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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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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

FutureTense

Protective vaccines and reliable diagnostics are essential tools for controlling viral diseases. However, the efficacy of these tools can be diminished by mutations in viral genomes. The delay between the emergence of new viral strains and the redesign of vaccines and diagnostics allows for continued viral transmission. Is it possible to address this challenge by computationally predicting viral genome sequence evolution? Can we “future-proof” vaccines and diagnostics by targeting both current and anticipated future sequence variants? While predicting viral evolution is still an unsolved, “grand challenge” problem in biology, the large, and rapidly growing, number of SARS-CoV-2 genome sequences provide an opportunity to quantify the ability of machine learning to predict viral genome sequence evolution. Towards this end, we have developed a simple computational model for predicting viral evolution at the level of individual nucleotides. The key metric for quantifying the per-base, prediction accuracy for viral evolution is the Mann-Whitney U statistic (or, equivalently, the area under the receiver operator curve). Since the Mann-Whitney U statistic is not a differentiable function, existing deep leaning packages (like Pytorch and Keras/TensorFlow) are not useful, as they require that the accuracy metric/objective function be analytically differentiable with respect to the model parameters. To overcome this challenge, we have implemented custom software, “FutureTense”, that can train a machine learning model by maximizing the non-differentiable Mann-Whitney U statistic. This software trains a machine learning model by exploring along the direction of the discrete gradient of the Mann-Whitney U statistic in the model parameter space. Parallel computing and genome sequence-specific optimizations are used to accelerate model training. The resulting machine learning model learns the observed high C->U mutation rates in the SARS-CoV-2 genome (which are potentially induced by host defenses) and provides prediction accuracies that are significantly better than one would expect from random chance. While predicting viral evolution is still quite far from a solved problem, the surprising performance of this simple model gives hope that the accuracy of predicting viral genome evolution can be further increased by more sophisticated approaches.

Gans, Jason↗
DOE OSTI2026

Surface Water Quality Data from Beaver-Impacted Streams; Trail Creek and East River, Colorado 2025

This data package contains surface water chemistry measurements collected in 2025 to evaluate how beaver damming and low-tech process-based stream restoration influence water quality and metal mobility in mountainous headwater systems of the Upper Colorado River Basin. Sampling was conducted at Trail Creek (Taylor Park watershed, Colorado), a tributary undergoing restoration through installation of low-tech process-based structures (i.e., beaver dam analogs), and at off-channel beaver ponds within the East River floodplain (East River watershed, Colorado). Samples were collected along longitudinal transects spanning upstream control reaches, beaver-influenced ponded reaches, and downstream segments. Additional samples were collected from near-surface pore waters within a beaver dam seepage face. The dataset includes concentrations of major and trace elements measured by inductively coupled plasma–mass spectrometry (ICP-MS) and inductively coupled plasma–optical emission spectrometry (ICP-OES), major anions measured by ion chromatography (IC), and dissolved organic carbon (DOC; reported as non-purgeable organic carbon, NPOC). Samples were size-fractionated at 0.45 micrometers (µm), 0.22 µm, and 0.02 µm to distinguish particulate (>0.45 µm), colloidal (0.22–0.02 µm), and dissolved (<0.02 µm) fractions. The data package consists of comma-separated value (.csv) files containing tabulated chemical concentration data, sample metadata (site identifiers, geographic coordinates, sampling dates, fraction type), and quality control flags. All files are provided in open, non-proprietary formats that can be accessed using standard data analysis software such as Microsoft Excel, R, Python, MATLAB, or other programs capable of reading .csv files. Units, detection limits, and analytical methods are documented in accompanying metadata files. The dataset is designed to support analyses of (1) how beaver impoundment and restoration structures alter elemental partitioning and transport, (2) the role of iron and organic carbon in mediating trace metal mobility, and (3) reach-scale changes in water quality across restoration gradients. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

Anions↗
DOE OSTI2023

Toward Machine Learning-Driven Mass Spectrometric Identification of Trichothecenes in the Absence of Standard Reference Materials

