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At least 685 records · Page 38

Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly

World is witnessing one of the worst pandemics of this century caused by SARS-CoV-2 virus which has affected millions of individuals. Despite rapid efforts to develop vaccines and drugs for COVID-19, the disease is still not under control. Chloroquine (CQ) and Hydroxychloroquine (HCQ) are two very promising inhibitors which have shown positive effect in combating the disease in preliminary experimental studies, but their use was reduced due to severe side-effects. Here, we performed a theoretical investigation of the same by studying the binding of the molecules with SARS-COV-2 Spike protein, the complex formed by Spike and ACE2 human receptor and a human serine protease TMPRSS2 which aids in cleavage of the Spike protein to initiate the viral activation in the body. Both the molecules had shown very good docking energies in the range of -6kcal/mol. Subsequently, we did a high throughput screening for other potential quinoline candidates which could be used as inhibitors. From the large pool of ligand candidates, we shortlisted the top three ligands (binding energy -8kcal/mol). We tested the stability of the docked complexes by running Molecular Dynamics (MD) simulations where we observed the stability of the quinoline analogues with the Spike-ACE2 and TMPRSS2 nevertheless the quinolines were not stable with the Spike protein alone. Thus, although the inhibitors bond very well with the protein molecules their intrinsic binding affinity depends on the protein dynamics. Moreover, the quinolines were stable when bound to electronegative pockets of Spike-ACE2 or TMPRSS2 but not with Viral Spike protein. We also observed that a Fluoride based compound: 3-[3-(Trifluoromethyl)phenyl]quinoline helps the inhibitor to bind with both Spike-ACE2 and TMPRSS2 with equal probability. The molecular details presented in this study would be very useful for developing quinoline based drugs for COVID-19 treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Opening band gaps of low-dimensional materials at the meta-GGA level of density functional approximations

The quasiparticle band structure can be properly described by Hedin's GW approximation (GW), at a high computational cost. For band gaps, semilocal density functionals up to the generalized gradient approximation (GGA) level cannot compete with the accuracy of hybrid-based approximations or GW. Meta-GGA density functionals with a strong dependence on the kinetic energy density ingredient can potentially give wider band gaps compared with GGAs. The recent TASK meta-GGA density functional from Aschebrock and Kümmel [ Phys. Rev. Research 1 , 033082 (2019) ], is constructed with an enhanced nonlocality in the generalized Kohn-Sham scheme and therefore harbors great opportunities for band gap prediction. Although this approximation was found to yield excellent band gaps of bulk solids, this accuracy cannot be straightforwardly transferred to low-dimensional materials. Additionally, the reduced screening of these materials results in larger band gaps compared with their bulk counterparts, as an additional barrier to overcome. In this paper we demonstrate how the alteration of this functional affects the band gaps of monolayers and nanoribbons and present accurate band gaps competing with the revised Heyd-Scuseria-Ernzerhof (HSE06) approximation. In order to achieve this goal, we have modified the TASK functional (a) by changing the tight upper bound for one- or two-electron systems ( h X 0 ) from 1.174 to 1.29 and (b) by changing the limit of the interpolation function f X ( α → ∞ ) of the TASK functional that interpolates the exchange enhancement factor F X ( s , α ) from α = 0 to 1. The resulting modified TASK (mTASK) was tested for various materials from three dimensions to two dimensions to one dimension (nanoribbons) and was compared with the results of the higher-level hybrid functional HSE06 or with the G 0 W 0 approximation within many-body perturbation theory. We find that mTASK systematically improves the band gaps and band structures of two-dimensional (2D) and 1D systems, without significantly affecting the accuracy of the original TASK for the bulk 3D materials, when compared with the Perdew-Burke-Ernzerhof (PBE) GGA and the strongly constrained and appropriately normed (SCAN) meta-GGA. We further demonstrate the applicability of mTASK by assessing the band structures of transition metal dichalcogenide nanoribbons with respect to various bending curvatures.

