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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 OSTI2018

Selenization of CIS and CIGS layers deposited by chemical spray pyrolysis

Cu(In1-xGax)Se2 (CIGS) thin films with x=0 (CIS) and x=0.3 (CIGS) were prepared on Mo-coated glass substrate by using chemical spray pyrolysis at a substrate temperature of 350 degrees C, followed by selenization treatment at 550 degrees C in selenium environment under N2 gas flow. X-ray diffraction patterns of as-deposited CIGS layers on Mo showed polycrystalline chalcopyrite phase with an intense (112) plane. Splitting of (204)/(220) and (116)/(312) planes for the film with x=0.3 reveals deviation of tetragonal nature. Field emission scanning electron microscopy cross-sectional images of selenized films showed clear re-crystallization of grains. During the selenization process of the CIGS absorber, a thin interface layer of MoSe2 is formed. Line mapping of Mo/CIGS layer showed more gallium segregation at the interface of back contact resulting in band gap grading. Chemical composition and mapping of the as-deposited and selenized samples were determined by energy dispersive analysis of X-rays. This work leads to fabrication of low cost and large scale Mo/CIGS/CdS/ZnO/ZnO:Al device structure.

14 SOLAR ENERGY↗
DOE OSTI2017

Propagator quantum chemical study of S-cis-(Z)-2-(2-formylethenyl)pyrrole: electronic structure and aspects of intramolecular hydrogen bond manifestation in ionization spectra

For the purpose of investigation of the electronic structures of functionalized pyrroles with potential biological activity the electronic structures and ionization spectra of S-cis-(Z)-2-(2-formylethenyl)pyrrole (FP) were calculated by the propagator quantum chemical method. The calculations were performed using the third-order algebraic diagrammatic construction method (ADC(3)) for one-particle Green´s function (electronic propagator) and the 6–31G** basis set. Going from FP (possessing the intramolecular hydrogen bond H⋯O) to its conformation FPR (without H⋯O bonding), the O1s-ionization energy and the ionization energy of the σ-type lone electron pair orbital of the O atom decrease by ~0.2 eV, which is a consequence of stopping the electron density transfer from the O atom. A strong electron density transfer through the hydrogen bond from the O atom to the NH group occurs in the nitrogen core level ionization spectrum as evidenced by a lower N1s-ionization energy of FP (by ~0.7 eV ) compared to that of FPR. The valence shell ionization spectra of FP and FPR calculated using the ADC(3) method are characterized by a high density of the satellite states. The results obtained indicate that the electronic structures of the compounds of the considered class are characterized by pronounced effects of electron correlation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Functional characterisation of parvulin-type peptidyl prolyl cis-trans isomerase, PinA in Dictyostelium discoideum

Pin1-type parvulins are unique among PPIases that can catalyse an otherwise slow cis-trans isomerisation of phosphorylated peptide bond preceding proline in target proteins. This prolyl isomerisation process can regulate activity, stability and localisation of target proteins and thus control cellular processes like eukaryotic cell proliferation, cell cycle progression and gene regulation. Towards understanding the function of Pin1-type prolyl isomerisation in Dictyostelium discoideum, a slime mould with distinct growth and developmental phases, we identified PinA as a novel Pin1-type parvulin by its ability to complement the temperature sensitivity phenotype associated with a mutation in ESS1 in S. cerevisiae. In D. discoideum, pinA is temporally and spatially regulated during growth and development. PinA is both nuclear as well as cytoplasmic in the growing cells. We further show that loss of pinA (pinA{sup −}) leads to decreased growth rate, reduced spore formation and abnormal prespore-prestalk patterning. We conclude that PinA is required for normal growth as well as development in D. discoideum. - Highlights: • PinA is a bona fide homologue of S. cerevisiae Ess1. • PinA is required for normal cell proliferation of D. discoideum. • PinA is spatially localised in developmental structures. • PinA is important for cell differentiation and patterning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Synthesis and reactivity of cis-FeH 2 (dcpe) 2 (dcpe=1,2-bis(dicyclohexylphosphino)ethane)

For this work, a new six-coordinate iron dihydride cis-FeH2(dcpe)2 (1) has been synthesized (dcpe = 1,2-bis(dicyclohexylphosphino)ethane). It has been found to react with either 1,4-cyclohexadiene or tert-butylethylene in toluene to give the respected hydrogenated hydrocarbon and the zero valent species Fe(dcpe)(toluene) (2). When this reaction with acceptor olefins was performed in methylcyclohexane, transfer dehydrogenation was observed to give low-yields of iron-bound toluene in 2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Floquet Study of Quantum Control of the Cis–Trans Photoisomerization of Rhodopsin

