Quantum-based Molecular Dynamics using Deep Neural Networks and AI Hardware
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Results for “core structure”
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Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis
Enediynes are among the most potent antitumor and antibacterial natural products. Studies on their biosynthetic pathways have identified a shared, linear polyene precursor generated from an iterative type I polyketide synthase (PKSE) as the source of the enediyne warhead. A key step is the release of this polyene from the PKSE by a discrete thioesterase (TE). Here, in this study, we used X-ray crystallography, site-directed mutagenesis, and heterologous coexpression of PKSEs and TEs to elucidate how enediyne TEs mediate the production of the polyene. We solved the structure of wild-type EspE7 from esperamicin producer Actinomodura verrucosospora. The substrate binding pocket was also defined upon serendipitous cocrystallization of an EspE7 mutant with a fatty acyl-CoA ligand. Structural data and in vitro activity assays with EspE7 mutants provide strong evidence that Glu68 in EspE7 and the analogous Glu residue in other enediyne TEs functions as a key catalytic residue, thus supporting a hydrolysis mechanism for enediyne TEs that aligns with that of Pseudomonas sp. 4-HB-CoA TE. Furthermore, combinations of 9- and 10-membered enediyne PKSEs and TEs produced 1,3,5,7,9,11,13-pentadecaheptaene (1) as the major product. Thus, the data further support previous conclusions that 1 serves as the sole precursor for the biosynthesis of all enediyne cores.
Enediynes↗
Covalent bond shortening and distortion induced by pressurization of thorium, uranium, and neptunium tetrakis aryloxides
Covalency involving the 5f orbitals is regularly invoked to explain the reactivity, structure and spectroscopic properties of the actinides, but the ionic versus covalent nature of metal-ligand bonding in actinide complexes remains controversial. The tetrakis 2,6-di- tert -butylphenoxide complexes of Th, U and Np form an isostructural series of crystal structures containing approximately tetrahedral MO 4 cores. We show that up to 3 GPa the Th and U crystal structures show negative linear compressibility as the OMO angles distort. At 3 GPa the angles snap back to their original values, reverting to a tetrahedral geometry with an abrupt shortening of the M-O distances by up to 0.1 Å. The Np complex shows similar but smaller effects, transforming above 2.4 GPa. Electronic structure calculations associate the M-O bond shortening with a change in covalency resulting from increased contributions to the M-O bonding by the metal 6d and 5f orbitals, the combination promoting MO 4 flexibility at little cost in energy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Influence of TMAO as co-solvent on the gelation of silica-PNIPAm core-shell nanogels at intermediate volume fractions
We study the structure and dynamics of poly(N-isopropylacrylamide) (PNIPAm) core-shell nanogels dispersed in aqueous trimethylamine N-oxide (TMAO) solutions by means of smallangle X-ray scattering and X-ray photon correlation spectroscopy (XPCS). Upon increasing the temperature above the lower critical solution temperature of PNIPAm at 33°C, a colloidal gel is formed as identified by an increase of I(q) at small q as well as a slowing down of sample dynamics by various orders of magnitude. With increasing TMAO concentration the gelation transition shifts linearly to lower temperatures. Above a TMAO concentration of approximately 0.40 mol/L corresponding to a 1:1 ratio of TMAO and NIPAm groups, collapsed PNIPAm states are found for all temperatures without any gelation transition. This suggests that reduction of PNIPAm-water hydrogen bonds due to the presence of TMAO results in a stabilisation of the collapsed PNIPAm state and suppresses gelation of the nanogel.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation
In neurodegenerative diseases including Alzheimer’s and amyotrophic lateral sclerosis, proteins that bind RNA are found in aggregated forms in autopsied brains. Evidence suggests that RNA aids nucleation of these pathological aggregates; however, the mechanism has not been investigated at the level of atomic structure. Here, we present the 3.4-Å resolution structure of fibrils of full-length recombinant tau protein in the presence of RNA, determined by electron cryomicroscopy (cryo-EM). The structure reveals the familiar in-register cross-β amyloid scaffold but with a small fibril core spanning residues Glu391 to Ala426, a region disordered in the fuzzy coat in all previously studied tau polymorphs. RNA is bound on the fibril surface to the positively charged residues Arg406 and His407 and runs parallel to the fibril axis. The fibrils dissolve when RNase is added, showing that RNA is necessary for fibril integrity. While this structure cannot exist simultaneously with the tau fibril structures extracted from patients’ brains, it could conceivably account for the nucleating effects of RNA cofactors followed by remodeling as fibrils mature.
