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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Multi-omics Resources for Understanding Gene Regulation in Response to ER Stress in Plants

Proteotoxic stress of the endoplasmic reticulum (ER) is a potentially lethal condition that ensues when the biosynthetic capacity of the ER is overwhelmed. A sophisticated and largely conserved signaling, known as the unfolded protein response (UPR), is designed to monitor and alleviate ER stress. In plants, the emerging picture of gene regulation by the UPR now appears to be more complex than ever before, requiring multi-omics-enabled network-level approaches to be untangled. In the past decade, with an increasing access and decreasing costs of next-generation sequencing (NGS) and high-throughput protein–DNA interaction (PDI) screening technologies, multitudes of global molecular measurements, known as omics, have been generated and analyzed by the research community to investigate the complex gene regulation of plant UPR. In this chapter, we present a comprehensive catalog of omics resources at different molecular levels (transcriptomes, protein–DNA interactomes, and networks) along with the introduction of key concepts in experimental and computational tools in data generation and analyses. Finally, this chapter will serve as a starting point for both experimentalists and bioinformaticians to explore diverse omics datasets for their biological questions in the plant UPR, with likely applications also in other species for conserved mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Quaternary i-MAX Phases (Mo 2/3 RE 1/3 ) 2 AlC (RE: Dy, Tb, Er): Experimental Characterization and First-Principles Insights into their Fundamental Properties

Rare earth (RE)-based materials have unique electronic, magnetic, and optical properties, leading to the recent discovery of atomically layered solids with the chemical formula (M' 2/3 RE 1/3 ) 2 AlC, which have since garnered significant attention in the scientific community. This study aims to synthesize, characterize, and investigate the structural and thermal stability of the RE i-MAX phases. We prepared i-MAX phases using molybdenum (Mo) as M′ and RE elements as Dy, Tb, and Er, namely (Mo 2/3 Dy 1/3 ) 2 AlC, (Mo 2/3 Tb 1/3 ) 2 AlC, and (Mo 2/3 Er 1/3 ) 2 AlC. Structural characterization through x-ray diffraction (XRD) and Raman spectroscopy confirms the formation of the RE-based i-MAX phase, along with the presence of minor impurity phases in the alloys. Thermogravimetric analysis (TGA) conducted up to 1000°C under ambient conditions reveals that the i-MAX phases remain thermally stable up to approximately 450°C, beyond which oxidation leads to a noticeable weight gain in all samples. Differential scanning calorimetry (DSC) measurements during heating and cooling cycles show endothermic and exothermic peaks for (Mo 2/3 Dy 1/3 ) 2 AlC i-MAX in the 410–420°C range, indicating a temperature-induced minor atomic arrangement. In contrast, these peaks are absent in the Tb- and Er-based i-MAX phases. These findings offer valuable insights into the thermal behavior and stability of these i-MAX phases under thermal stress, contributing to a deeper understanding of their unique properties. Furthermore, first-principles density functional theory (DFT) calculations were performed to investigate the electronic and optical properties of the i-MAX phases. The results reveal their metallic nature, with pronounced contributions from Mo and RE elements near the Fermi level and within the conduction band.

Rare earth↗
DOE OSTI2022

Transcriptional competition shapes proteotoxic ER stress resolution

Through dynamic activities of conserved master transcription factors (mTFs), the unfolded protein response (UPR) relieves proteostasis imbalance of the endoplasmic reticulum (ER), a condition known as ER stress. Because dysregulated UPR is lethal, the competence for fate changes of the UPR mTFs must be tightly controlled. However, the molecular mechanisms underlying regulatory dynamics of mTFs remain largely elusive. Here, we identified the abscisic acid-related regulator G-class bZIP TF2 (GBF2) and the cis-regulatory element G-box as regulatory components of the plant UPR led by the mTFs, bZIP28 and bZIP60. We demonstrate that, by competing with the mTFs at G-box, GBF2 represses UPR gene expression. Conversely, a gbf2 null mutation enhances UPR gene expression and suppresses the lethality of a bzip28 bzip60 mutant in unresolved ER stress. Here, by demonstrating that GBF2 functions as a transcriptional repressor of the UPR, we address the long-standing challenge of identifying shared signalling components for a better understanding of the dynamic nature and complexity of stress biology. Furthermore, our results identify a new layer of UPR gene regulation hinged upon an antagonistic mTFs-GFB2 competition for proteostasis and cell fate determination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

