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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Inverse methods for design of soft materials

Functional soft materials, comprising colloidal and molecular building blocks that self-organize into complex structures as a result of their tunable interactions, enable a wide array of technological applications. Inverse methods provide a systematic means for navigating their inherently high-dimensional design spaces to create materials with targeted properties. Furthermore, while multiple physically motivated inverse strategies have been successfully implemented in silico, their translation to guiding experimental materials discovery has thus far been limited to a handful of proof-of-concept studies. In this perspective, we discuss recent advances in inverse methods for design of soft materials that address two challenges: (1) methodological limitations that prevent such approaches from satisfying design constraints and (2) computational challenges that limit the size and complexity of systems that can be addressed. Strategies that leverage machine learning have proven particularly effective, including methods to discover order parameters that characterize complex structural motifs and schemes to efficiently compute macroscopic properties from the underlying structure. We also highlight promising opportunities to improve the experimental realizability of materials designed computationally, including discovery of materials with functionality at multiple thermodynamic states, design of externally directed assembly protocols that are simple to implement in experiments, and strategies to improve the accuracy and computational efficiency of experimentally relevant models.

36 MATERIALS SCIENCE↗
DOE OSTI2021

iBLAST: Incremental BLAST of new sequences via automated e-value correction

Search results from local alignment search tools use statistical scores that are sensitive to the size of the database to report the quality of the result. For example, NCBI BLAST reports the best matches using similarity scores and expect values (i.e., e-values) calculated against the database size. Given the astronomical growth in genomics data throughout a genomic research investigation, sequence databases grow as new sequences are continuously being added to these databases. As a consequence, the results (e.g., best hits) and associated statistics (e.g., e-values) for a specific set of queries may change over the course of a genomic investigation. Thus, to update the results of a previously conducted BLAST search to find the best matches on an updated database, scientists must currently rerun the BLAST search against the entire updated database, which translates into irrecoverable and, in turn, wasted execution time, money, and computational resources. To address this issue, we devise a novel and efficient method to redeem past BLAST searches by introducing iBLAST. iBLAST leverages previous BLAST search results to conduct the same query search but only on the incremental (i.e., newly added) part of the database, recomputes the associated critical statistics such as e-values, and combines these results to produce updated search results. Our experimental results and fidelity analyses show that iBLAST delivers search results that are identical to NCBI BLAST at a substantially reduced computational cost, i.e., iBLAST performs (1 + δ )/ δ times faster than NCBI BLAST, where δ represents the fraction of database growth. We then present three different use cases to demonstrate that iBLAST can enable efficient biological discovery at a much faster speed with a substantially reduced computational cost.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Engineering Computational Practices (Rev. 1)

This manual will attempt to motivate the use of an automated build system for the purposes of computational science and engineering. As part of this motivation, the surrounding computational practices of version control, documen tation, compute environment management, and regression testing will also be addressed as applied to the practice of computational engineering. Specifically, this manual intends to motivate the adoption of these traditional software engineering practices for use in research and production engineering simulation projects. This manual is not the first such effort in the greater scientific computing community. In fact, the authors relied heavily on the lesson plans of the Software Carpentry, established to teach computing skills to researchers in 1998. As the intention for this manual is to lay out fundamental practices of engineering computing, it will not attempt to fully teach the underlying concepts and will instead reference the well designed lesson plans of the Software Carpentry. Where possible, this manual will explain to general computing practices and concepts and limit discussion of specific software implementations to examples or vehicles for practice in concrete application. The specific software taught by the Software Carpentry curriculum is an excellent starting point to learn the core concepts of computational engi neering. However, the authors have found that applications to engineering simulation and analysis require translation of these software development concepts into the language and workflows of computational engineers. Adopting these computational tools may require engineers to re-imagine their workflows in some combination of traditional engineer ing and software concepts. It has also been necessary to extend existing software build systems for engineering practices beyond the simple wrap ping of engineering software execution. Where necessary, examples of specific software and their method of extension to engineering simulations will be given, with reference to the User Manual for recommended practical use. Where this manual relies on specific implementation examples, it should be understood that the practicing engineer may find that different software is more amenable to their specific work. It is always the overall collection of computational practices is more important than any specific software implementation. The ability to recognize which concepts are implemented by a software package will make a practicing engineer agile to changing project needs, computing resources, numeric solvers, programming languages, and even available funding.

