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At least 307 records · Page 17

Effect of Helium Flux on Near-surface Helium Accumulation in Plasma-Exposed Tungsten

We report results of object kinetic Monte Carlo (OKMC) simulations aimed at understanding the effect of helium flux on the near-surface helium accumulation in plasma-facing tungsten, which is initially defect-free and has a W(100) surface orientation. These OKMC simulations are performed at 933 K for fluxes ranging from 10 22 to 4 × 10 25 He/m 2 s, with 100 eV helium atoms impinging on a W(100) surface up to a maximum fluence of 4×10 19 He/m 2 . In the near-surface region, helium clusters interact elastically with the free surface. The interaction is attractive and results in the drift of mobile helium clusters towards the surface as well as increased trap mutation rates. The associated kinetics and energetics of the above-mentioned processes obtained from molecular dynamics simulations are also considered. The OKMC simulations indicate that as the flux decreases, the retention of implanted helium decreases, and its depth distribution shifts to deeper below the surface in initially pristine tungsten. Furthermore, the fraction of retained helium diffusing into the bulk increases as well, so much so that for 10 22 He/m 2 s, almost all of the retained helium diffused into the bulk with minimal/negligible near-surface helium accumulation. At a given flux, with increasing fluence, the fraction of retained helium initially decreases and then starts to increase after reaching a minimum. The occurrence of the retention minimum shifts to higher fluences as the flux decreases. Although the near-surface helium accumulation spreads deeper into the material with decreasing flux and increasing fluence, the spread appears to saturate at depths between 80 and 100 nm. Finally, we present a detailed analysis of the influence of helium flux on the size and depth distribution of total helium and helium bubbles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The mobility of small, over-pressurized helium bubbles in tungsten at 2000 K

Fusion reactor environments inevitably lead to the formation of high-pressure helium bubbles whose nucleation, growth, and diffusion strongly impact the performance of plasma-facing components. Here this research describes a diffusion mechanism of over-pressurized bubbles via a sequence of Frenkel pair nucleation, self-interstitial migration, and Frenkel pair annihilation. Molecular dynamics was used to simulate the diffusion of small bubbles in tungsten at 2000 K with helium-per-vacancy ratios in the range of 4.5 to 7. The diffusion coefficients are calculated and their dependence on helium content, number of vacancies, and number of attached self-interstitials is characterized. It is found that bubbles are most mobile when the nucleation/annihilation rates of Frenkel pairs are nearly equal and when the bubbles nucleate and annihilate a single self-interstitial. All bubbles experience a peak diffusivity, which can be as high as 10 -11 m 2 /s decreasing with bubble size. The calculated diffusion coefficients provide valuable insight into the mobility of small, high-pressure bubbles, and can be used as input parameters in mesoscale models to improve predictions of plasma-surface interactions. (LA-UR-21-21881)

36 MATERIALS SCIENCE↗

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synergistic catalysis by Mn promoted ceria for molecular oxygen assisted epoxidation

Mesoporous manganese doped cerium oxide catalysts were prepared by an inverse micelle method with different manganese loadings. These materials exhibited superior activity for epoxidation of alkenes with molecular oxygen. Highest active 10MnCe material showed an activity of 80 % conversion and >99 % selectivity for cyclooctene epoxidation. The fluorite crystal structure which facilitates the high oxygen mobility, low temperature reducibility, homogeneous distribution of manganese on ceria, nanoparticle nature, higher number of oxygen vacancies, low valent states of manganese and cerium, and the ability to generate reactive oxygen species of the manganese doped cerium oxide could be correlated to the high catalytic activity. The reaction followed first order kinetics with a rate constant of 0.31 h –1 at 100 °C, and the activation energy turned out to be 10.5 kJ/mol. In conclusion, the mechanistic study revealed that the reaction proceeds via a unique mechanism which involves in situ generated superoxide and singlet oxygen species..

