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At least 469 records · Page 26

Structural evolution of iodine on approach to the monatomic state

Here, we applied single-crystal x-ray diffraction and Raman spectroscopy in a diamond-anvil cell up to 36 GPa and first-principles theoretical calculations to study the molecular dissociation of solid iodine at high pressure. Unlike previously reported, we find that the familiar Cmce molecular phase transforms to a Cmc2 1 molecular structure at 16 GPa, and then to an incommensurate polymeric Fmmm⁡(00⁢$\gamma$)⁢s⁢00 structure, which can be viewed as a mixture of molecular I 2 and zigzag chains of three iodine atoms, at 20 GPa. The available data are consistent with metallization of iodine at the boundary between the commensurate Cmc⁢2 1 structure and the incommensurate Fmmm⁡(00⁢$\gamma$)s⁢00 structure at 20 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Revealing hidden defects through stored energy measurements of radiation damage

With full knowledge of a material’s atomistic structure, it is possible to predict any macroscopic property of interest. In practice, this is hindered by limitations of the chosen characterization techniques. For example, electron microscopy is unable to detect the smallest and most numerous defects in irradiated materials. Instead of spatial characterization, we propose to detect and quantify defects through their excess energy. Differential scanning calorimetry of irradiated Ti measures defect densities five times greater than those determined using transmission electron microscopy. Our experiments also reveal two energetically distinct processes where the established annealing model predicts one. Molecular dynamics simulations discover the defects responsible and inform a new mechanism for the recovery of irradiation-induced defects. The combination of annealing experiments and simulations can reveal defects hidden to other characterization techniques and has the potential to uncover new mechanisms behind the evolution of defects in materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Structural evolution of liquid silicates under conditions in Super-Earth interiors

Molten silicates at depth are crucial for planetary evolution, yet their local structure and physical properties under extreme conditions remain elusive due to experimental challenges. In this study, we utilize in situ X-ray diffraction (XRD) at the Matter in Extreme Conditions (MEC) end-station of the Linear Coherent Linac Source (LCLS) at SLAC National Accelerator Laboratory to investigate liquid silicates. Using an ultrabright X-ray source and a high-power optical laser, we probed the local atomic arrangement of shock-compressed liquid (Mg,Fe)SiO 3 with varying Fe content, at pressures from 81(9) to 385(40) GPa. We compared these findings to ab initio molecular dynamics simulations under similar conditions. Results indicate continuous densification of theO-O and Mg-Si networks beyond Earth’s interior pressure range, potentially altering melt properties at extreme conditions. This could have significant implications for early planetary evolution, leading to notable differences in differentiation processes between smaller rocky planets, such as Earth and Venus, and super-Earths, which are exoplanets withmasses nearly three times that of Earth.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Machine learning a molecular Hamiltonian for predicting electron dynamics

We develop a computational method to learn a molecular Hamiltonian matrix from matrix-valued time series of the electron density. As we demonstrate for three small molecules, the resulting Hamiltonians can be used for electron density evolution, producing highly accurate results even when propagating 1,000 time steps beyond the training data. As a more rigorous test, we use the learned Hamiltonians to simulate electron dynamics in the presence of an applied electric field, extrapolating to a problem that is beyond the field-free training data. We find that the resulting electron dynamics predicted by our learned Hamiltonian are in close quantitative agreement with the ground truth. Our method relies on combining a reduced-dimensional, linear statistical model of the Hamiltonian with a time-discretization of the quantum Liouville equation within time-dependent Hartree Fock theory. In conclusion, we train the model using a least-squares solver, avoiding numerous, CPU-intensive optimization steps. For both field-free and field-on problems, we quantify training and propagation errors, highlighting areas for future development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Dirks, Alden C↗

Modeling Novel Aqueous Particle and Cloud Chemistry Processes of Biomass Burning Phenols and Their Potential to Form Secondary Organic Aerosols

