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At least 1,063 records · Page 59

Exploring the Effects of Node Topology, Connectivity, and Metal Identity on the Binding of Nerve Agents and Their Hydrolysis Products in Metal–Organic Frameworks

Recent studies have shown that metal–organic frameworks (MOFs) built from hexanuclear M(IV) oxide cluster nodes are effective catalysts for nerve agent hydrolysis, where the properties of the active sites on the nodes can strongly influence the reaction energetics. The connectivity and metal identity of these M6 nodes can be easily tuned, offering extensive opportunities for computational screening to predict promising new materials. Thus, we used density functional theory (DFT) to examine the effects of node topology, connectivity, and metal identity on the binding energies of multiple nerve agents and their corresponding hydrolysis products. By computing an optimization metric based on the relative binding strengths of key hydrolysis reaction species (water, agent, and bidentate-bound products), we predicted optimal M6 nodes for hydrolyzing specific nerve agent and simulant molecules, where our results are in qualitative agreement with observed experimental trends. This analysis highlighted the notion that no single metal or node topology is optimal for all possible organophosphates, suggesting that MOFs should be selected based on the agent of interest. Using the large amount of data generated from our DFT calculations, we then derived quantitative structure–activity relationship (QSAR) models to help explain the complex trends observed in the binding energies. Through linear regression, we identified the most important descriptors for describing the binding of nerve agents and their hydrolysis products to M6 nodes. These results suggested that both molecular and node properties, including both structural and chemical features, collectively contribute to the binding energetics. By performing a thorough statistical analysis, we showed that our QSAR models are capable of making quantitatively accurate binding energy predictions for nerve agents and their hydrolysis products in a wide variety of M(IV)-MOFs. In conclusion, the insights gained herein can be used to guide future experiments for the synthesis of MOFs with enhanced catalytic activity for organophosphate hydrolysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-Throughput Computational Screening of Perovskites for Thermochemical Water Splitting Applications

The use of hydrogen as fuel is a promising avenue to aid in the reduction of greenhouse effect gases released in the atmosphere. In this work, we present a high-throughput density functional theory (HT-DFT) study of 5,329 cubic and distorted perovskite ABO 3 compounds to screen for thermodynamically favorable two-step thermochemical water splitting (TWS) materials. From a data set of more than 11,000 calculations, we screened materials based on the following: (a) thermodynamic stability and (b) oxygen vacancy formation energy that allow favorable TWS. From our screening strategy, we identify 139 materials as potential new candidates for TWS application. Several of these compounds, such as CeCoO 3 and BiVO 3 , have not been experimentally explored yet for TWS and present promising avenues for further research. We show that taking into consideration all phases present in the A–B–O ternary phase, as opposed to only calculating the formation energy of a compound, is crucial to assess correctly the stability of a compound as it reduces the number of potential candidates from 5,329 to 383. Finally, our large data set of compounds containing stabilites, oxidation states, and ionic sizes allowed us to revisit the structural maps for perovskites by showing stable and unstable compounds simultaneously.

08 HYDROGEN↗

Temperature effect on plasmons in bilayer graphene

We have theoretically investigated the plasmon dispersion and damping rate of doped bilayer graphene (BLG) at finite temperatures within the random phase approximation. Our computed results on plasmon dispersion show that plasmon frequency enhances with increasing temperatures in contrast to single layer graphene where it is suppressed. This can be attributed to the fact that the dynamic response of the electron gas or screening in bilayer graphene is different from that of single layer graphene. Further the temperature effect on damping rate is also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Microstrain screening towards defect-less layered transition metal oxide cathodes

Microstrain and the associated surface-to-bulk propagation of structural defects are known to be major roadblocks to developing high-energy and long-life batteries. However, the origin and effects of microstrain during the synthesis of battery materials remain largely unknown. Here, in this study, we perform microstrain screening during real-time and realistic synthesis of sodium layered oxide cathodes. Evidence gathered from multiscale in situ synchrotron X-ray diffraction and microscopy characterization collectively reveals that the spatial distribution of transition metals within individual precursor particles strongly governs the nanoscale phase transformation, local charge heterogeneity and accumulation of microstrain during synthesis. This unexpected dominance of transition metals results in a counterintuitive outward propagation of defect nucleation and growth. These insights direct a more rational synthesis route to reduce the microstrain and crystallographic defects within the bulk lattice, leading to significantly improved structural stability. The present work on microstrain screening represents a critical step towards synthesis-by-design of defect-less battery materials.