42 ENGINEERING↗
DOE OSTI2021

Deep Bayesian local crystallography

Abstract The advent of high-resolution electron and scanning probe microscopy imaging has opened the floodgates for acquiring atomically resolved images of bulk materials, 2D materials, and surfaces. This plethora of data contains an immense volume of information on materials structures, structural distortions, and physical functionalities. Harnessing this knowledge regarding local physical phenomena necessitates the development of the mathematical frameworks for extraction of relevant information. However, the analysis of atomically resolved images is often based on the adaptation of concepts from macroscopic physics, notably translational and point group symmetries and symmetry lowering phenomena. Here, we explore the bottom-up definition of structural units and symmetry in atomically resolved data using a Bayesian framework. We demonstrate the need for a Bayesian definition of symmetry using a simple toy model and demonstrate how this definition can be extended to the experimental data using deep learning networks in a Bayesian setting, namely rotationally invariant variational autoencoders.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Uncertainty in Synthetic Tropical Cyclone Hazard and Risk Estimates: Insights from RAFT, CHAZ, MIT, STORM, and CLIMADA

We synthesize five complementary tropical cyclone (TC) hazard frameworks—RAFT (physics-based machine learning), CHAZ and MIT (statistical–dynamical), STORM (fully statistical), and CLIMADA (observation-driven resampling)—to characterize uncertainty in wind-related TC metrics relevant to energy applications. All datasets and the IBTrACS observational record are harmonized to a common 6-hourly, 2.5° grid. We compare basin-wide and coastal properties using consistent definitions for TC frequency, mean and maximum intensity, 24-hour intensification, and 6-hour translation speed, and quantify agreement with Pearson r, RMSE, and Kling–Gupta efficiency (KGE) alongside resampling-based confidence intervals. CLIMADA is included for basin context but excluded from coastal skill scoring because it resamples historical IBTrACS; if supplied with projected future tracks from an external hazard model, CLIMADA can be used to simulate future TC scenarios. Results show robust, cross-model signals: (i) a corridor of activity from the tropical Atlantic through the Caribbean into the Bahamas and western subtropical Atlantic; (ii) a meridional dipole in 24-hour intensification (low-latitude strengthening, subtropical weakening); and (iii) a transition from slower tropical motion to faster midlatitude translation. Coastal winds (mean and maximum) consistently cluster from the eastern Gulf into the Bahamas–western Atlantic transition. The largest structural spread occurs in the amplitude and footprint of lifetime maximum intensity and, secondarily, in translation speed; intensification exhibits similar central behavior across frameworks with variability in extremes. Translation speed shows the most uniform coastal agreement. These findings provide a decision envelope for wind-focused risk screening and clarify where uncertainty should be carried forward; wind-only results represent a lower bound on total hazard, motivating integration of surge and rainfall modules and a companion, asset-level damage analysis.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (k app ) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Altogether, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Computational Workflow of Elucidating Viral Impact on Mediating Microbial Response to In-situ Experimental Warming: Bridging microbial modeling to carbon and mineral modeling

Viruses are abundant in soils and shape microbial communities in ways that can potentially influence ecosystem processes, yet their contributions to carbon cycling and mineral transformations remain poorly understood. Here we present a multi-phase framework that links virus-host interactions to soil biogeochemistry by combining ecological simulations, genome- and community-scale metabolic modeling, and statistical and machine-learning analyses. We first calibrated microbial abundance profiles under explicit infection scenarios to capture how viral pressure alters community structure, then explored alternative interaction strategies, including kill-the-winner, piggyback-the-winner, and mixed lytic-lysogenic modes, through forward simulations. These ecological shifts were translated into metabolic consequences using exchange fluxes summarized into biologically meaningful categories, while integrated statistical and machine-learning screens elevated subtle but consistent signals. Application of this framework revealed that viral infections shift the balance between organic and inorganic fluxes, redirecting metabolism from diffuse organic transformations toward inorganic pools such as protons and CO 2 , directly linking viral regulation to respiration and soil carbon balance. The roll-up analysis also isolated perturbations in critical mineral ions, including magnesium, manganese, zinc, and copper, which serve as essential enzymatic cofactors. In piggyback-the-winner scenarios, uptake of these ions was strongly suppressed. Contrasting viral strategies produced distinct community structures and metabolic outcomes, from broad suppression under kill-the-winner dynamics to dramatic redistributions under high-lytic and high-gain lysogenic regimes that collapsed vulnerable microbial populations while promoting opportunists. Together, these results provide a tractable path to trace viral perturbations from host abundance shifts to metabolic flux adjustments and ecosystem-scale processes, offering a practical way to include viruses in earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A parametrically programmable delay line for microwave photons