Phenols emitted from biomass burning contribute significantly to secondary organic aerosol (SOA) formation through the partitioning of semivolatile products formed from gas-phase chemistry and multiphase chemistry in aerosol liquid water and clouds. The aqueous-phase SOA (aqSOA) formed via hydroxyl radical (˙OH), singlet molecular oxygen ( 1 O 2 *), and triplet excited states of organic compounds ( 3 C*), which oxidize dissolved phenols in the aqueous phase, might play a significant role in the evolution of organic aerosol (OA). However, a quantitative and predictive understanding of aqSOA has been challenging. Here, we develop a stand-alone box model to investigate the formation of SOA from gas-phase ˙OH chemistry and aqSOA formed by the dissolution of phenols followed by their aqueous-phase reactions with ˙OH, 1 O 2 *, and 3 C* in cloud droplets and aerosol liquid water. Here, we investigate four phenolic compounds, i.e., phenol, guaiacol, syringol, and guaiacyl acetone (GA), which represent some of the key potential sources of aqSOA from biomass burning in clouds. For the same initial precursor organic gas that dissolves in aerosol/cloud liquid water and subsequently reacts with aqueous phase oxidants, we predict that the aqSOA formation potential (defined as aqSOA formed per unit dissolved organic gas concentration) of these phenols is higher than that of isoprene-epoxydiol (IEPOX), a well-known aqSOA precursor. Cloud droplets can dissolve a broader range of soluble phenols compared to aqueous aerosols, since the liquid water contents of aerosols are orders of magnitude smaller than cloud droplets. Further, our simulations suggest that highly soluble and reactive multifunctional phenols like GA would predominantly undergo cloud chemistry within cloud layers, while gas-phase chemistry is likely to be more important for less soluble phenols. But in the absence of clouds, the condensation of low-volatility products from gas-phase oxidation followed by their reversible partitioning to organic aerosols dominates SOA formation, while the SOA formed through aqueous aerosol chemistry increases with relative humidity (RH), approaching 40% of the sum of gas and aqueous aerosol chemistry at 95% RH for GA. Our model developments of biomass-burning phenols and their aqueous chemistry can be readily implemented in regional and global atmospheric chemistry models to investigate the aqueous aerosol and cloud chemistry of biomass-burning organic gases in the atmosphere.

09 BIOMASS FUELS↗

Large-Scale Molecular Dynamics Simulation of the Dehydration of a Suspension of Smectite Clay Nanoparticles

Fine-grained sediments and sedimentary rocks play important roles in a variety of modern energy technologies from petroleum geology to geological carbon sequestration and radioactive waste management. However, despite their utility and ubiquity, many of their properties remain poorly understood. In particular, the ability to predict the permeability and mechanics of these media remains a persistent fundamental challenge in the geosciences. In the present work, we show how large-scale classical molecular dynamics (MD) simulations can help interpret the properties of fine-grained sedimentary material. All-atom simulations containing 30 discrete clay particles are utilized to understand the evolution of a clay nanoparticle suspension during its progressive dehydration. Microstructural (pore size distribution, tortuosity, anisotropy), thermodynamic (enthalpy and free energy of hydration, anion exclusion), mechanical (total suction), and transport properties (diffusion coefficient tensors of water and sodium) are calculated and compared to the experiment. Overall, our results provide new insight into the coupled chemistry, mechanics, and transport properties of disordered nanoparticle assemblages and shed light upon the important role of water films in controlling these properties.

02 PETROLEUM↗

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases (FAPs) to catalyse unnatural photoredox radical C–C bond formation by leveraging strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases (RAPs) to facilitate decarboxylative radical cyclisation with excellent chemo-, enantio-, and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of FAPs. An orthogonal set of RAPs was engineered to access all four possible stereoisomers of stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved RAPs allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclisation. The development of stereoselective RAPs provides unnatural C–C bond forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free radical-mediated reactions.

