Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f
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99 GENERAL AND MISCELLANEOUS↗
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Correlative analysis of structure and chemistry of Li x FePO 4 platelets using 4D-STEM and X-ray ptychography
Lithium iron phosphate (Li x FePO 4 ), a cathode material used in rechargeable Li-ion batteries, phase separates upon de/lithiation under equilibrium. The interfacial structure and chemistry within these cathode materials affects Li-ion transport, and therefore battery performance. Here, correlative imaging of Li x FePO 4 was performed using four-dimensional scanning transmission electron microscopy (4D-STEM), scanning transmission X-ray microscopy (STXM), and X-ray ptychography in order to analyze the local structure and chemistry of the same particle set. Over 50,000 diffraction patterns from 10 particles provided measurements of both structure and chemistry at a nanoscale spatial resolution (16.6–49.5 nm) over wide (several micron) fields-of-view with statistical robustness. Li x FePO 4 particles at varying stages of delithiation were measured to examine the evolution of structure and chemistry as a function of delithiation. In lithiated and delithiated particles, local variations were observed in the degree of lithiation even while local lattice structures remained comparatively constant, and calculation of linear coefficients of chemical expansion suggest pinning of the lattice structures in these populations. Partially delithiated particles displayed broadly core–shell-like structures, however, with highly variable behavior both locally and per individual particle that exhibited distinctive intermediate regions at the interface between phases, and pockets within the lithiated core that correspond to FePO 4 in structure and chemistry. The results provide insight into the Li x FePO 4 system, subtleties in the scope and applicability of Vegard’s law (linear lattice parameter-composition behavior) under local versus global measurements, and demonstrate a powerful new combination of experimental and analytical modalities for bridging the crucial gap between local and statistical characterization.
25 ENERGY STORAGE↗
Cyanobacterial Phycobilisome Allostery as Revealed by Quantitative Mass Spectrometry
Phycobilisomes (PBSs) are the major photosynthetic light-harvesting complexes in cyanobacteria and red algae. PBS, a multisubunit protein complex, has two major interfaces that comprise intrinsically disordered regions (IDRs): rod–core and core-membrane. IDRs do not form regular, three-dimensional structures on their own. Their presence in the photosynthetic pigment–protein complexes portends their structural and functional importance. A recent model suggests that PB-loop, an IDR located on the PBS subunit ApcE and C-terminal extension (CTE) of the PBS subunit ApcG, forms a structural protrusion on the PBS core-membrane side, facing the thylakoid membrane. Here, the structural synergy between the rod–core region and the core-membrane region was investigated using quantitative mass spectrometry (MS). The AlphaFold-predicted CpcG-CTE structure was first modeled onto the PBS rod–core region, guided and justified by the isotopically encoded structural MS data. Quantitative cross-linking MS analysis revealed that the structural proximity of the PB-loop in ApcE and ApcG-CTE is significantly disturbed in the absence of six PBS rods, which are attached to PBS via CpcG-CTE, indicative of drastic conformational changes and decreased structural integrity. Furthermore, these results suggest that CpcG-rod attachment on the PBS rod–core side is essentially required for the PBS core-membrane structural assembly. The hypothesized long-range synergy between the rod–core interface (where the orange carotenoid protein also functions) and the terminal energy emitter of PBS must have important regulatory roles in PBS core assembly, light-harvesting, and excitation energy transmission. These data also lend strategies that genetic truncation of the light-harvesting antennas aimed for improved photosynthetic productivity must rely on an in-depth understanding of their global structural integrity.
