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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Models and Algorithms for Equilibrium Analysis of Mixed-Material Nucleic Acid Systems

Dynamic programming algorithms within the NUPACK software suite enable analysis of equilibrium base-pairing properties for complex and test tube ensembles containing arbitrary numbers of interacting nucleic acid strands. Currently, calculations are limited to single-material systems that are either all-RNA or all-DNA. Here, to enable analysis of mixed-material systems that are critical for modern applications in vitro, in situ, and in vivo, we develop physical models and dynamic programming algorithms that allow the material of the system to be specified at nucleotide resolution. Free energy parameter sets are constructed for both RNA/DNA and RNA/2'OMe-RNA mixed-material systems by combining available empirical mixed-material parameters with single-material parameter sets to enable treatment of the full complex and test tube ensembles. New dynamic programming recursions account for the material of each nucleotide throughout the recursive process. For a complex with N nucleotides, the mixed-material dynamic programming algorithms maintain the O(N 3 ) time complexity of the single-material algorithms, enabling efficient calculation of diverse physical quantities over complex and test tube ensembles (e.g., complex partition function, equilibrium complex concentrations, equilibrium base-pairing probabilities, minimum free energy secondary structure(s), and Boltzmann-sampled secondary structures) at a cost increase of roughly 2.0-3.5×. The results of existing single-material algorithms are exactly reproduced when applying the new mixed-material algorithms to single-material systems. Accuracy is significantly enhanced using mixed-material models and algorithms to predict RNA/DNA and RNA/2'OMe-RNA duplex melting temperatures from the experimental literature as well as RNA/DNA melt profiles from new experiments. In conclusion, mixed-material analyses can be performed online using the NUPACK web app (www.nupack.org) or locally using the NUPACK Python module.

2′OMe-RNA↗
DOE OSTI2026

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗
DOE OSTI2021

macroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. Furthermore, the web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ~2 s/sample.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

A Growing Freshwater Lens in the Arctic Ocean With Sustained Climate Warming Disrupts Marine Ecosystem Function

One of the most robust changes in the hydrological cycle predicted by Earth System Models (ESMs) during the remainder of 21st century is an increase in the difference between precipitation and evapotranspiration (P-E) in arctic and boreal regions. We explore the long-term consequences of this change for marine ecosystems in the Arctic Ocean using the Community Earth System Model forced with a business as usual scenario of future greenhouse gas concentrations. We find that by the year 2300 increases in freshwater delivery considerably reduce Arctic Ocean surface salinity, creating a freshwater lens that has far-reaching impacts on marine biogeochemistry. The expanding freshwater lens limits vertical nutrient supply into the euphotic zone by enhancing vertical stratification and accelerating surface lateral mixing with surface waters in the North Atlantic, which become increasingly nutrient depleted from weakening of the Atlantic Meridional Overturning Circulation (AMOC). The resulting increase in nutrient stress reduces marine export production in the Arctic Ocean by 53% in 2300 relative to the 1990s and triggers a shift in community composition with small phytoplankton replacing diatoms. At the same time, the seasonal timing of export production undergoes a 2-month forward shift, with the peak advancing from July to May. This suggests that the threat to food webs and higher trophic levels may intensify after the year 2100 as gains in productivity from sea ice loss saturate and freshwater impacts on nutrient stress continue to strengthen. Our analysis highlights the critical importance of changing terrestrial hydrology and land-ocean coupling as drivers of long-term biogeochemical change in the Arctic Ocean and the necessity of multi-century climate change projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

How Well do Earth System Models Capture Apparent Relationships Between Phytoplankton Biomass and Environmental Variables?

Abstract As phytoplankton form the base of the marine food web, understanding the controls on their abundance is fundamental to understanding marine ecology and its sensitivity to global climate change. While many Earth System Models (ESMs) predict phytoplankton biomass, it is unclear whether they properly capture the mechanistic relationships that control this quantity in the real ocean. We used Random Forest analysis to analyze the output of 13 ESMs as well as two observational data sets. The target variable was phytoplankton carbon and the predictors included environmental parameters known to influence phytoplankton, including nutrients, light, mixed layer depth, salinity, temperature, and upwelling. We examined the following: (a) What fractions of variability in ESMs and observations can be linked to the large‐scale environmental variables simulated by ESMs? (b) What are the dominant predictors and relationships affecting phytoplankton biomass? (c) How well do ESMs simulate phytoplankton carbon and do they simulate the relationships we see in observations? About 88%–96% of the variability in observational data sets and greater than 98% in the ESMs was accounted for by environmental variables known to influence phytoplankton biomass. The dominant predictors in the observational data sets were shortwave radiation and dissolved iron, with temperature and ammonium also relatively important. All the ESMs show that shortwave radiation is the most important variable and most of them predict the right sign of sensitivity to most variables. However, the models predict that biomass reaches maximum levels at unrealistically low levels of iron and unrealistically high levels of light.