Delay lines that store quantum information are crucial for advancing quantum repeaters and hardware efficient quantum computers. Traditionally, they are realized as extended systems that support wave propagation but provide limited control over the propagating fields. Here, we introduce a parametrically addressed delay line for microwave photons that provides a high level of control over the stored pulses. By parametrically driving a three-wave mixing circuit element that is weakly hybridized with an ensemble of resonators, we engineer a spectral response that simulates that of a physical delay line, while providing fast control over the delay line’s properties. We demonstrate this novel degree of control by choosing which photon echo to emit, translating pulses in time, and even swapping two pulses, all with pulse energies on the order of a single photon. We also measure the noise added from our parametric interactions and find it is much less than one photon.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2021

Accurate and scalable graph neural network force field and molecular dynamics with direct force architecture

Abstract Recently, machine learning (ML) has been used to address the computational cost that has been limiting ab initio molecular dynamics (AIMD). Here, we present GNNFF, a graph neural network framework to directly predict atomic forces from automatically extracted features of the local atomic environment that are translationally-invariant, but rotationally-covariant to the coordinate of the atoms. We demonstrate that GNNFF not only achieves high performance in terms of force prediction accuracy and computational speed on various materials systems, but also accurately predicts the forces of a large MD system after being trained on forces obtained from a smaller system. Finally, we use our framework to perform an MD simulation of Li 7 P 3 S 11 , a superionic conductor, and show that resulting Li diffusion coefficient is within 14% of that obtained directly from AIMD. The high performance exhibited by GNNFF can be easily generalized to study atomistic level dynamics of other material systems.

Chemistry↗
DOE OSTI2022

Efficient hybrid explicit-implicit learning for multiscale problems

Splitting method is a powerful method to handle application problems by splitting physics, scales, domain, and so on. Many splitting algorithms have been designed for efficient temporal discretization. Here, in this paper, our goal is to use temporal splitting concepts in designing machine learning algorithms and, at the same time, help splitting algorithms by incorporating data and speeding them up. We propose a machine learning assisted splitting scheme which improves the efficiency of the scheme meanwhile preserves the accuracy. We consider a recently introduced multiscale splitting algorithms, where the multiscale problem is solved on a coarse grid. To approximate the dynamics, only a few degrees of freedom are solved implicitly, while others explicitly. This splitting concept allows identifying degrees of freedom that need implicit treatment. In this paper, we use this splitting concept in machine learning and propose several strategies. First, the implicit part of the solution can be learned as it is more difficult to solve, while the explicit part can be computed. This provides a speed-up and data incorporation for splitting approaches. Secondly, one can design a hybrid neural network architecture because handling explicit parts requires much fewer communications among neurons and can be done efficiently. Thirdly, one can solve the coarse grid component via PDEs or other approximation methods and construct simpler neural networks for the explicit part of the solutions. We discuss these options and implement one of them by interpreting it as a machine translation task. This interpretation of the splitting scheme successfully enables us using the Transformer since it can perform model reduction for multiple time series and learn the connection between them. We also find that the splitting scheme is a great platform to predict the coarse solution with insufficient information of the target model: the target problem is partially given and we need to solve it through a known problem which approximates the target. Our machine learning model can incorporate and encode the given information from two different problems and then solve the target problems. We conduct four numerical examples and the results show that our method is stable and accurate.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Voltage waveform tailoring for high aspect ratio plasma etching of SiO 2 using Ar/CF 4 /O 2 mixtures: Consequences of low fundamental frequency biases