59 BASIC BIOLOGICAL SCIENCES↗
Explorations of the nonheme high-valent iron-oxo landscape: crystal structure of a synthetic complex with an [Fe IV 2 (μ-O) 2 ] diamond core relevant to the chemistry of sMMOH
Methanotrophic bacteria utilize methane monooxygenase (MMO) to carry out the first step in metabolizing methane. The soluble enzymes employ a hydroxylase component (sMMOH) with a nonheme diiron active site that activates O 2 and generates a powerful oxidant capable of converting methane to methanol. It is proposed that the diiron(II) center in the reduced enzyme reacts with O 2 to generate a diferric-peroxo intermediate called P that then undergoes O–O cleavage to convert into a diiron(IV) derivative called Q, which carries out methane hydroxylation. Most (but not all) of the spectroscopic data of Q accumulated by various groups to date favor the presence of an Fe IV 2 (μ-O) 2 unit with a diamond core. The Que lab has had a long-term interest in making synthetic analogs of iron enzyme intermediates. To this end, the first crystal structure of a complex with a Fe III Fe IV (μ-O) 2 diamond core was reported in 1999, which exhibited an Fe∙∙∙Fe distance of 2.683(1) Å. Now more than 20 years later, a complex with an Fe IV 2 (μ-O) 2 diamond core has been synthesized in sufficient purity to allow diffraction-quality crystals to be grown. Finally, its crystal structure has been solved, revealing an Fe∙∙∙Fe distance of 2.711(4) Å for comparison with structural data for related complexes with lower iron oxidation states.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquids close to Earth's liquid core conditions
Using an artificial neural-network machine learning interatomic potential, we have performed molecular dynamics simulations to study the structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid close to the Earth's liquid core conditions. Here, the simulation results reveal that the short-range structural order (SRO) in the $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid is very strong. About 80% of the atoms are arranged in crystallinelike SRO motifs. In particular, ~ $70$% of Fe-centered clusters can be classified as either hexagonal-close-packed-like or icosahedrallike SRO motifs. The SRO clusters centered on Fe, Si, or O atoms are strongly intermixed and homogenously distributed throughout the liquid. The atomic structure of the liquid and the fractions of dominant SRO clusters are not sensitive to pressure/temperature used in the simulations except that the SRO of the O-centered clusters is enhanced close to inner core pressures. The O-diffusion coefficient is about two to three times larger than the Fe and Si ions and increases more rapidly in the deeper core regions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Metal-Confined Synthesis of ZnS 2 Monolayer Catalysts for Dinitrogen Electroreduction
Atomically thin two-dimensional (2D) materials are of great significance in catalytic, energy storage, and electronic devices. So far, such materials are limited to several categories with layered structures. Herein, we predict an unusual atomically thin ZnS2 monolayer and exploit a metal-confined chemical vapor deposition strategy for the successful preparation of such an unprecedented 2D material, where a sulfide monolayer was first grown on metal nanosheets to form a sulfide/metal/sulfide sandwich structure, and then, the metal core was etched out to obtain freestanding sulfide monolayers. As shown in this work, the ZnS 2 monolayer possesses unique electron-deficient properties related to the atomic structure and exhibits high catalytic activity for dinitrogen electroreduction. Our work will enable creating 2D TMD materials that were previously inexistent or inaccessible.