25 ENERGY STORAGE↗

PyFaults: A Python Toolkit for Stacking Fault Screening

PyFaults is an open-source Python library designed to model stacking fault disorder in crystalline materials and qualitatively assess the characteristic selective broadening effects in powder X-ray diffraction (PXRD). Here, the main capabilities of PyFaults are presented, including unit cell and supercell model construction, PXRD pattern calculation, assessment against experimental PXRD, and methods for rapid screening of candidate models within a set of possible stacking vectors and fault occurrence probabilities. This program aims to serve as a computationally inexpensive tool for identifying and screening potential stacking fault models in materials with planar disorder. Three diverse case studies, involving GaN, Li2MnO3 and Li3YCl6, are presented to illustrate the program functionality across a range of structure types and stacking fault modalities.

MATHEMATICS AND COMPUTING↗

Inhibition of CRM1-mediated nuclear export of influenza A nucleoprotein and nuclear export protein as a novel target for antiviral drug development

An anti-influenza compound, DP2392-E10 based on inhibition of the nuclear export function of the viral nucleoprotein-nuclear export signal 3 (NP-NES3) domain was successfully identified by our previous high-throughput screening system. Here, we demonstrated that DP2392-E10 exerts its antiviral effect by inhibiting replication of a broad range of influenza A subtypes. In regard to the molecular mechanism, we revealed that DP2392-E10 inhibits nuclear export of both viral NP and nuclear export protein (NEP). More specifically, in vitro pull-down assays revealed that DP2392-E10 directly binds cellular CRM1, which mediates nuclear export of NP and NEP. In silico docking suggested that DP2392-E10 binds at a region close to the HEAT9 and HEAT10 domains of CRM1. Together, these results indicate that the CRM1-mediated nuclear export function of influenza virus represents a new potential target for antiviral drug development, and also provide a core structure for a novel class of inhibitors that target this function. - Highlights: •DP2392-E10 inhibits replication of a broad range of influenza A subtypes. •DP2392-E10 inhibits nuclear exports of NP and NEP via their NP-NES3 and NEP-NES2 domains, respectively. •DP2392-E10 is predicted to directly bind CRM1 in the region near the HEAT9 and HEAT10 repeats.

60 APPLIED LIFE SCIENCES↗

The Proximity and Josephson Effects in Niobium Nitride–Aluminum Bilayers

Highly disordered thin films of niobium nitride and the specific features of the proximity effect in NbN (S)–aluminum (N) bilayers with a large resistivity ratio, ρ{sub NbN}/ρ{sub Al}≫ 1, are studied. It is shown that magnetic screening and the critical current I{sub c} of such SN structures significantly increase compared to the S layer. The observed effect is associated with the induced superconductivity in the N layer due to the proximity effect. The Josephson effect is demonstrated in NbN/Al–NbN–NbN/Al variable thickness bridges made of such SN bilayers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electron Backstreaming Determination for Ion Thrusters

Electron backstreaming in ion thrusters is caused by the random flux of beam electrons past a potential barrier established by the accel grid. A technique that integrates this flux over the radial extent of the barrier reveals important aspects of electron backstreaming phenomena for individual beamlets, across the thruster beam, and throughout thruster life. For individual beamlets it was found that over 99% of the electron backstreaming occurs in a small annulus at the center of the beamlet that is less than 20% the area of the beamlet at the potential barrier established by the accel grid. For the thruster beam it was found that over 99% of the backstreaming current occurs inside of r = 6 cm for the over 28 cm diameter NSTAR grid. Initial validation against ELT data shows that the technique provides the correct behavior and magnitude of electron backstreaming limit, V(sub ebs). From the sensitivity analyses it is apparent that accel grid chamfering may be the dominant mechanism contributing to the sharp rise in the absolute value of V(sub ebs) observed in the ELT but does not explain the rise in ion transparency. Grid gap change also contributes to the absolute value of V(sub ebs) rise and large rises in ion transparency with thruster life for the center gridlet. Screen grid erosion contributes generally to rises in the absolute value of V(sub ebs) and ion transparency, but for the assumptions used herein, it appears to not have as much of an effect chamfering or grid gap change. Overall, it is apparent that accel grid chamfering, grid gap change, and screen grid erosion are important to the increase in electron backstreaming observed during the ELT.

