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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A Chemoselective and Stereodivergent Platform of Heme‐Nitrene Transferases to Access Chiral Aryl‐β‐Amino Esters and An Investigation of the Sequence‐Activity Landscape

Engineered biocatalysts can utilize nitrene precursors to access enantioenriched amination products, yet they have not been applied to produce valuable, enantiomerically enriched noncanonical β-amino esters. Current approaches to synthesizing β-amino acids rely on pre-oxidized precursors and multistep synthetic approaches involving various protecting groups. We engineered a platform of heme enzymes for stereoselective C–H bond amination of readily available carboxylic ester derivatives to install primary amines. A directed evolution campaign coupled with sequencing of over 1000 variants enabled us to develop engineered variants that use either O-pivaloylhydroxylamine triflic acid (PONT) or hydroxylamine hydrochloride (H 2 NOH∙HCl) as aminating reagents. An analysis of the resulting sequence–activity dataset revealed additional improvements that could be made to the final variant, highlighting the utility of sequencing data to guide future steps in directed evolution campaigns. Furthermore, the evolved nitrene transferases expand the scope of accessible chiral β-amino acid building blocks for peptidomimetic applications and provide new starting points for the design and synthesis of enantioenriched β-amino acid motifs.

amino ester building blocks↗
DOE OSTI2021

Evaluation of sequence tracking methods for Compton cameras based on CdZnTe arrays

In this study, the performance of sequence tracking methods for multiple interaction events in specific CdZnTe Compton imagers was evaluated using Monte Carlo simulations. The Compton imager consisted of a 6 × 6 array of virtual Frisch-grid CZT crystals, where the dimensions of each crystal were 5 × 5 × 12 mm 3 . The sequence tracking methods for another Compton imager that consists of two identical CZT crystals arrays were also evaluated. When 662 keV radiation was incident on the detectors, the percentages of the correct sequences determined by the simple comparison and deterministic methods for two sequential interactions were identical (~80 %), while those evaluated using the minimum squared difference method (55-59 %) and Three Compton method (45-55 %) for three sequential interactions, differed from each other. The reconstructed images of a 662 keV point source detected using single and double arrays were evaluated based on their angular resolution and signal-to-noise ratio, and the results showed that the double arrays outperformed single arrays.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Three-dimensional paganica fault morphology obtained from hypocenter clustering (L'Aquila 2009 seismic sequence, Central Italy)

In seismic modelling, fault planes are normally assumed to be flat due to the lack of data which can constrain fault morphology. However, incorporating 3D fault morphology is important for modelling several phenomena, for example calculating mainshock induced stress changes. Here we utilize a data-analytical method to unveil the 3D rupture morphology of faults using unsupervised clustering techniques applied to earthquake hypocenters in seismic sequences. We apply this method to the 2009 L'Aquila seismic sequence which involved a M W 6.1 mainshock on April 6th. We use a dataset of about 50,000 relocated events, mostly microearthquakes, reaching magnitude of completeness equal to 0.7. Clustering distinguishes the earthquakes as occurring in three main clusters along with other minor fault segments. We then represent the morphology of the main Paganica fault system (responsible for the largest mainshock) using splines. This method shows promise as a step toward robustly and quickly obtaining 3D rupture morphologies where earthquake sequences have been monitored. The 3D model is presented interactively online, and the processing is presented in an interactive Jupyter Notebook (https://bit.ly/2MnCFdj).

58 GEOSCIENCES↗
DOE OSTI2020

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Initial Stage of Nanoscale Imaging in Positive Tone Extreme UV Photoresists: The Influence of the Polymer Sequence

Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.