UV-Vis spectrophotometric determination of rare earth elements (REE) speciation at near-neutral to alkaline pH. Part II: hydrolysis of Er from 25 to 75 °C

Aqueous speciation of rare earth elements (REE) controls their mobilization, fractionation, and enrichment in the natural waters. Geochemical modeling of their speciation is key to improve our understanding of the formation of economic mineral deposits, for developing mineral separation and mine tailing recovery technologies, and for characterizing the geochemistry of thermal water. However, our ability to predict the fate of REE in a wide pH and temperature range is limited by the scarcity of thermodynamic data for the REE hydroxyl complexes. In part I of this study (H. J. Han and A. P. Gysi, Dalton Trans., 2024, 53, 13129–13141), the optical properties of m-cresol purple (mCP) were determined using UV-Vis spectrophotometry between 25 and 75 °C in order to develop a method for deriving the hydrolysis constants of erbium (Er). Here, UV-Vis spectrophotometry experiments were conducted as a function of temperature between 35 and 75 °C to determine the hydrolysis of Er in near-neutral to alkaline solutions using mCP as an in situ pH color indicator. Here, the experiments were conducted with Er concentrations from 0 to ~0.253 mmol kg –1 in low ionic strength solutions (≤0.001 mol kg –1 ).

58 GEOSCIENCES↗
DOE OSTI2024

Isolation of individual Er quantum emitters in anatase TiO 2 on Si photonics

Defects and dopant atoms in solid state materials are a promising platform for realizing single photon sources and quantum memories, which are the basic building blocks of quantum repeaters needed for long distance quantum networks. In particular, trivalent erbium (Er 3+ ) is of interest because it couples C-band telecom optical transitions with a spin-based memory platform. In order to produce quantum repeaters at the scale required for quantum networks it is imperative to integrate these necessary building blocks with mature and scalable semiconductor processes. Here, in this work, we demonstrate the optical isolation of single Er 3+ ions in CMOS-compatible titanium dioxide (TiO 2 ) thin films monolithically integrated on a silicon-on-insulator photonics platform. Our results demonstrate an initial step toward the realization of a monolithically integrated and scalable quantum photonics package based on Er 3+ doped thin films.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Lasing dynamics of diode-pumped Yb – Er laser with a passive Q switch exposed to high-power external light

The temporal dynamics of diode-side-pumped Yb – Er laser, with a passive Co{sup 2+} : MgAl{sub 2}O{sub 4} Q switch illuminated by a light beam (total fluence of 0.15 – 0.16 J cm{sup −2}) from a semiconductor pulsed module, is investigated. It is shown that, using this external illumination, one can change the lasing onset delay and the time jitter ΔT{sub gi}. The dependence of ΔT{sub gi} on the interval between the instant of switching the illumination module on and the lasing peak position t{sub i} has a minimum at |t{sub i}| ≈ 10 μs. The decrease in ΔT{sub gi} with a change in |t{sub i}| from 90 to 10 μs indicates that instant of lasing peak occurrence for the Yb – Er laser is partially controlled by the pulse from the highly stable semiconductor module. If |t{sub i}| < 10 μs, the enhanced luminescence fluence in the cavity of Yb – Er laser exceeds 0.16 J cm{sup −2}; the light beam from the module does not affect much the lasing process in the ytterbium – erbium laser; and, as a consequence, the time jitter recovers the initial value. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Magnetic properties of the Ising-like rare earth pyrosilicate: D-Er 2 Si 2 O 7

