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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing

Neurexins are presynaptic, cell-adhesion molecules that specify the functional properties of synapses via interactions with trans-synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing-dependent neurexin regulation are largely unknown. Here, we determined high-resolution structures of the complex of neurexophilin-1 and the second laminin/neurexin/sex-hormone-binding globulin domain (LNS2) of neurexin-1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin–neurexin binding interface that extends the jelly-roll β-sandwich of LNS2 of neurexin-1 into neurexophilin-1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin-1. Taken together, our data reveal an unexpected architecture of neurexophilin–neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Complexity and Simplicity: Putting Complexity Science in Perspective

As technical systems and social problems in modern society become ever more complex, many organizations are turning to what is commonly termed complexity science to find solutions. The problem many organizations face is that they frequently have no clear idea what they are trying to accomplish, no in-depth understanding of the nature, size and dimension of their problem, and only a limited understanding of what theoretical approaches and off-the-shelf analysis tools exist or are applicable to their particular problem. This paper examines the larger topic of complexity science, providing insight, and helping to place its promises in perspective.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2015

Influence of weak vibrational-electronic couplings on 2D electronic spectra and inter-site coherence in weakly coupled photosynthetic complexes

Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors (S) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small (S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations (S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S. This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.

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

CSI1, PATROL1, and exocyst complex cooperate in delivery of cellulose synthase complexes to the plasma membrane

Significance Cellulose is synthesized at the plasma membrane by cellulose synthase complexes (CSCs). The ability to deliver CSCs to discrete sites at the cell surface is critical for cellulose synthesis. We discovered that the de novo secretion of CSCs is mediated by cooperation among a recently identified cellulose synthase interacting protein, exocyst complex, and a plant-specific protein PATROL1 in Arabidopsis thaliana . We present a timeline of events for exocytosis of CSCs. CSCs represent unique cargo proteins that are not conserved in the mammalian or yeast system. Plants offer unique opportunities to characterize the function and regulation of exocytosis that may provide insight into the evolution of exocytosis in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

(Pentamethylcyclopentadienato)rhodium complexes for delivery of the curcumin anticancer drug [Rhodium pentamethylcyclopentadienato complexes for delivery of the curcumin anti-cancer drug]

[RhIII(*Cp)Cl(X,Y)] n+ complexes {X, Y = Cl, PTA, n = 0 (2); X, Y = en, n = 1 (3, Cl– salt; 4, PF 6 – salt); X, Y = acac, n = 0 (5); X, Y = cur, n = 0 (6), where *Cp = pentamethylcyclopentadienato, curH = curcumin; PTA = 1,3,5-triaza-7-phosphatricyclo[3.3.1.1]decane; en = 1,2-ethanediamine; acac = acetylacetonato = 2,4-pentanedionato(1–)} were synthesized from [Rh(*Cp)(µ-Cl)Cl] 2 (1). While 2–5 were inactive against human epithelial A549 lung-cancer cells in assays of cytotoxicity, and antimetastatic and proapoptotic behaviors, 6 had a cytotoxic activity similar to that of curH over 72 h, but at 24 h in real-time cell migration assays, it was less active, showing slow release of curH. All complexes underwent ligand-exchange reactions with biomolecules and cells within the timeframes of the assays (X-ray absorption spectroscopy). Intracellular elemental distributions (X-ray fluorescence microscopy) showed that 6 effectively delivered curH to cells, where it was released. Other elemental distributions and caspase activities were consistent with preapoptotic activities. As such, 6 is a promising delivery agent for bioactive ligands, such as curH. However, pure curcumin itself showed a previously unrecognized ability to promote migration of A549 cells at subtoxic concentrations in the presence of endothelial growth factor, which may be a concern for its widespread use as a nutritional supplement and as a potential drug. As a result, this aspect warrants further research.

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

A step forward from high-entropy ceramics to compositionally complex ceramics: a new perspective

High-entropy ceramics (HECs) have quickly gained attention since 2015. To date, nearly all work has focused on five-component, equimolar compositions. This perspective article briefly reviews different families of HECs and selected properties. Following a couple of our most recent studies, we propose a step forward to expand HECs to compositionally-complex ceramics (CCCs) to include medium-entropy and/or non-equimolar compositions. Here, using defective fluorite and ordered pyrochlore oxides as two primary examples, we further consider the complexities of aliovalent cations and anion vacancies as well as ordered structures with two cation sublattices. Better thermally-insulating yet stiff CCCs have been found in non-equimolar compositions with optimal amounts of oxygen vacancies and in ordered pyrochlores with large size disorder; it is demonstrated that medium-entropy ceramics (MECs) can prevail over their high-entropy counterparts. The diversifying classes of CCCs provide even more possibilities than HECs to tailor the composition, defects, disorder/order, and consequently various properties.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Gold core/ceria shell-based redox active nanozyme mimicking the biological multienzyme complex phenomenon

