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At least 775 records · Page 43

Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here, in this work, we introduce a modular strategy to generate conformations based on “backmapping” from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.

36 MATERIALS SCIENCE↗

Meta-Analysis of Advanced Nuclear Reactor Cost Estimations

Supporting Data can be downloaded at: https://gain.inl.gov/content/uploads/4/2024/06/INL-RPT-24-77048-R1.xlsx Nuclear energy is a critical cornerstone of the current United States clean energy supply and may play a larger role in the future in support of a transition to a net-zero economy. The current fleet of nuclear reactors predominantly consists of large light-water reactors (LWRs), while many of the reactor designs under consideration are smaller and/or different technologies. Because these new designs have not yet been built, there is a high degree of uncertainty associated with their cost. This complicates energy-planning efforts because cost projections are not always standardized, consistent, and centralized in an easily accessible location. To help support energy planning in the US, this report provides advanced nuclear cost ranges using a transparent methodology along with other relevant information that can be used to help support decision making and energy planning. The purpose of this work was to conduct a methodical process for cost evaluation using only public information that was vetted with the end-goal to provide reference cost projections for nuclear energy. To provide a solid basis for these values, the approach and assumptions are explicitly laid out throughout the report allowing any user of the data to challenge or reconsider them. Because future US nuclear-reactor costs are still unknown due to little recent observed data, the report opted to compile a comprehensive list of bottom-up estimates and evaluate averages/trends within the data to identify reference ranges. This was deemed preferable to opining on the robustness or validity of one cost estimation versus another. To that end, the work evaluated thousands of lines of cost subaccounts from several bottom-up cost estimates. A wide variety of different reactor types captured in the data are of various sizes and technologies. Some of these reactors will be representative of advanced reactors under development while others will not. Thus, the results here are dependent on the data that are available and the accuracy of the estimates that are used. Each bottom-up estimate was reviewed to determine whether it was complete. Incomplete data sets were corrected to ensure an adequate basis of cross-comparison. The report is not without limitations and should be interpreted as an initial step to develop cost ranges for nuclear technology. Ultimately, future work can build upon the methodology with refined cost estimates to reduce uncertainty. US-based overnight capital cost (OCC) estimates were compiled from extensive data sets into ranges for both large and small reactor sizes for 2030. To project the cost declines over time, learning rates were sampled from literature sources. No SMRs were previously built; hence, learning rates based on bottom-up approaches (e.g., by quantifying the impact stemming from fabrication of different components, modular work, site construction, commissioning) were prioritized. For larger reactors, actual learning rates from deployments were used to project future costs (adjusted to account for standardization or lack thereof between designs). Other costs included are fixed and variable operations and maintenance costs. The final variables were capacity factors and ramp rates to support energy planning.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Q1-2024 Solar Cost Benchmarks

Each year, the U.S. Department of Energy’s (DOE) Solar Energy Technologies Office (SETO) and its national laboratory partners develop cost benchmarks for U.S. solar photovoltaic (PV) systems. These benchmarks track progress toward reducing solar costs and guide R&D priorities. Unlike typical studies that report only $/W, SETO uses intrinsic units (e.g., $/m² for mounting structures) to better capture how technology improvements such as module efficiency would impact system costs. This allows flexible modeling where inputs can vary significantly to assess cost sensitivity. Costs are reported in two ways: Minimum Sustainable Price (MSP): Long term, financially viable price under stable market conditions. Modeled Market Price (MMP): Actual market price, influenced by short term distortions such as tariffs or subsidies. Three national labs collect cost data from industry stakeholders, ensuring no duplication in outreach to stakeholders. Data reflects real transactions (primarily from Q1) and is weighted based on the number of sources per cost element. The PV System Cost Model (PVSCM) divides total installed system cost into eight categories: 1. Module (PV) 2. Inverter 3. Energy Storage System (ESS) 4. Structural BOS (SBOS) 5. Electrical BOS (EBOS) 6. Fieldwork 7. Office work 8. Other (developer/EPC costs) The first five are hardware costs, while the last three are soft costs. Each category includes fixed and variable cost components, where “size” depends on context (e.g., manufacturing capacity for modules vs. system capacity for installation costs). Variable costs are expressed using appropriate intrinsic units. The model reflects the owner’s upfront overnight capital cost, excluding tax credits. Tariffs and subsidies are treated as temporary market distortions affecting MMP but not MSP. PVSCM is implemented in Excel, where cost elements are aggregated into total system cost. Additional sheets handle unit conversions and operation & maintenance (O&M), with O&M costs levelized over the system’s lifetime.