While a significant body of work exists on the detection of commonly known trichothecene toxins, biological, environmental, and other transformational processes can generate many under-characterized and unknown modified trichothecenes. Lacking both analytical reference standards and associated mass spectral databases, identification of these modified compounds reflects both a challenge and a critical gap from forensic and public health perspectives. Here we report here the application of machine learning (ML) techniques toward identification of discriminative fragment ions from mass spectrometric data that can be exploited to detect evidence of type A and B trichothecenes. The goal of this work is to establish a new method for the identification of unknown, though structurally similar trichothecenes, by leveraging objective ML techniques. Discriminative fragments derived from a series of gradient-boosted machine learners are then used to develop ML-driven precursor ion scan (PIS) methods on a triple quadrupole mass spectrometer (QQQ) for screening of “unknown unknown” trichothecenes. Specifically, we apply the PIS method to a laboratory-synthesized trichothecene, a first step in demonstrating the power of alternative, machine learning-driven mass spectrometric methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations

A generalization of the Lees-Edwards periodic boundary conditions (gLE-PBC) for molecular dynamics (MD) simulations is developed to allow for arbitrary deformations to be applied to the domain. The gLE-PBC domain remains a rectangular cuboid regardless of the applied deformation in contrast with the Lagrangian-rhomboid periodic boundary conditions (LR-PBC) where the domain deforms according to the applied deformation. Furthermore, the kinematics of gLE-PBC are validated against pure shear. The gLE-PBC method for interacting systems is then validated against the LR-PBC method and analytical solutions for a solid under isotropic compression, one-dimensional shearing, three-dimensional extension and shearing and for a liquid under Couette flow. Bulk physical properties extracted from the gLE-PBC simulations agree well with values calculated from equilibrium MD simulations. Three dimensional shearing and a deformation with a full velocity gradient matrix are also simulated, showing the range of problems gLE-PBC can explore.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Heat conduction in an irregular magnetic field. Part 2. Heat transport as a measure of the effective non-integrable volume

Given the large anisotropy of transport processes in magnetized plasmas, the magnetic field structure can strongly impact heat diffusion: magnetic surfaces and cantori form barriers to transport while chaotic layers and island structures can degrade confinement. When a small but non-zero amount of perpendicular diffusion is included, the structure of the magnetic field becomes less important, allowing pressure gradients to be supported across chaotic regions and island chains. We introduce a metric for the effective volume over which the local parallel diffusion dominates based on the solution to the anisotropic heat diffusion equation. To validate this metric, we consider model fields with a single island chain and a strongly chaotic layer for which analytic predictions of the relative parallel and perpendicular transport can be made. We also analyse critically chaotic fields produced from different sets of perturbations, highlighting the impact of the mode number spectrum on the heat transport. Our results indicate that this metric coincides with the effective volume of non-integrability in the limit $\kappa _{\perp } \rightarrow 0$ , where $\kappa_{\perp}$ is the perpendicular diffusion coefficient. We propose that this metric be used to assess the impact of non-integrability on the heat transport in stellarator equilibria.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Focusing of relativistic electron beams with permanent magnetic solenoid

Achieving strong focusing of MeV electron beams is a critical requirement for advanced beam applications such as compact laboratory x-ray sources, high gradient accelerators, and ultrafast electron scattering instrumentation. To address these needs, a compact radially magnetized permanent magnetic solenoid (PMS) has been designed, fabricated, and tested. The solenoid provides a compact and inexpensive solution for delivering high axial magnetic fields (1 T) to focus MeV electron beams. Field characterization of the solenoid demonstrates good agreement with analytical models, validating the PMS design. The electron beam test employs a high-brightness photoinjector to study the focusing properties of the PMS. The results indicate a focal length of less than 10 cm and a significant reduction in beam size with small spherical aberrations. Two application cases are evaluated: angular magnification in ultrafast electron diffraction setups and strong focusing for Compton scattering or other microfocus uses.

