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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Perpendicular crossing chains enable high mobility in a noncrystalline conjugated polymer

The nature of interchain π-system contacts, and their relationship to hole transport, are elucidated for the high-mobility, noncrystalline conjugated polymer C16-IDTBT by the application of scanning tunneling microscopy, molecular dynamics, and quantum chemical calculations. The microstructure is shown to favor an unusual packing motif in which paired chains cross-over one another at near-perpendicular angles. By linking to mesoscale microstructural features, revealed by coarse-grained molecular dynamics and previous studies, and performing simulations of charge transport, it is demonstrated that the high mobility of C16-IDTBT can be explained by the promotion of a highly interconnected transport network, stemming from the adoption of perpendicular contacts at the nanoscale, in combination with fast intrachain transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system 1 . Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis -element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Discovery of Ternary Antimonides A–Al–Sb (A = Rb or Cs) with Desired Structural Motifs Guided by Machine Learning

Specific structural motifs in inorganic solids are often related to their targeted physical properties. For many classes of solids, such as Zintl phases and polar intermetallics, the crystal structures are diverse and not easy to predict. Various antimonides that are potential thermoelectric materials were proposed to be synthesizable on the basis of their estimated formation energies. Their structures were broadly classified as clathrate, channel, layered, or network through a machine learning model trained on existing ternary phases and features based on elemental properties using the sure independence screening and sparsifying operator algorithm. Through experimental validation, three new ternary antimonides were synthesized and confirmed to form layered structures: tetragonal RbAlSb 2 and CsAlSb 2 , which are isopointal but not isotypic to LiBSi 2 ; and monoclinic Rb 2 Al 2 Sb 3 , which adopts the Na 2 Al 2 Sb 3 -type structure. Finally, reinvestigation of the related compound Cs 2 In 2 Sb 3 revealed a low thermal conductivity and p-type semiconducting behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Microhydration of the metastable N -Protomer of 4-Aminobenzoic acid by condensation at 80 K: H/D exchange without conversion to the more stable O- protomer

4-Aminobenzoic acid (4ABA) is a model scaffold for studying solvent-mediated proton transfer. Although protonation at the carboxylic group (O-protomer) is energetically favored in the gas phase, the N-protomer, where the proton remains on the amino group, can be kinetically trapped by electrospray ionization of 4ABA in an aprotic solvent such as acetonitrile. Here we report the formation of the hydrated deuterium isotopologues of the N-protomers, RND 3 + ·(H 2 O) n=1-3 , (R=C 6 H 4 COOD), which are generated by condensing water molecules onto the bare N-protomers in a liquid nitrogen cooled, radiofrequency octopole ion trap at 80 K. The product clusters are then transferred to a 20 K cryogenic ion trap where they are tagged with weakly bound D 2 molecules. The structures of these clusters are determined by analysis of their vibrational patterns obtained by resonant IR photodissociation. The resulting patterns confirm that the metastable N-protomer configuration remains intact even when warmed by sequential condensation of water molecules. Attachment of H 2 O molecules onto the RND 3 + head group also affords the opportunity to explore the possibility of H/D exchange between the acid scaffold and the proximal water network. The spectroscopic results establish that although the RND 3 + ·(H 2 O) n=1,2 clusters are formed without H/D exchange, the n = 3 cluster exhibits about 10% H/D exchange as evidenced by the appearance of the telltale HOD bands. Furthermore, the site of exchange on the acid is determined to be the acidic OH by the emergence of the OH stretching fundamental in the -COOH motif.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii

Abstract Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Kinetically versus thermodynamically controlled factors governing elementary pathways of GaP(111) surface oxidation

GaP and related III-V semiconductors have attracted interest as high-efficiency photoelectrochemical electrodes for solar water splitting. However, their efficacy is linked to the presence, identity, and integrity of native surface oxides, which are structurally and chemically complex and evolve during operation. Using ambient pressure X-ray photoelectron spectroscopy (APXPS) coupled with ab initio simulations, we track key chemical motifs expressed during evolution of GaP(111) surface oxides, their associated reaction kinetics, and their correlations with electronic properties. We identify two distinct thermal regimes corresponding to kinetically and thermodynamically controlled oxidation. Below 600 K, exposure to O2 generates kinetically facile Ga-O-Ga configurations, whereas higher temperatures cause activated oxygen to insert into Ga–P bonds as part of a thermodynamically driven transformation into a complex, heterogeneous 3D network of surface POx (1≤x ≤ 4) groups and Ga2O3 species, the latter of which eventually dominates upon depletion of surface phosphorus. Here our study highlights the critical competition between kinetic and thermodynamic factors during GaP oxidation, yielding insights for fabricating stable III-P-based photoelectrodes with precisely engineered surface properties.

08 HYDROGEN↗
DOE OSTI2025

Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus

Development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed genome-scale studies of transcription factor (TF)-binding sites with high reproducibility. Here, we apply this technique to the human opportunistic pathogen Rhizopus microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi. We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, we use the generated data to identify TFs involved in biologically relevant processes such as zinc metabolism and light response. Our work enhances our understanding of regulatory mechanisms in R. microsporus and provides broader insights into gene regulation across the fungal kingdom.

