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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 433 records · Page 24

Expanding the Scope of Genomic Security: Targeted Genome Editing within Microbiomes through Designer Bacteriophage Vectors

The ability to engineer the genome of a bacterial strain, not as an isolate, but while present among other microbes in a microbiome, would open new technological possibilities in the areas of medicine, energy and biomanufacturing. Our approach is to develop sets of phages (bacterial viruses) active on the target strain and themselves engineered to act not as killers but as vectors for gene delivery. This approach is rooted in our bioinformatic tools that map prophages accurately within bacterial genomes. We present new bioinformatic results in cross-contig search, design of phage genome assemblies, satellites that embed within prophages, alignment of large numbers of biological sequences, and improvement of reference databases for prophage discovery. We targeted a Pseudomonas putida strain within a lignin-degrading microbiome, but were unable to obtain active phages, and turned toward a defined microbiome of the mouse gut.

59 BASIC BIOLOGICAL SCIENCES↗

Computationally Guided and Experimentally Validated Design of Custom Chelators for Critical Mineral Recovery

Selective, high throughput separation of target critical metals from complex environments such as fly ash leachates and mining process streams presents a significant challenge for economical production. Custom chelators and sorbents are an attractive technology for selective metal extraction, however it can be difficult to predict their performance, and significant experimental efforts are often required to develop chelating technologies. Here, we present a computational strategy focused on modelling chelator-metal binding interactions and benchmark these results versus experimental data. A computational pipeline combining forcefield, semiempirical, and meta-GGA methods with a thermodynamic framework optimized for error cancellation has been developed to predict binding energies of chelator complexes towards critical mineral recovery applications. This approach, originally validated on [2.2.2] cryptates binding mono- and divalent cations, demonstrated robust predictive capabilities with an R2 of 0.850 against experimental aqueous binding energies. The workflow includes metadynamics for exploring high-dimensional potential energy surfaces and a cluster-continuum model for accurate yet computationally efficient solvation modeling. Error cancellation between solvation energies of free and chelator-coordinated ions enables faster convergence, even with finite cluster sizes. Initial studies on the cryptates revealed consistent metal-ligand coordination patterns, with systematic variations influenced by ion size and charge, highlighting key structural features linked to binding selectivity. Further studies of a proprietary chelator have resulted in identification of previously unreported selectivity towards economically significant metals, which in-house experiments have confirmed, demonstrating the feasibility of this approach. By applying this methodology to new chelators targeting critical minerals such as lithium, cobalt, nickel and other strategic metals, we aim to accelerate the discovery of next-generation chelators for efficient recovery, recycling, and separation processes. This computational framework serves as the backbone of a high-throughput design pipeline tailored for sustainable resource utilization and may be applied to a wide range of systems to meet experimental needs.

computational materials↗

Transboundary effects from idealized regional geoengineering

Regional geoengineering, by reflecting sunlight over a very limited spatial domain, might be considered as a means to target specific regional impacts of climate change. One of the obvious concerns raised by such approaches is the extent to which the resulting effects would be detectable well beyond the targeted region (e.g. in neighbouring countries). A few studies have explored this question for targeted regions that are still comparatively large. We consider idealized simulations with increased ocean albedo over relatively small domains; the Gulf of Mexico (0.23% of Earth's surface) and over the Australian Great Barrier Reef (0.07%), both with negligible global radiative forcing. Applied over these very small domains, the only statistically significant non-local changes we find are some limited reduction on summer precipitation in Florida in the Gulf of Mexico case (adjacent to the targeted region). The lack of transboundary effects suggests that governance needs for such targeted interventions are quite distinct from those for more global sunlight reflection.

54 ENVIRONMENTAL SCIENCES↗

A small-volume, high-throughput approach for surface tension and viscosity measurements of liquid fuels