Ising-like spin-1/2 magnetic materials are of interest for their ready connection to theory, particularly in the context of quantum critical behavior. In this work we report detailed studies of the magnetic properties of a member of the rare earth pyrosilicate family, D-Er 2 Si 2 O 7 , which is known to display a highly anisotropic Ising-like g-tensor and effective spin-1/2 magnetic moments. We used powder neutron diffraction, powder inelastic neutron spectroscopy (INS), and single crystal AC susceptibility to characterize its magnetic properties. Neutron diffraction enabled us to determine the magnetic structure below the known transition temperature (T N = 1.9 K) in zero field, confirming that the magnetic state is a four-sublattice antiferromagnetic structure with two non-collinear Ising axes, as was previously hypothesized. Our powder INS data revealed a gapped excitation at zero field, consistent with anisotropic (possibly Ising) exchange. An applied field of 1 T produces a mode softening, which is consistent with a field-induced second order phase transition. To assess the relevance of D-Er 2 Si 2 O 7 to the transverse field Ising model, we performed AC susceptibility measurements on a single crystal with the magnetic field oriented in the direction transverse to the Ising axes. This revealed a transition at 2.65 T at 0.1 K, a field significantly higher than the mode-softening field observed by powder INS, showing that the field-induced phase transitions are highly field-direction dependent as expected. Furthermore, these measurements suggest that D-Er 2 Si 2 O 7 may be a candidate for further exploration related to the transverse field Ising model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Understanding Reentrance in Frustrated Magnets: The Case of the Er 2 Sn 2 O 7 Pyrochlore

Reentrance, the return of a system from an ordered phase to a previously encountered less-ordered one as a controlled parameter is continuously varied, is a recurring theme found in disparate physical systems, yet its microscopic cause is often not investigated thoroughly. Here, through detailed characterization and theoretical modeling, we uncover the microscopic mechanism behind reentrance in the strongly frustrated pyrochlore antiferromagnet Er 2 Sn 2 O 7 . We use single crystal heat capacity measurements to expose that Er 2 Sn 2 O 7 exhibits multiple instances of reentrance in its magnetic field B vs temperature T phase diagram for magnetic fields along three cubic high symmetry directions. Through classical Monte Carlo simulations, mean field theory, and classical linear spin-wave expansions, we argue that the origins of the multiple occurrences of reentrance observed in Er 2 Sn 2 O 7 are linked to soft modes. These soft modes arise from phase competition and enhance thermal fluctuations that entropically stabilize a specific ordered phase, resulting in an increased transition temperature for certain field values and thus the reentrant behavior. Our work represents a detailed examination into the mechanisms responsible for reentrance in a frustrated magnet and may serve as a template for the interpretation of reentrant phenomena in other physical systems.

36 MATERIALS SCIENCE↗
DOE OSTI2021

High energy (0.8 J) mechanically Q-switched 2.94 μm Er:YAG laser

We report a flashlamp pumped mechanically Q-switched (MQS) 2.94 μm Er:YAG laser based on a spinning mirror with a highest output energy of 805 mJ at a pulse duration of 61 ns and 13 MW of peak power at 1 Hz repetition rate. This record output energy was achieved with the use of 300 mm long MQS Er:YAG laser cavity consisting of a 70% output coupler, 7 × 120 mm AR coated Er(50%):YAG crystal, and 4200 rad/s angular speed of the spinning mirror. The pulse jitter was also measured by using optical triggering and was smaller than 10 ns for 150 ns Q-switched pulses, which could be applicable to many laser applications where precise synchronization of pulses is required.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Application of Partial Least Squares Approaches to Pyroprocessing ER Data