14 SOLAR ENERGY↗

Jupiter's radiation belts

Fluxes of electrons and protons in Jupiter's radiation belts are calculated with the source (radial diffusion inward from the solar wind) and the loss (synchroton radiation). The calculations are tested against the measured radio-wave wavelength distribution, the radio-wave distribution with distance from Jupiter, and the degree of polarization of the radio waves. The Fokker-Planck equation is solved by using the method of Farley and Walt (1971) with the fixed flux at the outer boundary and the zero flux at Jupiter's surface. It is found, in agreement with Brice and McDonough (1973), Jacques and Davis (1973), and Birmingham et al. (1974), that the usual magnetic and electric diffusions, which vary as L to the 10th power and L to the 6th power, respectively, are insufficient to furnish the required electrons and that the diffusion driven by ionospheric winds of Brice and McDonough is strong enough to furnish Jupiter's belts. An additional loss mechanism close to Jupiter is required to remove the electrons, particularly those at low energies.

Stansberry, K. G.↗

Elliptic Grid Generation of Spiral-Bevel Pinion Gear Typical of OH-58 Helicopter Transmission

This paper discusses the source term treatment in the numerical solution of elliptic partial differential equations for an interior grid generation problem in generalized curvilinear coordinates. The geometry considered is that of a planar cross-section of a generic spiral-bevel gear tooth typical of a pinion in the OH-58 helicopter transmission. The source terms used are appropriate for an interior grid domain where all the boundaries are prescribed via a combination of Dirichlet and Neumann boundary conditions. New constraints based on the Green's Theorem are derived which uniquely determine the coefficients in the source terms. These constraints are designed for boundary clustered grids where gradients in physical quantities need to be resolved adequately. However, it is seen that the present formulation works satisfactorily for mild clustering also. Thus, a fully automated elliptic grid generation technique is made possible where there is no need for a parametric study of these parameters since the new relations fix these free parameters uniquely.

Kaul, Upender K.↗

An Inversion Analysis of Recent Variability in Natural CO2 Fluxes Using GOSAT and In Situ Observations

About one-half of the global CO2 emissions from fossil fuel combustion and deforestation accumulates in the atmosphere, where it contributes to global warming. The rest is taken up by vegetation and the ocean. The precise contribution of the two sinks, and their location and year-to-year variability are, however, not well understood. We use two different approaches, batch Bayesian synthesis inversion and variational data assimilation, to deduce the global spatiotemporal distributions of CO2 fluxes during 2009-2010. One of our objectives is to assess different sources of uncertainties in inferred fluxes, including uncertainties in prior flux estimates and observations, and differences in inversion techniques. For prior constraints, we utilize fluxes and uncertainties from the CASA-GFED model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates and two sets of fixed fossil CO2 emissions. Here, our inversions incorporate column CO2 measurements from the GOSAT satellite (ACOS retrieval, filtered and bias-corrected) and in situ observations (individual flask and afternoon-average continuous observations) to estimate fluxes in 108 regions over 8-day intervals for the batch inversion and at 3 x 3.75 weekly for the variational system. Relationships between fluxes and atmospheric concentrations are derived consistently for the two inversion systems using the PCTM atmospheric transport model driven by meteorology from the MERRA reanalysis. We compare the posterior fluxes and uncertainties derived using different data sets and the two inversion approaches, and evaluate the posterior atmospheric concentrations against independent data including aircraft measurements. The optimized fluxes generally resemble those from other studies. For example, the results indicate that the terrestrial biosphere is a net CO2 sink, and a GOSAT-only inversion suggests a shift in the global sink from the tropics south to the north relative to the prior and to an in-situ-only inversion. We also find a smaller terrestrial sink in higher-latitude northern regions in boreal summer of 2010 relative to 2009.