Environmental Sciences & Ecology↗
DOE OSTI2024

Expanded Understanding of the Western Antarctic Peninsula Sea‐Ice Environment Through Local and Regional Observations at Palmer Station

Abstract The Western Antarctic Peninsula (WAP) has been experiencing rapid regional warming since at least the 1950s, however, the impacts of this warming at the local scale are variable and nuanced. Previous studies that have linked sea‐ice variability to biogeochemical cycles and food web dynamics often combine local‐scale biogeochemical data with coarse‐resolution regional satellite sea‐ice data, which may not adequately capture local sea‐ice conditions. In this study, we analyzed local‐scale in situ sea‐ice observations collected as part of a 28‐year record (1992–2020) from the Palmer Long‐Term Ecological Research site at Anvers Island, mid‐WAP, in conjunction with isotopically‐derived sea‐ice meltwater (SIM) fractions and satellite‐derived sea‐ice motion and concentration, to quantify the variability and long‐term trends in local sea‐ice behavior. In situ sea ice observations at Palmer Station displayed higher variability than satellite observations and showed no significant declines over this time, despite region‐wide declines identified in prior studies. Higher spring SIM fractions were attributed to strong northward sea‐ice motion throughout the winter. Applying these local‐scale sea‐ice insights to similarly scaled stratification and chlorophyll‐ a measurements, we found that a longer‐lasting, more consistent sea‐ice pack led to greater water column stratification following the spring sea‐ice retreat. Greater sea‐ice persistence and stronger stratification led to larger peaks in chlorophyll‐ a , though sea‐ice metrics did not explain the positive temporal trends in either stratification strength or chlorophyll‐ a . Through this study, we identify how local sea‐ice observations and meltwater data can enhance satellite data to build an understanding of the intricate connections between ice, water column dynamics, and phytoplankton.

Goodell, E.↗
DOE OSTI2021

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants

The operation of modern wastewater treatment plants (WWTPs) is driven by activated sludge microbiota, a complex assemblage of trophically interacting microorganisms. Microbial predation is crucial to fundamental understanding of how biological interactions drive microbiome structuring and functioning of WWTPs. However, predatory bacteria have received little attention regarding their diversity, activity, and ecological function in activated sludge, limiting the exploitation of food web interactions for wastewater microbiome engineering. Here, by using rRNA-stable isotope probing of activated sludge microbiota with 13 C-labeled prey bacteria, we uncovered diverse as-yet-uncultivated putative predatory bacteria that actively incorporated 13 C-biomass. Myxobacteria, especially Haliangium and the mle1-27 clade, were found as the dominant active predators, refreshing conventional views based on a few predatory isolates of Bdellovibrionota from WWTPs. The identified predatory bacteria showed more selective predation on prey compared with the protists dominated by ciliates, providing in situ evidence for inter-domain predation behavior divergence in activated sludge. Putative predatory bacteria were tracked over a two-year microbiome monitoring effort at a local WWTP, revealing the predominance of Myxococcota (6.5 ± 1.3%) over Bdellovibrionota (1.0 ± 0.2%) lineages. Phylogenetic analysis unveiled highly diverse myxobacteria inhabiting activated sludge and suggested a habitat filtering effect in global WWTPs. Further mining of a global activated sludge microbiome dataset revealed the prevalence of Myxococcota (5.4 ± 0.1%) species and potential impacts of myxobacterial predation on process performance. Collectively, our findings provided unique insights into the predating activity, diversity, and prevalence of Myxococcota species in activated sludge, highlighting their links with wastewater treatment processes via trophic regulation of enteric and functional bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An in silico method to assess antibody fragment polyreactivity

Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models’ performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Guided construction of single cell reference for human and mouse lung