36 MATERIALS SCIENCE↗

Sequentially calibrating a Bayesian microsimulation model to incorporate new information and assumptions

Background: Microsimulation models are mathematical models that simulate event histories for individual members of a population. They are useful for policy decisions because they simulate a large number of individuals from an idealized population, with features that change over time, and the resulting event histories can be summarized to describe key population-level outcomes. Model calibration is the process of incorporating evidence into the model. Calibrated models can be used to make predictions about population trends in disease outcomes and effectiveness of interventions, but calibration can be challenging and computationally expensive. Methods: This paper develops a technique for sequentially updating models to take full advantage of earlier calibration results, to ultimately speed up the calibration process. A Bayesian approach to calibration is used because it combines different sources of evidence and enables uncertainty quantification which is appealing for decision-making. We develop this method in order to re-calibrate a microsimulation model for the natural history of colorectal cancer to include new targets that better inform the time from initiation of preclinical cancer to presentation with clinical cancer (sojourn time), because model exploration and validation revealed that more information was needed on sojourn time, and that the predicted percentage of patients with cancers detected via colonoscopy screening was too low. Results: The sequential approach to calibration was more efficient than recalibrating the model from scratch. Incorporating new information on the percentage of patients with cancers detected upon screening changed the estimated sojourn time parameters significantly, increasing the estimated mean sojourn time for cancers in the colon and rectum, providing results with more validity. Conclusions: A sequential approach to recalibration can be used to efficiently recalibrate a microsimulation model when new information becomes available that requires the original targets to be supplemented with additional targets.

60 APPLIED LIFE SCIENCES↗

Topological Superconductivity Based on Antisymmetric Spin–Orbit Coupling

Topological superconductivity (TSC) has drawn much attention for its fundamental interest and application in quantum computation. An outstanding challenge is the lack of intrinsic TSC materials with a p-wave pairing gap, which has led to the development of an effective p-wave theory of coupling s-wave gap with Rashba spin–orbit coupling (RSOC). However, the RSOC-strict mechanism and materials pose still both fundamental and practical limitations. Here, we generalize this theory to antisymmetric SOC (ASOC). Using k·p perturbation theory, we demonstrate that 2D crystals, with point groups of C 2 , C 4 , C 6 , C 2v , C 4v , C 6v , D 2 , D 4 , D 6 , S 4 , or D 2d , can all facilitate the desired ASOC. Remarkably, this enables us to discover 314 TSC candidates by screening 2D material databases, which are further confirmed by first-principles calculations of Majorana boundary modes and the topological invariant of the superconducting gap. As a result, our work fundamentally enriches TSC theory and greatly expands the classes of TSC materials for experimental exploration.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Machine-Learning-Driven Discovery of Water Splitting BaFe 2 O 4 and Human-in-the-Loop Improvement via Al-Substitution for Increased Thermal Stability

Thermochemical hydrogen (TCH) production offers a promising method for converting thermal energy into hydrogen fuel through heat-driven redox cycles of metal oxides. Here, in this work a defect graph neural network (dGNN) was used to predict oxygen vacancy formation energies ΔH V O combined with Materials Project predictions of oxygen chemical potential stability to screen candidate oxides via high-throughput database analysis. BaFe 2 O 4 was identified as a promising material for experimental validation based on its predicted ΔH V O , oxygen chemical potential stability range, and potential for tunable substitutions to improve thermal properties. Experimental validation using thermogravimetric analysis (TGA), stagnation flow reactor (SFR), X-ray diffraction (XRD), and electron microscopy confirmed positive water-splitting behavior but also revealed limitations in thermal stability under aggressive reduction conditions. To address this, a human-in-the-loop modification strategy was employed introducing Al substitution in BaFe 2–x Al x O 4 ; this modification improves thermal stability, alters the crystal structure and enhances overall performance. These results demonstrate a combined computational and experimental workflow in which machine learning accelerates identification of promising candidates, while targeted experimental design enables optimization of functional performance. This approach advances the development of robust, cost-effective TCH materials and highlights the importance of integrating data-driven discovery with human-guided materials design in paving the way for scalable hydrogen production technologies.