The use of non-sinusoidal waveforms in low pressure capacitively coupled plasmas intended for microelectronics fabrication has the goal of customizing ion and electron energy and angular distributions to the wafer. One such non-sinusoidal waveform uses the sum of consecutive harmonics of a fundamental sinusoidal frequency, f 0 , having a variable phase offset between the fundamental and even harmonics. In this paper, we discuss results from a computational investigation of the relation between ion energy and DC self-bias when varying the fundamental frequency f 0 for capacitively coupled plasmas sustained in Ar/CF 4 /O 2 and how those trends translate to a high aspect ratio etching of trenches in SiO 2 . The fundamental frequency, f 0 , was varied from 1 to 10 MHz and the relative phase from 0° to 180°. Two distinct regimes were identified. Average ion energy onto the wafer is strongly correlated with the DC self-bias at high f 0 , with there being a maximum at φ = 0° and minimum at φ = 180°. In the low frequency regime, this correlation is weak. Average ion energy onto the wafer is instead dominated by dynamic transients in the applied voltage waveforms, with a maximum at φ = 180° and minimum at φ = 0°. The trends in ion energy translate to etch properties. In both, the high and low frequency regimes, higher ion energies translate to higher etch rates and generally preferable final features, though behaving differently with phase angle.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Actuating Liquid Crystals Rapidly and Reversibly by Using Chemical Catalysis

Abstract Microtubules and catalytic motor proteins underlie the microscale actuation of living materials, and they have been used in reconstituted systems to harness chemical energy to drive new states of organization of soft matter (e.g., liquid crystals (LCs)). Such materials, however, are fragile and challenging to translate to technological contexts. Rapid (sub‐second) and reversible changes in the orientations of LCs at room temperature using reactions between gaseous hydrogen and oxygen that are catalyzed by Pd/Au surfaces are reported. Surface chemical analysis and computational chemistry studies confirm that dissociative adsorption of H 2 on the Pd/Au films reduces preadsorbed O and generates 1 ML of adsorbed H, driving nitrile‐containing LCs from a perpendicular to a planar orientation. Subsequent exposure to O 2 leads to oxidation of the adsorbed H, reformation of adsorbed O on the Pd/Au surface, and a return of the LC to its initial orientation. The roles of surface composition and reaction kinetics in determining the LC dynamics are described along with a proof‐of‐concept demonstration of microactuation of beads. These results provide fresh ideas for utilizing chemical energy and catalysis to reversibly actuate functional LCs on the microscale.

Chemistry↗
DOE OSTI2021

Local rules for fabricating allosteric networks

Mechanical properties of disordered networks can be significantly tailored by modifying a small fraction of their bonds. This procedure has been used to design and build mechanical metamaterials with a variety of responses. A long-range “allosteric” response, where a localized input strain at one site gives rise to a localized output strain at a distant site, has been of particular interest. This work presents an approach to incorporating allosteric responses in experimental systems by pruning disordered networks in situ. Previous work has relied on computer simulations to design and predict the response of such systems using a cost function where the response of the entire network to each bond removal is used at each step to determine which bond to prune. It is not feasible to follow such a design protocol in experiments where one has access only to local response at each site. This paper presents design algorithms that allow determination of what bonds to prune based purely on the local forces in the network without employing a cost function; using only local information, allosteric networks are designed in simulations and then built out of real materials. The results show that some pruning strategies work better than others when translated into an experimental system. A method is presented to measure local stresses experimentally in disordered networks. This approach is then used to implement pruning methods to design desired responses in situ. Results from these experiments confirm that the pruning methods are robust and work in a real laboratory material.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Spray Pyrolysis-Aerosol Deposition for the Production of Thick Yttria-Stabilized Zirconia Coatings