2D Materials↗
Observation of Core-Excited Dipole-Bound States
Polar molecules can bind an electron in a diffuse orbital due to the charge-dipole interaction. Electronic excited states of polar molecules can also bind an electron to form core-excited dipole-bound states (DBSs), analogous to core-excited Rydberg states. However, core-excited DBSs have not been observed because of the complicated electronic structure of molecular systems. Here we report the observation of a core-excited DBS in the pyrazolide anion as a result of the favorable electronic structure of the neutral pyrazolyl core, which has a low-lying excited state ($\tilde{A}$ 2 B 1 ) only 266 cm -1 above its ground state ($\tilde{X}$ 2 A 2 ). The binding energy of the DBS associated with the ground state is measured to be 221 cm -1 , while that of the core-excited DBS is 276 cm -1 , which is still a bound state relative to the detachment threshold. Furthermore, vibrational Feshbach resonances are observed for both DBSs and their autodetachment behaviors are studied by resonant photoelectron imaging.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Data from: 'Abiotic influences on continuous conifer forest structure across a subalpine watershed'
This package archives the core data used for analysis and inference in 'Abiotic influences on continuous conifer forest structure across a subalpine watershed' (Worsham et al., 2025). All data were collected in the East River, Washington Gulch, Slate River, and Coal Creek watersheds of Colorado. In the paper, we quantified the relative influence of climate, topographic, edaphic, and geologic factors on conifer stand structure and composition, and their functional relationships, at the watershed scale. We used waveform LiDAR data to derive spatially continuous stand structure metrics. We fused these with a species-level classification map to estimate tree species abundance. We applied generalized additive and generalized boosted models to evaluate the covariability of structural and compositional metrics with abiotic variables. The package contains the essential products required for reproducing our analysis and the tables and figures reported in the publication. The products comprise four classes: (1) geospatial data, (2) tabular data used for inferential analysis, (3) tabular data describing analytical results and performance statistics, and (4) a data user guide. (1) includes discretized waveform LiDAR data, locations and attributes of individual tree crowns, sampling locations and domain boundaries, a canopy height model, and raster files of estimated forest structural and compositional metrics at 100 m grid scale. (2) includes all response and explanatory variable values applied in inferential models. Response variables include conifer forest stand density, basal area, 95th percentile height, quadratic mean diameter, and others. Explanatory variables include climatic water deficit, actual evapotranspiration, elevation, heat load, soil available water content, and others. (3) includes results of training and testing several individual tree detection (ITD) algorithms, as well as inferential modeling results. (4) is a PDF user guide for this data package, including detailed descriptions and data dictionaries for all files. The data package root contains 17 assets: 8 compressed tape archive (.tar.gz) files, 5 comma-separated values (.csv) files, 3 Geographic Tagged Image File Format (GeoTIFF) (.tif) files, and 1 Portable Document Format (.pdf) file. The compressed .tar.gz archives contain ESRI shapefiles (.shp) .tif, compressed LASer (.laz), and .csv files. The archives must first be decompressed using the widely distributed command-line software utility TAR. All other files, including constituent files within the .tar.gz archives, can be opened in the open-source R statistical computing environment. Alternatively, .csv files may also be read in any simple text editor software or Microsoft Excel. Geospatial files including .shp and .tif files can also be opened in GIS software, such as QGIS (open-source) or ESRI ArcGIS (proprietary). The .pdf Data User Guide can be read with Adobe Acrobat Reader or other compatible readers.
2018 NEON and 2025 CHESS Campaigns↗
Multigroup Thermal Radiation Transport with Tensor Trains
We investigate the application of tensor-train (TT) algorithms to multigroup thermal radiation transport (i.e., photon radiation transport). The TT framework enables simulations at discretizations that might otherwise be computationally infeasible on conventional hardware. We show that solutions to certain multigroup problems possess an intrinsic low-rank structure, which the TT representation leverages effectively. This enables us to solve problems where the discretized solution size exceeds a trillion parameters on a single node. The solver is evaluated on a range of test problems with varying levels of complexity, consistently achieving compression factors greater than 100× and speedups exceeding 2×. We also investigate alternative TT topologies by analyzing the low-rank structure of the merged spatio-spectral core to assess the potential for greater compression. This analysis suggests that compression gains could increase by factors as large as 7. Our results indicate that the low-rank structure of the merged spatio-spectral core captures the spatio-spectral complexity of the solution, largely driven by the opacity structure of the medium. Beyond identifying opportunities for improved compression, this analysis highlights the types of errors that may arise in angle-integrated quantities when exploiting this low-rank structure.