Understanding how to control reaction dynamics of polyatomic systems by using ultrafast laser technology is a fundamental challenge of great technological interest. Here, we report a Floquet theoretical study of the effect of light-induced potentials on the ultrafast cis–trans photoisomerization dynamics of rhodopsin. The Floquet Hamiltonian involves an empirical 3-state 25-mode model with frequencies and excited-state gradients parametrized to reproduce the rhodopsin electronic vertical excitation energy, the resonance Raman spectrum, and the photoisomerization time and efficiency as probed by ultrafast spectroscopy. We simulate the excited state relaxation dynamics using the time-dependent self-consistent field method, as described by a 3-state 2-mode nuclear wavepacket coupled to a Gaussian ansatz of 23 vibronic modes. We analyze the reaction time and product yield obtained with pulses of various widths and intensity profiles, defining ’dressed states’ where the perturbational effect of the pulses is naturally decoupled along the different reaction channels. We find pulses that delay the excited-state photoisomerization for hundreds of femtoseconds, and we gain insights on the underlying control mechanisms. The reported findings provide understanding of quantum control, particularly valuable for the development of ultrafast optical switches based on visual pigments.

Videla, Pablo E.↗
DOE OSTI2021

Quantitative Proteomics and Quantitative PCR as Predictors of cis -1,2-Dichlorethene and Vinyl Chloride Reductive Dechlorination Rates in Bioaugmented Aquifer Microcosms

Quantitative measurement of process-specific biomarker genes of Dehalococcoides mccartyi (Dhc) supports monitoring at chlorinated ethene contaminated sites. In this study, we varied Dhc cell abundances from ~103 to 108 cells/mL in aquifer microcosms and correlated the corresponding reductive dehalogenase (RDase) gene and RDase protein abundances with measured reductive dechlorination (RD) rates of cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). An additional set of microcosms tested the RD rate-predictive power of the regression analyses. These efforts revealed (1) that targeted proteomics quantifies Dhc biomarker proteins (e.g., TceA and VcrA, OmeA) over a relevant range of Dhc cell densities, and (2) that protein and gene abundances can predict RD rates. Protein detection limits translated to a rate coefficient of 10 –4 day –1 (0.04 year –1 ) for both k cDCE and k vc , which is within the range observed at sites undergoing monitored natural attenuation (MNA) (i.e., without the implementation of enhanced bioremediation treatment). Rates predicted using a combination of quantitative biomarker gene and protein measurements generally resulted in the best match with experimentally determined rate constants. These new findings provide evidence that quantitative biomarker measurements may be useful predictors of in situ RD rates, which would constitute a major advance for the cost-effective management of contaminated sites.

42 ENGINEERING↗
DOE OSTI2019

COSY catalyses trans–cis isomerization and lactonization in the biosynthesis of coumarins

Coumarins, also known as 1,2-benzopyrones, comprise a large class of secondary metabolites that are ubiquitously found throughout the plant kingdom. In many plant species, coumarins are particularly important for iron acquisition and plant defence. Here, we show that COUMARIN SYNTHASE (COSY) is a key enzyme in the biosynthesis of coumarins. Arabidopsis thaliana cosy mutants have strongly reduced levels of coumarin and accumulate o-hydroxyphenylpropanoids instead. Accordingly, cosy mutants have reduced iron content and show growth defects when grown under conditions in which there is a limited availability of iron. Recombinant COSY is able to produce umbelliferone, esculetin and scopoletin from their respective o-hydroxycinnamoyl-CoA thioesters by two reaction steps—a trans–cis isomerization followed by a lactonization. This conversion happens partially spontaneously and is catalysed by light, which explains why the need for an enzyme for this conversion has been overlooked. The combined results show that COSY has an essential function in the biosynthesis of coumarins in organs that are shielded from light, such as roots. These findings provide routes to improving coumarin production in crops or by microbial fermentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗
DOE OSTI2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis -regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Identification of absolute geometries of cis and trans molecular isomers by Coulomb Explosion Imaging

