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At least 325 records · Page 18

Neural network potentials with effective charge separation for non-equilibrium dynamics of ionic solids: a ZnO case study

Developing neural network potentials (NNPs) accurate under non-equilibrium dynamics is challenging, as such systems require extensive sampling beyond equilibrium phases. Here we construct high-fidelity NNPs for zinc oxide (ZnO), a polymorphic ionic solid, using density functional theory (DFT) reference data. To efficiently capture transitional configurations, we combine enhanced-sampling molecular dynamics with empirical potentials, data distillation, and pretraining on short-range atomic energies (A-Train), followed by transfer learning with DFT-relabeled datasets. This hierarchical approach improves transferability across polymorphs and stress states. We further introduce effective charge separation, treating long-range Coulombic terms analytically while short-range residual interactions are learned by the NNP. The optimal effective charges fall in the range 0.5–1.0 q e , consistent with dielectric-screened values derived from formal charges but distinct from Bader estimates. Motivated by this observation, we propose a simple data-driven protocol in which effective charges are optimized by comparing DFT reference energies with explicit Coulomb calculations, without additional NNP training. This strategy improves accuracy and transferability in DFT-level predictions of energies, forces, and stress. Together, these results provide a practical charge-selection framework for robust NNP development in ionic solids, enabling reliable simulation of polymorphic phase transformations and non-equilibrium dynamics.

Chemistry↗

Additively manufactured high-entropy alloy mimics the pressure-induced structural transition of iron

We report a pressure-induced structural phase transformation in an additively manufactured (AM) AlCrFe 2 Ni 2 high-entropy alloy. High laser scan-speed processing during AM has been shown to strongly suppress FCC formation, yielding BCC/B2-dominant microstructures. Synchrotron x-ray diffraction reveals a reversible BCC/B2 → HCP transition near ∼13 GPa that mirrors the α-Fe → ɛ-Fe transformation in elemental iron. Notably, this iron-like phase change occurs despite substantial chemical disorder and multi-element site occupancy, demonstrating that the BCC lattice instability leading to close-packed polymorphs can persist in a highly disordered matrix. At ambient pressure, AlCrFe 2 Ni 2 exhibits robust ferromagnetic behavior associated with the BCC/B2 phase. The observation of an α-Fe–like polymorphic pathway in a chemically complex alloy shows that classic cubic-to-close-packed transformation physics is not extinguished by compositional complexity. As a result, AlCrFe 2 Ni 2 emerges as a model system for exploring pressure-driven polymorphism and potential magneto-structural coupling in high-entropy alloys.

36 MATERIALS SCIENCE↗

Viability, behavior, and color expression in the offspring of matings between common wall lizard Podarcis muralis color morphs

Abstract Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.

Abalos, Javier↗

Ferroelectric HfO 2 and the importance of strain

Ferroelectric oxides based on HfO 2 show tremendous promise for the next generation of memory and logic devices. The ferroelectric polymorph is one of several that can be derived from the high symmetry cubic fluorite structure of HfO 2 . A single grain of HfO 2 may consist of a coherent mixture of multiple orientational and translational variants of different polymorphs. Here, we use symmetry-adapted strain-order parameters to elucidate the relationship between the different HfO 2 polymorphs and their symmetrically equivalent variants. We use first-principles electronic structure methods to identify minimum energy pathways and map them in subspaces of the symmetry-adapted strain order parameters. We next investigate the atomic structure of domain boundaries that separate coexisting variants of ferroelectric HfO 2 . Further, we rely on Gibbsian excess quantities and a precise specification of mechanical boundary conditions to describe the thermodynamic properties of domain boundaries. Our first-principles calculations show that the O and Hf shuffle arrangement within a domain boundary is closely related to the intermediate shuffle patterns of the homogeneous pathways between ferroelectric variants. Furthermore, the preferred structure within a boundary is very sensitive to local strain constraints imposed by the adjacent ferroelectric variants, leading to highly anisotropic domain boundary energies.