Ju, Shuyun (ORCID:000000020322104X)↗

Dislocation nano-hydrides in nickel: Nucleation, evolution and effects on dislocation behaviors

Nano-hydrides have been predicted to precipitate at the core of edge dislocations in the Ni-H system, a mechanism that may promote hydrogen embrittlement. However, nano-hydride nucleation, growth, and effects on dislocation behavior have seldom been explored. This work combines molecular dynamics grand canonical Monte Carlo (MD-GCMC) simulations and continuum modeling to uncover a wide range of phenomena linked to dislocation nano-hydrides. Simulations reveal that nano-hydrides can be stabilized at dislocation cores with all character angles, including screw segments, due to the hydrostatic stresses around the cores of the Shockley partials. Nano-hydride nucleation takes place in these regions, and growth is dictated by the character angle θ of the perfect dislocation. The equilibrium stacking fault width d eq varies dynamically to increase the local hydrostatic stress field and facilitate the formation of the nano-hydride, forming a constriction-like feature and leading to three distinct behaviors: d eq decreases for θ > 30°, d eq remains unchanged for θ = 30°, and d eq increases for θ < 30°. Remote hydrostatic and Escaig stresses are also shown to influence the nucleation stage, implying stress concentrations such as those ahead of crack tips may facilitate nano-hydride precipitation. Moreover, we identify a new hydrogen-induced 60° dislocation reaction that emits a Shockley partial on a conjugate plane, with potential implications for twin nucleation. Testable predictions from this study are then used to reinterpret previous results from the literature. In conclusion, these findings provide a comprehensive framework to assess nano-hydride formation and evolution at dislocations in nickel and other face-centered cubic metals, with important implications to hydrogen embrittlement.

Dislocations↗

A Robotic High-Throughput Grid-Search Platform for Mapping Phase Behavior in Triblock Copolymer–Homopolymer Blends

We present a high-throughput experimental investigation of the phase behavior in triblock copolymers (PS-b-PB-b-PS and PS-b-PI-b-PS) and polystyrene (PS) homopolymer blends as a function of homopolymer molecular weight (MW) and blend ratio. Using a robotic thin-film processing platform (NOVA) integrated with Grazing Incidence Small-Angle X-ray Scattering (GISAXS) and Atomic Force Microscopy (AFM), we systematically mapped the order–disorder transition (ODT) boundaries and domain spacing evolution across a broad MW range (4.0–101.3 kDa) with varying homopolymer loadings (10% to 90%). The results reveal three distinct regimes: low-MW homopolymers, corresponding to the wet-brush regime produced only gradual domain swelling before disordering at high blend ratios (weight fraction); medium-MW homopolymers, corresponding to thedry-brush regime induced significant domain spacing increase up to 80% followed by earlier disordering, while high-MW homopolymers led to macrophase separation with minimal changes in domain spacing. Additionally, coarse-grained molecular dynamics simulations confirmed our experimental finding that in the low-MW region, the PS homopolymer uniformly distributed in the PS domain. These findings demonstrate that homopolymer molecular weight critically governs both the extent of domain swelling and the onset of disorder in triblock copolymer systems. This high-throughput platform enables the rapid mapping of composition–morphology relationships and can be integrated with AI/ML tools for designing next-generation nanostructured polymers.

36 MATERIALS SCIENCE↗

Cis-regulatory evolution shapes facial diversity in birds and mammals

Birds and mammals exhibit extraordinary facial diversity, reflecting adaptations to distinct ecological niches and feeding strategies. While core face-building developmental programs are conserved and orchestrated by interactions between ectodermal organizers and the underlying mesenchyme, mechanisms driving facial shape variation remain poorly understood. Here, we integrate single-cell transcriptomic and chromatin accessibility profiling of mouse and chicken developing face to construct a comparative regulatory map. Although both ectodermal and mesenchymal populations display distinct regulatory features in each species, the mesenchyme exhibits markedly greater divergence, pointing to its central role in shaping facial morphology. We further reveal unexpected molecular complexity in the main face-shaping organizer, including a mouse-specific Shh/Wnt5a expression domain. At key morphogen loci (Bmp4, Fgf8, and Wnt5a), conserved and lineage-specific enhancers exhibit spatially restricted activity patterns that mirror divergent signaling domains. These findings demonstrate how cis-regulatory evolution modulates conserved developmental programs to generate morphological novelty, providing a valuable resource for studying vertebrate facial evolution.