59 BASIC BIOLOGICAL SCIENCES↗
Constraining Flexibility in the MIL-88 Topology through Integration of 3-Dimensional Linkers
Metal–organic frameworks (MOFs) are a class of crystalline, nanoporous materials that are recognized for their tunability. While some MOFs demonstrate flexibility, this characteristic can pose challenges in achieving precise pore control or establishing permanent porosity. Specifically, MIL-88B, is notable for its high flexibility, as it is constructed from metal trimer clusters and 2-dimensional linkers (2DLs) featuring planar, aromatic cores, allowing significant structural changes. In this study, we synthesized two new MOFs, NU-2010 and NU-2011, which are structurally analogous to MIL-88B but incorporate ditopic 3-dimensional linkers (3DLs) with sterically bulky cores and higher symmetry. Our aim was to investigate whether the introduction of 3DLs could mitigate the flexibility observed in MIL-88B. We employed a combination of single crystal and powder X-ray diffraction techniques to assess the flexibility of MIL-88B, NU-2010, and NU-2011 under various conditions including thermal activation, solvent exchange, and temperature changes. Furthermore, our findings indicate that incorporating 3DLs significantly reduces framework flexibility in NU-2010 and NU-2011 relative to MIL-88B.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals
The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2’s nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5’ end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
60 APPLIED LIFE SCIENCES↗
In-situ X-ray scattering study of isotactic polypropylene/graphene nanocomposites under shear during fused deposition modeling 3D printing
Complementary techniques were applied to characterize the structure property relationships of FDM printed isotactic polypropylene/graphene nanocomposites. Raman spectroscopy indicated that graphene was mostly exfoliated during the nozzle extrusion process. Rheological measurements of the viscosity indicated that the presence of graphene induced shear thinning during extrusion. Azimuthal scans of wide angle x-ray scattering indicate correlated thermal fluctuations of the graphene platelets which stops abruptly at the onset of transcrystallization, or templating of the iPP chains on the graphene. X-ray microbeam SAXS analysis show the formation of ‘shish-kebab’ structures at the core of the unfilled filaments, where the ‘kebab’ component vanishes at the fiber-fiber interface enabling interdiffusion. Weak lamellar structure, and a corresponding decrease in the storage modulus are observed with the addition of 5% graphene. The lamellar structure disappears entirely with the addition of 10% graphene, while the storage modulus is decreased by nearly 50%. Thermal imaging of heat flux dissipation across molded and printed samples shows no orientational effects in pure iPP despite differences in crystal structure. Thermal conductivity increases dramatically in the samples with 10% graphene, and strong orientational effects are observed where the thermal coefficients differ by 180% between samples printed parallel or perpendicular to the heat flux.
36 MATERIALS SCIENCE↗
Machine Learning for DUNE Supernova Trigger
One of the major scientific goals of the Deep Underground Neutrino Experiment (DUNE) is to detect and measure the neutrino flux originating from galactic core-collapse supernovae. These neutrinos provide an opportunity to study the end of life evolution of massive stars, and reveal information about the structure of core-collapse that is not visible in observations of the electromagnetic spectrum. Because of the rarity of these events, it is crucial that DUNE is able to detect supernova neutrino interactions when they occur. However, this will require sifting through a large quantity of data, motivating the development of a trigger algorithm to identify significant events and discard irrelevant data. Machine learning provides a potential approach to building this trigger. This project generates ADC and ground truth images of simulated neutrino interactions in a LArTPC detector to be used for machine learning, and uses them to train a sparse Convolutional Neural Network (C NN). The performance of this model when applied to the task of pixel classification based on interaction type is examined. This project found that the sparse CNN approach has the potential to have high accuracy in pixel classification, meaning it may be highly relevant to the development of a supernova neutrino trigger for the DUNE far detector.
Damish, S.↗
Revealing Structural Evolution of Nickel Phosphide-Iron Oxide Core–Shell Nanocatalysts in Alkaline Medium for the Oxygen Evolution Reaction
Metal phosphide-containing materials have emerged as a potential candidate of non-precious metal-based catalysts for alkaline oxygen evolution reaction (OER). While it is known that metal phosphide undergoes structural evolution, considerable debate persists regarding the effects of dynamics on the surface activation and morphological stability of the catalysts. In this study, we synthesize NiP x -FeO x core-shell nanocatalysts with an amorphous NiP x core designed for enhanced OER activity. Using ex-situ X-ray absorption spectroscopy, we elucidate the local structural changes as a function of cyclic voltammetry cycles. Our studies suggest that the presence of corner-sharing octahedra in the FeO x shell improves structural rigidity through interlayer cross-linking, thereby inhibiting the diffusion of OH - /H 2 O. Thus, the FeO x shell preserves the amorphous NiP x core from rapid oxidation to Ni 3 (PO 4 ) 2 and Ni(OH) 2 . On the other hand, the incorporation of Ni from the core into the FeO x shell facilitates absorption of hydroxide ions for OER. As a result, the Ni/Fe(OH) x at the surface oxidizes to the active γ-(oxy)hydroxide phase under the applied potentials, promoting OER. This intriguing synergistic behavior holds significance as such synthetic route involving the FeO x shell can be extended to other systems, enabling manipulation of surface adsorption and diffusion of hydroxide ions. These findings also demonstrate that nanomaterials with core-shell morphology can be tuned to leverage the strength of each metallic component for improved electrochemical activities.