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward the predictive discovery of ambipolarly dopable ultra-wide-band-gap semiconductors: The case of rutile GeO 2

Ultrawide-band-gap (UWBG) semiconductors are promising for fast, compact, and energy-efficient power-electronics devices. Their wider band gaps result in higher breakdown electric fields that enable high-power switching with a lower energy loss. Yet, the leading UWBG semiconductors suffer from intrinsic materials' limitations with regard to their doping asymmetry that impedes their adoption in CMOS technology. Improvements in the ambipolar doping of UWBG materials will enable a wider range of applications in power electronics as well as deep-UV optoelectronics. These advances can be accomplished through theoretical insights on the limitations of current UWBG materials coupled with the computational prediction and experimental demonstration of alternative UWBG semiconductor materials with improved doping and transport properties. As an example, we discuss the case of rutile GeO2 (r-GeO 2 ), a water-insoluble GeO 2 polytype, which is theoretically predicted to combine an ultra-wide gap with ambipolar dopability, high carrier mobilities, and a higher thermal conductivity than β-Ga 2 O 3 . The subsequent realization of single-crystalline r-GeO 2 thin films by molecular beam epitaxy provides the opportunity to realize r-GeO 2 for electronic applications. Future efforts toward the predictive discovery and design of new UWBG semiconductors include advances in first-principles theory and high-performance computing software, as well as the demonstration of controlled doping in high-quality thin films with lower dislocation densities and optimized film properties.

36 MATERIALS SCIENCE↗

High Mobility SiGe/Si Transistor Structures on Sapphire Substrates Using Ion Implantation

High mobility n-type SiGe/Si transistor structures have been fabricated on sapphire substrates by ion implanting phosphorus ions into strained 100 Angstrom thick silicon channels for the first time. The strained Si channels were sandwiched between Si(sub 0.7)Ge(sub 0.3) layers, which, in turn, were deposited on Si(sub 0.7)Ge(sub 0.3) virtual substrates and graded SiGe buffer layers. After the molecular beam epitaxy (MBE) film growth process was completed, ion thick silicon channels implantation and post-annealing were used to introduce donors. The phosphorous ions were preferentially located in the Si channel at a peak concentration of approximately 1x10(exp 18)/cu cm. Room temperature electron mobilities exceeding 750 sq cm/V-sec at carrier densities of 1x10(exp 12)/sq cm were measured. Electron concentration appears to be the key factor that determines mobility, with the highest mobility observed for electron densities in the 1 - 2x10(exp 12)/sq cm range.

Alterovitz, S. A.↗

Discovery of a novel transcriptional regulator of sugar catabolism in archaea

Abstract The haloarchaeon Haloferax volcanii degrades D‐glucose via the semiphosphorylative Entner‐Doudoroff pathway and D‐fructose via a modified Embden‐Meyerhof pathway. Here, we report the identification of GfcR, a novel type of transcriptional regulator that functions as an activator of both D‐glucose and D‐fructose catabolism. We find that in the presence of D‐glucose, GfcR activates gluconate dehydratase, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase and also acts as activator of the phosphotransferase system and of fructose‐1,6‐bisphosphate aldolase, which are involved in uptake and degradation of D‐fructose. In addition, glyceraldehyde‐3‐phosphate dehydrogenase and pyruvate kinase are activated by GfcR in the presence of D‐fructose and also during growth on D‐galactose and glycerol. Electrophoretic mobility shift assays indicate that GfcR binds directly to promoters of regulated genes. Specific intermediates of the degradation pathways of the three hexoses and of glycerol were identified as inducer molecules of GfcR. GfcR is composed of a phosphoribosyltransferase (PRT) domain with an N‐terminal helix‐turn‐helix motif and thus shows homology to PurR of Gram‐positive bacteria that is involved in the transcriptional regulation of nucleotide biosynthesis. We propose that GfcR of H. volcanii evolved from a PRT‐like enzyme to attain a function as a transcriptional regulator of central sugar catabolic pathways in archaea.

