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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Strangers in a foreign land: ‘Yeastizing’ plant enzymes

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

EMI Mitigation of a Ćuk-Based Power-Electronic System Using Switching-Sequence-Based Control

Switching-sequence-based control (SBC) laws when designed based on topological switching behavior can have positive effects on slow- and fast-scale dynamics of a power-electronic system (PES). The slow-scale control can encompass fast PES state regulation and tracking, based on predefined objective, while fastscale control can address differential-mode (DM) and commonmode (CM) spectral-peak energy associated with PES switching operation. Such control laws may offer enhanced programmability to conventional PES design where bulky electromagnetic interference (EMI) filters have been traditionally used to reduce EMI of switching power converters to meet EMI regulatory standards. An EMI filter is always a less programmable solution since it is usually designed for the worst-case EMI mitigation and usually overkill for a PES operating under reduced load condition. The control scheme outlined in this article offers EMI mitigation across wide operating regions without compromising PES regulation. Moreover, it does so by use of switching sequences that guarantee the reachability of the PES dynamics using an advanced Lyapunov-function-based approach. SBC is a powerful tool to generate control actions for a PES based on multivariate PES state constraints. Hence, contemporary EMI regulatory standards are used as constraints in the SBC formulation to operate the PES under wide operating regime while autonomously mitigating the EMI levels. The work may be of paramount importance for operating the ultra-fast-transition recent wide-bandgap semiconductor devices like GaN–FET and SiC MOSFET under higher power with increasing switching frequencies, which is usually desirable for increased power density and reduced switching losses. Here, a hardware Cuk–PES operated ´ with GaN–FETs is fabricated and is used for case illustration. It is shown by experimental results how SBC mitigate DM and CM EMI noise of the PES while maintaining regulation even for the higher order nonminimum phase PES, while reducing sensor requirements using state observer derived from the switching model of the PES.

42 ENGINEERING↗
DOE OSTI2026

Construct design for precise DNA insertion in plants

Precise insertion of DNA sequences at targeted locations in plant genomes is pivotal for synthetic biology, genetics, and crop improvement. Construct design plays a critical role in achieving precise insertions, yet practical guidance remains limited. This review provides an in-depth overview of construct design principles and targeted DNA insertion (knock-in) strategies in plants. We assess the strengths, limitations, and construct requirements of current knock-in methods for specific applications, including short, large, and multifragment insertions. Additionally, we explore the potential of adopting advanced nonplant technologies to enhance knock-in efficiency and precision in plants. This review provides a valuable resource for facilitating the effective application of knock-in technologies to genetically improve crops with minimal off-target effects.

DNA construct↗
DOE OSTI2022

FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID ( http://isolate.fusariumdb.org/blast.php ) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ~680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

Plant Sciences↗
DOE OSTI2022

Evaluating the Impact of gRNA SNPs in CasRx Activity for Reducing Viral RNA in HCoV-OC43

Viruses within a given family often share common essential genes that are highly conserved due to their critical role for the virus’s replication and survival. In this work, we developed a proof-of-concept for a pan-coronavirus CRISPR effector system by designing CRISPR targets that are cross-reactive among essential genes of different human coronaviruses (HCoV). We designed CRISPR targets for both the RNA-dependent RNA polymerase (RdRp) gene as well as the nucleocapsid (N) gene in coronaviruses. Using sequencing alignment, we determined the most highly conserved regions of these genes to design guide RNA (gRNA) sequences. In regions that were not completely homologous among HCoV species, we introduced mismatches into the gRNA sequence and tested the efficacy of CasRx, a Cas13d type CRISPR effector, using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in HCoV-OC43. We evaluated the effect that mismatches in gRNA sequences has on the cleavage activity of CasRx and found that this CRISPR effector can tolerate up to three mismatches while still maintaining its nuclease activity in HCoV-OC43 viral RNA. This work highlights the need to evaluate off-target effects of CasRx with gRNAs containing up to three mismatches in order to design safe and effective CRISPR experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