Carbon dioxide↗

High- and Mid-Fidelity Modeling Comparison for a Floating Marine Turbine System: Preprint

There is a lack of suitable numerical tools, particularly open-source tools, that can be used for designing and optimizing marine turbine systems. The National Renewable Energy Laboratory (NREL) has added features to their widely used mid-fidelity wind turbine modeling code, OpenFAST, to enable modeling of axial flow marine turbines. This necessitated the addition of several physical effects relevant to marine turbines that can be neglected for wind turbines. These include buoyant loads, added mass and inertia loads, wave-current superposition, and changes to the coordinate systems. This updated version of OpenFAST allows for the modeling of both fixed and floating marine turbine systems at a speed comparable to real time. While efficient for long simulations, large sets of load cases, and design studies, mid-fidelity codes cannot capture all of the potentially important physical phenomenon impacting marine turbine systems. High-fidelity computational fluid dynamics (CFD) simulations can capture more flow effects with fewer assumptions and provide detailed body pressure mapping and flow-field information. It is important to compare predictions between mid-fidelity and high-fidelity codes, both to verify the models and to understand the limitations. A floating marine turbine system designed by NREL was modeled both with OpenFAST and with the commercial CFD code, STARCCM+. The CFD model used a 3-D unsteady Reynolds-averaged Navier-Stokes solver for a volume-of-fluid numerical wave and current tank. The blade-resolved simulations used the sliding-interface technique for the spinning rotor and an overset grid to accommodate the rigid-body motion of the floating system. The mooring system was modelled with a custom coupling of the CFD solver with the open-source code, MoorDyn. This improves upon the existing quasi-static catenary solver in STARCCM+, which lacks seabed contact or line-to-line connections. Spatial and temporal convergence studies were conducted. The simulation results for a combined current and wave condition are compared between OpenFAST and CFD, highlighting the capabilities of the mid-fidelity code and identifying the areas where a high-fidelity approach is needed.

CFD↗

Single-photoelectron collection efficiency in 4D ultrafast electron microscopy

In femtosecond (fs) 4D ultrafast electron microscopy (UEM), a tradeoff is made between photoelectrons per packet and time resolution. One consequence of this can be longer-than-desirable acquisition times for low-density packets, and particularly for low repetition rates when complete photothermal dissipation is required. Thus, gaining an understanding of photoelectron trajectories in the gun region is important for identifying factors that limit collection efficiency (CE; fraction of photoelectrons that enter the illumination system). Here, we continue our work on the systematic study of photoelectron trajectories in the gun region of a Thermo Fisher/FEI Tecnai Femto UEM, focusing specifically on CE in the single-electron regime. Using General Particle Tracer, calculated field maps, and the exact architecture of the Tecnai Femto UEM, we simulated the effects of fs laser parameters and key gun elements on CE. The results indicate CE strongly depends upon the laser spot size on the source, the (unbiased) Wehnelt aperture diameter, and the incident photon energy. The CE dispersion with laser spot size is found to be strongly dependent on aperture diameter, being nearly dispersionless for the largest apertures. A gun crossover is also observed, with the beam-waist position being dependent on the aperture diameter, further illustrating that the Wehnelt aperture acts as a simple, fixed electrostatic lens in UEM mode. This work provides further insights into the operational aspects of fs 4D UEM.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data from: Temporal dynamics of free‐living nitrogen fixation in the switchgrass rhizosphere

Here we present data associated with the manuscript, Temporal dyanmics of free-living nitrogen fixation in the switchgrass rhizosphere. Free-living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be reliant on FLNF when particularly when grown on low N marginal lands. These potential contributions of FLNF to switchgrass and the controls on this process are not well understood. We evaluated drivers of FLNF rates and N-fixing microbial community composition in field-grown switchgrass systems over two years with high temporal sampling. We found climate variables to be strong drivers of FLNF in switchgrass systems, compared to other environmental and biological factors including soil nutrients and N-fixing microbial community composition. Increased soil moisture availability tended to promote FLNF, but extreme rainfall events appeared to be detrimental. These climate-related responses suggest FLNF-derived N contributions may be reduced under projected climate shifts. We also found a significant, but weak correlation between N-fixing microbial community composition and FLNF rates including an observed shift in community composition between 2017 and 2018 and a similarly significant difference in FLNF rates between years. Lastly, we found that seasonal FLNF N contributions, based on measurement with high temporal resolution, may meet up to 80% of switchgrass N demands.

09 BIOMASS FUELS↗

MAGSAT anomaly map and continental drift

Anomaly maps of high quality are needed to display unambiguously the so called long wave length anomalies. The anomalies were analyzed in terms of continental drift and the nature of their sources is discussed. The map presented confirms the thinness of the oceanic magnetized layer. Continental magnetic anomalies are characterized by elongated structures generally of east-west trend. Paleomagnetic reconstruction shows that the anomalies found in India, Australia, and Antarctic exhibit a fair consistency with the African anomalies. It is also shown that anomalies are locked under the continents and have a fixed geometry.