organic↗

Ability of x‐ray computed tomography to resolve critical flaw size in laser‐based, paste stereolithography ceramic printing of alumina

Abstract Complex alumina parts were printed using vat photopolymerization (VPP), which is a stereolithography‐based additive manufacturing (AM) technique used to shape ceramic preforms, or green parts. The critical flaw size was determined using classical fracture mechanics techniques. The strength and fracture toughness were measured and compared to flaws detected in x‐ray computed tomography (XCT or CT) distributions as well as the fracture surfaces. The strength was lower compared traditionally made alumina, and that is due to layering effects, slurry defects, and printing defects. The critical flaw size from fracture mechanics was 206 µm. XCT has high enough resolution to detect the critical flaw size and much smaller features, where the average flaw size observed in CT scans was around 80–100 µm. The fracture surfaces indicate that flaws causing failure are larger than that of the critical flaw size (∼300 µm), but fracture surfaces do not show definitive features compared to traditionally made ceramics. Since XCT can observe flaws smaller than the critical flaw size, this method can be used as a screening technique.

36 MATERIALS SCIENCE↗

Sockeye Theory Manual

Sockeye is an application that models heat pipe performance, based on the MOOSE framework. Its primary focus is on liquid-metal heat pipes with annular screen or porous wick structures, with the intended application being the simulation of heat pipes in microreactors. The purpose of this capability is to evaluate and understand heat pipe performance under different conditions. Furthermore, this heat pipe performance is intended to be coupled to multiphysics applications for modeling microreactors, so that the effects of heat pipe performance on the larger reactor system can be simulated.

42 ENGINEERING↗

High-throughput spin-bath characterization of spin defects in semiconductors

Detailed knowledge of the local environments of spin defects in semiconductors, such as nitrogenvacancy (NV) centers in diamond or divacancies in silicon carbide, is crucial for optimizing control and entanglement protocols in quantum sensing and information applications. However, at present a direct experimental characterization of individual defect environments is not scalable, as conventional spin-bath measurements are time consuming and difficult to automate. Achieving high-throughput characterization requires short experiments to probe the spin bath. However, with fewer and noisier measurements, the inverse problem of recovering spin-bath properties from measured data becomes ill posed, with multiple spin baths having a high likelihood of yielding the same data. In this work, we present a set of computational tools to resolve the ill-posed inverse problem of recovering the atomic positions and hyperfine couplings of random nuclei surrounding spin defects from sparse, noisy experimental coherence data, which can be obtained in hours. Here, we use a trans-dimensional Bayesian approach that incorporates ab initio data to yield full posterior distributions over nuclear spin environments, enabling robust recovery from limited data. We also provide practical tools and guidelines to determine the limits of detectability for hyperfine couplings under specific dynamical decoupling sequences and sampling conditions. In addition, we demonstrate how the tools developed here, in combination with ab initio simulations of spin baths, can guide the design of efficient experimental protocols for application-specific high-throughput screening. To showcase the utility of our approach, we apply it to design fast dynamical decoupling experiments to characterize the spin baths often individual NV centers in diamond. While the primary focus is on accelerating spin-bath characterization of spin defects, this Bayesian approach also lays the foundation for digital-twin studies of spin defects, where a virtual model of the spin-defect system evolves in real time with ongoing experimental measurements. Together, the set of tools we designed and applied paves the way for scalable deployment of spin defects in semiconductors for quantum sensing and information applications.

Bayesian methods↗

Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling

Here, we investigate crystal nucleation in supersaturated colloid suspensions using enhanced molecular dynamics simulations augmented with machine learning techniques. The simulations reveal that crystallization in the model colloidal system studied here, with particles interacting through a repulsive screened Coulomb Yukawa potential, proceeds from vapor to dense liquid droplet to crystalline phases across multiple high barriers. Employing a one-dimensional reaction coordinate derived from the State Predictive Information Bottleneck framework, our simulations capture back-and-forth phase transitions across multiple barriers effectively in biased metadynamics simulations. We obtain relative free energy differences between different phases and also quantify the roles of different molecular level features in driving the phase changes.