Absorption↗
DOE OSTI2026

Polymorphism in Self-Assembly of Short Peptoid Sequences

Due to various applications enabled by diverse morphologies of self-assembled sequence-defined polymers, controlling the self-assembly of synthetic peptidomimetics into designed morphologies has emerged as a promising route for the development of bioinspired functional materials. Herein, we report morphological control over the assembly of a series of short peptoids, or poly-N-substituted glycines, that contain asymmetric hydrophobic domains. We demonstrate that the inherent flexibility of amphiphilic peptoid bilayers drives assembly polymorphism, resulting in the coexistence of nanosheets, twisted ribbons, and nanofibers three distinct morphologies. By tuning peptoid molecular interactions through variations in sequence design, solution pH, and temperature, we demonstrate precise control over the twisting and folding of peptoid bilayers, enabling the formation of well-defined nanosheets and nanohelices. Molecular dynamics simulations further unravel how the introduction of asymmetric hydrophobic domains enables the flexibility of peptoid bilayers and results in peptoid assembly polymorphism. By tuning peptoid molecular interactions through heating, we further demonstrate the transformation of nanosheets into nanohelices. We envision that our mechanistic investigation of peptoid assembly polymorphism provides a strong foundation for leveraging peptoid sequences and chemistries to achieve controlled molecular interactions, driving the creation of biomimetic materials with tailored morphologies and functionalities.

assembly polymorphism↗
DOE OSTI2025

Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing

Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. Mapping the genetics of gene expression in human microglia has identified several loci associated with disease-associated genetic variants in microglia-specific regulatory elements. However, identifying genetic effects on splicing is challenging because of the use of short sequencing reads. Here, we present the isoform-centric microglia genomic atlas (isoMiGA), which leverages long-read RNA sequencing to identify 35,879 novel microglia isoforms. We show that these isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ancestry meta-analysis of 555 human microglia short-read RNA sequencing samples from 391 donors, and found associations with genetic risk loci in Alzheimer’s and Parkinson’s disease. We nominate several loci that may act through complex changes in isoform and splice-site usage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

BMC Caller: a webtool to identify and analyze bacterial microcompartment types in sequence data

Bacterial microcompartments (BMCs) are protein-based organelles found across the bacterial tree of life. They consist of a shell, made of proteins that oligomerize into hexagonally and pentagonally shaped building blocks, that surrounds enzymes constituting a segment of a metabolic pathway. The proteins of the shell are unique to BMCs. They also provide selective permeability; this selectivity is dictated by the requirements of their cargo enzymes. We have recently surveyed the wealth of different BMC types and their occurrence in all available genome sequence data by analyzing and categorizing their components found in chromosomal loci using HMM (Hidden Markov Model) protein profiles. To make this a “do-it yourself” analysis for the public we have devised a webserver, BMC Caller (https://bmc-caller.prl.msu.edu), that compares user input sequences to our HMM profiles, creates a BMC locus visualization, and defines the functional type of BMC, if known. Shell proteins in the input sequence data are also classified according to our function-agnostic naming system and there are links to similar proteins in our database as well as an external link to a structure prediction website to easily generate structural models of the shell proteins, which facilitates understanding permeability properties of the shell. Additionally, the BMC Caller website contains a wealth of information on previously analyzed BMC loci with links to detailed data for each BMC protein and phylogenetic information on the BMC shell proteins. Our tools greatly facilitate BMC type identification to provide the user information about the associated organism’s metabolism and enable discovery of new BMC types by providing a reference database of all currently known examples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding

High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

16S rDNA↗
DOE OSTI2020

Bayesian Characterization of Main-sequence Binaries in the Old Open Cluster NGC 188

