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At least 91 records · Page 5

Structural biology at the National Synchrotron Light Source II

The structural biology program at the National Synchrotron Light Source II presents a coordinated set of instruments, software and research opportunities for the interested user. We describe in some detail the research capabilities enabled by the Center for BioMolecular Structure. The evolution of the resources is described in detail, considering three major themes: automation, micro-focusing and computation prediction.

36 MATERIALS SCIENCE↗

Development of electron source feedback for enhanced X-ray beam stability at NSLS-II

Future synchrotron light sources are being designed to deliver significantly higher brightness and coherence, enabling faster scanning and more advanced imaging techniques. However, realizing these capabilities requires improved X-ray beam stability, as vibrations directly limit measurement accuracy and image quality. At the NSLS-II Hard X-ray Nanoprobe (HXN), a local mechanical feedback system mitigates low-frequency motion but provides only limited suppression of dominant vibrations at 27 Hz and 120 Hz. To address this limitation, this work explores the use of the electron beam itself as the actuator for feedback by integrating X-ray beam position monitor signals into the fast orbit feedback system through a dedicated electrometer. Experimental results show that this approach effectively suppresses the dominant vibration peaks and enhances stability at the focusing point. Benchmark ptychography measurements further confirm that electron-beam-based feedback reduces background fluctuations and mitigates vibration-induced artifacts under fast-scanning conditions. These results establish the feasibility of using the electron beam as a feedback actuator for next-generation synchrotron applications and provide an experimental assessment of its potential and limitations.

36 MATERIALS SCIENCE↗

Nonpigmented PsbR is involved in the integrity of excitation landscape in higher plant photosystem II, a case study in Arabidopsis thaliana and a mutant

PsbR is a nonpigmented 10 kDa protein in Photosystem II (PSII) in algae and plants. A recent structural study clarified its enigmatic structural location in a Photosystem II megacomplex that has baffled the community for more than four decades. Our current study interrogates whether absence of PsbR affects the overall dynamics of excitation energy migration within light harvesting complexes (LHC) and PSII super assemblies using highly-active PSII membrane particles, so-called BBY particles, isolated from a PsbR deletion mutant (ΔPsbR) of Arabidopsis thaliana. A femto-second (fs)-time-resolved transient absorption experimentation recorded at 77 K with selective excitation of Chl b which is exclusively present in LHCs enabled us to resolve the temporal differences in LHC→LHC and LHC→PSII excitation energy transfer steps. By applying specific target spectro-kinetic models to the transient absorption datasets, we demonstrated that the time constants of Chl a LHC → Chl a LHC excitation transfer significantly elongates in the ΔPsbR LHC-PSII particles, suggestive of the decreased aggregation level of photosynthetic proteins in the mutant. These findings highlight excitation energy transfer integrity in LHC-PSII assembly is not only determined by the pigmented light-harvesting complexes, but also synergistically by the nonpigmented PSII components. Furthermore, the disturbed integrity in dynamics of excitation energy transfer pathway within LHC-PSII supercomplex is discussed in the context of the altered LHC-PSII megacomplexes type I and II architectures which result from the absence of the PsbR protein in higher plant PSII.

Chlorophyll↗

3D pore structure reconstruction of fluff region in top of EBR-II irradiated fuel by X-ray micro-computed tomography