36 MATERIALS SCIENCE↗

Crystal structure solution and high-temperature thermal expansion in NaZr 2 (PO 4 ) 3 -type materials

The NaZr 2 P 3 O 12 family of materials have shown low and tailorable thermal expansion properties. In this study, SrZr 4 P 6 O 24 (SrO·4ZrO 2 ·3P 2 O 5 ), CaZr 4 P 6 O 24 (CaO·4ZrO 2 ·3P 2 O 5 ), MgZr 4 P 6 O 24 (MgO·4ZrO 2 ·3P 2 O 5 ), NaTi 2 P 3 O 12 [½(Na 2 O·4TiO 2 ·3P 2 O 5 )], NaZr 2 P 3 O 12 [½(Na 2 O·4ZrO 2 ·3P 2 O 5 )], and related solid solutions were synthesized using the organic–inorganic steric entrapment method. The samples were characterized by in-situ high-temperature X-ray diffraction from 25 to 1500°C at the Advanced Photon Source and National Synchrotron Light Source II. The average linear thermal expansion of SrZr 4 P 6 O 24 and CaZr 4 P 6 O 24 was between −1 × 10 −6 per °C and 6 × 10 −6 per °C from 25 to 1500°C. The crystal structures of the high-temperature polymorphs of CaZr 4 P 6 O 24 and SrZr 4 P 6 O 24 with R 3 c symmetry were solved by Fourier difference mapping and Rietveld refinement. This polymorph is present above ∼1250°C. This work measured thermal expansion coefficients to 1500°C for all samples and investigated the differences in thermal expansion mechanisms between polymorphs and between compositions.

36 MATERIALS SCIENCE↗

The seventh blind test of crystal structure prediction: structure generation methods

A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.

Chemistry↗

Comparison of nested geometry treatments within GPU-based Monte Carlo neutron transport simulations of fission reactors

Monte Carlo (MC) neutron transport provides detailed estimates of radiological quantities within fission reactors. This involves tracking individual neutrons through a computational geometry. CPU-based MC codes use multiple polymorphic tracker types with different tracking algorithms to exploit the repeated configurations of reactors, but virtual function calls have high overhead on the GPU. The Shift MC code was modified to support GPU-based tracking with three strategies: dynamic polymorphism with virtual functions, static polymorphism, and a single tracker type with tree-based acceleration. On the Frontier supercomputer these methods achieve 77.8%, 91.2%, and 83.4%, respectively, of the tracking rate obtained using a specialized tracker optimized for rectilinear-grid-based reactors. This indicates that all three methods are suitable for typical reactor problems in which tracking does not dominate runtime. The flexibility of the single tracker method is highlighted with a hexagonal-grid microreactor problem, performed without hexagonal-grid-specific tracking routines, providing a 2.19× speedup over CPU execution.

97 MATHEMATICS AND COMPUTING↗

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗

Stability of goethite /alpha-FeOOH/ and lepidocrocite /gamma-FeOOH/ to dehydration by UV radiation - Implications for their occurrence on the Martian surface

The geochemistry of the FeOOH polymorphs is an important consideration when evaluating the likelihood of an occurrence of detectable amounts of these minerals on Mars. An investigation is conducted regarding the stability of the FeOOH polymorphs geothite and lepidocrocite to dehydration in the presence of UV radiation. A thorough characterization of the FeOOH powders used in the laboratory experiments is presented, and the irradiational facility and experimental procedures are described. The results obtained in the conducted experiments are discussed. It is found that there is as yet no basis in laboratory experiments for inferring that perceptible UV photodehydration of FeOOH polymorphs will occur naturally on the surface of Mars on a time scale of at least 10-100 years.

Morris, R. V.↗

Possible significance of cubic water-ice, H2O-Ic, in the atmospheric water cycle of Mars

The possible formation and potential significance of the cubic ice polymorph on Mars is discussed. When water-ice crystallizes on Earth, the ambient conditions of temperature and pressure result in the formation of the hexagonal ice polymorph; however, on Mars, the much lower termperature and pressures may permit the crystallization of the cubic polymorph. Cubic ice has two properties of possible importance on Mars: it is an excellant nucleator of other volatiles (such as CO2), and it undergoes an exothermic transition to hexagonal ice at temperatures above 170 K. These properties may have significant implications for both martian cloud formation and the development of the seasonal polar caps.