An ongoing effort looking at bioblendstocks to function as drop-in replacements or blending components for gasoline has identified a large number of candidate fuels. This work documents an approach for rapid screening of candidate fuels using relatively small sample sizes ($\mathcal{O}(\mu\,{\rm l})$) that targets two key physical properties of liquid fuels—surface tension and viscosity. The approach utilizes shape oscillation dynamics of single droplets generated by a piezo-electric device and their decay over time. Strobed imaging of the oscillation process is used along with image processing, edge detection, and data analysis to capture the decay of the oscillation over time. The time constant of the decay process along with oscillation frequency are then used to estimate viscosity and surface tension using a theory for small amplitude droplet oscillations. Measurements are obtained for primary reference fuels (isooctane and n-heptane) as well as candidate fuels from four bio-derived functional groups of interest. Measurement results for surface tension and viscosity are correlated with literature data as well as measurements from standard reference instruments. The measurement results show that the droplet oscillation based approach is capable of reproducing surface tension and viscosity values for the tested fuels within deviations of 7% and 13% respectively from literature data. Results are obtained using an average of 5 µl per fuel within about 20 s, thus demonstrating a small-volume, high-throughput approach that can be used for screening of candidate bioblendstock fuels.

09 BIOMASS FUELS↗

A Bayesian Calibration Framework with Embedded Model Error for Model Diagnostics

We study the utility and performance of a Bayesian model error embedding construction in the context of molecular dynamics modeling of metallic alloys, where we embed model error terms in existing interatomic potential model parameters. To alleviate the computational burden of this approach, we propose a framework combining likelihood approximation and Gaussian process surrogates. Here we leverage sparse Gaussian process techniques to construct a hierarchy of increasingly accurate but more expensive surrogate models. This hierarchy is then exploited by multilevel Markov chain Monte Carlo methods to efficiently sample from the target posterior distribution. We illustrate the utility of this approach by calibrating an interatomic potential model for a family of gold-copper alloys. In particular, this case study highlights effective means for dealing with computational challenges with Bayesian model error embedding in large-scale physical models, and the utility of embedded model error for model diagnostics.

Bayesian inference↗

Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-γ-semialdehyde Dehydrogenase

The proline catabolic pathway consisting of proline dehydrogenase (PRODH) and L-glutamate-γ-semialdehyde (GSAL) dehydrogenase (GSALDH) catalyzes the four-electron oxidation of L-proline to L-glutamate. Chemical probes to these enzymes are of interest for their role in cancer and inherited metabolic disease. Here, we report the results of a crystallographic fragment-screening campaign targeting both enzymes. A unique aspect of our approach is the screening of both enzymes simultaneously using crystals of the bifunctional PRODH-GSALDH enzyme, proline utilization A (PutA). A 288-fragment library from Zenobia was screened in crystallo in cocktails of six fragments. Validation X-ray crystallography with individual fragments identified seven crystal hits distributed in the PRODH active site, GSALDH aldehyde substrate-binding site, and GSALDH NAD+ adenine-binding site. The fragment bound in the PRODH active site, 4-methoxybenzyl alcohol, is structurally distinct from all known PRODH inhibitors as it lacks an anionic anchor and stabilizes open conformations of the active site, motivating the study of eighteen analogs. In total, thirteen crystal structures with resolutions ranging from 1.32 Å to 1.80 Å were determined, resolving the poses and interactions of seven fragments from the Zenobia library and five analogs of 4-methoxybenzyl alcohol. These results expand the chemical space of probes targeting proline catabolic enzymes and provide new structural information for further inhibitor development.

Biochemistry & Molecular Biology↗

Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors

Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Short-depth circuits for efficient expectation-value estimation

The evaluation of expectation values Tr[$\rho \mathcal{O}$] for some pure state $\rho$ and Hermitian operator $\mathcal{O}$ is of central importance in a variety of quantum algorithms. Near-optimal techniques have been developed in the past and require a number of measurements N approaching the Heisenberg limit N = O(1/ ε) as a function of target accuracy ε. The use of quantum phase estimation (QPE) requires, however, long circuit depths C = O(1/ ε) making its implementation difficult on near-term noisy devices. The more direct strategy of operator averaging is usually preferred as it can be performed using N = O(1/ε 2 ) measurements and no additional gates aside from those needed for the state preparation. In this work we use a simple but realistic model to describe the bound state of a neutron and a proton (the deuteron) to show that the latter strategy can require an overly large number of measurements in order to achieve a prefixed relative target accuracy ε r . Further, we propose to overcome this problem using a single step of QPE and classical postprocessing. This approach leads to a circuit depth C = O (ε μ ) (with μ ≥ 0) and to a number of measurements N = O (1/ε 2 + ν ) for 0 < ν ≤ 1 and a much smaller prefactor. We provide detailed descriptions of two implementations of our strategy for ν = 1 and ν ≈ 0.5 and derive appropriate conditions that a particular problem instance has to satisfy in order for our method to provide an advantage.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Data for Selected Ion Monitoring for Orbitrap-Based Metabolomics