Metallic fuels comprised of U-Zr binary and U-Pu-Zr ternary alloys are a promising fuel candidate for sodium-cooled fast reactors and possess many advantages over ceramic fuels such as higher uranium density and improved thermal conductivity. Fluff is a highly porous structure forming at the top of metallic fuel slugs during irradiation and was extensively observed in past sodium-cooled fast reactor (SFR) experiments such as Idaho National Laboratory’s Experimental Breeder Reactor II (EBR-II). Previous investigations have shown that fluff is rich in fissile atoms and hence could have neutronics implications, but its formation mechanisms are not understood. In this work, two cube-shaped lift outs were taken from the fluff and bulk fuel regions of a high burnup U-19Pu-10Zr composition EBR-II fuel slug and characterized by micro computed tomography (Micro-CT) and energy dispersive x-ray spectroscopy (EDS). This was used to characterize differences in microscale porosity and composition between fluff and bulk fuel, and to support or oppose postulated fluff formation mechanisms. Surface EDS showed minimal differences between the elemental compositions of the fluff and fuel cubes. However, three-dimensional (3D) pore analysis from the tomography scans showed significant differences between the fluff and fuel cube pore size distributions at the microscale level. The high porosity and irregular pore distribution seen in macroscale fluff was also present within the micro-scale fluff cube, having a much higher porosity than the fuel cube which was concentrated in a few large pore networks. In conclusion, these results indicate support for a creep driven mechanism of fluff formation.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Dedicated beam position monitor pair for model-independent lattice characterization at NSLS-II

This paper reports recent lattice characterization results obtained at the National Synchrotron Light Source II (NSLS-II) storage ring, conducted without reliance on a lattice model. A pair of beam position monitors (BPMs) with bunch-by-bunch (B$\times$B) resolution, were recently installed in a section of the storage ring free of magnetic fields. The new BPM pair measured the beam, or bunch’s transverse Poincaré map precisely after the beam was excited. Linear one-turn-matrices (OTM) were then derived, and from these, the 4-dimensional coupled Twiss parameters were extracted at the locations of the BPM pair. By normalizing beam oscillation amplitudes with the Twiss parameters, the global action-variables were obtained. Additionally, these action-variables facilitated the measurement of the local Twiss parameters observed by other BPMs independent on lattice model. This method is general, and particularly useful in certain scenarios such as a round beam mode in a diffraction-limited light source ring. We applied it to assess both weakly and strongly coupled lattices at the NSLS-II ring. Through analysis of the strongly coupled lattice, the quadrupole tilt errors were estimated to be less than 400 μrad. Utilizing the BPMs’ B$\times$B resolution, for the first time we observed the variations of the linear lattice along a long bunch-train.

36 MATERIALS SCIENCE↗

Cu(II) Stability and UV-Induced Electron Transfer in a Metal–Organic Hybrid: An EPR, DFT, and Crystallographic Characterization of Copper-Doped Zinc Creatininium Sulfate

Single-crystal X-ray diffraction and electron paramagnetic resonance (EPR) spectroscopic experiments, complemented by quantum chemical DFT calculations, were carried out on the copper-doped metal–organic hybrid and Tutton salt analogue zinc creatininium sulfate to determine its crystal structure, to characterize the electronic structure of the doped Cu(II) binding site, and to propose a pathway for an excited-state, proton-coupled electron transfer (PCET) process in UV-exposed crystals. The crystal structure is isomorphous to that of cadmium creatininium sulfate, which has the transition ion, not in direct coordination with the creatinine, but forming a hexahydrate complex, which is bridged to a creatininium through an intervening sulfate ion. The EPR g (2.446, 2.112, 2.082) and copper hyperfine (A Cu : -327, -59.6, 10.8 MHz) tensor parameters are consistent with doped copper replacing host zinc in the metal–hexahydrate complex. These parameters are similar to those observed for copper hexahydrate in doped Tutton salt systems at low temperature, where the unpaired electron occupies mainly the copper 3d x 2 –y 2 orbital. At room temperature in the Tutton systems, vibration couplings stemming from a dynamic Jahn–Teller effect cause tensor averaging which results in a reduction in their maximum g-tensor and hyperfine tensor values. However, like for the doped isomorphous Cd creatinine crystal, the Cu(II) EPR exhibits little, or no room temperature averaging compared to its low temperature pattern. Samples exposed to 254 nm UV light generate a carbon-centered free radical species, characterized by an isotropic g-tensor (g = 2.0029) and an alpha-proton hyperfine coupling (-24 -14 +4 G). These parameters identify it as a creatinine radical cation formed by the oxidative release of one of its C2 methylene hydrogens. DFT calculations confirm the unpaired electronic structures of both the Cu(II) site and free radical. The growth in radical concentration with an increase in the UV exposure time coincides with a decrease in the copper EPR signal, indicating a coupled light-induced oxidation reduction process. A comparison of the crystal structure with the EPR parameters and DFT results provides evidence for a UV-induced PCET.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