The binary fractions of open and globular clusters yield powerful constraints on their dynamical state and evolutionary history. We apply publicly available Bayesian analysis tools to a UBV RIJHK {sub S} photometric catalog of the open cluster NGC 188 to detect and characterize photometric binaries along the cluster main sequence. This technique has the advantage of self-consistently handling photometric errors, missing data in various bandpasses, and star-by-star prior constraints on cluster membership. Simulations are used to verify uncertainties and quantify selection biases in our analysis, illustrating that among binaries with mass ratios >0.5, we recover the binary fraction to better than 7% in the mean, with no significant dependence on binary fraction and a mild dependence on assumed mass-ratio distribution. Using our photometric catalog, we recover the majority (65% ± 11%) of spectroscopically identified main-sequence binaries, including eight of the nine with spectroscopically measured mass ratios. Accounting for incompleteness and systematics, we derive a mass-ratio distribution that rises toward lower mass ratios (within our q > 0.5 analysis domain). We observe a raw binary fraction for solar-type main-sequence stars with mass ratios q > 0.5 of 42% ± 4%, independent of the assumed mass-ratio distribution to within its uncertainties, consistent with literature values for old open clusters but significantly higher than the field solar-type binary fraction. We confirm that the binaries identified by our method are more concentrated than single stars, in agreement with previous studies, and we demonstrate that the binary nature of those candidates that remain unidentified spectroscopically is strongly supported by photometry from Gaia DR2.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Hierarchical Self‐Assembly of Multidimensional Functional Materials from Sequence‐Defined Peptoids

Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

Shao, Li↗
DOE OSTI2024

Hierarchical Self‐Assembly of Multidimensional Functional Materials from Sequence‐Defined Peptoids

Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

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

Submonomer synthesis of sequence defined peptoids with diverse side-chains.

Peptoids are a diverse family of sequence-defined oligomers of N-substituted glycine monomers, that can be readily accessed by the solid-phase submonomer synthesis method. Due to the versatility and efficiency of this chemistry, and the easy access to hundreds of potential monomers, there is an enormous potential sequence space that can be explored. This has enabled researchers from many different fields to custom-design peptoid sequences tailored to a wide variety of problems in biomedicine, nanoscience and polymer science. Here we provide detailed protocols for the synthesis of peptoids, using optimized protocols that can be performed by non-chemists. The submonomer method is fully compatible with Fmoc-peptide synthesis conditions, so the method is readily automated on existing automated peptide synthesizers using protocols provided here. Although the submonomer synthesis for peptoids is well established, there are special considerations required in order to access many of the most useful and desirable sidechains. Here we provide methods to include most of the amino-acid-like side chains, some of the most important non-natural monomer classes, as well as the creation of peptoid conjugates and peptide-peptoid hybrids.

Connolly, Michael D↗
DOE OSTI2020

Applicability of the Delplot method for the determination of catalytic reaction sequences: Hydrodeoxygenation of $\gamma$-valerolactone on Ni 2 P/MCM-41

Contact-time measurements based on sites are used to investigate the reaction sequence of the hydrodeoxygenation of γ-valerolactone (GVL) on Ni 2 P/MCM-41. Here the study is carried out at 300 °C and 0.5 MPa with site times of 0.29–6.1 s. A reaction network is proposed in which pentanoic acid and 2-methyltetrahydrofuran (2-MTHF) are formed in parallel initially and pentanal, butane and pentane are formed subsequently. A first-rank Delplot analysis (selectivity) gives a good fit, but higher-rank Delplots do not. The lack of applicability is explained by the magnitude of the rate constants, in which the rate constant for one of the later steps (the consumption of pentanal) is substantially larger than those for the preceding steps. For this reason, pentanal demonstrated the characteristics of a primary product and consequently affected the discrimination of higher rank products. A simulation of a model sequence with assumed rate constants confirms the reason why the Delplot method does not work for this reaction. Since the rate constants cannot be determined a priori to be of close magnitude, the Delplot method cannot be generally used to ascertain reaction sequences.

42 ENGINEERING↗
DOE OSTI2026

Hierarchical semi-Markov models with duration-aware dynamics for activity sequences