DNA origami protection and molecular interfacing through engineered sequence-defined peptoids

DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Crossing the Streams – Sampler and the TemplateEngine [Slides]

This presentation discusses Sampler, which is a versatile UQ and parametric study tool that can be applied to any SCALE Sequence. Sampler can perturb any quantity in any SCALE input. Recent work at ORNL has developed new types of covariance data that allow Sampler UQ to be applied to nearly all SCALE applications, including reactor depletion, UNF fuel characterization, source term analysis, and decay heat calculation. In SCALE 6.2 releases, CE data in transport cannot be perturbed. Sampler was originally designed for stochastic sampling with any sequence within SCALE and Parametric capability added in SCALE 6.2.2. Sampler can be used for uncertainty quantification, including sample data in static or depletion calculations and sample inputs for uncertainties in compositions and dimensions. The SCALE TemplateEngine allows for expanding templates to full inputs and the combination provides a powerful UQ tool.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Description and Use of SCALE Sampler Parametric Capability for Engineering Analysis and Optimization

The Sampler sequence was introduced into the SCALE nuclear modeling and simulation suite in SCALE 6.2 to perform uncertainty quantification via random sampling of nuclear data, material number densities, and dimensions. Sampler was expanded with the introduction of a parametric capability in SCALE 6.2.2. This paper discusses input for the Sampler parametric sequence and presents two case studies of analyses performed using the sequence. These case studies include preconceptual design of a package for transporting high assay low-enriched uranium (HALEU) oxide and scoping calculations to support subcritical limit development for a future update of the ANSI/ANS-8.1 (ANS-8.1) standard. The parametric capability within Sampler provides many benefits to analysts. For instance, parametric sweeps are frequently used to identify optimum parameter values as part of safety analysis or system design, but such sweeps can require substantial engineering time or may rely on custom-written scripts or scripts such as Write One, Run Many (or WORM) developed outside of any software quality assurance program. With the parametric capabilities in Sampler, however, a large number of inputs can be generated automatically without recourse to scripting by individual analysts. The parametric capability can also be used in lieu of the CSAS5S search sequence to identify optimum parameters more simply with straightforward inputs and outputs. Sampler can also be used to calculate input parameters from engineering specifications. For example, diameters can be converted to radii, or masses can be used to calculate number densities. Overall, the Sampler parametric capability provides a robust feature within SCALE, eliminating the need for user-developed scripting.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework

Motivation Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role in immune-mediated selection and can leave strong signatures in virus sequences; however, existing sequence-based within-host virus modeling frameworks do not explicitly include a human leukocyte antigen (HLA)-aware CTL response. Results We extended our previously published within-host sequence evolution simulator, wavess, to include an explicit CTL response, and share a method for identifying HLA-specific CTL epitopes given a founder virus sequence. We also updated the model to permit a variable recombination rate, which allows for modeling non-adjacent genes, segmented genomes, and recombination hotspots. These extensions to wavess allow for more accurate simulation of viruses and virus genes, particularly in regions of the genome where the immune response is dominated by CTLs (rather than antibodies). It also provides the foundation for investigations of how these newly-added biological mechanisms influence within-host evolution. Availability and implementation The core of wavess is written in Python 3, with helper functions written in R. It is available at https://github.com/MolEvolEpid/wavess.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Study of the Protection Improvements for a Weak Grid Area With High Inverter-Based Resources (IBRs)