An experimental route to identify and separate geometric isomers by means of coincident Coulomb explosion imaging is presented, allowing isomer-resolved photoionization studies on isomerically mixed samples. We demonstrate the technique on cis/trans 1,2-dibromoethene (C 2 H 2 Br 2 ). The momentum correlation between the bromine ions in a three-body fragmentation process induced by bromine 3d inner-shell photoionization is used to identify the cis and trans structures of the isomers. Lastly, the experimentally determined momentum correlations and the isomer-resolved fragment-ion kinetic energies are matched closely by a classical Coulomb explosion model.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Low temperature aging in a molecular glass: the case of cis -methyl formate

Glassy films of cis-methyl formate show spontaneous dipole orientation on deposition from the vacuum, the so-called ‘spontelectric effect’, creating surface potentials and electric fields within the films. We follow the decay of these fields, and their accompanying dipole orientation, on the hours timescale at deposition temperatures between 40 K and 55 K. Our data trace the low temperature ‘secondary decay’ mechanism, at tens of degrees below the glass transition temperature of 90 K. We show that secondary decay is due to molecular rotation, with associated activation energies lying between 0.1 and 0.2 eV. Diffusion is absent, as established from published neutron reflectivity data. Using an analytical model for the spontelectric effect, data are placed on a quantitative footing, showing that angular motion in excess of 50° reproduces the observed values of activation energies. Exploitation of the spontelectric effect is new in the study of glass aging and is shown here to give insight into the elusive processes which take place far from the molecular glass transition temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd) with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Quantum mechanical calculations on cis-2,6-bis(2-chlorophenyl)-3,3-dimethylpiperidin-4-one

Quantum mechanical calculations on cis-2, 6-bis (2-chlorophenyl)-3, 3-dimethylpiperidin-4-one were performed by using HSEH1PBE level of density functional theory (DFT) with 6-311++G (d, p) basis set. Geometric parameters of the title molecule in the ground state were found to be in good agreement with experimental data. The frontier molecular orbitals (HOMO and LUMO) were simulated by the same level. Small energy gap between the HOMO and LUMO is an indicator molecular charge transfer within the title molecule. The electronegativity, chemical hardness and softness were also calculated by using HOMO and LUMO energies. Dipole moment, polarizability and hyperpolarizability parameters were also calculated by using HSEH1PBE level. All calculations were carried out with the GAUSSIAN 09 package program.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Exploring Plant Cis –Regulatory Elements at Single–Cell Resolution: Overcoming Biological and Computational Challenges to Advance Plant Research

Cis-regulatory elements (CREs) are important sequences for gene expression and for plant biological processes such as development, evolution, domestication, and stress response. However, studying CREs in plant genomes has been challenging. The totipotent nature of plant cells, coupled with inability to maintain plant cell types in culture and the inherent technical challenges posed by the cell wall have limited our understanding of how plant cell types acquire and maintain their identities and respond to the environment via CRE usage. Furthermore, advances in single cell epigenomics have revolutionized the field identifying cell-type-specific CREs. These new technologies have the potential to significantly advance our understanding of plant CRE biology, and shed light on how the regulatory genome gives rise to diverse plant phenomena. However, there are significant biological and computational challenges associated with analyzing single cell epigenomic datasets. In this review, we discuss the historical and foundational underpinnings of plant single-cell research, challenges and common pitfalls in analysis of plant single-cell epigenomic data, and highlight biological challenges unique to plants. Additionally, we discuss how the application of single-cell epigenomic data in various contexts stands to transform our understanding of the importance of CREs in plant genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cis-regulatory evolution shapes facial diversity in birds and mammals

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Kyomen, Stella [Max Planck Institute for Evolution↗
DOE OSTI2012

Electron diffraction study of 1M illites with interstratified trans- and cis-vacant 2 : 1 layers

Illites from the volcanogenic Zn-Au-Ag sulfide deposit Galkinskoe (Northern Urals) have been investigated using oblique-texture electron diffraction patterns in combination with the simulation of diffraction effects. Along with single-phase tv/cv1M illites, the structures of which are formed by statistically interstratified dioctahedral 2: 1 layers with vacant trans- or cis-octahedra, illites in the form of a mixture of two interstratified tv/cv1M phases, with the dominance of tv- or cv layers, are identified. It is shown that in the latter case the diffraction pattern can also be interpreted within the single-phase tv/cv model, provided that the tv- and cv layers are distributed with some tendency to segregate. The structural features indicating the preference of the two-phase model are analyzed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