Gooding, James L.↗

Glass formation and crystallization in high-temperature glass-ceramics and Si3N4

The softening of glassy grain boundaries in ceramic matrix composites and Si3N4 at high temperatures reduces mechanical strength and the upper-use temperature. By crystallizing this glass to a more refractory crystalline phase, a material which performs at higher temperatures may result. Three systems were examined: a cordierite composition with ZrO2 as a nucleating agent; celsian compositions; and yttrium silicate glasses both in bulk and intergranular in Si3N4. For the cordierite compositions, a series of metastable phases was obtained. The crystallization of these compositions was summarized in terms of metastable ternary isothermal sections. Zircon formed at the expense of ZrO2 and spinel. In SiC composites, the transformations were slower. In celsian, two polymorphs were crystallized. One phase, hexacelsian, which always crystallized, even when metastable, had an undesirable volume change. The other phase, celsian, was very difficult to crystallize. In yttrium silicate bulk glasses, similar in composition to the intergranular glass in Si3N4, a number of polymorphs of Y2Si2O7 were crystallized. The conditions under which these polymorphs formed are compared with crystallization in Si3N4.

Drummond, Charles H., III↗

Mineralogy of Meteorite Groups

Approximately 275 mineral species have been identified in meteorites, reflecting diverse redox environments, and, in some cases, unusual nebular formation conditions. Anhydrous ordinary, carbonaceous and R chondrites contain major olivine, pyroxene and plagioclase; major opaque phases include metallic Fe-Ni, troilite and chromite. Primitive achondrites are mineralogically similar. The highly reduced enstatite chondrites and achondrites contain major enstatite, plagioclase, free silica and kamacite as well as nitrides, a silicide and Ca-, Mg-, Mn-, Na-, Cr-, K- and Ti-rich sulfides. Aqueously altered carbonaceous chondrites contain major amounts of hydrous phyllosilicates, complex organic compounds, magnetite, various sulfates and sulfides, and carbonates. In addition to kamacite and taenite, iron meteorites contain carbides, elemental C, nitrides, phosphates, phosphides, chromite and sulfides. Silicate inclusions in IAB/IIICD and lIE iron meteorites consist of mafic silicates, plagioclase and various sulfides, oxides and phosphates. Eucrites, howardites and diogenites have basaltic to orthopyroxenitic compositions and consist of major pyroxene and calcic plagioclase and several accessory oxides. Ureilttes .are made up mainly of calcic, chromian olivine and low-Ca clinopyroxene embedded in a carbonaceous matrix; accessory phases include the C polymorphs graphite, diamond, lonsdaleite and chaoite as well as metallic Fe-Ni, troilite and halides. Angrites are achondrites rich in fassaitic pyroxene (i.e. , AI-Ti diopside); minor olivine with included magnesian kirschsteinite is also present. Martian meteorites comprise basalts, Iherzolites, a dunite and an orthopyroxenite. Major phases include various pyroxenes and olivine; minor to accessory phases include various sulfides, magnetite, chromite and Ca-phosphates. Lunar meteorites comprise mare basalts with major augite and calcic plagioclase and anorthositic breccias with major calcic plagioclase. Several meteoritic phases were formed by shock metamorphism. Martensite (a2-fe,Ni) has a distorted body-centered-cubic structure and formed by a shear transformation from taenite during shock reheating and rapid cooling. The C polymorphs diamond, lonsdaleite and chaoite formed by shock from graphite. Suessite formed in the North Haig ureilite by reduction of Fe and Si (possibly from olivine) via reaction with carbonaceous matrix material. Ringwoodite, the spinel form of (Mg,Fe)2Si04, and majorite, a polymorph of (Mg,Fe)Si03 with the garnet structure, formed inside shock veins in highly shocked ordinary chondrites. Secondary minerals in meteorite finds that formed during terrestrial weathering include oxides and hy-. droxides formed directly from metallic Fe-Ni by oxidation, phosphates formed by the alteration of schreibersite, and sulfates formed by alteration of troilite.