Wirz, Richard E.↗

Functional coding and non-coding variants in human BRCA1 gene and their use in genetic screening

BRCA1 is involved in double-strand DNA damage repair pathways, and mutations in the gene are associated with hereditary breast and ovarian cancers. With great help of the development of high-throughput DNA sequencing techniques numerous single-nucleotide polymorphisms (SNPs) and insertion deletion (Indel) mutations are detected on both coding and non-coding/regulatory regions of the BRCA1. Mutations may cause pathogenic or benign changes on the protein function or affect its expression. In the last decade, use of genetic screening tests to detect mutations on such genes has become greatly popular. However, it is very important to know the effect of the detected mutations, which is mostly possible by the use of predictive softwares, and also the related family history to be able to correctly analyse the screening results and to inform the patient. Therefore, use of in silico and in vitro techniques to score the pathogenicity of detected variants on genes like BRCA1 is now of great importance. Otherwise, results obtained from screening tests and family history cannot be analysed precisely.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production

Abstract Branched-chain amino acid (BCAA) metabolism fulfills numerous physiological roles and can be harnessed to produce valuable chemicals. However, the lack of eukaryotic biosensors specific for BCAA-derived products has limited the ability to develop high-throughput screens for strain engineering and metabolic studies. Here, we harness the transcriptional regulator Leu3p from Saccharomyces cerevisiae to develop a genetically encoded biosensor for BCAA metabolism. In one configuration, we use the biosensor to monitor yeast production of isobutanol, an alcohol derived from valine degradation. Small modifications allow us to redeploy Leu3p in another biosensor configuration that monitors production of the leucine-derived alcohol, isopentanol. These biosensor configurations are effective at isolating high-producing strains and identifying enzymes with enhanced activity from screens for branched-chain higher alcohol (BCHA) biosynthesis in mitochondria as well as cytosol. Furthermore, this biosensor has the potential to assist in metabolic studies involving BCAA pathways, and offers a blueprint to develop biosensors for other products derived from BCAA metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Lead discovery for mammalian elongation of long chain fatty acids family 6 using a combination of high-throughput fluorescent-based assay and RapidFire mass spectrometry assay

A high-throughput RapidFire mass spectrometry assay is described for elongation of very long-chain fatty acids family 6 (Elovl6). Elovl6 is a microsomal enzyme that regulates the elongation of C12-16 saturated and monounsaturated fatty acids. Elovl6 may be a new therapeutic target for fat metabolism disorders such as obesity, type 2 diabetes, and nonalcoholic steatohepatitis. To identify new Elovl6 inhibitors, we developed a high-throughput fluorescence screening assay in 1536-well format. However, a number of false positives caused by fluorescent interference have been identified. To pick up the real active compounds among the primary hits from the fluorescence assay, we developed a RapidFire mass spectrometry assay and a conventional radioisotope assay. These assays have the advantage of detecting the main products directly without using fluorescent-labeled substrates. As a result, 276 compounds (30%) of the primary hits (921 compounds) in a fluorescence ultra-high-throughput screening method were identified as common active compounds in these two assays. It is concluded that both methods are very effective to eliminate false positives. Compared with the radioisotope method using an expensive {sup 14}C-labeled substrate, the RapidFire mass spectrometry method using unlabeled substrates is a high-accuracy, high-throughput method. In addition, some of the hit compounds selected from the screening inhibited cellular fatty acid elongation in HEK293 cells expressing Elovl6 transiently. This result suggests that these compounds may be promising lead candidates for therapeutic drugs. Ultra-high-throughput fluorescence screening followed by a RapidFire mass spectrometry assay was a suitable strategy for lead discovery against Elovl6. - Highlights: • A novel assay for elongation of very-long-chain fatty acids 6 (Elovl6) is proposed. • RapidFire mass spectrometry (RF-MS) assay is useful to select real screening hits. • RF-MS assay is proved to be beneficial because of its high-throughput and accuracy. • A combination of fluorescent and RF-MS assays is effective for Elovl6 inhibitors.