25 ENERGY STORAGE↗
Multi-scale investigation of heterogeneous swift heavy ion tracks in stannate pyrochlore
Er 2 Sn 2 O 7 pyrochlore was irradiated with swift heavy Au ions (2.2 GeV), and the induced structural modifications were systematically examined using complementary characterization techniques including transmission electron microscopy (TEM), X-ray diffraction (XRD), and neutron total scattering with pair distribution function (PDF) analysis. Each technique probes different aspects and length scales of the transformed material regions. TEM revealed a core–shell ion track structure—an amorphous core surrounded by a disordered, anion-deficient fluorite shell—which was confirmed by XRD. Neutron total scattering, with sensitivity to the oxygen sublattice, provided relative fractions of amorphous and disordered fluorite phases and confirmed the presence of a defective pyrochlore phase, which largely maintains its structural ordering but is clearly distinct from the pristine pyrochlore matrix. This defect-rich pyrochlore phase forms a halo extending radially beyond the well-characterized core–shell track morphology observed in electron micrographs. Despite their differing long-range periodicity, the short-range structures of the amorphous, disordered, and defective pyrochlore phases are all modeled well with a weberite-type configuration. Evolution of the phase fractions with increasing ion fluence was examined to ascertain the phase-to-phase pathways that occur during primary and secondary ion impact. Furthermore, this approach extends knowledge about the multi-scale response of stannate pyrochlores to swift heavy ion irradiation in the electronic energy loss regime and improves existing track-overlap models.
36 MATERIALS SCIENCE↗
Self-radiography of imploded shells on OMEGA based on additive-free multi-monochromatic continuum spectral analysis
Radiographs of pure-DT cryogenic imploding shells provide critical validation of progress toward ignition-scalable performance of inertial confinement fusion implosions. Cryogenic implosions on the OMEGA Laser System can be self-radiographed by their own core spectral emission near ≈2 keV. Utilizing the distinct spectral dependences of continuum emissivity and opacity, the projected optical-thickness distribution of imploded shells, i.e., the shell radiograph, can be distinguished from the structure of the core emission distribution in images.Importantly, this can be done without relying on spectral additives (shell dopants), as in previous applications of implosion self-radiography. Furthermore, demonstrations with simulated data show that this technique is remarkably well-suited to cryogenic implosions and can also be applied to self-radiography of imploded room-temperature CH shells at higher spectral energy (hv ≈ 3–5 keV) based on the very similar continuum spectrum of carbon. Experimental demonstration of additive-free self-radiography with warm CH shell implosions on OMEGA will provide an important proof of principle for future applications to cryogenic DT implosions.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Probing the atomically diffuse interfaces in Pd@Pt core-shell nanoparticles in three dimensions
Deciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We quantify the rich structural variety of core-shell nanoparticles with heteroepitaxy in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is found to be atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle’s morphology or crystallographic texture. The high concentration of Pd in the diffusive interface is highly related to the free Pd atoms dissolved from the Pd seeds, which is confirmed by atomic images of Pd and Pt single atoms and sub-nanometer clusters using cryogenic electron microscopy. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into precise nanomaterial manipulation and chemical property regulation.