79 ASTRONOMY AND ASTROPHYSICS↗
Hydrogen solubility in FeSi alloy phases at high pressures and temperatures
Abstract Light elements alloying with metallic Fe can change the properties and therefore play a key role in the structure and dynamics of planetary cores. Hydrogen and silicon are possible light elements in the rocky planets’ cores. However, hydrogen storage in Fe-Si alloy systems remains unclear at high pressures and high temperatures because of experimental difficulties. Taking advantage of pulsed laser heating combined with high-energy synchrotron X-ray diffraction, we studied reactions between FeSi and H in laser-heated diamond-anvil cells (LHDACs) up to 61.9 GPa and 3500 K. We found that under H-saturated conditions the amount of H alloying with FeSi (0.3 and <0.1 wt% for the B20 and B2 structures, respectively) is much smaller than that in pure Fe metal (>1.8 wt%). Our experiments also suggest that H remains in the crystal structure of FeSi alloy when recovered to 1 bar. Further density functional theory (DFT) calculations indicate that the low-H solubility likely results from the highly distorted interstitial sites in the B20 and B2 structures, which are not favorable for H incorporation. The recovery of H in the B20 FeSi crystal structure at ambient conditions could open up possibilities to understand geochemical behaviors of H during core formation in future experiments. The low-H content in FeSi alloys suggests that if a planetary core is Si-rich, Si can limit the ingassing of H into the Fe-rich core.
Geochemistry & Geophysics↗
Explorations of the nonheme high-valent iron-oxo landscape: crystal structure of a synthetic complex with an [FeIV2(μ-O) 2 ] diamond core relevant to the chemistry of sMMOH
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99 GENERAL AND MISCELLANEOUS↗
Advances in Coring Procedures of Silicon Photovoltaic Modules
We describe advances on procedures used for the coring of silicon photovoltaic modules. These procedures involve coring specific locations, starting from the back of the modules, and removing selected parts of the cell structure, while preserving the front tempered glass. The standard coring procedures had to be modified from case to case due to the different cell structures and measurement requirements. We provide examples of the characterization of the cored samples by scanning electron microscopy and energy-dispersive X-ray spectroscopy. Finally, we describe a simple process to create small openings at specific locations on the back of photovoltaic modules to allow for efficiency-related measurement of individual cells and groups of cells.
41 EE - Solar Energy Technologies Office (EE-4S)↗
Structural deformation and host–guest properties of doubly-reduced cycloparaphenylenes, [ n ]CPPs 2– ( n = 6, 8, 10, and 12)
Chemical reduction of several cycloparaphenylenes (CPPs) ranging in size from [8]CPP to [12]CPP has been investigated with potassium metal in THF. The X-ray diffraction characterization of the resulting doubly-reduced [n]CPPs provided a unique series of carbon nanohoops with increasing dimensions and core flexibility for the first comprehensive structural analysis. The consequences of electron acquisition by a [n]CPP core have been analyzed in comparison with the neutral parents. The addition of two electrons to the cyclic carbon framework of [n]CPPs leads to the characteristic elliptic core distortion and facilitates the internal encapsulation of sizable cationic guests. Molecular and solid-state structure changes, alkali metal binding and unique size-dependent host abilities of the [n]CPP 2– series with n = 6–12 are discussed. This in-depth analysis opens new perspectives in supramolecular chemistry of [n]CPPs and promotes their applications in size-selective guest encapsulation and chemical separation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Norm-Conserving Pseudopotentials and Basis Sets to Explore Actinide Chemistry in Complex Environments
We constructed and tested a new set of norm-conserving pseudopotentials, as well as companion Gaussian basis sets, for the actinide series (Ac–Lr) using the Goedecker, Teter and Hutter (GTH) formalism within the generalized gradient approximation (GGA) functional for exchange-correlation of Perdew, Burke and Ernzerhof (PBE). This fills a critical void in the literature for studying the chemistry of 5f–block elements in condensed phase. The accuracy and reliability of the newly parameterized An–GTH pseudopotentials and basis sets, a variety of tests on actinide-containing molecules were carried out and compared to all-electron and available experimental results. The new pseudopotentials include both medium ( [Xe]4f 14 ) and large core ( [Xe]4f 14 5d 10 ) options that successfully reproduced structure and energetics, particularly redox processes. The medium core size set, in particular, reproduced all electron calculations over multiple oxidation states from 0 to VII, whereas the large core set was suitable only for the early series elements and low oxidation states.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Rays for Roots - Integrating Backscatter X-Ray Phenotyping, Modeling and Genetics to Increase Carbon Sequestration and Switchgrass Resource Use (Final Report)