Electron diffraction↗
DOE OSTI2023

Experimental and computational investigation into the hydrodynamics and chemical dynamics of laser ablation aluminum plasmas

Laser ablation plasma chemistry is governed by a complex interplay between hydrodynamic plasma-gas mixing processes, thermodynamics, and rapid high-temperature chemical reactions. Here, in this work, we investigate the gas-phase oxidation chemistry of ns-laser ablation aluminum plasmas in air using optical spectroscopy combined with advanced multi-physics modeling. Experimental measurements demonstrate the formation of AlO in the plasma plume as early as 1 μs while computational results reveal that several Al x O y species are distributed in the periphery of the plume at even earlier times (<20 ns) in the presence of large temperature gradients and strong shockwaves. Interactions with the ablation crater during rapid plume expansion are shown to initiate vortex formation, followed by mixing dynamics that work to pull AlO into the vortices to react with gas-phase Al to form Al 2 O. Oxygen and several aluminum oxides are simultaneously pulled up through the stem of the fireball, encouraging further intermixing between reacting species and enhanced molecular formation. This work concludes that chemical dynamics in laser ablation plasmas is driven by diffusion processes, concentration gradients, and plume hydrodynamics while strong shockwaves generated during laser ablation do not impede chemical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Benchmarking Adaptive Variational Quantum Eigensolvers

By design, the variational quantum eigensolver (VQE) strives to recover the lowest-energy eigenvalue of a given Hamiltonian by preparing quantum states guided by the variational principle. In practice, the prepared quantum state is indirectly assessed by the value of the associated energy. Novel adaptive derivative-assembled pseudo-trotter (ADAPT) ansatz approaches and recent formal advances now establish a clear connection between the theory of quantum chemistry and the quantum state ansatz used to solve the electronic structure problem. Here we benchmark the accuracy of VQE and ADAPT-VQE to calculate the electronic ground states and potential energy curves for a few selected diatomic molecules, namely H 2 , NaH, and KH. Using numerical simulation, we find both methods provide good estimates of the energy and ground state, but only ADAPT-VQE proves to be robust to particularities in optimization methods. Another relevant finding is that gradient-based optimization is overall more economical and delivers superior performance than analogous simulations carried out with gradient-free optimizers. The results also identify small errors in the prepared state fidelity which show an increasing trend with molecular size.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A deterministic gradient-based approach to avoid saddle points

Abstract Loss functions with a large number of saddle points are one of the major obstacles for training modern machine learning (ML) models efficiently. First-order methods such as gradient descent (GD) are usually the methods of choice for training ML models. However, these methods converge to saddle points for certain choices of initial guesses. In this paper, we propose a modification of the recently proposed Laplacian smoothing gradient descent (LSGD) [Osher et al., arXiv:1806.06317 ], called modified LSGD (mLSGD), and demonstrate its potential to avoid saddle points without sacrificing the convergence rate. Our analysis is based on the attraction region, formed by all starting points for which the considered numerical scheme converges to a saddle point. We investigate the attraction region’s dimension both analytically and numerically. For a canonical class of quadratic functions, we show that the dimension of the attraction region for mLSGD is $\lfloor (n-1)/2\rfloor$ , and hence it is significantly smaller than that of GD whose dimension is $n-1$ .

Mathematics↗
DOE OSTI2020

Iron mineral dissolution releases iron and associated organic carbon during permafrost thaw

It has been shown that reactive soil minerals, specifically iron(III) (oxyhydr)oxides, can trap organic carbon in soils overlying intact permafrost, and may limit carbon mobilization and degradation as it is observed in other environments. However, the use of iron(III)-bearing minerals as terminal electron acceptors in permafrost environments, and thus their stability and capacity to prevent carbon mobilization during permafrost thaw, is poorly understood. We have followed the dynamic interactions between iron and carbon using a space-for-time approach across a thaw gradient in Abisko (Sweden), where wetlands are expanding rapidly due to permafrost thaw. We show through bulk (selective extractions, EXAFS) and nanoscale analysis (correlative SEM and nanoSIMS) that organic carbon is bound to reactive Fe primarily in the transition between organic and mineral horizons in palsa underlain by intact permafrost (41.8 ±10.8 mg carbon per g soil, 9.9 to 14.8% of total soil organic carbon). During permafrost thaw, water-logging and O 2 limitation lead to reducing conditions and an increase in abundance of Fe(III)-reducing bacteria which favor mineral dissolution and drive mobilization of both iron and carbon along the thaw gradient. By providing a terminal electron acceptor, this rusty carbon sink is effectively destroyed along the thaw gradient and cannot prevent carbon release with thaw.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Tuning nonequilibrium phase transitions with inertia