WO 3 /CuWO 4 Ratio Controls Open-Circuit Photovoltage and Photocurrent in Type II Heterojunction Solar Fuel Photoelectrodes

WO 3 /CuWO 4 photoelectrodes for the oxygen evolution reaction benefit from a type II heterojunction for charge separation. However, the impact of the WO 3 /CuWO 4 ratio on the photocurrent and the photovoltage is not clear. To probe the effect of composition, Cu x W 1-x O y thin films with variable W:Cu ratio were prepared on FTO by reactive magnetron co-sputtering of W and Cu, followed by air annealing at 500ºC. EDS, XRD, Rietveld refinement, and Raman spectroscopy confirm the presence of crystalline WO 3 and CuWO 4 in the W rich films and increasing amounts of amorphous copper oxides in the Cu rich films. Bandgaps were determined by optical absorption spectroscopy, surface photovoltage spectroscopy (SPS), and photoaction spectra and are found to decrease from 2.7 eV to 1.2 eV with increasing copper oxide content. SPS reveals n-type semiconductor photoanode behavior for WO 3 /CuWO 4 samples and p-type photocathode behavior for CuO x rich films. Photoelectrochemical experiments confirm stable water oxidation with Faraday efficiency near unity for all W rich films and photocurrents that are increasing with CuWO 4 content. Optimal performance is seen for WO 3 /CuWO 4 mixed phases containing 47-75 mass% CuWO 4 . These compositions maximize charge separation at the type II heterojunction interface between the two materials. Additionally, according to incident photon to current efficiency (IPCE) data, the WO 3 improves photon conversion below 350 nm, while CuWO 4 improves conversion at 450-525 nm. Overall, this work shows for the first time how the WO 3 /CuWO 4 ratio controls the photovoltage and the photocurrent in type II heterojunction solar fuel photoelectrodes, and how copper oxides in the copper rich films severely degrade the performance. Furthermore, these results are useful in the context of bulk-heterojunction electrodes for the conversion of solar energy into fuels.

CuWO4↗

Coloring Tetrahedral Semiconductors: Synthesis and Photoluminescence Enhancement of Ternary II-III 2 -VI 4 Colloidal Nanocrystals

Ternary tetrahedral II-III 2 -VI 4 semiconductors, where II is Zn or Cd, III In or Ga, and VI S, Se, or Te, are of interest in UV radiation detectors in medicine and space physics as well as CO 2 photoreduction under visible light. We synthesize colloidal II-III 2 -VI 4 semiconductor nanocrystals from readily available precursors and ascertain their ternary nature by structural and spectroscopic methods, including 77 Se solid-state NMR spectroscopy. The pyramidally shaped nanocrystals range between 2 and 12 nm and exhibit optical gaps of 2–3.9 eV. In the presence of excess anions on the particle surface, treatment with Lewis acidic, Z-type ligands results in better passivation and enhanced photoluminescence. Electronic structure calculations reveal the most stable, lowest energy polymorphs and coloring patterns. This work will pave the way toward more environmentally friendly, ternary semiconductors for optoelectronics and electrocatalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site

During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.

60 APPLIED LIFE SCIENCES↗

Optimization and quantification of silver( II ) for mediated electrochemical oxidation applications

Mediated electrochemical oxidation (MEO) is a low-temperature, low-pressure, aqueous mineralization process used to treat organic waste. A powerful metal oxidant is used as a mediator in an acidic solution. Although Ce and Co are thoroughly studied mediators, Ag is a preferred choice because of the higher efficiency rates of mineralization observed with this system. Importantly, the quantification methodology and spectroscopic characteristics of the Ag(II) ion must be obtained. In this study, we determined molar extinction coefficients of the primary absorption band associated with the Ag(II) ion in 2–9 M HNO 3 solution. The optimization of Ag(II) electrooxidation was also determined by altering parameters such as HNO 3 concentration, mediator concentration, and temperature. The optimization studies and extinction coefficient data provide parameters for implementation of Ag as a suitable mediator for MEO processing of organic waste.