Rubin, Alan E.↗

One-Carbon Metabolism and SANS 2022 Update

Spaceflight Associated Neuro-ocular Syndrome, or SANS, affects a subset of astronauts (1, 2), and biochemical evidence has documented differences in those astronauts (3). Specifically, they had higher circulating concentrations of metabolites of the one-carbon metabolic pathway (1C), including homocysteine, and these concentrations were higher before flight (3). After ruling out many potential confounding factors in these otherwise healthy individuals (e.g., sex, kidney function, vitamin status, coffee consumption), a study of genetics was warranted. In an initial pilot effort, we documented a genetic predisposition to develop ophthalmic changes after long-duration space flight (4). That is, from a limited study of 5 single-nucleotide polymorphisms (SNPs), we found that the G allele for the MTRR A66G SNP was associated with a greater risk of choroidal folds and cotton-wool spots after flight, and the C allele for SHMT1 C1420T was protective against optic disc edema (4). These data provide a potential pathway for understanding why some individuals develop SANS, while others do not. The initial pilot study of 5 SNPs yielded striking findings, but the 1C pathway is far more complex. An effort was undertaken to examine more than 500 1C SNPs to see if a broader examination could help illuminate this association. That work is ongoing. The astronaut findings led us to advocate for the inclusion of 1C pathway genetic and biochemistry testing on other SANS-related projects, noting that genetics might help identify responders, non-responders, or outliers. The first such effort yielded evidence of an association of specific forms of the MTRR and SHMT-1 SNPs and vitamin B12 status with end-tidal CO2 after acute carbon dioxide exposure (5). The second such effort led to the identification that individuals exposed to strict head-down tilt and CO2 for 30-d who developed optic disc edema also had risk alleles for the two SNPs described above (6). Additionally, we identified a clinical population with many characteristics either attributed or purported to be involved in the ocular changes seen in affected astronauts: women with polycystic ovary syndrome (PCOS). PCOS is a condition of androgen excess and anovulatory menstrual cycles. The shared characteristics and clinical findings between SANS and PCOS generally include higher circulating homocysteine concentrations, increased retinal nerve fiber layer thickness, increased androgen concentrations (or responses), and altered carbohydrate metabolism. To our knowledge, no study has examined whether women with PCOS have asymptomatic ophthalmic anomalies observed in astronauts with SANS. While researchers have evaluated the one-carbon metabolism pathway polymorphisms of PCOS patients, and initial studies show an association with certain one-carbon polymorphisms, none have looked at the set of SNPs identified in our studies that are associated with ophthalmic changes in astronauts. Accordingly, we designed a study to evaluate the association of one-carbon pathway SNPs and ophthalmic findings in patients with PCOS and/or IIH compared to controls. Subjects provided blood samples for vitamin and one carbon biochemistry analyses, an extensive analysis of >500 SNPs associated with one carbon metabolism and had eye examinations and ocular imaging. Data analysis are underway. The data collected to date have shown associations between one carbon pathway biochemistry and genetics and incidence of SANS. The mechanisms for SANS has yet to be identified, although many hypotheses exist. Based on our data, we have developed (8, 9) and expanded (6) a multi-hit hypothesis for how these seemingly disparate findings could be linked. While intriguing, the hypothesis represents the starting point for further research. We aim to clarify the relationship between B-vitamin status and genetics with regard to the risk of SANS. Ultimately, understanding the mechanism(s) behind this will provide a means to predict, prevent, or treat these ophthalmologic pathologies in astronauts, and terrestrial populations.

S M Smith↗

Search for High-Pressure Silicon Phases: Reaching the Extreme Conditions with High-Intensity Laser Irradiation

Controlling electronic and optical properties of semiconducting materials could substantially expand their functionality and enable new pathways for the formation of ‘smart’ materials for emerging innovative applications. An emerging new path for the synthesis of exotic silicon (Si) polymorphs is irradiation of bulk diamond-cubic Si by ultrashort laser pulses at relativistic intensity above 1019 W/cm2. Exotic polymorphs are formed due to interaction with MeV-energy electrons generated in laser-produced high-temperature plasma state. The unusual Si structures are found in the form of 5–10 nm nanoparticles confined deep in the bulk of 500-μm-thick Si samples. Raman spectroscopy, electron microscopy and X-ray diffraction studies provide an unequivocal evidence of exotic Si phase formation. A key advantage of such relativistic irradiation lies thereby in the fact that large quantities of such exotic Si is synthesised embedded within the bulk diamond-cubic Si and that further the formed Si polymorphs are stable at ambient temperature and pressure. They are thus available for further studies for electronic applications in selective band gap engineering.