Residential electricity demand at granular scales is driven by what people do and for how long. Accurately forecasting this demand for applications like microgrid management and demand response therefore requires generative models for activities that can produce realistic daily activity sequences, capturing both the timing and duration of human behavior. This paper develops a generative model of human activity sequences using nationally representative time-use diaries at a 10-min resolution. We use this model to quantify which demographic factors are most critical for improving predictive performance. We propose a hierarchical semi-Markov framework that addresses two key modeling challenges. First, a time-inhomogeneous Markov router learns the patterns of “which activity comes next.” Second, a semi-Markov hazard component explicitly models activity durations, capturing “how long” activities realistically last. To ensure statistical stability when data are sparse, the model pools information across related demographic groups and time blocks. The entire framework is trained and evaluated using survey design weights to ensure our findings are representative of the U.S. population. On a held-out test set, we demonstrate that explicitly modeling durations with the hazard component provides a substantial and statistically significant improvement over purely Markovian models. Furthermore, our analysis reveals a clear hierarchy of demographic factors: Sex, Day-Type, and Household Size provide the largest predictive gains, while Region and Season, though important for energy calculations, contribute little to predicting the activity sequence itself. The result is an interpretable and robust generator of synthetic activity traces, providing a high-fidelity foundation for downstream energy systems modeling.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2023

Data-driven prediction of geometry- and toolpath sequence-dependent intra-layer process conditions variations in laser powder bed fusion

Geometrical features and toolpath sequence are two important factors that cause process condition variations, such as variations in the meltpool temperature or meltpool size, that might lead to undesired material properties in the laser powder bed fusion (LPBF) process. Due to the high dynamics and complex physics of the LPBF process, it is difficult to predict variations in process conditions with simulations alone. Advances in measurement technology and computational technologies open up new possibilities for smart manufacturing. In this paper, a data-driven method to predict intra-layer variations in the processing conditions that source from the toolpath sequence and part geometry is presented. The approach is demonstrated using two-color on-axis pyrometer measurements. Three demonstration cases are presented in which it is demonstrated (1) how the trained predictive model can be used as a filter to ease the interpretation of process variations and discover patterns related to toolpath and part geometry, and (2) how to generate predictions that can be used for feedforward control, i.e., for adjusting laser power or scanning speed along the toolpath using a meltpool temperature prediction model generated based on on-axis measurements. Results show that the developed prediction model is able to meaningfully predict process variations resulted from toolpath sequence and geometry. Predictions are aligned with the results from the related work of others and for the case of 180° laser path turnarounds in our high-speed X-ray imaging experiments. In conclusion, the potential issues related to the current maturity status of the process and measuring equipment that could in practice affect the performance of the proposed solutions are also discussed.

42 ENGINEERING↗
DOE OSTI2024

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

The ability to program chain conformation and structure through control over the monomer sequence of synthetic polymers has broad implications for next-generation material design. While related problems of protein-folding and de novo design have generated accurate predictions of 3D folded chain structures, generalization to synthetic polymers remains intractable due to the requirement of large structural databases and the intrinsically disordered nature of polymer building blocks. In this work, polypeptoids, a class of peptidomimetic synthetic polymers, are utilized to build a general workflow for the study of relationships between monomer sequence and dynamic 3D chain structure in solution. Furthermore, this work demonstrates how control over the monomer sequence can alter the conformational landscape of synthetic polymers to deviate dramatically from classical chain statistics. Specifically, the distribution of end-to-end distances, as measured by double electron-electron resonance spectroscopy in dilute solvent, is systematically skewed towards shorter distances with an increasing number of hydrophobes and further refined by hydrophobe arrangement in amphiphilic polypeptoid chains.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Generation of Tunable Stochastic Sequences Using the Insulator–Metal Transition

Probabilistic computing is a paradigm in which data are not represented by stable bits, but rather by the probability of a metastable bit to be in a particular state. The development of this technology has been hindered by the availability of hardware capable of generating stochastic and tunable sequences of “1s” and “0s”. The options are currently limited to complex CMOS circuitry and, recently, magnetic tunnel junctions. Here, we demonstrate that metal–insulator transitions can also be used for this purpose. We use an electrical pump/probe protocol and take advantage of the stochastic relaxation dynamics in VO 2 to induce random metallization events. A simple latch circuit converts the metallization sequence into a random stream of 1s and 0s. The resetting pulse in between probes decorrelates successive events, providing a true stochastic digital sequence.

97 MATHEMATICS AND COMPUTING↗