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.f

Mass Spectrometry↗

Atomically Precise Membranes for the Separation of Gases

Industrial separations require enormous amounts of energy, accounting for approximately half the industrial energy use and 10–15% of the total energy consumption. Distillation alone accounts for about half the energy demand for industrial separations. If these processes could be replaced by an energy-efficient membrane separation process, this energy demand could be reduced by 90%. However, although some membrane processes have made inroads into thermal distillation, for membrane-based separations to replace the distillation process to a far more significant and practical level, new membranes with higher robustness, selectivity, and flux still need be developed. In this membrane development program, we leveraged Temple University’s prior work in spiroligomers to develop robust membrane structures. These structures can be formed into atomically precise pores by controlling the chemical synthesis and the oligomer building blocks to first build precisely controlled macrocycles and then subsequently crosslinking these macrocycles to produce a membrane. Furthermore, through the highly controllable chemistry of our molecular building blocks, not only can we integrate pores with highly controllable and reproducible size and morphology, but we can also target internal functionalization. By using a range of scalable membrane synthesis approaches, combined with control of each and every pores internal chemistry and molecular conformation we can achieve membrane structures that can display the ultimate in high selectivity and permeance. The Mainstream-Temple University membranes can be designed to achieve ultra-selective separations based on the key factors of molecular size, shape, and functionality. In our approach to fabricate scalable atomically precise membranes, we used our molecular Lego nanostructures. We demonstrated an approach to create atomically precise pores within the membrane with pores that are the dimensions of the molecule we are trying to separate. Moreover, in addition to controlling the morphology of the membrane structure by controlling the size of every pore, we can also decorate every pore with precisely targeted and placed functional groups. These accurately placed functional groups can provide selective binding to molecules and provide enhanced selectivity via a facilitated transport mechanism. In Phase II, the Mainstream-Temple University team demonstrated the scalable synthesis of oligomers and the ability to control the pore internal and external functionality, or chemistry, to allow the fabrication of a thin-film membrane. The initial steps of the spiroligomer synthesis to produce the two key bis-amino enantiomer building blocks were scaled from the gram scale to the kilogram scale, obtaining 25 kg of the materials by transferring the procedure to a toll manufacturer. Finally, we successfully optimized the fabrication of these macrocycles into robust membranes. We successfully transitioned from a laboratory based, hard-to-scale Langmuir trough synthesis to a highly scalable, roll-to-roll applicable, interfacial polymerization process. During this Phase II program, we established a platform of atomically precise membranes where our highly controllable, atomically precise macrocycles served as a scaffold with precisely and uniformly controlled pores. Furthermore, this layer can be tailored to accommodate a diverse range of functional groups, which both further controlled the pore size to enhance the sieving effect as well as imparting precisely controlled targeted selectivity through biomimetic molecular interactions. In this Phase II, we established and scaled up a platform approach to both tune the pore size and chemistry as well as scale it to produce membranes that can be applied to a wide range of industries. In future development, the project team expects to scale up both the macrocycle building block production and interfacial polymerization process to produce the atomically precise membrane with targeted pore sizes and pore chemistries.

36 MATERIALS SCIENCE↗

A matched-filter approach to radio variability and transients: searching for orphan afterglows in the VAST Pilot Survey

Radio transient searches using traditional variability metrics struggle to recover sources whose evolution time-scale is significantly longer than the survey cadence. Motivated by the recent observations of slowly evolving radio afterglows at gigahertz frequency, we present the results of a search for radio variables and transients using an alternative matched-filter approach. We designed our matched-filter to recover sources with radio light curves that have a high-significance fit to power-law and smoothly broken power-law functions; light curves following these functions are characteristic of synchrotron transients, including ‘orphan’ gamma-ray burst afterglows, which were the primary targets of our search. Applying this matched-filter approach to data from Variables and Slow Transients Pilot Survey conducted using the Australian SKA Pathfinder, we produced five candidates in our search. Subsequent Australia Telescope Compact Array observations and analysis revealed that: one is likely a synchrotron transient; one is likely a flaring active galactic nucleus, exhibiting a flat-to-steep spectral transition over 4 months; one is associated with a starburst galaxy, with the radio emission originating from either star formation or an underlying slowly evolving transient; and the remaining two are likely extrinsic variables caused by interstellar scintillation. The synchrotron transient, VAST J175036.1–181454, has a multifrequency light curve, peak spectral luminosity, and volumetric rate that is consistent with both an off-axis afterglow and an off-axis tidal disruption event; interpreted as an off-axis afterglow would imply an average inverse beaming factor $\langle f^{-1}_{\text{b}} \rangle = 860^{+1980}_{-710}$, or equivalently, an average jet opening angle of $\langle \theta _{\textrm {j}} \rangle = 3^{+4}_{-1}\,$ deg.

