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At least 19 records

AlphaFold Protein Structure Database for Sequence-Independent Molecular Replacement

Crystallographic phasing recovers the phase information that is lost during a diffraction experiment. Molecular replacement is a commonly used phasing method for crystal structures in the protein data bank. In one form it uses a protein sequence to search a structure database to find suitable templates for phasing. However, sequence information is not always available, such as when proteins are crystallized with unknown binding partner proteins or when the crystal is of a contaminant. The recent development of AlphaFold published the predicted protein structures for every protein from twenty distinct species. In this work, we tested whether AlphaFold-predicted E. coli protein structures were accurate enough to enable sequence-independent phasing of diffraction data from two crystallization contaminants of unknown sequence. Using each of more than 4000 predicted structures as a search model, robust molecular replacement solutions were obtained, which allowed the identification and structure determination of YncE and YadF. Our results demonstrate the general utility of the AlphaFold-predicted structure database with respect to sequence-independent crystallographic phasing.

59 BASIC BIOLOGICAL SCIENCES↗

Large-scale 2D heterostructures from hydrogen-bonded organic frameworks and graphene with distinct Dirac and flat bands

The current strategies for building 2D organic-inorganic heterojunctions involve mostly wet-chemistry processes or exfoliation and transfer, leading to interface contaminations, poor crystallizing, or limited size. Here we show a bottom-up procedure to fabricate 2D large-scale heterostructure with clean interface and highly-crystalline sheets. As a prototypical example, a well-ordered hydrogen-bonded organic framework is self-assembled on the highly-oriented-pyrolytic-graphite substrate. The organic framework adopts a honeycomb lattice with faulted/unfaulted halves in a unit cell, resemble to molecular “graphene”. Interestingly, the topmost layer of substrate is self-lifted by organic framework via strong interlayer coupling, to form effectively a floating organic framework/graphene heterostructure. The individual layer of heterostructure inherits its intrinsic property, exhibiting distinct Dirac bands of graphene and narrow bands of organic framework. Our results demonstrate a promising approach to fabricate 2D organic-inorganic heterostructure with large-scale uniformity and highly-crystalline via the self-lifting effect, which is generally applicable to most of van der Waals materials.

36 MATERIALS SCIENCE↗

Twelve-crystal prototype of Li 2 MoO 4 scintillating bolometers for CUPID and CROSS experiments

An array of twelve 0.28 kg lithium molybdate (LMO) low-temperature bolometers equipped with 16 bolometric Ge light detectors, aiming at optimization of detector structure for CROSS and CUPID double-beta decay experiments, was constructed and tested in a low-background pulse-tube-based cryostat at the Canfranc underground laboratory in Spain. Performance of the scintillating bolometers was studied depending on the size of phonon NTD-Ge sensors glued to both LMO and Ge absorbers, shape of the Ge light detectors (circular vs. square, from two suppliers), in different light collection conditions (with and without reflector, with aluminum coated LMO crystal surface). The scintillating bolometer array was operated over 8 months in the low-background conditions that allowed to probe a very low, μBq/kg, level of the LMO crystals radioactive contamination by 228 Th and 226 Ra.

47 OTHER INSTRUMENTATION↗

Investigating Influential Parameters for High-Purity Germanium Crystal Growth

This paper focuses on the research and development of high-purity germanium (HPGe) crystals for detector fabrication, specifically targeting applications in rare-event physics searches. The primary objective was to produce large-scale germanium crystals weighing >1 kg with a controlled diameter of ∼10 cm and an impurity range of approximately 1010/cm 3. Ensuring structural integrity and excellent crystalline quality requires a thorough assessment of dislocation density, a critical aspect of the crystal development process. Dislocation density measurements play a crucial role in maximizing the sensitivity of HPGe detectors, and our findings confirmed that the dislocation density fell within acceptable ranges for detector fabrication. Additionally, this paper examines the segregation coefficient of various contaminants during the crystal development process. Comprehensive analysis of impurity segregation is essential for reducing contaminant quantities in the crystal lattice and customizing purification processes. This, in turn, minimizes undesired background noise, enhancing signal-to-noise ratios for rare-event physics searches and overall detector performance. The investigation included the segregation coefficients of three major acceptors and one donor in crystals grown at the University of South Dakota, providing valuable insights for optimizing crystal purity and detector efficiency.