Multivariate approaches show promise for application to process monitoring for safeguards of pyroprocessing. Past MPACT work explored the application of Principal Component Analysis (PCA) to detect off-normal conditions in pyroprocessing electrorefiner (ER) data from in the Hot Fuel Examination Facility (HFEF) at Idaho National Laboratory (INL) known as the Scalable Pyrochemical Recycling testbed (SPyRe) ER. PCA, however, does not consider the output variables. In FY24, multivariate analysis was extended from PCA to Partial Least Squares (PLS) analysis. PLS maximizes the variance between both the input signals and output variables. In the case of this work, PLS was applied in two different manners: Predictive PLS and Discriminant PLS. Predictive PLS maximizes the covariance between the process variables of the ER and the measured U concentration from in-situ voltammetry. Discriminant PLS maximizes the covariance between the process variables and a set of training process “states” such as known off-normal conditions. By projecting into the latent variable space in PLS, the process variables can be regressed onto the outputs and predictions can be made for new data sets. In this work, by applying predictive PLS, a penalized non-linear PLS approach was able to make predictions of concentration based on test and training data and detect when operations were off-normal. However, the predictive PLS does not classify the signals to which off-normal operations are attributable. Discriminant PLS can be used to classify off-normal operations but is inadequate to properly classify specific off-normal classes like power supply faults when the Discriminant PLS model is only specifically trained to detect that off-normal class. When all faults are trained against the observation data, all three operational classes are accurately classified and distinguished. Thus, future application of latent variable techniques should not select any given method, but should use a mixture of PCA, Predictive PLS, and Discriminant PLS.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Materials Data on Er(CuO2)2 by Materials Project

Er(CuO2)2 crystallizes in the tetragonal I4_1/a space group. The structure is three-dimensional. Er3+ is bonded in a 8-coordinate geometry to eight equivalent O2- atoms. There are four shorter (2.36 Å) and four longer (2.38 Å) Er–O bond lengths. Cu+2.50+ is bonded in a square co-planar geometry to four equivalent O2- atoms. There is two shorter (1.89 Å) and two longer (1.92 Å) Cu–O bond length. O2- is bonded to two equivalent Er3+ and two equivalent Cu+2.50+ atoms to form a mixture of distorted edge and corner-sharing OEr2Cu2 tetrahedra.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(HO)3 by Materials Project

Er(OH)3 crystallizes in the hexagonal P6_3/m space group. The structure is three-dimensional. Er3+ is bonded in a 9-coordinate geometry to nine equivalent O2- atoms. There are six shorter (2.39 Å) and three longer (2.47 Å) Er–O bond lengths. H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.97 Å. O2- is bonded in a single-bond geometry to three equivalent Er3+ and one H1+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(SiAu)2 by Materials Project

Er(AuSi)2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Er3+ is bonded to eight equivalent Si4- atoms to form ErSi8 hexagonal bipyramids that share corners with sixteen equivalent AuSi4 tetrahedra, edges with four equivalent ErSi8 hexagonal bipyramids, edges with eight equivalent AuSi4 tetrahedra, and faces with four equivalent ErSi8 hexagonal bipyramids. All Er–Si bond lengths are 3.22 Å. Au+2.50+ is bonded to four equivalent Si4- atoms to form AuSi4 tetrahedra that share corners with eight equivalent ErSi8 hexagonal bipyramids, corners with four equivalent AuSi4 tetrahedra, edges with four equivalent ErSi8 hexagonal bipyramids, and edges with four equivalent AuSi4 tetrahedra. All Au–Si bond lengths are 2.56 Å. Si4- is bonded in a 9-coordinate geometry to four equivalent Er3+, four equivalent Au+2.50+, and one Si4- atom. The Si–Si bond length is 2.28 Å.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(CoB)2 by Materials Project

Er(CoB)2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Er3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Er–B bond lengths are 2.84 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of corner and edge-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.01 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Er3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(Bi3O5)4 by Materials Project