Kyomen, Stella [Max Planck Institute for Evolution↗

Dispersed Nickel Phthalocyanine Molecules on Carbon Nanotubes as Cathode Catalysts for Li-CO 2 Batteries

The Li-CO 2 battery has great potential for both CO 2 utilization and energy storage, but its practical application is limited by low energy efficiency and short cycle life. Efficient cathode catalysts are needed to address this issue. Herein, this work reports on molecularly dispersed electrocatalysts (MDEs) of nickel phthalocyanine (NiPc) anchored on carbon nanotubes (CNTs) as the cathode catalyst for Li-CO 2 batteries. The dispersed NiPc molecules efficiently catalyze CO 2 reduction, while the conductive and porous CNTs networks facilitate CO 2 evolution reaction, leading to enhanced discharging and charging performance compared to the NiPc and CNTs mixture. Octa-cyano substitution on NiPc (NiPc-CN) further enhances the interaction between the molecule and CNTs, resulting in better cycling stability. The Li-CO 2 battery with the NiPc-CN MDE cathode shows a high discharge voltage of 2.72 V and a small discharging–charging potential gap of 1.4 V, and can work stably for over 120 cycles. The reversibility of the cathode is confirmed by experimental characterizations. Finally, this work lays a foundation for the development of molecular catalysts for Li-CO 2 battery cathodes.

25 ENERGY STORAGE↗

A Laboratory-driven Multiscale Investigation of X-Ray Induced Mass Loss and Photochemical Evolution in Cosmic Carbon and Silicate Dust

We present the results of an integrated laboratory and modeling investigation into the impact of stellar X-rays on cosmic dust. Carbonaceous grains were prepared in a cooled (< 200 K) supersonic expansion from aromatic molecular precursors, and were later irradiated with 970 eV X-rays. Silicate (enstatite) grains were prepared via laser ablation, thermally annealed, and later irradiated with 500 eV X-rays. Infrared spectra of the 3.4 μm band of the carbon sample prepared with benzene revealed 84% ± 5% band area loss for an X-ray dose of 5.2 x 10 23 eV.cm -2 . Infrared spectra of the 8 -12 μm Si-O band of the silicate sample revealed band area loss up to 63% ± 5% for doses of 2.3 x 10 23 eV.cm -2 . A hybrid Monte Carlo particle trajectory approach was used to model the impact of X-rays and ensuing photoelectrons, Auger and collisionally ionized electrons through the bulk. As a result of x-ray ionization and ensuing Coulomb explosions on surface molecules, the calculated mass loss is 60% for the carbonaceous sample and 46% for the silicate sample, within a factor of 2 of the IR band loss, supporting an X-ray induced mass-loss mechanism. We apply the laboratory X-ray destruction rates to estimate the lifetimes of dust grains in protoplanetary disks surrounding 1 M ⊙ and 0.1 M ⊙ G and M stars. In both cases, X-ray destruction timescales are short (a few million years) at the disk surface, but are found to be much longer than typical disk lifetimes (≳10 Myr) over the disk bulk.

79 ASTRONOMY AND ASTROPHYSICS↗

Theory and modeling of molecular modes in the NMR relaxation of fluids

Traditional theories of the nuclear magnetic resonance (NMR) autocorrelation function for intra-molecular dipole pairs assume a single-exponential decay, yet the calculated autocorrelation of realistic systems displays a rich, multi-exponential behavior, resulting in anomalous NMR relaxation dispersion (i.e., frequency dependence). We develop an approach to model and interpret the multi-exponential intra-molecular autocorrelation using simple, physical models within a rigorous statistical mechanical development that encompasses both rotational diffusion and translational diffusion in the same framework. Here, we recast the problem of evaluating the autocorrelation in terms of averaging over a diffusion propagator whose evolution is described by a Fokker–Planck equation. The time-independent part admits an eigenfunction expansion, allowing us to write the propagator as a sum over modes. Each mode has a spatial part that depends on the specified eigenfunction and a temporal part that depends on the corresponding eigenvalue (i.e., correlation time) with a simple, exponential decay. The spatial part is a probability distribution of the dipole pair, analogous to the stationary states of a quantum harmonic oscillator. Drawing inspiration from the idea of inherent structures in liquids, we interpret each of the spatial contributions as a specific molecular mode. These modes can be used to model and predict the NMR dipole–dipole relaxation dispersion of fluids by incorporating phenomena on the molecular level. We validate our statistical mechanical description of the distribution in molecular modes with molecular dynamics simulations interpreted without any relaxation models or adjustable parameters: the most important poles in the Padé–Laplace transform of the simulated autocorrelation agree with the eigenvalues predicted by the theory