Accurate cell type identification is a key and rate-limiting step in single-cell data analysis. Single-cell references with comprehensive cell types, reproducible and functionally validated cell identities, and common nomenclatures are much needed by the research community for automated cell type annotation, data integration, and data sharing. Here, we develop a computational pipeline utilizing the LungMAP CellCards as a dictionary to consolidate single-cell transcriptomic datasets of 104 human lungs and 17 mouse lung samples to construct LungMAP single-cell reference (CellRef) for both normal human and mouse lungs. CellRefs define 48 human and 40 mouse lung cell types catalogued from diverse anatomic locations and developmental time points. We demonstrate the accuracy and stability of LungMAP CellRefs and their utility for automated cell type annotation of both normal and diseased lungs using multiple independent methods and testing data. We develop user-friendly web interfaces for easy access and maximal utilization of the LungMAP CellRefs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre

Photosynthesis fuels primary production at the base of marine food webs. Yet, in many surface ocean ecosystems, diel-driven primary production is tightly coupled to daily loss. This tight coupling raises the question: which top-down drivers predominate in maintaining persistently stable picocyanobacterial populations over longer time scales? Motivated by high-frequency surface water measurements taken in the North Pacific Subtropical Gyre (NPSG), we developed multitrophic models to investigate bottom-up and top-down mechanisms underlying the balanced control of Prochlorococcus populations. Here, we find that incorporating photosynthetic growth with viral- and predator-induced mortality is sufficient to recapitulate daily oscillations of Prochlorococcus abundances with baseline community abundances. In doing so, we infer that grazers in this environment function as the predominant top-down factor despite high standing viral particle densities. The model-data fits also reveal the ecological relevance of light-dependent viral traits and non-canonical factors to cellular loss. Finally, we leverage sensitivity analyses to demonstrate how variation in life history traits across distinct oceanic contexts, including variation in viral adsorption and grazer clearance rates, can transform the quantitative and even qualitative importance of top-down controls in shaping Prochlorococcus population dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The structural basis for 2′−5′/3′−5′-cGAMP synthesis by cGAS

Abstract cGAS activates innate immune responses against cytosolic double-stranded DNA. Here, by determining crystal structures of cGAS at various reaction stages, we report a unifying catalytic mechanism. apo-cGAS assumes an array of inactive conformations and binds NTPs nonproductively. Dimerization-coupled double-stranded DNA-binding then affixes the active site into a rigid lock for productive metal•substrate binding. A web-like network of protein•NTP, intra-NTP, and inter-NTP interactions ensures the stepwise synthesis of 2′−5′/3′−5′-linked cGAMP while discriminating against noncognate NTPs and off-pathway intermediates. One divalent metal is sufficient for productive substrate binding, and capturing the second divalent metal is tightly coupled to nucleotide and linkage specificities, a process which manganese is preferred over magnesium by 100-fold. Additionally, we elucidate how mouse cGAS achieves more stringent NTP and linkage specificities than human cGAS. Together, our results reveal that an adaptable, yet precise lock-and-key-like mechanism underpins cGAS catalysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data-driven organic solubility prediction at the limit of aleatoric uncertainty

Abstract Small molecule solubility is a critically important property which affects the efficiency, environmental impact, and phase behavior of synthetic processes. Experimental determination of solubility is a time- and resource-intensive process and existing methods for in silico estimation of solubility are limited by their generality, speed, and accuracy. This work presents two models derived from the FASTPROP and CHEMPROP architectures and trained on BigSolDB which are capable of predicting solubility at arbitrary temperatures for a wide range of small molecules in organic solvent. Both extrapolate to unseen solutes 2–3 times more accurately than the current state-of-the-art model and we demonstrate that they are approaching the aleatoric limit (0.5–1$$\log S$$ log S ) of available test data, suggesting that further improvements in prediction accuracy require more accurate datasets. The FASTPROP-derived model (called FASTSOLV) and the CHEMPROP-based model are open source, freely accessible via a Python package and web interface, highly reproducible, and up to 2 orders of magnitude faster than current alternatives.