Bhattarai, Sanjay↗

Plutonium Co-precipitation with Calcite

The mobility of plutonium (Pu) in the environment is affected by Pu–mineral interactions, such as adsorption–desorption and structural incorporation. Calcite (CaCO 3 ) is a common secondary phase in near surface environments and a major component of many rocks and soils and is expected to form as an alteration product of cement-based materials planned for use in geological repositories. The reactivity of the calcite surface and its ability to tolerate significant variations in its chemical composition through substitution of Ca for other cations make calcite a potentially important sink for environmental contaminants. Here, single crystals of calcite were synthesized from aqueous solutions in equilibrium with air containing Pu as either Pu(VI) or Pu(IV) and characterized using a combination of laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) and X-ray absorption spectroscopy (XAS). These data are used to assess the amount, structure, and oxidation state of Pu co-precipitated into calcite, providing insight into the potential for Pu sequestration in calcite precipitates. Overall, the XAS and LA–ICP–MS data support the co-precipitation of plutonyl [Pu(VI/V)] in the bulk calcite, although the exact nature of the co-precipitated Pu complex is difficult to elucidate in the synthesized material. Co-precipitated plutonyl could be incorporated in either distorted Ca lattice sites or defect sites, and we provide evidence to suggest that Pu(VI) is reduced mainly to Pu(V) in the precipitated solid. LA–ICP–MS additionally shows that the co-precipitation of Pu(VI/V) is favored over the co-precipitation of Pu(IV). Altogether, our results suggest that Pu sequestration in calcite under environmental conditions could immobilize Pu and isolate it from groundwater interactions in contaminated environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Background identification in cryogenic calorimeters through $\alpha -\alpha$ delayed coincidences

Localization and modeling of radioactive contaminations is a challenge that ultra-low background experiments are constantly facing. These are fundamental steps both to extract scientific results and to further reduce the background of the detectors. Here we present an innovative technique based on the analysis of $\alpha -\alpha$ delayed coincidences in 232 Th and 238 U decay chains, developed to investigate the contaminations of the ZnSe crystals in the CUPID-0 experiment. This method allows to disentangle surface and bulk contaminations of the detectors relying on the different probability to tag delayed coincidences as function of the $\alpha$ decay position.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase)

The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with two molecules as asymmetric unit. Both crystal forms were obtained from trace contaminants of an old commercial lipase preparation. Structures were determined and refined to 1.65 Å and 1.43 Å resolution respectively. The latter crystal has a non-crystallographic (NCS) twofold axis within the asymmetric unit. Glycosylation at Asn197 is evident, and in the tetragonal crystal can be seen to include three, partially disordered sugar residues following the initial N-acetyl glucosamine (NAG). Superposition of the tetragonal crystal model on the α-amylases from Bacillus subtilis (PDB:1BAG), pig pancreas (PDB:3L2L), and barley (PDB:1AMY), show a high degree of coincidence, particularly for the (β/α)8-barrel domains, and especially within the active site. Using this structural agreement between amylases, we extrapolated the binding model of a six residue, limit dextrin found in pig pancreas α-amylase to the A. oryzae enzyme model, which predicts substrate interacting amino acid residues.

59 BASIC BIOLOGICAL SCIENCES↗

Solvent-driven aqueous separations for hypersaline brine concentration and resource recovery

Solvent-driven separation processes can extract water and high-value minerals from high salinity or contaminated brines, simultaneously reducing the environmental impact of brine disposal and enabling resource recovery. The efficient dewatering of hypersaline brines is essential for the sustainable minimal and zero liquid discharge processing of industrial wastewaters. Fractional crystallization can selectively extract ions from contaminated waste streams, allowing critical materials to be recycled, including transition and lanthanide metals required for renewable energy generation and storage. Mass transfer in solvent-driven water extraction occurs across a liquid–liquid interface, eliminating the scaling and fouling of membrane and heat exchanger surfaces and limiting the need for extensive pretreatment. Solvent-driven fractional crystallization can leverage sequential treatment and control of process conditions to rapidly recover salts without requiring evaporation of water. Despite promising applications, the principles and potential of solvent-driven aqueous separations remain poorly understood. This critical review explores the opportunities presented by solvent-based aqueous separations from the molecular to process scale, evaluating the chemistry of solvation and system design in the broader context of desalination, resource recovery, water softening, and mineral production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Closed-loop recycling of mixed polyesters via catalytic methanolysis and monomer separations

A sustainable plastics future will require high recycling rates and the use of biogenic feedstocks, which together are catalyzing interest in replacing fossil fuel-derived, noncircular polyolefin packaging materials with bio-based, chemically recyclable polyesters. Here, in this study, we present a catalytic methanolysis process capable of depolymerizing both fossil fuel- and bio-based polyesters, including polyethylene terephthalate (PET), polylactic acid, polybutylene adipate terephthalate and polybutylene succinate in one reactor under mild conditions with high monomer yields. We scaled this process to 1 kg and integrated separations engineering using activated carbon, crystallization, extraction and distillation to remove contaminants and recover individual monomers from depolymerized mixed polyesters with high yield and purity. PET synthesized from monomers isolated from postconsumer materials showed comparable mechanical and thermal properties to PET from commercial monomers. Techno-economic analysis and life cycle assessment show that this process is economically viable and exhibits lower environmental impacts than primary production of respective polymers.