Lax, Carlos [Universidad de Murcia (Spain)] (ORCID↗
NASA NTRS2004

Structural Basis for the Catalytic Activity of Human SER/THR Protein Phosphatase-5

Serinekhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth. Here we report the 1.6 Angstrom resolution crystal structure of PP5 catalytic domain with metal and phosphate ions in the active site. The structure reveals a mechanism for PPS-mediated catalysis that requires the precise positioning of two metal ions within a conserved Asp(sup 271)-M(sub 1),-M(sub 2)-His(sup 427)-W(sup 2)-His(sup 304)-Asp(sup 274) catalytic motif, and provides a structural basis for the exceptional catalytic proficiency of protein phosphatases placing them among the most powerful catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of PP5 should aid development of specific inhibitors.

Swingle, M. R.↗
DOE OSTI2020

Unexpected crystalline homogeneity from the disordered bond network in La(Cr 0.2 Mn 0.2 Fe 0.2 Co 0.2 Ni 0.2 )O 3 films

Designing and understanding functional electronic and magnetic properties in perovskite oxides requires controlling and tuning the underlying crystal lattice. In this work, we report the structure, including oxygen and cation positions, of a single-crystal, entropy stabilized perovskite oxide film of La(Cr 0.2 Mn 0.2 Fe 0.2 Co 0.2 Ni 0.2 )O 3 grown on SrTiO3 (001). The parent materials range from orthorhombic (LaCrO 3 , LaMnO 3 , and LaFeO 3 ) to rhombohedral (LaCoO 3 and LaNiO 3 ), and first principles calculations indicate that these structural motifs are nearly degenerate in energy and should be highly distorted site to site. Despite this extraordinary local configurational disorder on the B-site sublattice, we find a structure with unexpected macroscopic crystalline homogeneity with a clear orthorhombic unit cell, whose orientation is demonstrated to be controlled by the strain and crystal structure of the substrate for films grown on (La 0.3 Sr 0.7 )(Al 0.65 Ta 0.35 )O 3 and NdGaO 3 (110). Furthermore, quantification of the atom positions within the unit cell reveals that the orthorhombic distortions are small, close to LaCrO 3, which may be driven by a combination of disorder averaging and the average ionic radii. This is a step toward understanding the rules for designing crystal motifs and tuning functional properties through controlled configurational complexity.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquids close to Earth's liquid core conditions

Using an artificial neural-network machine learning interatomic potential, we have performed molecular dynamics simulations to study the structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid close to the Earth's liquid core conditions. Here, the simulation results reveal that the short-range structural order (SRO) in the $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid is very strong. About 80% of the atoms are arranged in crystallinelike SRO motifs. In particular, ~ $70$% of Fe-centered clusters can be classified as either hexagonal-close-packed-like or icosahedrallike SRO motifs. The SRO clusters centered on Fe, Si, or O atoms are strongly intermixed and homogenously distributed throughout the liquid. The atomic structure of the liquid and the fractions of dominant SRO clusters are not sensitive to pressure/temperature used in the simulations except that the SRO of the O-centered clusters is enhanced close to inner core pressures. The O-diffusion coefficient is about two to three times larger than the Fe and Si ions and increases more rapidly in the deeper core regions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2004

Structural Basis for the Catalytic Activity of Human Serine/Threonine Protein Phosphatase-5

Serinehhreonine protein phosphatase-5 (PP5) affects many signaling networks that regulate cell growth and cellular responses to stress. Here we report the crystal structure of the PP5 catalytic domain (PP5c) at a resolution of 1.6 A. From this structure we resolved the mechanism for PP5-mediated hydrolysis of phosphoprotein substrates, which requires the precise positioning of two metal ions within a con served Aspn-271-M(sub 1):M(sub 2)-W(sup 1)-His-427-His-304-Asp-274 catalytic motif. The structure of PPSc provides a structural basis for explaining the exceptional catalytic proficiency of protein phosphatases, which are among the most powerful known catalysts. Resolution of the entire C-terminus revealed a novel subdomain, and the structure of the PP5c should also aid development of type-specific inhibitors.