In striking contrast to equilibrium systems, inertia can profoundly alter the structure of active systems. Here, we demonstrate that driven systems can exhibit effective equilibrium-like states with increasing particle inertia, despite rigorously violating the fluctuation–dissipation theorem. Increasing inertia progressively eliminates motility-induced phase separation and restores equilibrium crystallization for active Brownian spheres. This effect appears to be general for a wide class of active systems, including those driven by deterministic time-dependent external fields, whose nonequilibrium patterns ultimately disappear with increasing inertia. The path to this effective equilibrium limit can be complex, with finite inertia sometimes acting to accentuate nonequilibrium transitions. The restoration of near equilibrium statistics can be understood through the conversion of active momentum sources to passive-like stresses. Unlike truly equilibrium systems, the effective temperature is now density dependent, the only remnant of the nonequilibrium dynamics. Further, this density-dependent temperature can in principle introduce departures from equilibrium expectations, particularly in response to strong gradients. Our results provide additional insight into the effective temperature ansatz while revealing a mechanism to tune nonequilibrium phase transitions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A hybrid calibration approach to Hertz-type contact parameters for discrete element models

This study aims at providing a hybrid calibration framework to estimate Hertz-type contact parameters (particle-scale shear modulus and Poisson ratio) for both two-dimensional and three-dimensional discrete element modelling (DEM). On the basis of statistically isotropic granular packings, a set of analytical formulae between macroscopic material parameters (Young modulus and Poisson ratio) and particle-scale Hertz-type contact parameters for granular systems are derived under small-strain isotropic stress conditions. However, the derived analytical solutions are only estimated values for general models. By viewing each DEM modelling as an implicit mathematical function taking the particle-level parameters as independent variables and employing the derived analytical solutions as the initial input parameters, an automatic iterative scheme is proposed to obtain the calibrated parameters with higher accuracies. Considering highly nonlinear features and discontinuities of the macro-micro relationship in Hertz-based discrete element models, the adaptive moment estimation algorithm is adopted in this study because of its capacity of dealing with noise gradients of cost functions. Here, the proposed method is validated with several numerical cases including randomly distributed monodisperse and polydisperse packings. Noticeable improvements in terms of calibration efficiency and accuracy have been made.

Constitutive law↗
DOE OSTI2025

Near Resonance between the Shelf Ocean and Semidiurnal Atmospheric Tidal Winds

This manuscript illustrates the resonance between continental shelf oceans and the semidiurnal atmospheric tidal wind, explaining O(10 −2 ) m semidiurnal sea surface height (SSH) variations in detided datasets. The resonance, similar to amplification of semidiurnal oceanic tides on the gentle and wide shelf, results in pronounced, offshore-attenuated standing waves on the shelf which is driven by the cross-shore pressure gradient force, Coriolis force, and the rotary wind stress. Observations and numerical results from the Texas–Louisiana shelf confirm this mechanism, where a significant presence of the semidiurnal tidal wind couples with O(10 −1 ) m s −1 ocean currents, influencing SSH distribution and sustaining the wave structure. The consistency of the interaction and momentum budgets with the analytical solution suggests the robustness of the semidiurnal atmospheric tidal wind interacting with the shelf ocean. Notably, these findings suggest that similar resonances could occur on other gentle shelves known for enhancing semidiurnal oceanic tides and contribute 3%–10% of the wind work.

