability and pharmacokinetics for both parts and antiviral activity among viremic adults living with HIV and not on ART for part 2 of the study. The secondary endpoints were changes in CD4 + T cell counts and development of HIV-1 sequence variations associated with PGDM1400, PGT121 and VRC07-523LS resistance in part 2. Intravenously administered PGDM1400 was safe and well-tolerated at doses up to 30 mg kg -1 and when given in combination with PGT121 and VRC07-523LS. A single intravenous infusion of 20 mg kg -1 of each of the three antibodies reduced plasma HIV RNA levels in viremic individuals by a maximum mean of 2.04 log10 copies per ml; however, viral rebound occurred in all participants within a median of 20 days after nadir. Rebound viruses demonstrated partial to complete resistance to PGDM1400 and PGT121 in vitro, whereas susceptibility to VRC07-523LS was preserved. Viral rebound occurred despite mean VRC07-523LS serum concentrations of 93 µg ml -1 . The trial met the pre-specified endpoints. Our data suggest that future bNAb combinations likely need to achieve broad antiviral activity, while also maintaining high serum concentrations, to mediate viral control.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Crystal Prediction and Design of Tunable Light Emission in BTB–Based Metal–Organic Frameworks

Metal-organic frameworks (MOFs) have recently been shown to exhibit unique mechanisms of luminescence based on charge transfer between structural units in the framework. These MOFs have the potential to be structural tuned for targeted emission with little or no metal participation. Here a computationally led, material design and synthesis methodology is presented that elucidates the mechanisms of light emission in interpenetrated structures comprised of metal centers (M = In, Ga, InGa, InEu) and BTB (1,3,5-Tris(4-carboxyphenyl)benzene) linkers, forming unique luminescent M-BTB MOF frameworks. Gas phase and periodic electronic structure calculations indicate that the intensity of the emission and the wavelength are overwhelmingly controlled by a combination of the number of interacting stacked linkers and their interatomic spacings, respectively. In the MOF, the ionic radii of the metal centers primarily control the expansion or shrinkage of the linker stacking distances. Experimentally, multiple M-BTB-based MOFs are synthesized and their photoluminescence was tested. Experiments validated the modeling by confirming that shifts in the crystal structure result in variations in light emission. Through this material design method, the mechanisms of tuning luminescence properties in interpenetrated M-BTB MOFs have been identified and applied to the design of MOFs with specific wavelength emission based on their structure.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Verification and Validation Tests of Gamma Library of MC2-3 for Coupled Neutron and Gamma Heating Calculation

For the accurate assessment of the heat generation rate in fast reactors, the gamma library of MC2 -3 and the MC2 -3 + GAMSOR procedure employing the coupled neutron and gamma heating calculation has been thoroughly verified against Monte Carlo results and validated using the ZPPR-15D gamma dose measurement data. NJOY outputs are post-processed in a consistent way with the NJOY procedure to avoid any missing data or double counting of data. Prompt heating for 379 out of 391 isotopes in the gamma library was verified against MCNP6.2 to within 1% relative error in total heating for most isotopes. For both a simple one-dimensional slab problem representing a sodium cooled fast reactor and the Experimental Breeder Reactor II (EBR-II) benchmark problem, the root-mean-square values of assembly power error were less than 0.5% for fuel assemblies, ~1% in blankets and ~1 to ~3% in reflectors compared to MCNP6.2 results. The most plausible cause for the 3% error in a reflector assembly is believed to be the error in the multigroup neutron cross sections for the reflector assembly. For validation, gamma doses measured with thermoluminiscent dosimeters (TLDs) in the ZPPR-15D experiment were calculated using GAMSOR. Due to the uncertainty in the TLD measurement with regards to the energy deposition of photons and neutrons, the validation data leads to a 12.7% uncertainty on the experimental measurement. With this uncertainty bound, the calculated doses all fell within one standard deviation of the measured value. Combined with the accurate calculation of reaction rate distributions and neutron spectrum measurements, these results indicate good agreement for the neutron and gamma heating calculations that were performed.

coupled neutron and gamma heating↗

DOE OSTI2022

Managing weather- and market price-related financial risks in algal biofuel production

Large-scale algae production has garnered interest due to its potential as a biofuel feedstock. Previous research assessing the profitability of algae products has been mostly based on values averaged over time, but algae production and resulting financial returns exhibit significant variability due to weather and fluctuations in selling prices for algae-based products. In other sectors, producers often reduce weather- and market price-related financial risk with financial instruments such as insurance, but little research has been performed on the design of insurance products to protect algae producers. Furthermore, this study develops a novel index-based insurance instrument that pays-out during unfavorable weather and market conditions, then explores the instrument's effectiveness, combined with a cash reserve, in reducing revenue stream variability for an algae producer. Results indicate that a biophysically based index-insurance product tailored to the specific financial risks in algae production can reduce variability in net revenues and can do so at a lower cost than relying solely on cash reserves, the most common financial risk management tool. Assessing the performance of index-insurance in algae production is particularly timely given the passage of the 2018 Farm Bill, which newly opens opportunities for the USDA to provide crop insurance to algae producers.

09 BIOMASS FUELS↗

DOE OSTI2024

Parts-Per-Million Carbonate Mineral Quantification with Thermogravimetric Analysis–Mass Spectrometry

Mitigating the deleterious effects of climate change requires the development and implementation of carbon capture and storage technologies. To expand the monitoring, verification, and reporting (MRV) capabilities of geologic carbon mineralization projects, we developed a thermogravimetric analysis–mass spectrometry (TGA–MS) methodology to enable quantification of <100 ppm calcite (CaCO 3 ) in complex samples. We extended TGA–MS calcite calibration curves to enable a higher measurement resolution and lower limits of quantification for evolved CO 2 from a calcite–corundum mixture. We demonstrated <100 ppm carbonate mineral quantification with TGA–MS for the first time, an outcome applicable across earth, environmental, and materials science fields. We applied this carbonate quantification method to a suite of Columbia River Basalt Group (CRBG) well cuttings recovered in 2009 from Pacific Northwest National Laboratory’s Wallula #1 Well. Our execution of this new combined calcite and calcite–corundum calibration curve TGA–MS method on our CRBG sample suite indicated average carbonate contents of 0.050 wt % in flow interiors (caprocks) and 0.400 wt % in interflow zones (reservoirs) in the upper 1250 m of the Wallula #1 Well. Finally, by advancing our knowledge of continental flood basalt-hosted carbonates in the mafic subsurface and reaching new TGA–MS quantification limits for carbonate minerals, we expand MRV capabilities and support the commercial-scale deployment of carbon mineralization projects in the Pacific Northwest United States and beyond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