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

Abstract Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN + ) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN + -based reducing power. This is based on an orthogonal, NMN + -dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN + . With a throughput of >10 6 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Towards the Ultimate Strength of Medium‐Entropy Alloys Through Pulsed Lasers

The tensile strength of metals at extreme strain rates is a key predictor of their performance in ballistic and structural impact applications. An important experimental method to reach these extreme strain rates is the use of high-amplitude, short-duration pulsed lasers. The Jupiter Laser Facility at the Lawrence Livermore National Laboratory enabled probing for the first time the mechanical response of several promising High Entropy Alloys at times on the order of nanoseconds (strain rates of ∼10 7 and ∼10 9 s −1 ). The measured strength is in the range of 6 to 10 GPa, ten times the quasistatic value. The mechanisms of plastic deformation and failure were identified and quantified through analysis and molecular dynamics simulation. The reflected wave amplitudes, obtained by VISAR, were used to determine the tensile (spall) stress. The high tensile strength obtained is due to two factors: the strain-rate dependence of plastic flow and the kinetics of void nucleation, growth, and coalescence. The experimental results are compared with an analytical prediction considering both grain-interior and grain-boundary void initiation. Molecular dynamics simulations, conducted at strain rates of 10 8 and 10 9 s −1 , rationalize the experimental results. In conclusion, they provide valuable information about the process of failure evolution, and reveal that grain boundary separation plays a pivotal role in spalling.

Materials science↗

Pinhole-seeded lateral epitaxy and exfoliation of GaSb films on graphene-terminated surfaces

Abstract Remote epitaxy is a promising approach for synthesizing exfoliatable crystalline membranes and enabling epitaxy of materials with large lattice mismatch. However, the atomic scale mechanisms for remote epitaxy remain unclear. Here we experimentally demonstrate that GaSb films grow on graphene-terminated GaSb (001) via a seeded lateral epitaxy mechanism, in which pinhole defects in the graphene serve as selective nucleation sites, followed by lateral epitaxy and coalescence into a continuous film. Remote interactions are not necessary in order to explain the growth. Importantly, the small size of the pinholes permits exfoliation of continuous, free-standing GaSb membranes. Due to the chemical similarity between GaSb and other III-V materials, we anticipate this mechanism to apply more generally to other materials. By combining molecular beam epitaxy with in-situ electron diffraction and photoemission, plus ex-situ atomic force microscopy and Raman spectroscopy, we track the graphene defect generation and GaSb growth evolution a few monolayers at a time. Our results show that the controlled introduction of nanoscale openings in graphene provides an alternative route towards tuning the growth and properties of 3D epitaxial films and membranes on 2D material masks.

36 MATERIALS SCIENCE↗

Lithium oxidation and electrolyte decomposition at Li-metal/liquid electrolyte interfaces

In this work, we examine the evolution of events occurring when a Li metal surface is in contact with a 2 M solution of a Li salt in a solvent or mixture of solvents, via classical molecular dynamics simulations with a reactive force field allowing bond breaking and bond forming. The main events include Li oxidation and electrolyte reduction along with expansion of the Li surface layers forming a porous phase that is the basis for the formation of the solid-electrolyte interphase (SEI) components. Nucleation of the main SEI components (LiF, Li oxides, and some organics) is characterized. The analysis clearly reveals the details of these physical–chemical events as a function of time, during 20 nanoseconds. The effects of the chemistry of the electrolyte on Li oxidation and dissolution in the liquid electrolyte, and SEI nucleation and structure are identified by testing two salts: LiPF 6 and LiCF 3 SO 3 , and various solvents including ethers and carbonates and mixtures of them. The kinetics and thermodynamics of Li 6 F, the core nuclei in the LiF crystal, are studied by analysis of the MD trajectories, and via density functional theory calculations respectively. The SEI formed in this computational experiment is the “native” film that would form upon contact of the Li foil with the liquid electrolyte. As such, this work is the first in a series of computational experiments that will help elucidate the intricate interphase layer formed during battery cycling using metal anodes.

25 ENERGY STORAGE↗