59 BASIC BIOLOGICAL SCIENCES↗

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

biocuration↗

The influence of surface impurities on photoelectric currents driven by intense soft x rays

In an x-ray driven cavity experiment, an intense flux of soft x rays on the emitting surface produces significant emission of photoelectrons having several kiloelectronvolts of kinetic energy. At the same time, rapid heating of the emitting surface occurs, resulting in the release of adsorbed surface impurities and subsequent formation of an impurity plasma. This numerical study explores a simple model for the photoelectric currents and the impurity plasma. In this work, attention is given to the effect of varying the composition of the impurity plasma. The presence of protons or hydrogen molecular ions leads to a substantially enhanced cavity current, while heavier plasma ions are seen to have a limited effect on the cavity current due to their lower mobility. Additionally, it is demonstrated that an additional peak in the current waveform can appear due to the impurity plasma. A correlation between the impurity plasma composition and the timing of this peak is elucidated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Polymer Retention Evaluation in a Heavy Oil Sand for a Polymer Flooding Application on Alaska’s North Slope

For a polymer flooding field trial in a heavy oil reservoir on Alaska’s North Slope, polymer retention is a key parameter. Because of the economic impact of retention, this parameter was extensively studied using field core material and conditions. Several important findings were noted. Polymer retention based on effluent viscosity measurements can be overestimated unless the correct (non-linear) relation between polymer concentration and viscosity is used. Polymer degradation (either mechanical or oxidative) can also lead viscosity-based measurements to overestimate retention. Inaccessible pore volume (IAPV) can be overestimated if insufficient brine is flushed through the sand between polymer banks. Around 100 pore volumes (PV) of brine may be needed to displace mobile polymer to approach a true residual resistance factor and properly measure IAPV. Even for a sand pack with kwsor = 20 mD, IAPV was zero for HPAM with molecular weight (Mw) of 18 million g/mol. Fine-grain particles (<20 μm) strongly impacted polymer retention values. Native NB#1 sand with a significant component of particles <20 μm exhibited 290 μg/g, while the same sand exhibited 28 μg/g after these small particles were removed. Polymer retention did not necessarily correlate with mineral composition. The NB#1, NB#3, and OA sands had similar elemental and clay compositions, but the NB#1 sand exhibited ~10 times higher retention than the NB#3 sand. Polymer retention did not necessarily correlate with permeability. NB#1 sand exhibited much higher retention than OA sand, even though NB#1 sand was twice as permeable as OA sand. No evidence of chromatographic separation of HPAM molecular weights was found in our experiments. Although retention tended to be greater without a residual oil saturation (than at Sor), the effect was not strong. Aging a core (with high oil saturation) at 60°C reduced HPAM retention by a factor of two. As expected, under similar conditions, polymer retention was greater for a higher Mw HPAM (18 million g/mol) than for a lower Mw HPAM (10-12 million g/mol). In many cases with high polymer retention values (e.g., 240 μg/g), polymer arrival at the end of the core was relatively quick, but achieving the injected concentration occurred gradually over many pore volumes. This effect was not due chromatographic separation of polymer molecular weights. Results from modeling of this behavior was consistent with concentrationdependent polymer retention. The form assumed for the retention function in a simulator can have an important impact on the timing and magnitude of the oil response from a polymer flood. Field-based observations can underestimate polymer retention, depending on when the tracer and polymer concentrations were measured and the assumptions made about reservoir heterogeneity.

Wang, Dongmei↗

The Effect of Surface Chemical Functionality Upon Ice Adhesion

In nature, anti-freeze proteins present in fish utilize specific organic functionalities to disrupt ice crystal formation and propagation. Based on these structures, surfaces with controlled chemical functionality and chain length were evaluated both experimentally and computationally to assess the effect of both parameters in mitigating ice formation. Linear aliphatic dimethylethoxysilanes terminated with methyl or hydroxyl groups were prepared, characterized, and used to coat aluminum. The effect upon icing using a microdroplet freezing apparatus and the Adverse Environment Rotor Test Stand found hydroxyl-terminated materials exhibited a greater propensity for ice formation and adhesion. Molecular dynamics simulations of a silica substrate bearing functionalized species of similar composition were brought into contact with a pre-equilibrated ice crystal. Several parameters including chain mobility were monitored to ascertain the size of a quasi-liquid layer. The studies suggested that chain mobility affected the interface between ice and the surface more than terminal group chemical composition.