To increase carbon (C) deposition in the soil and enhance crop resource use efficiency, characterizing root form and function is essential. Several root and soil traits have been linked to increased root-to-soil C transfer. Technology that could provide high-resolution characterization of many of these traits in field conditions would revolutionize our ability to study and understand how to increase C sequestration. In this effort, we developed an initial early prototype backscatter X-ray system for non-destructive imaging of root traits. We collected initial backscatter X-ray data in field and lab settings and carried out early analysis of these data. Along with this prototype, we also developed a suite of root phenotyping approaches including advanced minirhizotron image analysis, soil core imaging, and mesocosm imaging. Minirhizotron (MR) tubes are clear tubes inserted into the soil in the field and used to image roots and the surrounding soil. Our team has developed deep learning-based methods that can segment roots from soil that can learn from imprecise image-level labels. The ability to learn or fine-tune our deep learning algorithms from image-level labels allows easier and faster application of these approaches to new locations and new plant species. We have successfully implemented and applied our MR analysis approaches to thousands of switchgrass MR images collected across geographical regions. An advantage of MR imaging is the ability to collect root and soil images over time. Our soil core analysis included collecting hundreds of soil core samples from harvested switchgrass fields and imaging these cores with both X-ray CT and backscatter X-ray imaging. Initial segmentation approaches for the X-ray CT images of these cores have been developed and applied. An advantage of soil core analysis is that it preserves the three-dimensional structures of the roots and soil in the core collected. Our group also developed photogrammetry-based mesocosm root imaging and phenotyping approaches. In this approach, a plant was grown in a large mesocosm with a three-dimensional grid of thin supporting lines inserted throughout the mesocosm. After the plant (and, correspondingly, the root architecture is grown and established) the soil media was removed and the supporting lines approximately preserved the three-dimensional root architecture. Then, we applied photogrammetry techniques to create a three-dimensional digital representation of the root architecture for which we developed analysis algorithms including skeletonization. We carried out our phenotyping development with powerful switchgrass resources and physiological and agroecosystem modeling to deliver novel technology. This project contributes to multiple ARPA-E missions including reduction of foreign imports of energy, reduction of energy-related emissions including greenhouse gases, and ensuring that the United States maintains a technological lead in developing and deploying advanced energy technology. Furthermore, the developed tools could transform public and private plant breeding and could be broadly applicable to other crops and, potentially, other application areas. Our team of engineers, plant and soil scientists, and modelers i) developed an early prototype backscatter X-ray platform that can operate in field conditions; ii) developed a suite of root phenotyping and characterization approaches as described above; iii) developed and carried out plant biology and physiology roots studies and; iv) developed and implemented mechanistic physiological modeling.
42 ENGINEERING↗
Microbial O 2 consumption as a function of pore structure in soils of sorghum, switchgrass, and prairie vegetation systems
Abstract Microscale O 2 availability in soil, a main factor influencing microbial processing of soil carbon and nitrogen, is a function of O 2 diffusion and microbial O 2 consumption. While O 2 diffusivity is widely studied, it is difficult to quantify the rate of microbial O 2 consumption ( MO ). In this study, we quantified the MO using O 2 microsensor profiling to compare MO in different soils and vegetation systems while manipulating the soil pore structure. Soil samples were collected from three bioenergy vegetation systems, sorghum ( Sorghum bicolor L. Moench), switchgrass ( Panicum virgatum L.), and prairie, at an experimental site in Southeast Michigan, and from switchgrass and prairie systems at two sites in South and North Wisconsin. We prepared soil cores with two contrasting pore structures, that is, large (>30 µm Ø) pore‐dominated soil (LP) and small (<10 µm Ø) pore‐dominated soil (SP), from the same 1‐ to 2‐mm soil size fraction. We quantified MO (nmol O 2 cm −3 s −1 ) using a microprofiler with an oxygen (OX‐100 µm) microsensor (Unisense) pre‐ and post‐38‐day incubation. Across all studied systems, there was a trend for a decrease in SP MO post‐incubation, suggesting a change in microbial metabolism to lower O 2 utilization. However, sizeable microbial O 2 consumption continued in the LP soils, further corroborated by a positive correlation between the C‐CO 2 emission rate and the post‐incubation MO , highlighting that LP provided a better physical microenvironment for the soil microbes.
Chakraborty, Poulamee [Department of Plant Soil an↗