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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2001

Homology and the optimization of DNA sequence data

Three methods of nucleotide character analysis are discussed. Their implications for molecular sequence homology and phylogenetic analysis are compared. The criterion of inter-data set congruence, both character based and topological, are applied to two data sets to elucidate and potentially discriminate among these parsimony-based ideas. c2001 The Willi Hennig Society.

Non-NASA Center↗
NASA NTRS1994

The beetle Tribolium castaneum has a fushi tarazu homolog expressed in stripes during segmentation

The genetic control of embryonic organization is far better understood for the fruit fly Drosophila melanogaster than for any other metazoan. A gene hierarchy acts during oogenesis and embryogenesis to regulate the establishment of segmentation along the anterior-posterior axis, and homeotic selector genes define developmental commitments within each parasegmental unit delineated. One of the most intensively studied Drosophila segmentation genes is fushi tarazu (ftz), a pair-rule gene expressed in stripes that is important for the establishment of the parasegmental boundaries. Although ftz is flanked by homeotic selector genes conserved throughout the metazoa, there is no evidence that it was part of the ancestral homeotic complex, and it has been unclear when the gene arose and acquired a role in segmentation. We show here that the beetle Tribolium castaneum has a ftz homolog located in its Homeotic complex and expressed in a pair-rule fashion, albeit in a register differing from that of the fly gene. These and other observations demonstrate that a ftz gene preexisted the radiation of holometabolous insects and suggest that it has a role in beetle embryogenesis which differs somewhat from that described in flies.

NASA Discipline Developmental Biology↗
NASA NTRS1993

The Tribolium homeotic gene Abdominal is homologous to abdominal-A of the Drosophila bithorax complex

The Abdominal gene is a member of the single homeotic complex of the beetle, Tribolium castaneum. An integrated developmental genetic and molecular analysis shows that Abdominal is homologous to the abdominal-A gene of the bithorax complex of Drosophila. abdominal-A mutant embryos display strong homeotic transformations of the anterior abdomen (parasegments 7-9) to PS6, whereas developmental commitments in the posterior abdomen depend primarily on Abdominal-B. In beetle embryos lacking Abdominal function, parasegments throughout the abdomen are transformed to PS6. This observation demonstrates the general functional significance of parasegmental expression among insects and shows that the control of determinative decisions in the posterior abdomen by homeotic selector genes has undergone considerable evolutionary modification.

Non-NASA Center↗
DOE OSTI2020

Special Issue on Nitrogenases and Homologous Systems

The nitrogenase superfamily comprises homologous enzyme systems that carry out fundamentally important processes, including the reduction of N 2 and CO, and the biosynthesis of bacteriochlorophyll and coenzyme F430. This special issue provides a cross-disciplinary overview of the ongoing research in this highly diverse and unique research area of metalloprotein biochemistry.

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

The Arabidopsis thaliana nucleotide sugar transporter GONST2 is a functional homolog of GONST1

Abstract Glycosylinositolphosphorylceramides (GIPCs) are the predominant lipid in the outer leaflet of the plasma membrane. Characterized GIPC glycosylation mutants have severe or lethal plant phenotypes. However, the function of the glycosylation is unclear. Previously, we characterized Arabidopsis thaliana GONST1 and showed that it was a nucleotide sugar transporter which provides GDP‐mannose for GIPC glycosylation. gonst1 has a severe growth phenotype, as well as a constitutive defense response. Here, we characterize a mutant in GONST1’s closest homolog, GONST2. The gonst2‐ 1 allele has a minor change to GIPC headgroup glycosylation. Like other reported GIPC glycosylation mutants, gonst1‐1gonst2‐1 has reduced cellulose, a cell wall polymer that is synthesized at the plasma membrane. The gonst2‐1 allele has increased resistance to a biotrophic pathogen Golovinomyces orontii but not the necrotrophic pathogen Botrytis cinerea . Expression of GONST2 under the GONST1 promoter can rescue the gonst1 phenotype, indicating that GONST2 has a similar function to GONST1 in providing GDP‐D‐Man for GIPC mannosylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nuclear Magnetic Resonance ‐based fragment screen of the E3 ligase Fem‐1 homolog B