Smith, Joseph G., Jr.↗

Concentration Dependent Interfacial Chemistry of the NaOH(aq):Gibbsite Interface

Caustic conditions are often employed for dissolution of a wide variety of minerals, where ion sorption, surface diffusion, and interfacial organization impact surface reactivity. In the case of gibbsite, gamma-Al(OH)3, the chemistry at the NaOH(aq) interface is deeply intertwined with industrial processing of aluminum, including metal production and the disposition of Al-containing wastes. To date, little is known about the structure, speciation, and dynamic behavior of gibbsite interfaces (and that of many other minerals) with NaOH(aq)—particularly as a function of ionic strength. Yet concentration-dependent interfacial organization and dynamics are a critical starting point to develop a fundamental understanding of the factors that influence dissolution. This work reports equilibrium molecular dynamics simulations of the gamma-Al(OH)3:NaOH(aq) interface, revealing the sorption behavior and speciation of ions from 0.5–10 M [NaOH]. As inner-sphere complexes, Na+ primarily coordinates to the side of the gibbsite hexagonal cavities, while OH accepts hydrogen-bonding from the surface-OH groups. The mobility of inner-sphere Na+ and OH ions is significantly reduced due to a strong surface affinity in comparison to previous reports of NaCl, CaCl2, or BaCl2 electrolytes. At high [NaOH], contact ion pairing that is observed in the bulk solution is partially disrupted upon sorption to the gibbsite surface by the individual ion–surface interactions. The molecular-scale changes to surface speciation and competition between ion–surface vs. ion–ion interactions influence surface characterization of gibbsite and potential dissolution processes, providing a valuable baseline for starting conditions needed within future reactive molecular simulations.

alkaline solutions, IDREAM, gibbsite, molecular dy↗

Elucidating the Molecular Origins of the Transference Number in Battery Electrolytes Using Computer Simulations

The rate at which rechargeable batteries can be charged and discharged is governed by the selective transport of the working ions through the electrolyte. Conductivity, the parameter commonly used to characterize ion transport in electrolytes, reflects the mobility of both cations and anions. The transference number, a parameter introduced over a century ago, sheds light on the relative rates of cation and anion transport. This parameter is, not surprisingly, affected by cation–cation, anion–anion, and cation–anion correlations. In addition, it is affected by correlations between the ions and neutral solvent molecules. Computer simulations have the potential to provide insights into the nature of these correlations. We review the dominant theoretical approaches used to predict the transference number from simulations by using a model univalent lithium electrolyte. In electrolytes of low concentration, one can obtain a quantitative model by assuming that the solution is made up of discrete ion-containing clusters–neutral ion pairs, negatively and positively charged triplets, neutral quadruplets, and so on. These clusters can be identified in simulations using simple algorithms, provided their lifetimes are sufficiently long. In concentrated electrolytes, more clusters are short-lived and more rigorous approaches that account for all correlations are necessary to quantify transference. Elucidating the molecular origin of the transference number in this limit remains an unmet challenge.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Hypernetworks for Exploration of Multi-Dimensional Metabolomics Data (Chyper)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and help address the challenge of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used, for example, in the Global Natural Products Social Molecular Networking platform, are an increasingly popular computational strategy for exploring and visualizing molecular relationships and improving annotation. MNs use graph representations to show the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated to a single molecular identity. However, more advanced methods may better represent the complexity present in samples. Our work aims to increase confidence in annotation propagation by extending molecular network methods to include “molecular hypernetworks” (MHNs), able to natively represent multiway relationships among observations supporting both human and analytical processing. In this paper we first introduce MHNs illustrated with simple examples, and demonstrate how to build them from liquid chromatography- and ion mobility spectrometry- separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

59 BASIC BIOLOGICAL SCIENCES↗

Non-covalent planarizing interactions yield highly ordered and thermotropic liquid crystalline conjugated polymers