Catalytically active individual gold (Au) and cerium oxide (CeO2) nanoparticles are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. These activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. A functional nanozyme depicting multienzyme like properties that functions as a synthetic super enzyme has eluded the researchers in the nanoscience community for past decade. In current report, we have designed a functional multienzyme in the form of Gold (core)-CeO2 (shell) nanoparticles (Au@CeO2 CSNPs) exhibiting excellent peroxidase, catalase and superoxide dismutase enzyme-like activities that are controlled simply by tuning the pH. The reaction kinetic parameters reveal that the peroxidase-like activity of this core shell nanozyme is comparable to natural HRP enzyme. Unlike peroxidase-like activity exhibited by other nanomaterials, Au@CeO2 CSNPs showed decrease in hydroxyl radical formation, suggesting that the bio catalytic reactions are performed by efficient electron transfers. A significant enzyme-like activity of this core shell nanoparticle was conserved at extreme pH (2 – 11) and temperatures (up to 90 °C), clearly suggesting the superiority over natural enzymes. Further, the utility of peroxidase-like activity of this core shell nanoparticles was extended for the detection of glucose, which showed a linear range of detection between (100 µM – 1 mM). It is hypothesized that the proximity of the redox potentials of Au+/Au and Ce (III)/Ce (IV) may result in a redox couple promoting the multienzyme activity of core shell nanoparticles. Au@CeO2 CSNPs may open new directions for development of single platform sensors in multiple biosensing applications.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

The impact of crystal symmetry on the electronic structure and functional properties of complex lanthanum chromium oxides

Complex oxides exhibit a wide range of crystal structures, chemical compositions and physical properties. The underlying drivers determining the complicated structure-composition-property phase diagrams are the relative positions and orbital overlaps between the metal cations and the oxygen anions. Here we report a combined experimental and theoretical investigation of the structure and bonding in a series of lanthanum chromium oxides prepared by reactive molecular beam epitaxy. Of particular interest is the charge state and local coordination of the Cr. We have stabilized LaCrO 3 , LaCrO 4 and La 2 CrO 6 films by controlling the three elemental fluxes during deposition, and have carried out x-ray diffraction, x-ray photoemission, and x-ray absorption spectroscopy, as well as first-principles calculations, to determine structure, charge state, chemical bonding, and electronic structure. Significant changes in bonding character and orbital interaction are revealed with decreasing ligand symmetry from octahedral to tetrahedral Cr coordination. Both LaCrO 4 and LaCrO 6 with tetrahedrally coordinated Cr show strong pre-edge features in the Cr K-edge near-edge structure whereas LaCrO 3 with octahedrally coordinated Cr exhibits very weak pre-edge features. The origin of these pre-edge features is discussed based on various selection rules and ligand symmetry. We also demonstrate an increase in cation-anion orbital hybridization and a decrease in long-range ligand coupling induced by this symmetry reduction. These in turn result in dramatic modifications of the macroscopic optical and magnetic properties.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Calculus structure on the Lie conformal algebra complex and the variational complex

We construct a calculus structure on the Lie conformal algebra cochain complex. By restricting to degree one chains, we recover the structure of a g-complex introduced in [A. De Sole and V. G. Kac, Commun. Math. Phys. 292, 667 (2009)]. A special case of this construction is the variational calculus, for which we provide explicit formulas.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Efficient estimators for likelihood ratio sensitivity indices of complex stochastic dynamics

We demonstrate that centered likelihood ratio estimators for the sensitivity indices of complex stochastic dynamics are highly efficient with low, constant in time variance and consequently they are suitable for sensitivity analysis in long-time and steady-state regimes. These estimators rely on a new covariance formulation of the likelihood ratio that includes as a submatrix a Fisher information matrix for stochastic dynamics and can also be used for fast screening of insensitive parameters and parameter combinations. The proposed methods are applicable to broad classes of stochastic dynamics such as chemical reaction networks, Langevin-type equations and stochastic models in finance, including systems with a high dimensional parameter space and/or disparate decorrelation times between different observables. Furthermore, they are simple to implement as a standard observable in any existing simulation algorithm without additional modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface

We exploit gas-phase cluster ion techniques to provide insight into the local interactions underlying divalent metal ion-driven changes in the spectra of carboxylic acids at the air-water interface. This information is used to clarify the experimental findings of surface sensitive spectroscopies that the CO stretching bands of long chain acids appear at very similar energies when the head group is deprotonated by high sub-phase pH or is exposed to relatively high concentrations of Ca2+ divalent metal ions (e.g., Ca2+ and Mg2+). To this end, we report the evolution of the vibrational spectra of size-selected [Ca2+·RCO2¯]+·(H2O)n=0-14 and RCO2¯·(H2O)n=0-14 cluster ions obtained using infrared photofragmentation mass spectrometry toward the features observed at the air-water interface. The carboxylate with R = -CD2CD3 was chosen in order to capture the longer chain behavior and to suppress band congestion that complicates the spectra of the light isotopologue. Surprisingly, not only does stepwise hydration of the RCO2¯ anion and the [Ca2+·RCO2¯]+ contact ion pair yield solvatochromic responses in opposite directions, but in both cases the responses of the two CO bands (?_s^COO and ?_as^COO) to hydration are opposite to each other! The result is that the two CO bands evolve toward their interfacial and bulk asymptotes from opposite directions. Theoretical simulations of the [Ca2+·RCO2¯]+·(H2O)n clusters indicate that the metal ion remains directly bound to the head group in a contact ion pair motif as the asymmetric CO stretch converges at the bulk value by n = 12, establishing that direct metal complexation can account for the interfacial and bulk behavior. We discuss these effects in the context of a qualitative model that invokes the water network-dependent local electric field along the C-C bond connecting the head group to the tail as the key parameter driving the observed trends. M.A.J. and H.C.A. thank the National Science Foundation through the NSF Center for Aerosol Impacts on Chemistry of the Environment (NSF-CAICE), CHE-1305427 for supporting this work. M.A.J. thanks the Air Force Office of Scientific Research for the cryogenic spectrometer used in the gas phase experiments. K.D.J. thanks the Department of Energy under grant no. DE-FG02-00ER15066. C.J. Mundy and S.M. Kathmann are supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. M.D. Baer was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract No. DE-AC05- 76RL01830. Computing resources for the calculation of harmonic spectra were allocated by PNNL’s Institutional Computing program.

Denton, Joanna↗
DOE OSTI2013

The Impacts of Cation Stoichiometry and Substrate Surface Quality on Nucleation, Structure, Defect Formation, and Intermixing in Complex Oxide Heteroepitaxy–LaCrO3 on SrTiO3(001)

Our ability to design and fabricate electronic devices with reproducible properties using complex oxides is critically dependent on our ability to controllably synthesize these materials in thin-film form. Structure-property relationships are intimately tied to film and interface composition. Here we report on the effects of cation stoichiometry in LaCrO3 heteroepitaxial films prepared using molecular beam epitaxy. We show that LaCrO3 films grow pseudomorphically on SrTiO3(001) over an wide range of La-to-Cr atom ratios. However, the growth mode and structural quality are sensitive to the La-to-Cr ratio, with La-rich films being of considerably lower structural quality than Cr-rich films. Cation mixing occurs at the interface for all La-to-Cr ratios investigated, and is not quenched by deposition at ambient temperature. Indiffused La atoms occupy Sr sites in the substrate. The presence of defects in the SrTiO3 substrate is implicated in promoting La indiffusion by comparing the properties of LaCrO3/SrTiO3 with those of LaCrO3/Si, both prepared at ambient temperature. Additionally, pulsed laser deposition is shown to result in more extensive interfacial mixing than molecular beam epitaxy for deposition at ambient temperature on Si.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2018

Oxidation of Naphthalene with a Manganese(IV) Bis(hydroxo) Complex in the Presence of Acid [Naphthalene Oxidation of Manganese(IV)-Bis(Hydroxo) Complex in the Presence of Acid]

Naphthalene oxidation with metal–oxygen intermediates is a difficult reaction in environmental and biological chemistry. Herein, we report that a Mn IV bis(hydroxo) complex, which was fully characterized by various physicochemical methods, such as ESI–MS, UV/Vis, and EPR analysis, X–ray diffraction, and XAS, can be employed for the oxidation of naphthalene in the presence of acid to afford 1,4–naphthoquinone. Redox titration of the Mn IV bis(hydroxo) complex gave a one–electron reduction potential of 1.09 V, which is the most positive potential for all reported nonheme Mn IV bis(hydroxo) species as well as Mn IV oxo analogues. Here, kinetic studies, including kinetic isotope effect analysis, suggest that the naphthalene oxidation occurs through a rate–determining electron transfer process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