74 ATOMIC AND MOLECULAR PHYSICS↗
Satellites, core hole excitations, and spin-resolved electronic structure in the spectroscopy of half-metallic CrO 2
Photoelectron satellites—the structures appearing on the low kinetic or high binding-energy side of the “main” or “elastic” photopeak—betray the complex many-body interactions set in motion by the sudden creation of the core hole. In this work, we demonstrate, using the technologically important ferromagnetic half-metal CrO 2 , how such satellites can manifest themselves in other core-level spectroscopies of the material and how they can reveal important details pertinent to its electronic structure. Specifically, we identify a fluorescence satellite in the Cr 𝐿 3 resonant x-ray-emission spectra that radiates at a constant emission energy across the Cr 𝐿 3 x-ray edge with energy ≈1.3 eV above the ordinary valence fluorescence. Here, we provide evidence that this feature arises from the valence recombination of the Cr 2𝑝 core hole “dressed” by the same shakeup charge-transfer process present in both the Cr x-ray photoelectron and the Cr x-ray absorption spectra with its energy uniquely measuring the exchange splitting of the Cr 3𝑑 level. Further analysis of the x-ray emission data reveals three additional features that radiate at constant loss energy that are attributed to combinations of Cr 3𝑑(𝑡 2𝑔 ) → Cr 3𝑑(𝑡 2𝑔 ), charge-transfer O 2𝑝→Cr 3𝑑, and crystal-field Cr 3𝑑(𝑡 2𝑔 )→Cr 3𝑑(𝑒 𝑔 ) excitations. These assignments and their energies are supported by density-functional theory calculations, the accuracy of which we demonstrate by hard x-ray valence-photoemission measurements. Atomic multiplet calculations, which include crystal-field effects, help interpret x-ray photoelectron and x-ray absorption spectra of the covalently mixed Cr ion. Resonant Cr K-𝐿 2,3 𝐿 2,3 Auger-electron emission spectra support a ligand-to-metal nature of the charge-transfer process while highlighting the charge sensitivity differences between photon-in/electron-out and photon-in/photon-out spectroscopies.
36 MATERIALS SCIENCE↗
Out of the Lab: 3D Printing on Non-Ideal Surfaces
In this work, coaxial direct ink writing is utilized to print sensitive or encapsulated materials onto heterogeneous and rough substrates. By enclosing the core fluid within a rigid ceramic shell, continuity is maintained even when printing on substrates traditionally considered challenging. This work presents the development of a coaxial ceramic direct ink writing system and investigates co-flow dynamics through microfluidic principles. A specially designed coaxial nozzle enables the co-extrusion of an alumina shell, with indium-tin-oxide inks serving as the core material. This approach allows the fabrication of core-shell ceramic structures suitable for future high-temperature applications on rough surfaces. The colloidal inks are tailored to achieve the necessary rheological properties and sintering performance. Additionally, flow simulations, guided by microfluidic co-flow principles, are employed to define the processing parameters for coaxial printing, ensuring precise control over the core-shell architectures. Physical modeling is further applied to study core deformation and eccentricity. These simulations are experimentally validated, supporting the successful deposition of coaxial ceramic features on heterogeneous, high-temperature ceramic substrates.
20 FOSSIL-FUELED POWER PLANTS↗
Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5
Kinetoplastid protists such as Trypanosoma brucei undergo an unusual process of mitochondrial uridine (U) insertion and deletion editing termed kinetoplastid RNA editing (kRNA editing). This extensive form of editing, which is mediated by guide RNAs (gRNAs), can involve the insertion of hundreds of Us and deletion of tens of Us to form a functional mitochondrial mRNA transcript. kRNA editing is catalyzed by the 20 S editosome/RECC. However, gRNA directed, processive editing requires the RNA editing substrate binding complex (RESC), which is comprised of 6 core proteins, RESC1-RESC6. To date there are no structures of RESC proteins or complexes and because RESC proteins show no homology to proteins of known structure, their molecular architecture remains unknown. RESC5 is a key core component in forming the foundation of the RESC complex. To gain insight into the RESC5 protein we performed biochemical and structural studies. We show that RESC5 is monomeric and we report the T . brucei RESC5 crystal structure to 1.95 Å. RESC5 harbors a dimethylarginine dimethylaminohydrolase-like (DDAH) fold. DDAH enzymes hydrolyze methylated arginine residues produced during protein degradation. However, RESC5 is missing two key catalytic DDAH residues and does bind DDAH substrate or product. Implications of the fold for RESC5 function are discussed. This structure provides the first structural view of an RESC protein.