Abstract Targeted protein degradation using PROTACs (PROteolysis TArgeting Chimeras) has emerged as a transformative therapeutic strategy, largely relying on a small number of E3 ubiquitin ligases such as CRBN and VHL. However, resistance, toxicity, and poor oral bioavailability limit the utility of PROTACs and highlight the need to expand the E3 ligase toolbox. Fem‐1 homolog B (FEM1B) is a lesser‐known E3 ligase that offers a promising alternative due to its broad expression and ability to recognize diverse degron motifs. Here, we describe the development of a stable construct of FEM1B, the results of a protein‐observed NMR‐based fragment screen using this construct, and the X‐ray structures of some of the fragment hits when bound to the protein. From these results, new PROTACs utilizing FEM1B as the E3 ligase may be discovered, providing an alternative E3 ligase for targeted protein degradation.

Katinas, Jade M. [Department of Biochemistry Vande↗
DOE OSTI2024

Homological Invariants of Pauli Stabilizer Codes

Abstract We study translationally invariant Pauli stabilizer codes with qudits of arbitrary, not necessarily uniform, dimensions. Using homological methods, we define a series of invariants called charge modules. We describe their properties and physical meaning. The most complete results are obtained for codes whose charge modules have Krull dimension zero. This condition is interpreted as mobility of excitations. We show that it is always satisfied for translation invariant 2D codes with unique ground state in infinite volume, which was previously known only in the case of uniform, prime qudit dimension. For codes all of whose excitations are mobile we construct a p-dimensional excitation and a $$(D-p-1)$$ ( D - p - 1 ) -form symmetry for every element of thep-th charge module. Moreover, we define a braiding pairing between charge modules in complementary degrees. We discuss examples which illustrate how charge modules and braiding can be computed in practice.

Physics↗
DOE OSTI2024

Processing and characterization of the homologous Zr x Ta 2 O 2x+5 series

In this study, Zr x Ta 2 O 2x+5 (ZTOx) was systematically studied to determine ideal solid-state synthesis and pressureless sintering conditions. For Zr 6 Ta 2 O 17 (ZTO6) and other compositions with values of x in ZTOx the optimal synthesis temperature of 1100 °C with 1 h dwell time was optimal. XRD phase analysis of the homologous series indicated that for ZTOx, x = 5, 6, 7, and 8 were within the phase stability field while x = 4 and x = 9 were outside the phase stability field. Unit cell lattice parameters changed anisotropically with Zr:Ta ratio with an overall <0.1% change in unit cell volume across the solid solution. Some Raman modes red shifted while others blue shifted, indicating competing tensile and compressive strains. Sintering of ZTOx required a progressively higher temperature as Zr-content increased despite the same starting powder grain sizes and synthesis temperature. Higher Vickers hardness for Zr-rich (12.7–12.8 GPa) than Ta-rich Zr x Ta 2 O 2x+5 (11.6–11.7 GPa) disappeared when accounting for different sintering temperatures. Indentation toughness was similar for all compositions (1.2–1.4 MPa m 1/2 ). Properties of Zr x Ta 2 O 2x+5 series indicate tunability of Zr:Ta composition ratio while maintaining the structure and room temperature mechanical properties comparable to Hf 6 Ta 2 O 17 and 8 mol% yttria stabilized zirconia ceramics.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ironing out the transition metal contribution to the magnetism of the n = 3 members of the homologous series Pr n +1 M n Ge 3 n +1 (M = Fe, Co): Pr 4 Fe 3 Ge 10 vs. Pr 4 Co 3 Ge 10

The Ln n+1 M n X 3n+1 (Ln = lanthanide, M = transition metal, and X = tetrel) homologous series provides a platform to study collective phenomena in quantum materials. Here, in this work, we compare the crystal growth, structure, and magnetic properties of the n = 3 members of the Pr n+1 M n Ge 3n+1 (M = Fe, Co) analogues, Pr 4 Fe 3 Ge 10 (a = 4.3207 (10) Å, b = 35.523 (8) Å, c = 4.2982 (15) Å, and V = 659.7 (3) Å 3 ) and Pr 4 Co 3 Ge 10 (a = 4.3091 (12) Å, b = 35.750 (9) Å, c = 4.2807 (11) Å, and V = 659.4 (3) Å 3 ). We determined that the ideal flux growth conditions for each compound are highly dependent on the concentration of Sn flux and quench temperature. Pr 4 Fe 3 Ge 10 orders ferromagnetically at 10 K along the c-direction while Pr 4 Co 3 Ge 10 orders antiferromagnetically at 16 K along the b-direction. For both compounds, we observed a magnetic moment higher than that expected for only Pr 3+ ions (3.58 µ B /Pr), implying that the transition metal ions contribute to magnetic ordering (3.91, 3.48, and 3.69 µ B /Pr for Pr 4 Fe 3 Ge 10 , and 3.76, 4.04, and 3.83 µ B /Pr for Pr 4 Co 3 Ge 10 measured along the a-, b-, and c-directions, respectively). Moreover, the zero-field Mössbauer spectrum obtained at 4.2 K for Pr 4 Fe 3 Ge 10 demonstrates that the iron sites participate in magnetic ordering.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea

Pea (legume plant defense) phytoalexin pterocarpans (–)-maackiain and (+)-pisatin have opposite C6a and C11a configurations, but how this occurs biosynthetically is unknown. Herein, pea dirigent-protein (DP) PsPTS2, which generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), was investigated as regards stereoselectivity towards four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers. Each DMDI stereoisomer configuration was determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF, this being 20-fold faster than with the trans-(3R,4S)-isomer. The 4R-configured substrate’s near ß-axial OH orientation significantly enhanced its leaving group abilities in creating intermediate A-ring mono-quinone methide (QM), whereas the 4S-isomer’s 4-OH group α-equatorial orientation was a poorer leaving group. Substrate docking simulations also indicated that the 4R-configured ß-axial OH was closest to the Asp catalytic center, whereas the 4S-isomer’s α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S, 4R)-DMDIs were substrates, even with the former having the same C3/C4 stereochemistry as (+)-pisatin. PsPTS2, assayed with cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and its C3/C4 stereoisomers, gave 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF), with the same substrate stereoselectivity. DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and the tree legume Bolusanthus speciosus, as DMIF is found in both. PsPTS1 preferentially utilized cis-(3R,4R)-DMDI to give (–)-maackiain, this being 2200-fold more efficient than with cis-(3R,4R)-DMI. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, again reflecting the better 4R configured OH leaving group. Pea PsPTS2 and PsPTS1 provisionally provide a facile DP-engendered means to enable differing C6a and C11a configurations in (+)-pisatin and (–)-maackiain. Both DP transformations are considered to occur via DP-engendered generation of an identical mono-QM bound intermediate, which with PsPTS2 either re-aromatizes to give DMDIF or with PsPTS1 undergoes intramolecular cyclization to afford (–)-maackiain. Substrate docking simulations using PsPTS2 (2.5 Å resolution) and PsPTS1 (1.5 Å resolution) plausibly indicate that cis-(3R,4R)-DMDI binds in the anti-configuration in the PsPTS2 active site to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.

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

Homologous Alkali Metal Copper Rare-Earth Chalcogenides A 2 Cu 2 n Ln 4 Q 7+ n ( n = 1, 2, 3)

Twenty-seven new members of the A 2 Cu 2n Ln 4 Q 7+n (A = Cs, Rb; Ln = La-Nd, Sm, Gd-Yb; Q = S, Se) homologous series were synthesized in one of three structural types (indicated by n = 1, 2, 3). All the compounds contained 3D frameworks with alkali-metal-containing tunnels. For each increment in n, one Cu 2 Q was added, which was incorporated into the framework as an edge-sharing tetrahedron by replacing a square planar chalcogenide site. High-throughput DFT calculations predicted many of the phases to be thermodynamically stable. These predictions were compared with the synthesis results for the phases formed in each composition space. In the syntheses, heavier lanthanides showed a preference to start forming the n = 3 ACu 3 Ln 2 Q 5 , which is consistent with the predictions. RbCuNd 2 Se 4 and RbCuTb 2 Se 4 were found to be thermally stable under vacuum at temperatures up to 1000 °C. Optical measurements revealed band gaps of 1.55(5) and 1.62(5) eV for CsCuCe 2 Se 4 and RbCuTb 2 Se 4 , respectively, and a work function of 4.83(5) eV for CsCuPr 2 Se 4 . Additionally, some n = 3 ACu 3 Ln 2 Qs compounds exhibit a negative phonon mode because of a copper atom coordination, which may distort to a trigonal planar geometry at sufficiently low temperatures. The dynamic instabilities and the predicted distortion in the copper tetrahedra for the n = 3 ACu 3 Ln 2 Q 5 compounds were found to have a linear relationship with the atomic number of the lanthanides and the electronegativity of the lanthanides. In conclusion, the A 2 Cu 2 n Ln 4 Q 7+n compounds can potentially find application as high-temperature thermoelectric materials and other semiconductors.