Schrage, Briana R. [Oak Ridge National Laboratory ↗

Ion implantation of magnesium guests into type II silicon clathrate films: an alternate approach to doping a cage-like silicon allotrope

Type II silicon clathrates, with their unique cage-like structure, offer exciting potential for applications in thermoelectrics, photovoltaics, and quantum materials due to their tunable electronic and thermal properties. This study investigates the use of ion implantation to introduce targeted guest atoms, which act as dopants, into type II Si clathrate films. The focus is on Mg as a test case for implantation, a dopant previously unreported in type II Si clathrates. The effects of ion implantation on the metastable Si clathrate structure were examined through systematic investigation of implant parameters. Time-of-flight secondary ion mass spectrometry depth profiling confirmed the successful implantation of Mg, while X-ray diffraction and confocal Raman spectroscopy demonstrated minimal structural damage at lower fluences, with the clathrate framework retaining its integrity without converting to other phases. At the higher end of the fluence range implantation caused localized transitions from clathrate to amorphous silicon. Implant activation using rapid thermal annealing was examined with the clathrate structure stable up to 500 °C and being converted to diamond silicon above this temperature. Post-implantation and activation structural characterization showed evidence of damage reversal. Electron paramagnetic resonance studies provided indirect evidence of dopant incorporation. These findings establish a foundation for introducing alternative guests/dopants into the Si clathrate cages through ion implantation, advancing their tunability for next-generation quantum and optoelectronic devices.

36 MATERIALS SCIENCE↗

Rigid cationic ligands enable high-efficiency NIR-II photoluminescence in copper( i ) iodide hybrid semiconductors

Near-infrared (NIR) luminescent materials are pivotal for advanced optoelectronic and biomedical applications, yet attaining efficient emission in the NIR-II region (950-1400 nm) remains challenging. Here, we introduce a ligand cationization strategy for designing copper(i) iodide-organic hybrid materials that emit in the NIR-II region (920-1120 nm) with PLQYs up to 8.58%. By incorporating rigid cationic ligands with CuI modules, we synergistically achieve bandgap narrowing (to 1.51 eV) and structural rigidification via ionic-dative bonding, effectively suppressing non-radiative decay while extending emission beyond 1100 nm. Coupled with solution processability-enabled by the successful synthesis of nanometer-sized nanoparticles in various shapes-and excellent thermal stability (≥210 °C), this work establishes ligand cationization as a universal approach for designing efficient NIR-II emitters.

Chen, Jingwen↗

Publication of the Belle II Software

The Belle II software was developed by a few hundred individual contributors over several years. Following the rising desire of making it publicly available, the collaboration established open source software policies and procedures. The political and technical challenges and their solutions at Belle II are discussed in this article. With the publication of the Belle II software, basf2, on GitHub and Zenodo in 2021 an important milestone towards open science was reached.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Fast and efficient Sb-based type-II phototransistors integrated on silicon

Increasing the energy efficiency and reducing the footprint of on-chip photodetectors enable dense optical interconnects for emerging computational and sensing applications. While heterojunction phototransistors (HPTs) exhibit high energy efficiency and negligible excess noise factor, their gain-bandwidth product (GBP) has been inferior to that of avalanche photodiodes at low optical powers. Here, we demonstrate that utilizing type-II energy band alignment in an Sb-based HPT results in six times smaller junction capacitance per unit area and a significantly higher GBP at low optical powers. These type-II HPTs were scaled down to 2 μm in diameter and fully integrated with photonic waveguides on silicon. Thanks to their extremely low dark current and high internal gain, these devices exhibit a GBP similar to the best avalanche devices (∼270 GHz) but with one order of magnitude better energy efficiency. Their energy consumption is about 5 fJ/bit at 3.2 Gbps, with an error rate below 10−9 at −25 dBm optical power at 1550 nm. These features suggest new opportunities for creating highly efficient and compact optical receivers based on phototransistors with type-II band alignment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Type-I and type-II interfaces in a MoSe 2 /WS 2 van der Waals heterostructure