09 BIOMASS FUELS↗

Mercury Detection Utilizing an Aquatic Animal as a Remote-Sensing Platform

Mercury species in open water, especially the accumulated methylmercury ion, pose a threat to fish and environment. Therefore, it is important to develop a small sensor package that can be integrated into a biotelemetry sensor carried by an aquatic animal, enhancing the ability to detect mercury contamination in large water areas. A quartz crystal microbalance (QCM) sensor using metal-organic framework (MOF) as sensing material was developed to detect mercury and methylmercury ions in real time based on acoustic wave perturbation. Thiol groups were introduced into the MOF UiO-66 through the organic linker to prepare the UiO-66-SH which was confirmed by infrared spectroscopy results. Batch adsorption experiments were conducted for the Hg 2+ , CH 3 Hg + , and Ca 2+ ions adsorption in the UiO-66-SH. The adsorption capacities of the mercury ions were more than an order of magnitude higher than those of the competing Ca 2+ ions at the same concentration. The frequency changes of the QCM sensor with the UiO-66-SH sensing film were an order of magnitude higher than those of the controlled baseline QCM sensor without a sensing film. Additionally, the frequency change can be tailored by adjusting the thickness of the MOF film and the adsorption properties of the sensing material. The sensor frequency change correlates well with ion adsorption capacities.

47 OTHER INSTRUMENTATION↗

Isolating p- and n-Doped Fingers With Intrinsic Poly-Si in Passivated Interdigitated Back Contact Silicon Solar Cells

Polycrystalline silicon on silicon oxide (poly-Si/SiO x ) passivating contacts enable ultra high efficiency interdigitated back contact silicon solar cells. To prevent shunt between n- and p-type doped fingers, an insulating region is required between them. We evaluate the use of intrinsic poly Si for this isolation region. Interdigitated fingers were formed by plasma deposition of doped hydrogenated amorphous silicon through mechanically aligned shadow masks, on top of a full-area intrinsic amorphous silicon layer. High temperature annealing then crystallized the a-Si:H to poly Si and drove in the dopants. Two mechanisms were identified which cause contamination of the intrinsic poly Si gap during processing. During deposition of doped fingers, we show using secondary ion mass spectrometry and conductivity measurements that the intrinsic gap becomes contaminated by doped a-Si:H tails several nanometers thick to concentrations of ~10 20 cm -3 . Another source of contamination occurs during high-temperature annealing, where dopants desorb from doped regions and readsorb onto intrinsic a Si:H. Both pathways reduce the resistivity of the intrinsic gap from ~10 5 Ω·cm to ~10 -1 Ω·cm. We show that plasma etching of the a-Si:H surface before crystallizing with a capping layer can eliminate the contamination of the intrinsic poly-Si, maintaining a resistivity of ~10 5 Ω·cm. Lastly, this demonstrates masked plasma deposition as a dopant patterning method for Si solar cells.

14 SOLAR ENERGY↗

GaAs Solar Cells Grown on Intentionally-Contaminated GaAs Substrates

III-V solar cells have the best performance of any semiconductor materials, but deposition of these materials relies on high-quality single crystal GaAs wafers for their superior performance. Unfortunately, the cost of these wafers makes these high-efficiency devices only accessible in high-value or niche markets. Here, we explored the effect of growing bulk GaAs crystals with lower purity input materials in order to reduce their cost. We observe that intentional impurities added to the melt before the crystal growth occurs segregate to the top of the boule. Single junction GaAs solar cells grown on wafers made from contaminated boules showed no performance degradation compared to a high-purity control wafer. These results suggest that lower purity Ga and As source materials can be used during crystal growth to reduce the cost of wafers.

41 EE - Solar Energy Technologies Office (EE-4S)↗

Improved robustness of sequentially deposited potassium cesium antimonide photocathodes achieved by increasing the potassium content towards theoretical stoichiometry

Alkali antimonide semiconductor photocathodes are promising candidates for high-brightness electron sources for advanced accelerators, including free-electron lasers (FEL), due to their high quantum efficiency (QE), low emittance, and high temporal resolution. Two challenges with these photocathodes are (1) the lack of a universal deposition recipe to achieve crystal stoichiometries and (2) their high susceptibility to vacuum contamination, which restricts their operation pressure to ultrahigh vacuums and leads to a short lifetime and low extraction charge. To resolve these issues, it is essential to understand the elemental compositions of deposited photocathodes and correlate them to robustness. Here, we report depth profiles for potassium cesium antimonide photocathodes, which were investigated using synchrotron radiation x-ray photoelectron spectroscopy, and the robustness of those photocathodes. We prepared two types of photocathodes with different potassium contents via sequential thermal evaporation. Depth profiles revealed that the photocathodes with a potassium deficit had excess cesium at the surface, while the ratio of potassium and cesium to antimony decreased rapidly within the film. In contrast, the photocathodes with sufficient potassium had close to the theoretical stoichiometry of K 2 CsSb at the surface and maintained that stoichiometry for over half the entire film thickness. Both photocathode types had a similar maximum QE at 532 nm; however, exposure to oxygen revealed that the photocathode with a crystalline stoichiometry of K 2 CsSb maintained QE at one order of magnitude higher pressure compared to its potassium-deficit counterpart. These results highlight the importance of synthesizing potassium cesium antimonide photocathodes with sufficient potassium to achieve the theoretical crystalline stoichiometry for both high QE and improved robustness.