Chemistry↗

The Novel Hybrid Ab Initio Model of High-Performance Structural Alloys Design for Fossil Energy Power Plants

The current project developed a novel HT-CALPHAD/DFT approach, which can quickly design new high-performance structural alloys for the application of FE power plants. The PI will mainly take charge of high-throughput DFT simulations and computational thermodynamics of the selected multicomponent alloy systems for the FE power plant applications. At the end of the project, a novel hybrid model based on high throughput CALPHAD/DFT simulations and computational thermodynamics will be developed to provide guidance on how to identify multi-component new high-performance structural alloys with much less computational effort needed. It will address the extensive computation time needed for DFT on the new alloys design. In addition, it will also address the well-known headache of DFT, i.e. how to make the accurate prediction of the high-temperature equilibria. The novel hybrid model the PI proposed will not only be applied to the design of high-performance structural alloys in FE power plants but in many different applications, such as nuclear reactors. This hybrid modeling approach includes four sections: 1) HT-CALPHAD modeling of Al-Co-Cr-Ni-Fe system with FCC and BCC phase. In this section, 3561 non-equiatomic compositions were randomly generated in order to investigate the phase stability of single FCC and BCC phases. Meanwhile, we proposed a data screening procedure to screen out the good candidates within these compositions, considering the temperature range, average density, and melting temperature, etc. 2) Investigation of FCC-Cr lattice stability in Fe-Cr system. We systematically assessed the reliability of FCC-Cr lattice stability derived by DFT and CALPHAD approaches. Meanwhile, the Fe-Cr binary system was chosen as a case study to verify the Cr lattice stability obtained by both approaches. 3) High-throughput DFT modeling on elastic properties of Al-Co-Cr-Ni-Fe systems. We predicted and established the FCC quinary elastic constant database of the Al-Co-Cr-Fe-Ni systems at 0K by using special quasi-random structure (SQS) approach. The predictions will start with pure elements of Al-Co-Cr-Fe-Ni system and will be continued with binaries, ternaries, quaternaries, and finally the quinary compositions. 3) Modeling of temperature-dependent elastic properties in Al-Co-Cr-Ni-Fe systems. In this part, we predict the thermal expansion coefficient and elastic stiffness coefficient as a function of temperature by applying quasiharmonic approximation. With this approach, the elastic properties of HEAs at elevate temperature can be estimated.

01 COAL, LIGNITE, AND PEAT↗

A database of ultrastable MOFs reassembled from stable fragments with machine learning models

High-throughput screening of hypothetical metal-organic framework (MOF) databases can uncover new materials, but their stability in real-world applications is often unknown. We leverage community knowledge and machine learning (ML) models to identify MOFs that are thermally stable and stable upon activation. We separate these MOFs into their building blocks and recombine them to make a new hypothetical MOF database of over 50,000 structures with orders of magnitude more (1) connectivity nets and (2) inorganic building blocks than were present in prior databases. Further, this database shows a 10-fold enrichment of ultrastable MOF structures that are stable upon activation and more than 1 standard deviation more thermally stable than the average experimentally characterized MOF. For nearly 10,000 ultrastable MOFs, we compute elastic moduli to confirm that these materials have good mechanical stability, and we report methane deliverable capacities. We identify privileged metal nodes in ultrastable MOFs that optimize gas storage and mechanical stability simultaneously.

36 MATERIALS SCIENCE↗

Radiological Safety Analysis Computer (RSAC) Program Version 7.4 Users’ Manual

The Radiological Safety Analysis Computer (RSAC) Program Version 7.4 (RSAC-7) is the newest version of the RSAC legacy code. RSAC-7 calculates the consequences of a release of radionuclides to the atmosphere. Users generates a fission product inventory from either reactor operating history or a nuclear criticality event. RSAC-7 models the effects of high-efficiency particulate air filters or other cleanup systems and calculates the decay and ingrowth during transport through processes, facilities, and the environment. Doses are calculated for inhalation, air immersion, ground surface, ingestion, and cloud gamma pathways. RSAC-7 is used as a tool to evaluate accident conditions in emergency response scenarios, radiological sabotage events, and safety basis accident consequences. This users’ manual contains the mathematical models and operating instructions for RSAC-7. Instructions, screens, and examples are provided to guide the user through the functions provided by RSAC-7. This program is designed for users who are familiar with radiological dose assessment methods.