We report experimental evidence that MoSe 2 and WS 2 allow the formation of type-I and type-II interfaces, according to the thickness of the former. Heterostructure samples are obtained by stacking a monolayer WS 2 flake on top of a MoSe 2 flake that contains regions of thickness from one to four layers. Photoluminescence spectroscopy and transient absorption measurements reveal a type-II interface in the regions of monolayer MoSe 2 in contact with monolayer WS 2 . In other regions of the heterostructure formed by multilayer MoSe 2 and monolayer WS 2 , features of type-I interface are observed, including the absence of charge transfer and dominance of intralayer excitons in MoSe 2 . Furthermore, the coexistence of type-I and type-II interfaces in a single heterostructure offers opportunities to design sophisticated two-dimensional materials with finely controlled photocarrier behaviors.

2D materials↗

Photoelectron Spectroscopy and Structural Characterization of [EDTA·M(II)]2-·nH2O (M = Ni, Cu, Zn; n = 0-2) Complexes

We investigated microhydrated transition metal-EDTA dianion complexes [EDTA·M(II)]2-·nH2O (M = Ni, Cu, and Zn; n = 1, 2) using cryogenic photoelectron spectroscopy in conjunction with theoretical calculations. The measured spectra of [EDTA·Ni/Zn(II)]2-·nH2O closely resemble those of their corresponding bare dianions, with a systematic shift towards high electron binding energy side upon stepwise hydration and featuring a hexadentate metal-EDTA binding motif. In contrast, the spectra of hydrated [EDTA·Cu(II)]2- exhibit broadened first detachment bands, implying coexistence of multiple metal-ligand binding forms, as a consequence of the Jahn-Teller effect associated with its d9 electron arrangement. These findings showcase molecular-level insights into the structural adaptability of EDTA-based supramolecular assemblies comprising transition metal ions, water molecules, and multidentate ligand environments.

Ling, Zicheng↗

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗

Linking transients to their host galaxies – II. A comparison of host galaxy properties and rate dependencies across supernova types

ABSTRACT We use the latest data set of supernova (SN) host galaxies to investigate how the host properties – stellar mass, star formation rate (SFR), metallicity, absolute magnitude, and colour–differ across SN types, with redshift-driven selection effects controlled. SN Ib and Ic host galaxies, on average, are more massive, metal-rich, and redder than SN II hosts. For subtypes, SN Ibn and Ic-BL have bluer hosts than their normal SN Ib and Ic siblings; SN IIb has consistent host properties with SN Ib, while hosts of SN IIn are more metal-rich than those of SN II. Hydrogen-deficient superluminous SNe feature bluer and lower luminosity hosts than most subtypes of core-collapse supernova (CC SN). Assuming simple proportionality of CC SN rates and host SFRs does not recover the observed mean host properties; either a population of long-lived progenitors or a metallicity-dependent SN production efficiency better reproduces the observed host properties. Assuming the latter case, the rates of SN II are insensitive to host metallicity, but the rates of SN Ib and Ic are substantially enhanced in metal-rich hosts by a factor of $\sim 10$ per dex increase in metallicity. Hosts of SN Ia are diverse in their observed properties; subtypes including SN Ia-91T, Ia-02cx, and Ia-CSM prefer star-forming hosts, while subtypes like SN Ia-91bg and Ca-rich prefer quiescent hosts. The rates of SN Ia-91T, Ia-02cx, and Ia-CSM are closely dependent on, or even proportional to, their host SFRs, indicating relatively short-lived progenitors. Conversely, the rates of SN Ia-91bg and Ca-rich transients are proportional to the total stellar mass, favouring long-lived progenitors.

Qin, Yu-Jing (ORCID:0000000336586026)↗