59 BASIC BIOLOGICAL SCIENCES↗
A review on the state of thermal hydraulics research on air ingress scenarios in High-Temperature Gas-cooled Reactors following a D-LOFC
With the expectation of near-immediate carbon neutrality, widespread implementation of proven High-Temperature Gas-cooled Reactors (HTGRs) embodies a viable solution pathway given their inherent, passive safety features and high thermal efficiency. This study provides an overview of the current state of research involving the thermal hydraulics associated with air ingress from a depressurized loss of forced cooling (D-LOFC) in HTGRs. Accurately characterizing and predicting the physical phenomena underlying air ingress is of paramount concern, as the integrity of the fuel and core graphite support structures are threatened by the presence of oxygen. Broadly speaking, the air ingress scenario can be delineated into three main stages: (1) Depressurization, (2) Density-Driven Flow, and (3) Natural Convection. In tandem with the underlying fundamental theory, this review collates and synthesizes the existing body of contemporary research concerning the air ingress scenario following a D-LOFC. As evinced by this review, our current understanding and predictive abilities have benefited from extensive research, predominantly concentrated on the rate of air ingestion into the core. Here, additional research is necessary to holistically capture the phenomenology of an air ingress scenario following a D-LOFC by considering an additional variable: the oxygen content of the ingressing air. The latter variable requires investigation into the complex interactions of the fully integrated system. Additionally, while numerical tools are evolving domestically through the Nuclear Energy Advanced Modeling and Simulation program, a sufficiently validated code remains absent.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Size-dependent second-order-like phase transitions in Fe nanocluster melting from low-temperature structural isomerization
Here, in this work, the melting phase transitions of Fe n nanoclusters with 10 ≤ n ≤ 100 atoms are investigated using classical many-body molecular dynamics simulations. For many cluster sizes, surface melting occurs at much lower temperatures than core melting. Surface and core melting points and energetic melting points (temperatures of maximum heat capacity, C v ) are calculated for all cluster sizes. Melting properties are found to be strong functions of cluster structure. Cluster sizes with closed-shell structures always have first-order-like phase transitions. Almost one-third of cluster sizes in the analyzed range exhibit second-order-like phase transitions due to the presence of multiple structural configurations close in energy. 1-shell clusters with one to a few more atoms than a neighboring closed-shell structure have very low surface melting points and very high energetic melting points compared to their closed-shell counterparts. In clusters above 50 atoms with certain core structures, melting of the surface before the core was observed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Microsolvation in V + (H 2 O) n Clusters Studied with Selected-Ion Infrared Spectroscopy
Gas phase ion-molecule clusters of the form V + (H 2 O) n (n = 1-30) are produced by laser vaporization in a supersonic expansion. These ions are analyzed and mass-selected with a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy. The small clusters (n ≤ 7) are studied with argon tagging, while the larger clusters are studied via the elimination of water molecules. The vibrational spectra for the small clusters include only free O-H stretching vibrations, while larger clusters exhibit red-shifted hydrogen bonding vibrations. The spectral patterns reveal that the coordination around V + ions is completed with four water molecules. A symmetric square-planar structure forms for the n = 4 ion, and this becomes the core ion in larger structures. Clusters up to n = 8 have mostly two-dimensional structures, but hydrogen bonding networks evolve to three-dimensional structures in larger clusters. The free O-H vibration of AAD (acceptor-acceptor-donor) coordinated surface molecules converges to a frequency near that of bulk water by the cluster size of n = 30. However, the splitting of this vibration for AAD- versus AD-coordinated molecules is still different compared to other singly-charged or doubly-charged cation-water clusters. Finally, this indicates that cation identity and charge-site location in the cluster can produce discernible spectral differences for clusters in this size range.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The crystal structure of Fe2S at 90 GPa based on single-crystal X-ray diffraction techniques
The Fe-S system was explored in a laser-heated diamond-anvil cell at 89(2) GPa and 2380(120) K to better understand the phase stability of Fe 2 S. Upon temperature quenching, crystallites of Fe 2 S were identified, and their structure was investigated using single-crystal X-ray diffraction techniques. At these conditions, Fe 2 S adopts the C23 structure (anti-PbCl 2 , Co 2 P) with space group Pnma (Z = 4). This structure consists of columns of corner-sharing, FeS 4 tetrahedra, and columns of edge-sharing FeS 5 square pyramids linked along edges in the b direction. Sulfur is in ninefold coordination with Fe. This work marks the first high-pressure structural solution and refinement of Fe 2 S synthesized in a multigrain Fe+FeS sample at 90 GPa and 2400 K and establishes the stability of C23 Fe 2 S at these conditions. A previous powder diffraction study reports an orthorhombic Fe 2 S phase with a C37, Co 2 Si-like unit cell above 190 GPa. A C23–C37 structural transition is inferred to explain the previously observed unit-cell parameters at higher pressures and temperatures. These results highlight the utility of applying single-crystal X-ray diffraction techniques to high P-T multigrain samples to explore the structural properties of iron-rich phases in Earth and planetary cores.
36 MATERIALS SCIENCE↗