73 - NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Incorporation of aerosol into the COSPv2 satellite lidar simulator for climate model evaluation

Abstract. Atmospheric aerosol has substantial impacts on climate, air quality and biogeochemical cycles, and its concentrations are highly variable in space and time. A key variability to evaluate within models that simulate aerosol is the vertical distribution, which influences atmospheric heating profiles and aerosol–cloud interactions, to help constrain aerosol residence time and to better represent the magnitude of simulated impacts. To ensure a consistent comparison between modeled and observed vertical distribution of aerosol, we implemented an aerosol lidar simulator within the Cloud Feedback Model Intercomparison Project (CFMIP) Observation Simulator Package version 2 (COSPv2). We assessed the attenuated total backscattered (ATB) signal and the backscatter ratios (SRs) at 532 nm in the U.S. Department of Energy's Energy Exascale Earth System Model version 1 (E3SMv1). The simulator performs the computations at the same vertical resolution as the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), making use of aerosol optics from the E3SMv1 model as inputs and assuming that aerosol is uniformly distributed horizontally within each model grid box. The simulator applies a cloud masking and an aerosol detection threshold to obtain the ATB and SR profiles that would be observed above clouds by CALIOP with its aerosol detection capability. Our analysis shows that the aerosol distribution simulated at a seasonal timescale is generally in good agreement with observations. Over the Southern Ocean, however, the model does not produce the SR maximum as observed in the real world. Comparison between clear-sky and all-sky SRs shows little differences, indicating that the cloud screening by potentially incorrect model clouds does not affect the mean aerosol signal averaged over a season. This indicates that the differences between observed and simulated SR values are due not to sampling errors, but to deficiencies in the representation of aerosol in models. Finally, we highlight the need for future applications of lidar observations at multiple wavelengths to provide insights into aerosol properties and distribution and their representation in Earth system models.

54 ENVIRONMENTAL SCIENCES↗

Multiple Phase Screen Scintillation Code Execution and Examples

The phenomenon of random fluctuations in the amplitude and phase of received transionospheric radio frequency (RF) signals is well known and documented. For wide band signals, sometimes a set of frequencies in the the band or even the whole band can suffer degradation or complete drop out at the receiver. The former is known as frequency selective scintillation where only a fraction of the signal bandwidth is affected, whereas the latter is known as flat fading.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Meshing, Language Server Protocol, and other User-Oriented MOOSE Framework Improvements to Enhance Reactor Analysis Capabilities and Workflows

The open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) framework underpins most of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) physics applications and coupling methods. Users interact with MOOSE in multiple ways to enable the construction of complex multiphysics models, including but not limited to compilation, input creation and syntax validation, meshing, solving the physics problem via MOOSE-based solvers and coupling, and output inspection. In FY23, numerous enhancements have been made to MOOSE to enhance the user experience. Reactor-oriented meshing capabilities in MOOSE have been expanded, an online tutorial was created and hosted on the MOOSE site, and a hands-on workshop was held for more than 100 users. The Language Server Protocol (LSP) capability has been implemented in MOOSE to better communicate correct syntax to the NEAMS Workbench user interface which is commonly used to validate input and submit jobs by users. Finally, several other user-facing improvements were made including the implementation of improved screen output and logging control, enhancements to the initial condition system, and enhancements of the MultiApp system commonly used for coupling. Collectively, these enhancements were driven by user needs and directly improve user ability to construct complex multiphysics models for nuclear reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Rotational Millimeter-Wave Shoe Scanner Using the Discrete Fourier Transform for Backprojection-Based Image Reconstruction

