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At least 739 records · Page 41

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗

Erosion resistance test of SiC mirror sample for ITER divertor VUV spectrometer

A series of tests have been performed to validate the resistance of the Silicon Carbide (SiC) mirror as the first mirror material of ITER VUV spectrometers to all ITER environmental conditions. Here we focused on the erosion (and deposition) of the SiC mirror sample caused by high-energy neutral particles. The flux of neutral particles reaching the first mirror was calculated using the ZEMAX software with a simplified entrance duct model. In the calculation, the particle flux reaching the first wall is necessary and the previously reported values derived from the SOLPS calculations were used. Based on this estimated particle flux, the erosion resistance tests were performed to check the erosion effect due to the high-energy neutral particles on the first mirror of ITER divertor VUV spectrometer. In the experiment, erosion was induced by exposing the SiC mirror sample to hydrogen and deuterium plasmas (and ions). The target fluence of incident ions in experiment is based on the estimation of the flux of neutral particles in ITER. The surface shape, composition, erosion depth, and surface roughness were measured to check the damage of the mirror surface after erosion test. Based on simulations and erosion resistance tests, it was concluded that the SiC mirror can be used as the first mirror of ITER divertor VUV spectrometer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Monte Carlo N-Particle Transport Performance of Predicting Digital Radiographic IQI Inspection

The identification of porosity, geometric noncompliance, and other defect types are critical to the qualification of materials and components. X-ray radiographic nondestructive testing is a common industrial inspection method for process quality control and component qualification and certification. Digital radiography provides a quick and efficient alternative when compared to traditional film-based inspection. The quality of radiographic inspection is dependent on equipment specifications, such as the source spot size and detector pixel size, and the specific parameters selected for use for the radiographic technique. To evaluate if an x-ray system and technique is sufficient for a given requirement, a radiographic image quality indicator (IQI) can be used. Radiographic IQIs in hard to machine materials or hard to manufacture defects can be time consuming and expensive to manufacture. This study was conducted to evaluate current Savannah River National Laboratory (SRNL) x-ray imaging systems with a custom tantalum IQI and using Monte Carlo simulations to predict the performance of future systems. The tantalum IQI was tested using a Siefert Isovolt 420 keV x-ray tube with a Perkin Elmer XRD 1611 flat panel with 100-micron pixels. Using the Monte Carlo N-Particle transport software, the radiographic tally was used to simulate the photon flux through an identical tantalum IQI. These simulations provided a benchmark as to the best theoretical identification on a given system using our tantalum IQI. The simulations were refined to match SRNL’s current systems’ noise levels, leading to confidence in their ability to predict the performance of other systems that may be purchased and deployed in the future at the Savannah River Site. Future studies will be conducted to prove this research can be extended to artificially evaluate the ability for systems to identify critical defect sizes through x-ray radiographic inspection, drastically reducing the cost and time burdens of producing high-fidelity radiographic test articles.

digital X-ray radiography↗

Enhancements supporting IC usage of PEM libraries on next-gen platforms

This milestone reports on the culmination of several years of effort by multiple PEM support software development teams to provide capabilities for use in LLNL-developed integrated codes on next-gen ASC platforms, including GPU support. We will provide a survey of relevant Application Program Interfaces (API) that are required to support LLNL IC code capability on relevant architectures, with a focus on Sierra and El Capitan. We will identify and summarize all dependencies between PEM supported libraries and IC supported physics codes. We will provide an assessment of algorithmic improvements that have been deployed, as well as future developments that are required to complete the GPU porting efforts. This assessment will include a description of programming models adopted by each of the PEM projects, distinct algorithmic challenges for each of the capabilities, and information about sharing GPU memory between the APIs and host codes. We will develop targeted test problems to assess computational performance. Finally, this milestone will result in identification of gaps in our effort to assist the LLNL ASC program in prioritization of effort for porting software to El Capitan.