60 APPLIED LIFE SCIENCES↗

Investigation of the therapeutic potential of N-acetyl cysteine and the tools used to define nigrostriatal degeneration in vivo

The glutathione precursor N-acetyl-L-cysteine (NAC) is currently being tested on Parkinson's patients for its neuroprotective properties. Our studies have shown that NAC can elicit protection in glutathione-independent manners in vitro. Thus, the goal of the present study was to establish an animal model of NAC-mediated protection in which to dissect the underlying mechanism. Mice were infused intrastriatally with the oxidative neurotoxicant 6-hydroxydopamine (6-OHDA; 4 μg) and administered NAC intraperitoneally (100 mg/kg). NAC-treated animals exhibited higher levels of the dopaminergic terminal marker tyrosine hydroxylase (TH) in the striatum 10d after 6-OHDA. As TH expression is subject to stress-induced modulation, we infused the tracer FluoroGold into the striatum to retrogradely label nigrostriatal projection neurons. As expected, nigral FluoroGold staining and cell counts of FluoroGold{sup +} profiles were both more sensitive measures of nigrostriatal degeneration than measurements relying on TH alone. However, NAC failed to protect dopaminergic neurons 3 weeks following 6-OHDA, an effect verified by four measures: striatal TH levels, nigral TH levels, nigral TH{sup +} cell counts, and nigral FluoroGold levels. Some degree of mild toxicity of FluoroGold and NAC was evident, suggesting that caution must be exercised when relying on FluoroGold as a neuron-counting tool and when designing experiments with long-term delivery of NAC—such as clinical trials on patients with chronic disorders. Finally, the strengths and limitations of the tools used to define nigrostriatal degeneration are discussed. - Highlights: • N-acetyl cysteine (NAC) was injected into animals infused with the toxicant 6-OHDA. • Retrograde tracing with FluoroGold was used to define nigrostriatal cell loss. • Infrared Odyssey imaging and cell counts were used to screen for nigral cell loss. • NAC protected transiently against 6-OHDA but this effect waned over time. • Mildly toxic effects of chronic NAC delivery may influence future clinical trials.

60 APPLIED LIFE SCIENCES↗

Thickness dependence of La 0.7 Sr 0.3 MnO 3 /PbZr 0.2 Ti 0.8 O 3 magnetoelectric interfaces

Magnetoelectric materials have great potential to revolutionize electronic devices due to the coupling of their electric and magnetic properties. Thickness varying La 0.7 Sr 0.3 MnO 3 (LSMO)/PbZr 0.2 Ti 0.8 O 3 (PZT) heterostructures were built and measured in this article by valence sensitive x-ray absorption spectroscopy. The sizing effects of the heterostructures on the LSMO/PZT magnetoelectric interfaces were investigated through the behavior of Mn valence, a property associated with the LSMO magnetization. Here, we found that Mn valence increases with both LSMO and PZT thickness. Piezoresponse force microscopy revealed a transition from monodomain to polydomain structure along the PZT thickness gradient. The ferroelectric surface charge may change with domain structure and its effects on Mn valence were simulated using a two-orbital double-exchange model. The screening of ferroelectric surface charge increases the electron charges in the interface region, and greatly changes the interfacial Mn valence, which likely plays a leading role in the interfacial magnetoelectric coupling. The LSMO thickness dependence was examined through the combination of two detection modes with drastically different attenuation depths. The different length scales of these techniques' sensitivity to the atomic valence were used to estimate the depth dependence Mn valence. Finally, a smaller interfacial Mn valence than the bulk was found by globally fitting the experimental results.

36 MATERIALS SCIENCE↗

The ‘grey’ assessment practice of IA screening: Prevalence, influence and applied rationale

Research focusing on the practices surrounding screening in Impact Assessment (IA) is limited. Yet, it has been found that development proposals sometimes are adjusted through an informal dialog with IA practitioners prior to or during screening. Such practice is often referred to as ‘grey IA’ in Denmark. This article explores the prevalence, influence and applied rationale of grey IA. Through a questionnaire, data was collected from 121 IA practitioners working within the fields of environmental impact assessment and strategic environmental assessment. It was found that grey IA is a common practice, which influences the outcomes of formal screening procedures through consideration of impacts on neighbours and spatial zones of protection. Grey IA is to some extent motivated by the opportunity to save the resources required for full-scale IA, but an additional ‘green’ rationale also exists. Grey IA may influence the effectiveness of IA systems, but further research is needed before any conclusions can be made. - Highlights: • Screening procedures may function as an informal, ‘grey’ assessment. • Grey assessment is common and influences formal screening outcomes. • Grey assessment is motivated by an opportunity to cut IA costs. • Yet, an environmental, ‘green’ rationale for grey assessment also exists.