Atmosphere-ocean interaction↗
DOE OSTI2020

Determining Design Criteria for Feeding Biomass into a Fluidized Bed Using a Feed Screw

Many pathways have been discovered for the thermochemical conversion of biomass to products. These pathways often show very promising results on the benchtop scale and could be economical with the appropriate scale up. However, many of the fundamental challenges of scaling up thermochemical reactions are not well understood. One primary problem area that rarely receives much upfront attention is feeding large quantities of biomass into thermochemical reactors. As biomass transitions from ambient to reactor conditions, it undergoes chemical and physical changes that affect its flowability. Often these changes lead to agglomeration of feed particles within the transfer screw, leading to large clumps of feed entering and disrupting the fluidized bed, or more critically leading to a plug in the feed screw causing costly downtime and maintenance to remove. This transitional phase must be better understood for scale up of conversion technologies to be successful. The Feedstock-Conversion Interface Consortium (FCIC) is a collaboration of eight National Laboratories. FCIC is currently conducting research on screw feeding of biomass into thermochemical fluidized bed reactors. Heat transfer models have been constructed for the screw/reactor interface. Mechanical forces on biomass within screw feeder are being determined, as well as how those forces change by varying feed screw design. Feedstock physical and chemical properties are then being measured along these temperature and mechanical force gradients. This work will better inform feed screw design for scale up, increasing the success rate of future biorefineries. Discussion will include research approach, testing, and preliminary results.

09 BIOMASS FUELS↗
DOE OSTI2025

Data for Stetten et al. (2025), "Biogeochemical controls on iron speciation and cycling across upland to shoreline gradients in freshwater and estuarine coastal soils (Lake Erie and Chesapeake Bay, United States)"

Coastal environments are dynamic interfaces that mediate carbon and nutrient exchanges between terrestrial landscapes and open waters, but it is unclear how biogeochemical reactions, in particular iron (Fe) redox transformations, affect the understanding and prediction of coastal ecosystem functions. This dataset includes measurements from two freshwater sites in the Western and Central basins of Lake Erie (Ohio, United States) and two estuarine sites in the Chesapeake Bay (Maryland, United States); the analytical results were reported by Stetten et al. (2025) in Science of the Total Environment. It was produced as part of the COMPASS-FME project, which seeks to advance a scalable, predictive understanding of the fundamental biogeochemical processes, ecological structure, and ecosystem dynamics that distinguish coastal terrestrial-aquatic interfaces from the purely terrestrial or aquatic systems to which they are coupled. The sites were sampled in November 2022 (CRC), December 2022 (MSM), February 2023 (GCW), and March 2023 (OWC); site codes follow those used by Pennington et al. (2025).The dataset consists of the following soil data:- Solid data (Fe concentration, etc.)- Porewater data (sulfate, sulfide, etc.)- Linear combination fitting results of X-ray absorption near edge structure (XANES) spectra; i.e., quantitative results of the oxidation state of Fe, indicated as a proportion of pure Fe(III) and Fe(II) model compounds- Linear combination fitting results of EXAFS (extended X-ray absorption fine structure) spectra, indicated as proportion of of Fe-model compounds (illite, smectite, etc.)Each data type has a single file in comma-separated value (CSV) format. No special software is required to read it.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Steep sulfur gradient in CZTSSe solar cells by H 2 S-assisted rapid surface sulfurization

Sulfur/selenium grading is a widely used optimization strategy in kesterite thin-film solar cells to obtain a bandgap-graded absorber material and to optimize optical and electrical properties of the solar-cell device. In this work, we present a novel approach to introduce a [S]/([S] + [Se]) grading for Cu 2 ZnSn(S,Se) 4 solar cells. In contrast to commonly used methods with slow process dynamics, the presented approach aims to create a fast sulfurization reaction on the surface of pure selenide kesterite absorbers by using highly reactive H 2 S gas and high sulfurization temperatures in a rapid flash-type process. With a combination of X-ray photoelectron spectroscopy, X-ray emission spectroscopy, Raman spectroscopy, and Raman-shallow angle cross sections spectroscopy, we gain depth-varied information on the [S]/([S] + [Se]) ratio and discuss the impact of different process parameter variations on the material and device properties. The results demonstrate the potential of the developed process to generate a steep gradient of sulfur that is confined mainly to the surface region of the absorber film.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