Swingle, M. R.↗
DOE OSTI2023

Interpretable design of Ir-free trimetallic electrocatalysts for ammonia oxidation with graph neural networks

The electrochemical ammonia oxidation to dinitrogen as a means for energy and environmental applications is a key technology toward the realization of a sustainable nitrogen cycle. The state-of-the-art metal catalysts including Pt and its bimetallics with Ir show promising activity, albeit suffering from high overpotentials for appreciable current densities and the soaring price of precious metals. Herein, the immense design space of ternary Pt alloy nanostructures is explored by graph neural networks trained on ab initio data for concurrently predicting site reactivity, surface stability, and catalyst synthesizability descriptors. Among a few Ir-free candidates that emerge from the active learning workflow, Pt 3 Ru-M (M: Fe, Co, or Ni) alloys were successfully synthesized and experimentally verified to be more active toward ammonia oxidation than Pt, Pt 3 Ir, and Pt 3 Ru. More importantly, feature attribution analyses using the machine-learned representation of site motifs provide fundamental insights into chemical bonding at metal surfaces and shed light on design strategies for high-performance catalytic systems beyond the d-band center metric of binding sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer

Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number. The natural lanthanide-binding protein lanmodulin (LanM) is a sustainable alternative to conventional solvent-extraction-based separation. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM’s quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM’s greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Graph characterization of higher-order structure in atmospheric chemical reaction mechanisms

Atmospheric chemical reactions play an important role in air quality and climate change. While the structure and dynamics of individual chemical reactions are fairly well understood, the emergent properties of the entire atmospheric chemical system, which can involve many different species that participate in many different reactions, are not well described. In this work, we leverage graph-theoretic techniques to characterize patterns of interaction (“motifs”) in three different representations of gas-phase atmospheric chemistry, termed “chemical mechanisms.” These widely used mechanisms, the master chemical mechanism, the GEOS-Chem mechanism, and the Super-Fast mechanism, vary dramatically in scale and application, but they all generally aim to simulate the abundance and variability of chemical species in the atmosphere. This motif analysis quantifies the fundamental patterns of interaction within the mechanisms, which are directly related to their construction. For example, the gas-phase chemistry in the very small Super-Fast mechanism is entirely composed of bimolecular reactions, and its motif distribution matches that of an individual bimolecular reaction well. The larger and more complex mechanisms show emergent motif distributions that differ strongly from any specific reaction type, consistent with their complexity. The proposed motif analysis demonstrates that while these mechanisms all have a similar design goal, their higher-order structure of interactions differs strongly and thus provides a novel set of tools for exploring differences across chemical mechanisms.

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

Tunable and Robust Optical and Structural Properties of a Cooperative Squaraine-Dye Aggregate-DNA DX-DAE Tile System

Molecular excitons, which are excitations delocalized over multiple dyes in a wavelike manner, are of interest for a wide range of applications, including quantum information science. Numerous studies have templated a variety of synthetic dyes via a DNA scaffold to induce dye aggregation to create molecular excitons upon photoexcitation. Dye aggregate optical properties are critically dependent on relative dye geometry and local environment; therefore, an understanding of dye-dye and DNA-dye interactions is critical for advancing toward more complex DNA-dye systems. The extensively studied DNA Holliday junction (HJ) and less-studied double-crossover (DX) tile motif are fundamental test beds for designing complex and ultimately modular DNA-dye architectures. Here, we report the first study of single-linked squaraine dye aggregation and exciton delocalization on a larger and more stable (compared with the HJ) DX tile motif. We first highlight a few DNA-dye constructs that support single dyes and aggregates with distinct optical properties that are both tunable—through sample design, buffer conditions, and heat treatment—and robust to environment changes, including transfer to solid phase. Next, we assess several experimental and design considerations that demonstrate directed dye-driven assembly of a novel double-tile DNA configuration. Our results demonstrate that single-linked squaraine dyes templated to DX tiles provide a viable research path to design and evaluate dye aggregate networks that support exciton delocalization. We include herein the first report of exciton delocalization in the solid phase in a DNA-dye construct. Additionally, our findings indicate that dye aggregation impacts the assembly of the DNA-dye construct, and, in some cases, thereby cooperates with the DNA to determine a final robust system configuration. Finally, we show that a controlled annealing schedule can be employed to promote the homogeneous assembly of DNA-dye constructs. The findings in this study contribute to the understanding of DNA-dye systems and the relevant factors involved in their directed assembly to achieve specific constructs with desirable properties.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Proxy Applications for Converged Workloads: DMC LDRD Initiative

Modern scientific applications are complicated and require coordination of several components. Proxy application driven software-hardware co-design plays a vital role in driving innovation among the developments of applications, software infrastructure and hardware architecture. Proxy applications are self-contained and simplified codes that are intended to model the performance-critical computations within applications. Applications executing on modern High Performance Computing (HPC) systems are susceptible to network congestion, insufficient memory bandwidth within and across compute nodes, and inadvertent loss of performance due to bugs and unoptimized programming models. Modern numerical simulations and machine learning models play a critical role in studying physical phenomenon under myriad uncertainties. Such applications often exhibit irregular computation and memory accesses at specific regions of the application code, which can contribute to various performance bottlenecks at scale. To mitigate such issues and prepare the next generation hardware for a variety of computation and data movement contingencies, a well-known practice is to consider "proxy" applications as representative motifs for various classes of scientific applications. While there is disagreement in the HPC community on the mechanisms of construction of the proxy applications, there is a strong consensus on their positive impact in co-design. Proxy Applications for Converged Workloads (PACER) is about facilitating software-hardware co-design through proxy applications with the goal of improving the performance of converged science workflows on heterogeneous systems.

97 MATHEMATICS AND COMPUTING↗