97 MATHEMATICS AND COMPUTING↗

Nuclear Thermal Rocket Emulator for a Hardware-in-the-Loop Test Bed

To support NASA’s mission to use nuclear thermal rockets for future Mars missions, an instrumentation and control test bed has been built at Oak Ridge National Laboratory. The system is designed as a hardware-in-the-loop test bed for testing control elements and autonomous control algorithms for nuclear thermal propulsion rockets. The mock reactor system consists of a modular and scalable framework, using inexpensive components and open-source software. The hardware system consists of a two-phase flow loop and a mock reactor with six control drums. A single-board computer (NVIDIA Jetson) handles reactor core emulation and hosts a message queuing telemetry transport broker that allows user-deployed control algorithms to interact with the system hardware. The reactor emulator receives sensor data from the hardware and provides the simulated performance of the reactor under steady-state, transient, and fault conditions. The emulator uses a reactivity lookup table and the point kinetics equations to solve for the reactor dynamics in real time. Emulated reactor dynamics and sensor input inform the autonomous control algorithm’s decision-making in a closed-loop manner. The current system is capable of operating at 10 Hz, but faster cycle rates are an area of ongoing research. This test bed will enable NASA and other space vendors to rigorously test their autonomous control systems for NTP rockets under transient (reactor startup and shutdown), steady-state, and fault conditions to reduce development time and risk for autonomous control systems in future missions.

autonomous control↗

Differential Power Processing for Ultra-Efficient Data Storage

Here this paper presents the hardware, software, and power codesign of an ultra-efficient data storage server with differential power processing (DPP). DPP can reduce the power conversion stress, improve the efficiency, and enhance the functionality of modular power electronics systems. The power inputs of a large number of hard disk drives (HDDs) were connected in series and supported by a multiport ac-coupled differential power processing (MAC-DPP) converter through a multiwinding transformer. Methods for controlling the multi-input multi-output power flow in the multiwinding transformer while avoiding core saturation were investigated. A ten-port MAC-DPP prototype with 700-W/in 3 power density was built to support a 450-W HDD storage system with ten series-stacked voltage domains. The prototype was tested on a 50-HDD server testbench, and the overall system loss is below 1 W (99.77% system efficiency). The server was able to maintain high-speed reading and writing operation of all 50 HDDs against the worst hot-swapping scenarios. A variety of hardware/software configurations and many cloud storage techniques were tested on the fully functioning server. Experimental results show that the energy efficiency of large-scale information systems (CPU/GPU clusters, memory banks, HDD arrays, etc.) can be greatly improved by software, hardware, and power codesign.

42 ENGINEERING↗

LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING↗

Accurate frozen core approximation for all-electron density-functional theory

We implement and benchmark the frozen core approximation, a technique commonly adopted in electronic structure theory to reduce the computational cost by means of mathematically fixing the chemically inactive core electron states. The accuracy and efficiency of this approach are well controlled by a single parameter, the number of frozen orbitals. Explicit corrections for the frozen core orbitals and the unfrozen valence orbitals are introduced, safeguarding against seemingly minor numerical deviations from the assumed orthonormality conditions of the basis functions. A speedup of over twofold can be achieved for the diagonalization step in all-electron density-functional theory simulations containing heavy elements, without any accuracy degradation in terms of the electron density, total energy, and atomic forces. This is demonstrated in a benchmark study covering 103 materials across the Periodic Table and a large-scale simulation of CsPbBr3 with 2560 atoms. Our study provides a rigorous benchmark of the precision of the frozen core approximation (sub-meV per atom for frozen core orbitals below −200 eV) for a wide range of test cases and for chemical elements ranging from Li to Po. The algorithms discussed here are implemented in the open-source Electronic Structure Infrastructure software package.