Lemouel, J. L.↗

The energetic ion signature of an O-type neutral line in the geomagnetic tail

An energetic ion signature is presented which has the potential for remote sensing of an O-type neutral line embedded in a current sheet. A source plasma with a tailward flowing Kappa distribution yields a strongly non-Kappa distribution after interacting with the neutral line: sharp jumps, or ridges, occur in the velocity space distribution function f(nu-perpendicular, nu-parallel) associated with both increases and decreases in f. The jumps occur when orbits are reversed in the x-direction: a reversal causing initially earthward particles (low probability in the source distribution) to be observed results in a decrease in f, while a reversal causing initially tailward particles to be observed produces an increase in f. The reversals, and hence the jumps, occur at approximately constant values of perpendicular velocity in both the positive nu parallel and negative nu parallel half planes. The results were obtained using single particle simulations in a fixed magnetic field model.

Martin, R. F., Jr.↗

Previous model comparisons

The first model comparison workshop examined 14 mathematical models. Issues discussed included: transport methodologies; transport of nuclear test debris; transport algorithms; source gases; NO(y), Cl(x), HO(x), and O3; photolysis rates; diurnal averaging; and rainout. The second model comparison meeting examined 16 models. More real model-model intercomparisons were undertaken and several topics were addressed including: photochemistry and radiation; transport; current atmosphere 1980; and assessment runs. The models computed different values for photolysis rates even when O3 and O2 were fixed, thus more time should be spent at future model comparison meeting on radiation codes.

Jackman, Charles H.↗

The Abacus/Reflector and Integrated Symmetrical Concentrator: Concepts for Space Solar Power Collection and Transmission

New energy sources are vital for the development of emerging nations, and the growth of industry in developed economies. Also vital is the need for these energy sources to be clean and renewable. For the past several years, NASA has been taking a new look at collecting solar energy in space and transmitting it to Earth, to planetary surfaces, and to orbiting spacecraft. Several innovative concepts are being studied for the space segment component of solar power beaming. One is the Abacus/Reflector, a large sun-oriented array structure fixed to the transmitter, and a rotating RF reflector that tracks a receiving rectenna on Earth. This concept eliminates the need for power-conducting slip rings in rotating joints between the solar collectors and the transmitter. Another concept is the Integrated Symmetrical Concentrator (ISC), composed of two very large segmented reflectors which rotate to collect and reflect the incident sunlight onto two centrally-located photovoltaic arrays. Adjacent to the PV arrays is the RF transmitter, which as a unit track the receiving rectenna, again eliminating power-conducting joints, and in addition reducing the cable lengths between the arrays and transmitter. The metering structure to maintain the position of the reflectors is a long mast, oriented perpendicular to the equatorial orbit plane. This paper presents a status of ongoing systems studies and configurations for the Abacus/Reflector and the ISC concepts, and a top-level study of packaging for launch and assembly.

Carrington, Connie↗

Low-Frequency Electromagnetic Exploration for Groundwater on Mars

Water with even a small amount of dissolved solids has an electrical conductivity orders of magnitude higher than dry rock and is therefore a near-ideal exploration target on Mars for low frequency, diffusive electromagnetic methods. Models of the temperature- and frequency-dependent electrical properties of rock-ice-water mixtures are used to predict the electromagnetic response of the Martian subsurface. Detection of ice is difficult unless it is massively segregated. In contrast, liquid water profoundly affects soundings, and even a small amount of adsorbed water in the cryosphere can be detected. Subcryospheric water is readily distinguishable at frequencies as low as 100 Hz for fresh water to 10 mHz for brines. These responses can be measured using either natural or artificial sources. Ultra low frequency signals from solar wind and diurnal-heating perturbations of the ionosphere are likely, and disturbances of regional crustal magnetic fields may also be observable. Spherics, or extremely to very low frequency signals from lightning discharge, would provide optimal soundings; however, lightning may be the least likely of the possible natural sources. Among the active techniques, only the time-domain electromagnetic (TDEM) method can accommodate a closely spaced transmitter and receiver and sound to depths of hundreds of meters or more. A ground- or aircraft-based TDEM system of several kilograms can detect water to a depth of several hundred meters, and a system of tens of kilograms featuring a large, fixed, rover- or ballistically deployed loop can detect water to several kilometers depth.