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

Role of CeNiSi 2 and BaNiSn 3 Structure Types in the Emergent Magnetism of the Homologous Series Ln n +1 M n X 3 n +1 :Ce 4 Fe 3 Ge 10

The synthesis and characterization of Ce 4 Fe 3 Ge 10 , n =3 member of the homologous series Ln n+1 M n X 3n+1 (Ln = lanthanides, M = transition metal, X = tetrel), is reported. The structure can be modelled with the Cmcm space group adopting the Eu 2 Ni 2-x Sn 5 structure type, with lattice parameters of a = 4.3323 (15) Å, b = 35.507 (9) Å, and c = 4.3069 (12) Å. Members of the series for n > 2 consist of stacking of ordered (CeNiSi 2 type) and disordered (BaNiSn 3 / AuCu 3 type) subunits with the acting as a “spacer” between CeNiSi 2 subunits. Although neither CeFeGe 3 nor CeFe 0.63 Ge 2 order magnetically down to 2 K, Ce 4 Fe 3 Ge 10 is an antiferromagnet below 3.6 K. To rationalize the emergent magnetism: (i) we established the Kondo and RKKY interaction dominant regions for the Ce analogues adopting the BaNiSn 3 and CeNiSi 2 by creating an electronic landscape for each, (ii) mapped the strained subunits, due to stacking, within the series. Here, we established the CeFeGe 3 subunit within Ce 4 Fe 3 Ge 10 contracts and is located within the Kondo-interaction dominant region, while the CeFe 0.63 Ge 2 subunit expands and is in the RKKY-interaction dominant region.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Abstract Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in bothSalinibacter ruber, an environmental halophilic organism, andEscherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Science & Technology - Other Topics↗
DOE OSTI2020

Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP

Abstract The Orange Carotenoid Protein (OCP) is a water-soluble protein that governs photoprotection in many cyanobacteria. The 35 kDa OCP is structurally and functionally modular, consisting of an N-terminal effector domain (NTD) and a C-terminal regulatory domain (CTD); a carotenoid spans the two domains. The CTD is a member of the ubiquitous Nuclear Transport Factor-2 (NTF2) superfamily (pfam02136). With the increasing availability of cyanobacterial genomes, bioinformatic analysis has revealed the existence of a new family of proteins, homologs to the CTD, the C-terminal domain-like carotenoid proteins (CCPs). Here we purify holo-CCP2 directly from cyanobacteria and establish that it natively binds canthaxanthin (CAN). We use small-angle X-ray scattering (SAXS) to characterize the structure of this carotenoprotein in two distinct oligomeric states. A single carotenoid molecule spans the two CCPs in the dimer. Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critical residues for carotenoid binding that likely contribute to the extreme red shift (ca. 80 nm) of the absorption maximum of the carotenoid bound by the CCP2 dimer and a further 10 nm shift in the tetramer form. These data provide the first structural description of carotenoid binding by a protein consisting of only an NTF2 domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material’s structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal–organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25–30% decrease in root-mean-squared-deviation and an average increase of 40–50% in R 2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure–property relationships for materials design.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Interpretation of autoencoder-learned collective variables using Morse–Smale complex and sublevelset persistent homology: An application on molecular trajectories

Dimensionality reduction often serves as the first step toward a minimalist understanding of physical systems as well as the accelerated simulations of them. In particular, neural network-based nonlinear dimensionality reduction methods, such as autoencoders, have shown promising outcomes in uncovering collective variables (CVs). However, the physical meaning of these CVs remains largely elusive. In this work, we constructed a framework that (1) determines the optimal number of CVs needed to capture the essential molecular motions using an ensemble of hierarchical autoencoders and (2) provides topology-based interpretations to the autoencoder-learned CVs with Morse–Smale complex and sublevelset persistent homology. Furthermore, this approach was exemplified using a series of n-alkanes and can be regarded as a general, explainable nonlinear dimensionality reduction method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