This project designs enhanced protection scheme for the real-world weak grid area with a high penetration of IBRs. As the existing protection schemes are originally designed for traditional synchronous machines, we first evaluate if the protection scheme will continue to operate reliably in systems with high levels of IBRs. Hardware relays are tested using a controller-hardware-in-the-loop setup. PSCAD electromagnetic transient simulation with IBR original equipment manufacturer black-box models is used to perform fault studies and generate COMTRADE data, which are replayed by a real-time digital simulator (RTDS) to feed input to the hardware relays. Three scenarios are analyzed: normal operation, an N-1 contingency, and an IBR-only scenario. The evaluation results reveal the following: 1) the protection scheme remains reliable under normal conditions and N-1 contingencies and 2) in IBR-only scenarios, differential protection (87L) continues to operate reliably, whereas local protection elements, such as distance and directional elements, fail because of the lack of regulated negative sequence current contributed by IBRs. Enhanced protection is designed to address the challenge of lack of negative sequence current from IBRs, including increased restraining factors a2 and k2 to block 32Q or using V instead QV ORDER for ground faults, enhanced mho distance element with voltage and phase angle supervision for L-L faults. The efficacy of enhanced protection logic is validated and proven to work reliably. Additionally, IEEE Std. 2800-2022 negative sequence current compliant GFL and GFM IBRs from another vendor are tested and proven to work reliably without need for enhanced logic. Therefore, this work provides valuable decision-making for utilities facing protection system challenges due to IBRs, either designing enhanced protection scheme or requesting their IBRs being IEEE Std. 2800-2022 compliant to produce regulated negative sequence current for protection relay to make correct decision.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Bottom-Up Simulation, Reconstruction, and Quantification of Macromolecule Sequences from Experimental Polymerizations

Motivated by the canonical sequence–structure–function paradigm, tools to characterize chemical patterning in natural biomacromolecules, from proteins to nucleic acids, have grown exponentially in recent years. However, analogous strategies for synthetic macromolecules remain in nascent stages, complicated by sequence polydispersity and analytical limitations. To address this, we have developed a comprehensive and open-source Python package, PRISM (polymer rate insights and sequence modeling), an end-to-end workflow that provides a path from experimental kinetics measurements to quantitative and qualitative metrics for describing chemical patterning in stochastic polymers. First, a numerical integration strategy was constructed to simulate and fit experimental data from reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics, enabling the facile estimation of relevant reactivity ratios. These ratios were then used in a mechanism-specific stochastic kinetic simulation strategy to simulate sequence ensembles corresponding to model systems spanning experimental copolymers, classes of statistical polymers (e.g., alternating, block, and gradient), and multiblock copolymers. Lastly, inspired by sequence homology metrics from bioinformatics, we introduce visualization strategies and quantitative metrics to facilitate comparisons of different sequence ensembles. As the sequence–structure–function paradigm becomes increasingly central in de novo design of synthetic macromolecules, this toolkit provides a first step toward accurate and representative sequence description and featurization.

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

Regulatory Treatment of Low Frequency External Events under a Risk-Informed Performance-Based Licensing Pathway

Significant efforts are underway to develop and implement a risk-informed performance-based licensing framework for advanced reactors built on the establishment of an affirmative safety case. Such approaches offer the benefits of increased flexibility regarding key design and licensing decisions based on a detailed assessment and understanding of plant risk. These methods include the comprehensive analysis of scenarios that have historically been addressed through conservative and deterministic licensing analysis approaches, such as the evaluation of event sequences at frequencies of occurrence beyond the design basis. While the detailed analysis of low frequency events provides insights that can help justify alternative treatments to past conservatism, the findings are dependent on the quality and confidence associated with the analyses. The assessment of external hazards presents a unique challenge, as their potential frequency of occurrence, especially of large magnitude events, is inherently uncertain given the long return periods in question. The current project seeks to further explore the regulatory treatment of low frequency external events as part of a risk-informed performance-based framework. The goals are to identify the benefits and challenges of such approaches for advanced reactor vendors and to aid in the development of consistent and appropriate methodologies. As part of this effort, the current report summarizes initial project findings, with a focus on the evaluation of the seismic hazard. This includes an exploration of the implementation of a risk-informed performance-based approach through an example analysis. Based on the identified challenges associated with the probabilistic treatment of low frequency event sequences, additional performance-based methods were explored as complementary tools for demonstrating regulatory compliance. The report highlights key challenges and opportunities associated with the methods and outlines recommendations and future activities to assist with their implementation.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