79 ASTRONOMY AND ASTROPHYSICS↗

Array-Based Machine Learning for Functional Group Detection in Electron Ionization Mass Spectrometry

Mass spectrometry is a ubiquitous technique capable of complex chemical analysis. The fragmentation patterns that appear in mass spectrometry are an excellent target for artificial intelligence methods to automate and expedite the analysis of data to identify targets such as functional groups. To develop this approach, we trained models on electron ionization (a reproducible hard fragmentation technique) mass spectra so that not only the final model accuracies but also the reasoning behind model assignments could be evaluated. The convolutional neural network (CNN) models were trained on 2D images of the spectra using transfer learning of Inception V3, and the logistic regression models were trained using array-based data and Scikit Learn implementation in Python. Our training dataset consisted of 21,166 mass spectra from the United States’ National Institute of Standards and Technology (NIST) Webbook. The data was used to train models to identify functional groups, both specific (e.g., amines, esters) and generalized classifications (aromatics, oxygen-containing functional groups, and nitrogen-containing functional groups). We found that the highest final accuracies on identifying new data were observed using logistic regression rather than transfer learning on CNN models. It was also determined that the mass range most beneficial for functional group analysis is 0–100 m/z. We also found success in correctly identifying functional groups of example molecules selected from both the NIST database and experimental data. Beyond functional group analysis, we also have developed a methodology to identify impactful fragments for the accurate detection of the models’ targets. The results demonstrate a potential pathway for analyzing and screening substantial amounts of mass spectral data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Turbulence and Control of Wind Farms

The dynamics of the turbulent atmospheric boundary layer play a fundamental role in wind farm energy production, governing the velocity field that enters the farm as well as the turbulent mixing that regenerates energy for extraction at downstream rows. Understanding the dynamic interactions among turbines, wind farms, and the atmospheric boundary layer can therefore be beneficial in improving the efficiency of wind farm control approaches. Anticipated increases in the sizes of new wind farms to meet renewable energy targets will increase the importance of exploiting this understanding to advance wind farm control capabilities. This review discusses approaches for modeling and estimation of the wind farm flow field that have exploited such knowledge in closed-loop control, to varying degrees. We focus on power tracking as an example application that will be of critical importance as wind farms transition into their anticipated role as major suppliers of electricity. The discussion highlights the benefits of including the dynamics of the flow field in control and points to critical shortcomings of the current approaches.

Automation & Control Systems↗

Coupled cluster Green's function: Past, Present, and Future

Coupled cluster Green's function (CCGF) approach has drawn much attention in recent years for targeting the molecular and material electronic structure problems from a many-body perspective in a systematically improvable way. Here, we will present a brief review of the history of how the Green's function method evolved with the wavefunction, early and recent development of CCGF theory, and more recently scalable CCGF software development. We will highlight some of the recent applications of CCGF approach and propose some potential applications that would emerge in the near future.

Peng, Bo↗

Design and Commissioning of a Deuterium-Tritium Gas Delivery System for Muon Catalyzed Fusion in a Diamond Anvil Cell