Yu, Victor Wen-zhe↗

Image quality indicator and dechromator setup for static LANSCE proton radiography experiment

This document describes a static geometry consisting of a sphere of gold and Ti-6Al-4V alloy, along with an energy-loss matching dechromator composed of polycarbonate, to field with the X3 electromagnetic magnifying lens at LANSCE during the next beam cycle. This static configuration will allow us to: (1) characterize the system’s resolution at the material interface between the gold and titanium alloy, and test the image quality for fine features associated with the screws used to fasten the titanium alloy hemispheres; (2) tune our models of proton scattering and imaging for these materials; and (3) test a procedure to align the polycarbonate dechromator and the sphere within the proton beamline. The data will also be suitable for validation of the software options available for proton radiography simulations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Utility of Big Area Additive Manufacturing for Part Production for Low-Head Hydropower

ORNL worked with Cadens, LLC to explore the use of additive manufacturing (AM) for the production of low-cost parts for low-head hydropower systems. Cadens develops design optimization software that leverages the flexible, low-cost, high-strength benefits of AM and composite materials, and operates a micro-hydro lab to test AM components in controlled environments. Until now Cadens’ tests have been limited in size to components that they can cost-effectively manufacture using local commercial systems. This project provided an opportunity for Cadens to scale up their modular AM hydropower parts using the capabilities of Big Area Additive Manufacturing (BAAM). This project was a success and resulted in the design and fabrication of several end use parts of a hydropower system using a Big Area Additive Manufacturing (BAAM) system. The fabricated parts include draft tube, thimble, runner housing mold, PVC end fitting and two PVC pipe supports. The components have been in use for more than three years without a 3D printed component failing.

13 HYDRO ENERGY↗

Sierra/SD – Verification Test Manual – 5.22

Verification and validation (V&V) of scientific computing programs are important at Sandia National Labs due to the expanding role of computational simulation in managing the United States nuclear stockpile. The complexities of structural response calculations used to analyze physical problems, the varieties of codes applied to the calculations, and the importance of accurate predictions when assessing field conditions demand confidence in the consistency and accuracy of computer codes. Confidence in the accuracy of the predictions arising from computer simulations must ultimately be gained through verification and validation. The Sierra salinas structural dynamics analysis code, Sierra/SD, is used at the DOE Laboratories, and in several DOD projects. The roles of Sierra/SD in the qualification of weapon systems and components for normal and hostile environments throughout the Stockpile-to-Target Sequence include to, • Redesign weapon components. • Certify weapon components and systems for target environments such as hypersonic vehicles. • Certify that components will survive the thermal mechanical shock loads associated with hostile environments. • Evaluate current stockpile issues, including issues associated with uncertainty quantification. • Address many other problems that are encountered in stockpile management. The Sierra/SD verification plan is described, and an evolving set of key verification tests are described in detail. The verification tests ensure the correctness of the mathematics and numerical algorithms associated with functionality describing engineering phenomena. Development is in accordance with a set of tailored Software Quality Engineering (SQE) practices. SQE practices guide the overall verification and validation effort.

97 MATHEMATICS AND COMPUTING↗

Open Building Operating System: An Open-Source Grid Responsive Control Platform for Buildings

Grid-interactive efficient buildings (GEBs) with flexible loads are a promising method to decarbonize buildings, shift loads during peak hours, and lower energy use and electricity costs. Despite the promising benefits of GEBs, automation systems that manage flexible loads in response to energy prices or other grid signals are still uncommon in small and medium commercial buildings. Recent literature demonstrates such control solutions, but they often rely on custom integrations lacking the tools and drivers needed for scalability. To address these gaps, our team has created a fully open-source software stack capable of integrating heterogeneous flexible building loads and implementing integrated portable control applications called the Open Building Operating System (OpenBOS). The software can be deployed over existing control architecture with a small capital cost. OpenBOS leverages semantic models, which have been the subject of recent investigations to facilitate application portability. The use of semantic data reduces the labor and expense required to deploy and update smart control applications, increasing scalability. In this paper, the semantic modeling schema "Brick" was used, but the proposed approach can also be applied to ASHRAE standard 223P, when released. This paper describes the methodology and software components of OpenBOS and demonstrates its functionality with a rule-based demand flexibility control application configured using a semantic model. This application was tested at a real building in NY that uses a dual-fuel heating system made up of five ductless heat pump mini-splits and a central furnace serving a single zone. The demonstration reduced electricity costs at the site by 27%, demand during a shed event by 49%, and furnace usage by 35%.