A molecular view of peptoid-induced acceleration of calcite growth

The extensive deposits of calcium carbonate (CaCO 3 ) generated by marine organisms constitute the largest and oldest carbon dioxide (CO 2 ) reservoir. These organisms utilize macromolecules like peptides and proteins to facilitate the nucleation and growth of carbonate minerals, serving as an effective method for CO 2 sequestration. However, the precise mechanisms behind this process remain elusive. In this study, we report the use of sequence-defined peptoids, a class of peptidomimetics, to achieve the accelerated calcite step growth kinetics with the molecular level mechanistic understanding. By designing peptoids with hydrophilic and hydrophobic blocks, we systematically investigated the acceleration in step growth rate of calcite crystals using in situ atomic force microscopy (AFM), varying peptoid sequences and concentrations, CaCO 3 supersaturations, and the ratio of Ca 2+ / HCO 3 − . Mechanistic studies using NMR, three-dimensional fast force mapping (3D FFM), and isothermal titration calorimetry (ITC) were conducted to reveal the interactions of peptoids with Ca 2+ and HCO 3 − ions in solution, as well as the effect of peptoids on solvation and energetics of calcite crystal surface. Our results indicate the multiple roles of peptoid in facilitating HCO 3 − deprotonation, Ca 2+ desolvation, and the disruption of interfacial hydration layers of the calcite surface, which collectively contribute to a peptoid-induced acceleration of calcite growth. These findings provide guidelines for future design of sequence-specific biomimetic polymers as crystallization promoters, offering potential applications in environmental remediation (such as CO 2 sequestration), biomedical engineering, and energy storage where fast crystallization is preferred.

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

Programmable Matter: The Nanoparticle Atom and DNA Bond

Colloidal crystal engineering with DNA has led to significant advances in bottom-up materials synthesis and a new way of thinking about fundamental concepts in chemistry. Here, programmable atom equivalents (PAEs), comprised of nanoparticles (the “atoms”) functionalized with DNA (the “bonding elements”), are assembled through DNA hybridization into crystalline lattices. Unlike atomic systems, the “atom” (e.g., the nanoparticle shape, size, and composition) and the “bond” (e.g., the DNA length and sequence) can be tuned independently, yielding designer materials with unique catalytic, optical, and biological properties. Here in this review, nearly three decades of work that have contributed to the evolution of this class of programmable matter is chronicled, starting from the earliest examples based on gold-core PAEs, and then delineating how advances in synthetic capabilities, DNA design, and fundamental understanding of PAE-PAE interactions have led to new classes of functional materials that, in several cases, have no natural equivalent.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Metals and methylotrophy: Via global gene expression studies

A number of minerals, such as copper, cobalt, and rare earth elements (REE), are essential modulators of microbial one-carbon metabolism. This chapter provides an overview of the gene expression study design and analysis protocols for uncovering REE-induced changes in methylotrophic bacteria. By interrogating relationships and differences in total gene expression induced by mineral micronutrients, a deeper understanding of gene regulation at a systems scale can be gained. With careful design and execution of RNA-sequencing experiments, thorough processing and assessment of read quality can be utilized to assess and adjust for possible biases. Here, by ensuring only quality data are utilized in downstream processes, differential gene expression, overrepresented analyses, and gene-set enrichment analyses provide reliable and reproducible representation of pathways and functions which are being affected by changes in environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗
DOE OSTI2023

ctrl-flow v0.0.1

ctrl-flow is a software that assists users in selecting a building control sequence from a library of control sequences that are implemented in the Modelica Buildings Library. The software allows selecting, configuring and editing the control sequences. It also allows exporting the sequence for use in building project design documents in Modelica-based simulations. The export will be in a json intermediate format, in the Modelica Language, in the Control Description Language and in English language format, such as in a Word document. The software functions as a web based application that includes a graphical user interface.

Wetter, Michael↗