We report the design, commissioning, and operation of deuterium-deuterium (DD) and deuterium-tritium (DT) gas delivery systems developed to load a diamond anvil cell (DAC) beam target for muon-catalyzed fusion (muCF). The DAC approach enables DT fuel to be compressed to GPa pressures at more than twice the liquid density and heated from cryogenic temperatures through 500 K, opening access to a substantially expanded parameter range for muCF kinetics and yield measurements. In this approach, DT is cryo-condensed to a liquid in a minichamber and then compressed in the DAC using a helium-driven pneumatic membrane, achieving high pressures in a millimeter-scale DT sample volume. A DD gas delivery system was designed and used to validate the experimental apparatus, measure the gas quantities needed for filling, develop operational experience, and collect kinetics and yield data with DD targets. The DT gas delivery system adds tritium-specific capabilities for inventory minimization, secondary containment, and activity monitoring. The DT system integrates depleted uranium storage beds and a liquid helium cryogenic condenser used for pressure building and cryopumping. High-purity delivery is provided by a rapid-response palladium permeator. The system is housed in a helium-atmosphere glovebox held at negative pressure with continuous cleanup. We present the process and instrumentation design, a failure modes and effects analysis (FMEA), and data from the experiment's in situ Raman spectrometer, which provides direct confirmation of target loading and composition through the optically clear diamond anvils. The 2024 and 2025 DT campaigns achieved repeatable target fills and operation with no measurable tritium releases to the stack, demonstrating safe, high-purity DT loading at novel density-temperature conditions for muCF studies.

Koukina, Elena [Acceleron Fusion]↗

Identifying a list of Salmonella serotypes of concern to target for reducing risk of salmonellosis

There is an increasing awareness in the field of Salmonella epidemiology that focusing control efforts on those serotypes which cause severe human health outcomes, as opposed to broadly targeting all Salmonella , will likely lead to the greatest advances in decreasing the incidence of salmonellosis. Yet, little guidance exists to support validated, scientific selection of target serotypes. The goal of this perspective is to develop an approach to identifying serotypes of greater concern and present a case study using meat- and poultry-attributed outbreaks to examine challenges in developing a standardized framework for defining target serotypes.

59 BASIC BIOLOGICAL SCIENCES↗

High-Order Mesh hr-adaptivity for Surface Fitting to Implicit Geometries

We present an ℎ𝑟-adaptivity framework for morphing a given mesh to fit a target surface prescribed as the zero isocontour of a discrete function. In this framework, high-order meshing is posed as a variational minimization problem that depends on the mesh quality prescribed via the target matrix optimization paradigm (TMOP) and position of a subset of mesh nodes with respect to the target surface. The proposed formulation ensures that the variational problem is converged and mesh quality degradation near the surface is limited, even when the mesh topology is incompatible with the target surface. Additionally, a mesh subset-based approach and ℎ-refinement is introduced to efficiently increase fitting accuracy while reducing the computational cost of the mesh morphing problem. The ℎ𝑟-adaptivity technique extends to different element types in two- and three-dimensions, and can be used in existing finite element and spectral element frameworks to obtain high-order body-fitted meshes. Various numerical experiments demonstrate the robustness and accuracy of the fitting approach for problems of practical interest such as Lagrangian hydrodynamics and topology optimization.

97 MATHEMATICS AND COMPUTING↗

Tuning transition metal nanoparticles on a non-traditional support via experimental design

The ability to control metal nanoparticle size and morphology on supported catalysts is crucial for optimizing catalytic performance in targeted applications. Here, this work presents a systematic approach for tuning Ni particle and crystallite size on an unconventional, low-porosity silica fume support through select thermal treatments. The catalyst was synthesized via the deposition of nickelocene onto silica fume, resulting in well-dispersed Ni nanoparticles. A face-centered central composite design was employed to systematically assess the effects of time, temperature, and sintering gas environment on metal particle growth. The results demonstrate that the sintering gas environment is the primary factor governing particle and crystallite evolution, with temperature as the next most significant influence. Nickel nanoparticles sintered at temperatures of 650 °C and above under inert conditions exhibited substantial growth and polycrystalline structures, whereas samples treated in oxidative environments formed NiO, restricting particle mobility. Minimally oxidative (500 ppm O₂) environments facilitated rapid sintering while effectively removing residual ligands from the one-step nickelocene deposition process. Extensive structural characterization via a combination of scanning transmission electron microscopy, X-ray diffraction, hydrogen temperature programmed reduction, and small-angle X-ray scattering revealed that oxidative treatments enhanced metal-support interactions, as evidenced by increased reduction temperatures and narrower particle size distributions. These findings establish quantitative relationships between sintering parameters and Ni nanoparticle characteristics, providing a framework for rational catalyst design through controlled thermal treatments. This methodology is broadly applicable to other catalytic systems and provides a quantitative foundation for catalyst design.

CVD↗