Er(Bi3O5)4 crystallizes in the cubic I23 space group. The structure is three-dimensional. Er3+ is bonded to four equivalent O2- atoms to form ErO4 tetrahedra that share corners with twelve equivalent BiO5 square pyramids. All Er–O bond lengths are 2.15 Å. Bi+3.08+ is bonded to five O2- atoms to form distorted BiO5 square pyramids that share corners with eight equivalent BiO5 square pyramids, a cornercorner with one ErO4 tetrahedra, and an edgeedge with one BiO5 square pyramid. There are a spread of Bi–O bond distances ranging from 2.11–2.55 Å. There are three inequivalent O2- sites. In the first O2- site, O2- is bonded to one Er3+ and three equivalent Bi+3.08+ atoms to form corner-sharing OErBi3 tetrahedra. In the second O2- site, O2- is bonded in a distorted trigonal non-coplanar geometry to three equivalent Bi+3.08+ atoms. In the third O2- site, O2- is bonded in a trigonal planar geometry to three equivalent Bi+3.08+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(ReO4)3 by Materials Project

Er(ReO4)3 crystallizes in the trigonal R3c space group. The structure is three-dimensional. Er3+ is bonded in a 9-coordinate geometry to nine O2- atoms. There are a spread of Er–O bond distances ranging from 2.25–2.65 Å. Re7+ is bonded in a tetrahedral geometry to four O2- atoms. There are a spread of Re–O bond distances ranging from 1.72–1.78 Å. There are four inequivalent O2- sites. In the first O2- site, O2- is bonded in a single-bond geometry to one Re7+ atom. In the second O2- site, O2- is bonded in a distorted single-bond geometry to one Er3+ and one Re7+ atom. In the third O2- site, O2- is bonded in a bent 150 degrees geometry to one Er3+ and one Re7+ atom. In the fourth O2- site, O2- is bonded in a distorted water-like geometry to one Er3+ and one Re7+ atom.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(CuS)3 by Materials Project

ErCu3S3 crystallizes in the trigonal P-31c space group. The structure is three-dimensional. there are two inequivalent Er3+ sites. In the first Er3+ site, Er3+ is bonded to six equivalent S2- atoms to form ErS6 octahedra that share corners with twelve equivalent CuS4 tetrahedra, edges with three equivalent ErS6 octahedra, and edges with six equivalent CuS4 tetrahedra. All Er–S bond lengths are 2.72 Å. In the second Er3+ site, Er3+ is bonded to six equivalent S2- atoms to form ErS6 octahedra that share corners with twelve equivalent CuS4 tetrahedra, edges with three equivalent ErS6 octahedra, and edges with six equivalent CuS4 tetrahedra. All Er–S bond lengths are 2.72 Å. Cu1+ is bonded to four equivalent S2- atoms to form CuS4 tetrahedra that share corners with four ErS6 octahedra, corners with six equivalent CuS4 tetrahedra, edges with two ErS6 octahedra, and edges with three equivalent CuS4 tetrahedra. The corner-sharing octahedra tilt angles range from 16–55°. There are a spread of Cu–S bond distances ranging from 2.33–2.41 Å. S2- is bonded in a 6-coordinate geometry to two Er3+ and four equivalent Cu1+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Er(NiB)2 by Materials Project

Er(NiB)2 crystallizes in the monoclinic C2/c space group. The structure is three-dimensional. Er3+ is bonded in a 6-coordinate geometry to six equivalent B3- atoms. There are a spread of Er–B bond distances ranging from 2.69–2.89 Å. Ni+1.50+ is bonded in a 4-coordinate geometry to four equivalent B3- atoms. There are a spread of Ni–B bond distances ranging from 2.02–2.07 Å. B3- is bonded in a 8-coordinate geometry to three equivalent Er3+, four equivalent Ni+1.50+, and one B3- atom. The B–B bond length is 1.74 Å.

36 MATERIALS SCIENCE↗