An active 3D microwave / millimeter-wave shoe scanner was previously developed at the Pacific Northwest National Laboratory (PNNL) using two linear arrays scanned over a rectilinear aperture. The radar system chirps a frequency sweep from 10-40 GHz. These frequencies allow imaging through optically opaque material such as leather, rubber, plastics, and other dielectrics. The system was designed to detect concealed items in the soles of shoes while allowing people to leave their shoes on through a security checkpoint. To shrink the footprint of the system, a new iteration of the design has been developed that scans the two linear arrays over a circular aperture. This new footprint opens the possibility of it being installed in the floor of a cylindrical millimeter-wave body scanner. The backprojection-based multilayer dielectric image reconstruction developed at PNNL can easily handle arbitrary spatial sampling, accommodating the new rotational shoe scanner design. Commonly, the fast Fourier transform (FFT) is used to efficiently compute the range response from the data collected by the system as a preprocessing step to the backprojection algorithm. It was found that converting to range using the discrete Fourier transform (DFT) directly has some advantages over the FFT. For example, nonlinear and non-uniform frequency sweeps can easily be compensated for during the computation of the DFT and only the range bins of interest need to be computed and their spacing can be chosen arbitrarily. Because the range conversion step of the image reconstruction is the fastest part of the process there is very little speed penalty for using the DFT over the FFT and it can even increase the speed of image reconstruction when the ranges of interest are fewer than the total span that is calculated in the FFT.

Millimeter-wave imaging, microwave imaging, shoe s↗

User’s Manual for RESRAD-RDD&IND Code Version 2: Vol. 1—Methodology and Models Used in RESRAD-RDD&IND Code

RESRAD-RDD&IND is part of the RESRAD family of codes that Argonne National Laboratory developed for the U.S. Department of Energy (DOE). An earlier version, RESRAD-RDD published in 2009, dealt only with radiological dispersal device (RDD) incidents (DOE 2009). This new version, RESRAD-RDD&IND, is designed to evaluate both RDD incidents and improvised nuclear device (IND) incidents. This report is Volume 1 of the RESRAD-RDD&IND User’s Manual that documents the methodology, models, and radionuclide-specific data used in RESRAD-RDD&IND code Version 2.0. Volume 2 of the RESRAD-RDD&IND User’s Manual is called the User’s Guide for RESRAD-RDD&IND Code . It describes how to use RESRAD-RDD&IND code Version 2.0 and includes screen shots and parameter information.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Deep Learning for Modeling Enhanced Geothermal Systems

Enhanced Geothermal Systems (EGS) offer a vast potential to expand the use of geothermal energy. Heat is extracted from this engineered system by injecting cold water into a subsurface fractures, which are in contact with the hot dry rock, and pulled through the production wells. Creating EGS requires improving the natural permeability of hot crystalline rocks. To develop economically viable EGS reservoirs, significant technical barriers (e.g., better stimulation technologies without adequate water and/or permeability) and non-technical barriers (e.g., land access and permitting) must be overcome. In this short conference paper, we present a workflow to address a part of this challenge – “How to develop economically viable EGS using existing technologies?”. Our workflow called the GeoThermalCloud (GTC) for EGS, leverages recent advances in machine learning, deep learning, and cloud computing. This GTC framework is open-source and available at https://github.com/SmartTensors/GeoThermalCloud.jl. The GTC framework provides trained deep learning (DL) models to estimate the net present value of a given EGS design scenario. The Geothermal Design Tool (https://github.com/GeoDesignTool/GeoDT.git), a fast and simplified multi-physics solver, is used to develop a database for training DL models. The database consists of EGS design parameters (inputs to DL model) and their net present value (output of DL model) in uncertain geologic systems. The EGS design parameters for constructing this training database are based on Utah FORGE but include the options of more wells and deeper depths. The DL models are trained by ingesting the EGS design parameters and estimating the corresponding net present value. Such an emulation allows us to screen various EGS designs quickly and identify good development strategies by coupling them with optimization techniques. Our preliminary results show promise in DL emulation of net present value. However, a lot more work is needed to improve the predictive capability of DL models (i.e., extensive hyperparameter tuning is necessary). This will be the primary focus of our future work.

artificial neural networks, geothermal↗