Science & Technology - Other Topics↗
DOE OSTI2026

Revealing multiscale competing processes in the solid-state synthesis of single-crystalline layered oxide positive electrodes

Solid-state synthesis involves a web of coupled chemical reactions and physical changes that unfold across multiple scales. Efforts to fine-tune its parameters have historically followed heuristic, trial-driven workflows that demand significant time and resources. In this study, we aimed to open this black box by employing multiscale in situ synchrotron imaging and diffraction. Using LiNi 0.5 Mn 0.3 Co 0.2 O 2 battery positive electrode material as a model system and Ba-based sintering aids, we reveal dopant segregation, intergranular mass transport, and porosity evolution as key drivers of single-crystalline particle formation. Notably, we uncovered a dynamic competition between particle-level grain coalescence and atomic-scale cation disordering, both of which are thermally activated yet have opposing impacts on battery performance. These findings highlight the coupled, multiscale nature of structure development and offer a mechanistic basis for optimizing the solid-state synthesis process. This framework provides a path toward more controlled, efficient, and scalable production of high-performance battery positive electrode materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure

Abstract Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, wetland soil may be exposed to oxygen (O 2 ) during droughts, or to sulfate (SO 4 2- ) as a result of sea level rise. How these stressors – separately and together – impact microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, and stoichiometric modeling to characterize the impact of elevated SO 4 2- and O 2 levels on microbial methane (CH 4 ) and carbon dioxide (CO 2 ) emissions. The results uncovered the adaptive responses of this community to changes in SO 4 2- and O 2 availability and identified altered microbial guilds and metabolic processes driving CH 4 and CO 2 emissions. Elevated SO 4 2- reduced CH 4 emissions, with hydrogenotrophic methanogenesis more suppressed than acetoclastic. Elevated O 2 shifted the greenhouse gas emissions from CH 4 to CO 2 . The metabolic effects of combined SO 4 2- and O 2 exposures on CH 4 and CO 2 emissions were similar to those of O 2 exposure alone. The reduction in CH 4 emission by increased SO 4 2- and O 2 was much greater than the concomitant increase in CO 2 emission. Thus, greater SO 4 2- and O 2 exposure in wetlands is expected to reduce the aggregate warming effect of CH 4 and CO 2 . Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism that converts lactate and SO 4 2- to produce acetate, H 2 S, and CO 2 when SO 4 2- is elevated under oxic conditions. This study provides greater quantitative resolution of key metabolic processes necessary for the prediction of CH 4 and CO 2 emissions from wetlands under future climate scenarios.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Visualizing temperature-dependent phase stability in high entropy alloys

High entropy alloys (HEAs) contain near equimolar amounts of five or more elements and are a compelling space for materials design. In the design of HEAs, great emphasis is placed on identifying thermodynamic conditions for single-phase and multi-phase stability regions, but this process is hindered by the difficulty of navigating stability relationships in high-component spaces. Traditional phase diagrams use barycentric coordinates to represent composition axes, which require ( N – 1) spatial dimensions to represent an N -component system, meaning that HEA systems with N > 4 components cannot be readily visualized. Here, we propose forgoing barycentric composition axes in favor of two energy axes: a formation-energy axis and a ‘reaction energy’ axis. These Inverse Hull Webs offer an information-dense 2D representation that successfully captures complex phase stability relationships in N ≥ 5 component systems. We use our proposed diagrams to visualize the transition of HEA solid-solutions from high-temperature stability to metastability upon quenching, and identify important thermodynamic features that are correlated with the persistence or decomposition of metastable HEAs.

Chemistry↗
DOE OSTI2022

High-throughput predictions of metal–organic framework electronic properties: theoretical challenges, graph neural networks, and data exploration

Abstract With the goal of accelerating the design and discovery of metal–organic frameworks (MOFs) for electronic, optoelectronic, and energy storage applications, we present a dataset of predicted electronic structure properties for thousands of MOFs carried out using multiple density functional approximations. Compared to more accurate hybrid functionals, we find that the widely used PBE generalized gradient approximation (GGA) functional severely underpredicts MOF band gaps in a largely systematic manner for semi-conductors and insulators without magnetic character. However, an even larger and less predictable disparity in the band gap prediction is present for MOFs with open-shell 3 d transition metal cations. With regards to partial atomic charges, we find that different density functional approximations predict similar charges overall, although hybrid functionals tend to shift electron density away from the metal centers and onto the ligand environments compared to the GGA point of reference. Much more significant differences in partial atomic charges are observed when comparing different charge partitioning schemes. We conclude by using the dataset of computed MOF properties to train machine-learning models that can rapidly predict MOF band gaps for all four density functional approximations considered in this work, paving the way for future high-throughput screening studies. To encourage exploration and reuse of the theoretical calculations presented in this work, the curated data is made publicly available via an interactive and user-friendly web application on the Materials Project.

36 MATERIALS SCIENCE↗