Grimm, Robert E.↗

Fossil Microorganisms and Formation of Early Precambrian Weathering Profiles

Weathering crusts are the only reliable evidences of the existence of continental conditions. Often they are the only source of information about exogenous processes and subsequently about conditions under which the development of the biosphere occurred. A complex of diverse fossil microorganisms was discovered as a result of Scanning Electron Microscope investigations. The chemical composition of the discovered fossils is identical to that of the host rocks and is represented by Si, Al, Fe, Ca and Mg. Probably, the microorganisms fixed in rocks played the role of catalyst. The decomposition of minerals comprising the rocks and their transformation into clayey (argillaceous) minerals, most likely occurred under the influence of microorganisms. And may be unique weathering crusts of Early Precambrian were formed due to interaction between specific composition of microorganism assemblage and conditions of hypergene transformations. So it is possible to speak about colonization of land by microbes already at that time and about existence of single raw from weathering crusts (Primitive soils) to real soils.

Rozanov, A. Yu↗

Inductive Position Sensor

An inductive position sensor uses three parallel inductors, each of which has an axial core that is an independent magnetic structure. A first support couples first and second inductors and separate them by a fixed distance. A second support coupled to a third inductor disposed between the first and second inductors. The first support and second support are configured for relative movement as distance changes from the third inductor to each of the first and second inductors. An oscillating current is supplied to the first and second inductors. A device measures a phase component of a source voltage generating the oscillating current and a phase component of voltage induced in the third inductor when the oscillating current is supplied to the first and second inductors such that the phase component of the voltage induced overlaps the phase component of the source voltage.

Youngquist, Robert C.↗

Direct Conversion of CO 2 to Olefins over a Cr 2 O 3 /ZSM-5@CaO Cooperative and Bifunctional Material Under Isothermal Conditions

Direct conversion of point-source CO 2 into fine chemicals over cooperative and bifunctional materials (BFMs) – composed of adsorbents and catalysts – has emerged as a promising approach to improve the energy efficiency of the carbon capture and conversion processes. In this study, a bifunctional material consisting of Cr 2 O 3 /ZSM-5 catalyst and CaO adsorbent was developed and tested in the CO 2 -oxidative dehydrogenation of propane (CO 2 –ODHP) for reactive capture of CO 2 in a fixed bed reactor. First, CaO was prepared using two distinct methods: solid-state and citrate sol–gel. The citrate sol–gel method resulted in small and finely-distributed CaO particles, allowing more accessible sites for CO 2 adsorption. Consequently, a high CO 2 adsorption capacity of ~14 mmol/g was achieved with fast adsorption kinetics compared to CaO prepared by the solid-state method. The CaO adsorbent was then combined with the Cr 2 O 3 /ZSM-5 catalyst for BFM synthesis and tested in the CO 2 –ODHP process, targeting propylene production. The BFM was extensively characterized to provide insights into the BFM’s surface chemistry, morphology, and reaction mechanism in the reactive capture process of CO 2 –ODHP. The results revealed that under isothermal adsorption–reaction conditions at 600 °C, a propane conversion of 22.5%, a propylene selectivity of 55.3%, and an olefin selectivity of 67.3% were achieved. The excellent propylene selectivity was attributed to the catalyst acidity and redox property of the Cr 2 O 3 /ZSM-5 catalyst, which facilitated the reaction pathway of propane dehydrogenation in the process of CO 2 –ODHP. Overall, this study renders Cr 2 O 3 /ZSM-5@CaO as promising BFMs with high CO 2 capture capacity and catalytic activity for integrated CO 2 capture and conversion in the ODHP reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Photoionization from the Ground and Excited Vibrational States of H$^+_2$ and Its Deuterated Isotopologues

Photoionization cross sections and rate coefficients have been calculated for all bound vibrational levels of the 1sσ g state of H$^+_2$, HD+, and D$^+_2$. The Born–Oppenheimer approximation is employed in our calculation of vibrationally resolved photoionization cross sections. Vibrationally resolved and local thermal equilibrium photoionization rate coefficients are presented for photon temperatures less than 50,000 K and are found to be several orders of magnitude larger than previous results in the literature. Analytic fits for the vibrationally resolved and local thermal equilibrium photoionization rate coefficients are provided. Near-threshold oscillations in the vibrationally resolved photoionization are observed. A benchmark set of photoionization cross sections are presented. Fixed-nuclei photoionization cross sections are calculated using two-center true continuum wave functions and are verified by comparison with previous calculations and are found to be in excellent agreement in all cases. Data files for our set of benchmark cross sections, rate coefficients, and fitting parameters for H$^+_2$, HD + , and D$^+_2$ are available on Zenodo under an open-source Creative Commons Attribution license at doi:10.5281/zenodo.8304061.

74 ATOMIC AND MOLECULAR PHYSICS↗