Rapp, Ludovic↗

Assessing Single-Source Reproducibility of Human Head Hair Peptide Profiling from Different Regions of the Scalp

Neither microscopical hair comparisons nor mitochondrial DNA sequencing alone, or together, constitutes a basis for personal identification. Due to these limitations, a complementary technique to compare questioned and known hair shafts was investigated. Recently, scientists from Lawrence Livermore National Laboratory's Forensic Science Center and other collaborators developed a peptide profiling technique, which can infer non-synonymous single nucleotide polymorphisms (SNPs) preserved in hair shaft proteins as single amino acid polymorphisms (SAPs). In this study, peptide profiling was evaluated to determine if it can meet forensic expectations when samples are in limited quantities with the possibility that hair samples collected from different areas of a single donor’s scalp (i.e., single source) might not exhibit the same SAP profile. The average dissimilarity, percent differences in SAP profiles within each source, ranged from 0% difference to 29%. This pilot study suggests that more work is needed before peptide profiling of hair can be considered for forensic comparisons.

59 BASIC BIOLOGICAL SCIENCES↗

Topological effects on separation of alkane isomers in metal–organic frameworks

Polymorphism in metal–organic frameworks (MOFs) means that the same chemical building blocks (nodes and linkers) can be used to construct isomeric MOFs with different topological networks. The choice of topology can substantially impact the pore network of the MOF, changing the sizes and shapes of the pores, which has implications for adsorption and separation applications. Here, we look at the influence of topology in 38 polymorphic MOFs on the separation of linear and branched C4–C6 alkane isomers, a separation of great importance to the petrochemical industry. We find that the MOF Cu 2 (1,4-benzenedicarboxylate) in nbo topology (nbo-Cu 2 BDC) has particularly high affinity for linear alkanes due to its small pore size, which excludes the branched isomers. Upon studying this MOF in further detail, we find that it can take either of two conformations: a cubic conformation, which is typical of nbo MOFs, and a unique star conformation that contains 1D triangular and hexagonal channels. The determination of which conformation the MOF will adopt depends on steric effects between the nodes and linkers.

42 ENGINEERING↗

High temperature stability and transport characteristics of hydrogen in alumina via multiscale computation

Here, the impact of hydrogen charge states on the stability and transport characteristics of hydrogen interstitials in alumina polymorphs is evaluated by multiscale computational methods including density functional theory (DFT), ab initio molecular dynamics (AIMD) and machine learned force fields. Thermodynamic calculations show that the protonic H i +1 interstitial is the most stable defect species for most values of the electronic bandgap in both and amorphous alumina (Al 2 O 3 ). Further, active learned Gaussian approximation potentials (GAP) were developed using AIMD data to study temperature dependent long time proton diffusion in alumina. Diffusivity calculations from GAP-MD simulations are found to be comparable with of the AIMD data, while being ~340 times faster and scalable to larger systems. Comparisons with diffusivity values for other interstitial charge states (H i 0 and H i -1 ) and published experimental literature indicate that H i +1 diffusion is the likely mechanism of hydrogen transport. A good agreement is obtained between H i +1 diffusivity calculated in α-Al 2 O 3 from DFT: 5.05 10 -3 exp(-0.81 eV/k B /T) cm 2 /s and reported experiment: 9.7X10 -4 exp(-0.83 eV/k B /T) cm 2 /s. Computationally and experimentally calculated energy barriers (0.81 and 0.83 eV respectively) only differ by 2.5%. Similarly, the pre-exponential diffusion coefficients only differ by 0.5 orders of magnitude. Moreover, the diffusivity of H i +1 in amorphous Al 2 O 3 in the 1000–2000 K range is calculated to be 2.53X10 -2 exp(-0.89 eV/k B /T), just one order of magnitude higher than the corresponding value in α-Al 2 O 3 . This suggests that local structural disorder does not significantly affect the energy landscape and diffusion behavior of H i +1 in Al 2 O 3 . Overall, these results show promise for the application of alumina polymorphs as hydrogen permeation barriers.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