Aerosol deposition (AD) is a coating technique wherein particles are impacted onto a target substrate at reduced pressures, and supersonic particle impact velocities lead to coating consolidation. The limiting step in AD application is often not supersonic deposition operation, but aerosolization of powder particles with the proper size distribution; the translational impact velocity is strongly size-dependent. It is demonstrated that by directly synthesizing particles in the gas phase, size-controlled ceramic particles can be injected into AD systems. This in situ formation step obviates the need for particle aerosolization. Ultrasonic spray pyrolysis (USP) is applied to produce yttria-stabilized zirconia (YSZ), and USP is directly coupled with AD to produce consolidated, thick, YSZ coatings on metal substrates. USP-AD yields YSZ coatings on stainless steel and aluminum substrates with porosities <0.20, which grow to thicknesses beyond 100 μm. Aerodynamic particle spectrometry and electron microscopy reveal that the depositing particles are 200 nm–1.2 μm in diameter, though each particle is composed of nanocrystalline YSZ. Supporting computational fluid dynamics calculations demonstrate that the YSZ particle impact speeds are above 300 m s -1 . Thermal conductivity measurements demonstrate that USP-AD coatings have conductivities consistent with those produced from high-temperature processes.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Er Al :Al 2 ⁢O 3 for telecom-band photonics: Electronic structure and optical properties

Er-doped Al 2 ⁢O 3 is a promising host for telecom-band integrated photonics. Here, in this study, we combine ab initio calculations with a symmetry-resolved analysis to elucidate substitutional Er on the Al site (Er Al ) in 𝛼−Al 2 ⁢O 3 . First-principles relaxations confirm the structural stability of Er Al . We then use the local trigonal crystal-field symmetry to classify the Er-derived impurity levels by irreducible representations and to derive polarization-resolved electric-dipole selection rules, explicitly identifying the symmetry-allowed 𝑓−𝑑 hybridization channels. Kubo-Greenwood absorption spectra computed from Kohn-Sham states quantitatively corroborate these symmetry predictions. Furthermore, we connect the calculated intra-4⁢𝑓 line strengths to Judd-Ofelt theory, clarifying the role of 4⁢𝑓−5⁢𝑑 admixture in enabling optical activity. Notably, we predict a characteristic absorption near 1.47 µ⁢m (telecom band), relevant for on-chip amplification and emission. To our knowledge, a symmetry-resolved first-principles treatment of Er:Al 2 ⁢O 3 with an explicit Judd-Ofelt interpretation has not been reported, providing a transferable framework for tailoring rare-earth dopants in wide-band-gap oxides for integrated photonics. Our results for the optical spectra are in good agreement with experimental data. The resulting symmetry-based selection rules translate directly to polarization-dependent coupling in Al 2 ⁢O 3 integrated photonic waveguides and resonators, enabling device-level design of TE/TM-mode interaction with Er emitters in the 1.5-µ⁢m telecom band.

Er-doped Al2O3↗
DOE OSTI2023

Erasure conversion in a high-fidelity Rydberg quantum simulator

Minimizing and understanding errors is critical for quantum science, both in noisy intermediate scale quantum (NISQ) devices and for the quest towards fault-tolerant quantum computation. Rydberg arrays have emerged as a prominent platform in this context with impressive system sizes and proposals suggesting how error-correction thresholds could be significantly improved by detecting leakage errors with single-atom resolution, a form of erasure error conversion. However, two-qubit entanglement fidelities in Rydberg atom arrays have lagged behind competitors and this type of erasure conversion is yet to be realized for matter-based qubits in general. Here we demonstrate both erasure conversion and high-fidelity Bell state generation using a Rydberg quantum simulator. When excising data with erasure errors observed via fast imaging of alkaline-earth atoms, we achieve a Bell state fidelity of $\ge 0.997{1}_{-13}^{+10}$ , which improves to $\ge 0.998{5}_{-12}^{+7}$ when correcting for remaining state-preparation errors. We further apply erasure conversion in a quantum simulation experiment for quasi-adiabatic preparation of long-range order across a quantum phase transition, and reveal the otherwise hidden impact of these errors on the simulation outcome. Our work demonstrates the capability for Rydberg-based entanglement to reach fidelities in the 0.999 regime, with higher fidelities a question of technical improvements, and shows how erasure conversion can be utilized in NISQ devices. These techniques could be translated directly to quantum-error-correction codes with the addition of long-lived qubits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