54 ENVIRONMENTAL SCIENCES↗

Full-wave simulations on helicon and parasitic excitation of slow waves near the edge plasma

Helicon waves are thought to be promising in various tokamaks, such as DIII-D, because they can penetrate reactor-grade high-density cores and drive the off-axis current with higher efficiency. In the frequency regime ~476 MHz, both slow electrostatic and fast electromagnetic helicon waves can coexist in DIII-D. If the antenna parasitically excites the slow mode, these waves can propagate along the magnetic field line into the scrape-off layer (SOL). Although the importance of the misalignment of the Faraday screen and the electron density in the SOL on the excitation and propagation of slow modes is well known, the conditions for minimizing slow mode excitation have yet to be optimized. Using the Petra-M simulation code in the 2D domain, we analyze the effects of the misalignment of the antenna in the poloidal direction, the misalignment of the Faraday screen in the toroidal direction, and the density in front of the antenna on slow mode generation. Our results suggest that the misalignment of the Faraday screen is a critical factor in reducing the slow mode and that the misalignment angle should be below ~5° to minimize the slow wave excitation. When the electron density is higher than 3.5 x 10 18 m –3 in the SOL, the generation of the slow mode from the antenna is minimized and unaffected by the misalignment of the Faraday screen.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation on gate oxide reliability under gate bias screening for commercial SiC planar and trench MOSFETs

This paper evaluates the impact of the fast high gate-voltage screening technique on gate oxide reliability of commercial 1.2 kV 4H-SiC power metal-oxide-semiconductor field-effect transistors (MOSFETs) with planar and trench gate structures. The measurements are conducted on packaged devices with the intent that the results will be applicable to wafer-level screening. The threshold voltage (V th ) of SiC MOSFETs is measured before and after various screening treatments and recovery process. In addition, constant-voltage time-dependent dielectric breakdown (TDDB) measurements are performed on SiC MOSFETs to obtain the intrinsic lifetime of gate oxide. The objective of this study is to determine the optimal screening conditions and improve screening efficiency without degradation of gate oxide reliability, such as V th shift and reduced oxide intrinsic lifetime. Due to the differences in the gate oxidation process and structural design of SiC planar and trench MOSFETs, the two types of devices exhibit different oxide reliability in the screening process. The recommended screening conditions obtained in this paper reveal that SiC trench MOSFETs can accept higher screening voltages compared to SiC planar MOSFETs. Hence, it can be concluded that more efficient screening techniques can be adopted for SiC MOSFETs with thicker gate oxide to meet the requirements of industrial applications.

36 MATERIALS SCIENCE↗

Boron-Based Neutron Scintillator Screens for Neutron Imaging

In digital neutron imaging, the neutron scintillator screen is a limiting factor of spatial resolution and neutron capture efficiency and must be improved to enhance the capabilities of digital neutron imaging systems. Commonly used neutron scintillators are based on 6 LiF and gadolinium oxysulfide neutron converters. This work explores boron-based neutron scintillators because 10 B has a neutron absorption cross-section four times greater than 6Li, less energetic daughter products than Gd and 6 Li, and lower γ-ray sensitivity than Gd. These factors all suggest that, although borated neutron scintillators may not produce as much light as 6 Li-based screens, they may offer improved neutron statistics and spatial resolution. This work conducts a parametric study to determine the effects of various boron neutron converters, scintillator and converter particle sizes, converter-to-scintillator mix ratio, substrate materials, and sensor construction on image quality. The best performing boron-based scintillator screens demonstrated an improvement in neutron detection efficiency when compared with a common 6 LiF/ZnS scintillator, with a 125% increase in thermal neutron detection efficiency and 67% increase in epithermal neutron detection efficiency. The spatial resolution of high-resolution borated scintillators was measured, and the neutron tomography of a test object was successfully performed using some of the boron-based screens that exhibited the highest spatial resolution. For some applications, boron-based scintillators can be utilized to increase the performance of a digital neutron imaging system by reducing acquisition times and improving neutron statistics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