47 OTHER INSTRUMENTATION↗

Cluster Analysis of Combined EDS and EBSD Data to Solve Ambiguous Phase Identifications

A common problem in analytical scanning electron microscopy (SEM) using electron backscatter diffraction (EBSD) is the differentiation of phases with distinct chemistry but the same or very similar crystal structure. X-ray energy dispersive spectroscopy (EDS) is useful to help differentiate these phases of similar crystal structures but different elemental makeups. However, open, automated, and unbiased methods of differentiating phases of similar EBSD responses based on their EDS response are lacking. This paper describes a simple data analytics-based method, using a combination of singular value decomposition and cluster analysis, to merge simultaneously acquired EDS + EBSD information and automatically determine phases from both their crystal and elemental data. I use hexagonal TiB 2 ceramic contaminated with multiple crystallographically ambiguous but chemically distinct cubic phases to illustrate the method. Code, in the form of a Python 3 Jupyter Notebook, and the necessary data to replicate the analysis are provided as Supplementary material.

47 OTHER INSTRUMENTATION↗

Exploring the phase space of Zn 2 SbN 3 , a novel semiconducting nitride

The novel semiconductor Zn 2 SbN 3 is one of a growing list of ternary nitrides with promise for optoelectronic and energy applications. Previous work by Arca et al. [Materials Horizons, 2019, 6, 1669–1974] first reported synthesis of this material, but did not explore the effects of growth conditions on material formation. In this work, we present a semi-automated study of the relationship between growth conditions and crystallinity via high-throughput RF sputtering and a custom X-ray diffraction analysis routine. Zn 2 SbN 3 is found to crystallize in a wide range of growth conditions, and the formation of several contaminant phases is examined. Electron microscopy of these secondary phases, caused both by off-stoichiometry and by growth conditions, provides insight into the growth mechanisms of Zn 2 SbN 3 . Furthermore, computational work relates this material to other Zn-based ternary nitrides and offers an explanation for the difficulty of growing cation-ordered material despite the wide range of growth conditions explored.

36 MATERIALS SCIENCE↗

Relationship of Chemical Composition and Moisture Sensitivity in LiNi x Mn y Co 1-x-y O 2 for Lithium-Ion Batteries

Chemical composition–moisture sensitivity relationship of LiNi x Mn y Co 1-x-y O 2 (NMC) cathode materials was investigated by exploring crystal structures, surface properties, and electrochemical performance behaviors of various commercial NMC powders: LiNi 1/3 Mn 1/3 Co 1/3 O 2 (NMC111), LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC532), LiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC622), and LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811). The NMC powders were stored in different moisture conditions: moisture-free, humidified air, or immersed in water. Rietveld refinement analysis of X-ray diffraction (XRD) data and scanning electron microscopy (SEM) were used to characterize the crystal structure changes and the evolution of particle surfaces morphologies. The effect of moisture contamination on the electrochemical properties of NMC cathodes was studied by galvanostatic cycling and electrochemical impedance spectroscopy (EIS). The moisture contamination resulted in either structural disorder or unwanted surficial deposition products, which increased a charge-transfer impedance and consequent performance degradation of battery cells. The results showed that NMC’s moisture vulnerability increased with Ni content (x) despite protective coatings on commercial particles, which stressed the necessity of alternative surface passivation strategies of Ni-rich NMC for broad applications such as electric vehicles and electrified aircraft propulsion.

25 ENERGY STORAGE↗

Remote epitaxy and selective epitaxy on vdW materials for layer transfer

Remote epitaxy is recently gaining huge attention forthe growth of single-crystal thin films and their isolation from the substrate for heterogeneous integration.Despite the recent progress, there are challenges inengineering the interface and optimizing the materialquality. Here, we introduce two approaches that could overcome the issues. As the first approach, we show directly grown 2D materials as a template for remote epitaxy of III-V and III-N materials. This ensuresa pristine interface without transfer process-related contaminations and damages. Second, we show theuse of nanopatterned graphene for selective epitaxyand lateral overgrowth of single-crystal films. This allows for the use of materials as substrates and epilayers which is not possible in remote epitaxy.

Kim, Hyunseok↗