Controlling the multi-level assembly and morphological properties of conjugated polymers through structural manipulation has contributed significantly to the advancement of organic electronics. In this work, a redox active conjugated polymer, TPT–TT, composed of alternating 1,4-(2-thienyl)-2,5-dialkoxyphenylene (TPT) and thienothiophene (TT) units is reported with non-covalent intramolecular S⋯O and S⋯H–C interactions that induce controlled main-chain planarity and solid-state order. As confirmed by density functional theory (DFT) calculations, these intramolecular interactions influence the main chain conformation, promoting backbone planarization, while still allowing dihedral rotations at higher kinetic energies (higher temperature), and give rise to temperature-dependent aggregation properties. Thermotropic liquid crystalline (LC) behavior is confirmed by cross-polarized optical microscopy (CPOM) and closely correlated with multiple thermal transitions observed by differential scanning calorimetry (DSC). This LC behavior allows us to develop and utilize a thermal annealing treatment that results in thin films with notable long-range order, as shown by grazing-incidence X-ray diffraction (GIXD). Specifically, we identified a first LC phase, ranging from 218 °C to 107 °C, as a nematic phase featuring preferential face-on π–π stacking and edge-on lamellar stacking exhibiting a large extent of disorder and broad orientation distribution. A second LC phase is observed from 107 °C to 48 °C, as a smectic A phase featuring sharp, highly ordered out-of-plane lamellar stacking features and sharp tilted backbone stacking peaks, while the structure of a third LC phase with a transition at 48 °C remains unclear, but resembles that of the solid state at ambient temperature. Furthermore, the significance of thermal annealing is evident in the ∼3-fold enhancement of the electrical conductivity of ferric tosylate-doped annealed films reaching 55 S cm −1 . More importantly, thermally annealed TPT–TT films exhibit both a narrow distribution of charge-carrier mobilities (1.4 ± 0.1) × 10 −2 cm 2 V −1 s −1 along with a remarkable device yield of 100% in an organic field-effect transistor (OFET) configuration. This molecular design approach to obtain highly ordered conjugated polymers in the solid state affords a deeper understanding of how intramolecular interactions and repeat-unit symmetry impact liquid crystallinity, solution aggregation, solution to solid-state transformation, solid-state morphology, and ultimately device applications.

Chemistry↗

Indium as a surfactant: Effects on growth morphology and background impurity in GaN films grown by ammonia-assisted molecular beam epitaxy

We report on the improvement of the surface morphology of c-plane GaN films grown at high growth rates (~1 µm/h) using ammonia molecular beam epitaxy through a series of growth optimizations as well as the introduction of indium as a surfactant. The indium surfactant was expected to help with the adatom mobility and, thus, provide smoother growth surfaces. Through a combination of varying V/III ratios, In flux, and growth temperatures, an optimal condition for surface morphology, characterized by atomic force microscopy, was achieved. At higher Ga fluxes for fast growth rates (~1 µm/h and beam equivalent pressures of ~5 × 10 –7 Torr), higher ammonia flows were necessary to preserve the surface morphology. In addition, indium was an effective surfactant—reducing the roughness and improving the overall surface morphology. However, excessive indium causes the surface morphology to degrade, potentially due to the enhancement of the Ga desorption from the surface as a result of the reaction of indium with ammonia for high indium fluxes. The indium surfactant also resulted in a reduction of background Si impurity concentrations in the film. These effects allow for the growth of thick drift layers with low background dopant concentrations for vertical GaN power devices.

36 MATERIALS SCIENCE↗

Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex

Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport.

59 BASIC BIOLOGICAL SCIENCES↗

Formation and stability of long basal-prismatic facets in Mg

Long BP facets bounding {101¯2} 1¯011 twins in Mg ( ≥ 4nm) have been observed experimentally. However, the formation of these long BP facets has not been studied and their contribution/role to the twin growth remains unclear. We observed a long straight BP facet (27 nm) using high-resolution transmission electron microscopy (HRTEM) and investigated its formation, stability, and mobility by atomistic simulations. Experimentally, a serrated twin interface containing short CTBs and short BP facets near a (101¯2) twin tip is observed to transform under the effects of the electron beam into a long straight semi-coherent BP facet that contains disclination dipoles. Molecular dynamics (MD) simulations of the relaxation of a 3D twin domain reveals another process whereby a long partially-relaxed BP interface forms and contains an I 2 stacking fault. A comparison between the energy of these configurations as obtained by atomistic simulations suggests that these transformations occur in two steps: (1) serrated interfaces composed of coherent BP segments with lengths less than 2 nm combine and form a long and straight coherent BP facets and (2) these long coherent BP facets quickly transform into relaxed ones with misfit defects. Importantly, it is found that long BP facets are relatively immobile, and upon reloading, decay into more mobile serrated interfaces prior to migrating. Here, the work presented suggests that the atomistic configurations of BP facets during twin growth processes differ significantly from relaxed BP interfaces that would be observed by TEM.

36 MATERIALS SCIENCE↗