24 POWER TRANSMISSION AND DISTRIBUTION↗

CFD modeling and simulation for corrosive wear of refractory in molten slag

The development of high-wear resistant refractories having minimal production costs is facilitated by characterizing the wear mechanisms associated with their corrosive wear. Static cup testing is a commonly used method for comparing the corrosion resistance performance of two or more refractory materials. Although the static cup test conditions are not as severe as dynamic tests, this study shows that the thermal gradient present within the system during heating and cooling stages serves to generate movement of the slag leading to mechanical wear. The thermal gradient within the refractory, and between the slag and the refractory, occurs during the ramp stage of the test and lasts until the soaking stage is reached bringing the system to a thermal equilibrium. Using computational fluid dynamics (CFD) capabilities embedded within ANSYS software, this study modelled and quantified the convection currents within the slag and associated shear stresses generated on the refractory walls due to the thermal gradient. A traditional ladle furnace was employed as a case study to verify the results of the studied CFD model. The corrosion rate of the refractory lining was found to depend on the mass transfer coefficient of the refractory dissolution into the slag, and a velocity term which governs the extent of corrosion at any given location. This velocity term is a function of slag viscosity, as well as the concentration gradient and/or temperature gradient at the triple points. In this study, wall shear stress was used as a reliable proxy for identifying high-velocity regions prone to excessive corrosive wear. Elevated wall shear stress near the slag/air and slag/molten steel interfaces align with observed corrosion grooves, which reflects the intensified corrosive wear at these locations.

Ramteke, Rajat Rajat Durgesh Ramteke [University o↗

A machine-learning-aided data recovery approach for predicting multi-material thermal behaviors in advanced test reactor capsules

Instrumented experiments conducted at test reactors are essential to the deployment of new advanced reactor systems. Designing new experiments and generating data on specific reactor conditions require significant investments in terms of both time and cost. Finite element analysis software can be used to create high-fidelity models of experiment environments in order to support the actual experiments, but computation time remains a concern in terms of applying outcomes to real-time usage of data (e.g., a digital twin [DT]). Here, the present research proposes a machine-learning (ML) aided approach to making temperature and displacement predictions based on the thickness of the outer gas gap on the experimental capsule used for in-pile demonstration of a novel new thermal conductivity probe in the Advanced Test Reactor (ATR). This capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. Gas gaps existed between the fuel and the rodlet, and between the inner and the outer capsule. The learning data pertained to an experimental capsule's radial distributions of temperature and displacement, as obtained based on Abaqus and the physical features. For the first step of ML sequence, the temperature was predicted using three positional parameters. Next, the displacement was predicted using seven additional parameters. Each physical feature was normalized in order to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement with the simulation results in all cases involving interpolation and extrapolation. Furthermore, data similarity enhancement increased the similarity between the training and the target data, thereby increasing the predictive accuracy of the ML models. In certain extrapolation cases involving limited original ML model accuracy, data similarity enhancement and data recovery was able to somewhat improve this accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗

Machine-Learning-aided Approach for Predicting the Thermal Expansion Behaviors in Advanced Test Reactor Capsules (NURETH-20 full paper)

Instrumented experiments at test reactors are essential to deploying new advanced reactor systems. Designing new experiments and generating data on specific conditions require both time and cost investment. A high-fidelity model of the experiment environment can be created using finite element analysis software to support the actual experiments, but computation time is still a concern in applying outcomes to real-time usage (e.g., a digital twin). This research proposes a machine-learning-aided approach to temperature and displacement predictions, based on the thickness of the outer gas gap on the experimental capsule used for the in-pile demonstration of a novel thermal conductivity probe in the Advanced Test Reactor. The capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. There were gas gaps between the fuel and rodlet and between the inner and outer capsule. The learning data consisted of an experimental capsule’s radial distributions of temperature and displacement, as obtained from Abaqus and the physical features. For the first step, temperature was predicted using three positional parameters. Then the displacement was predicted using six different positional parameters. Each physical feature was normalized to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement in all cases involving interpolation and extrapolation. Also, data similarity enhancement increased the similarity between training and target data increasing the predictive accuracy of machine-learning models. In some cases of extrapolation, the accuracy of the machine-learning model showed limited performance, but still data similarity enhancement improved the accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Comparative analysis of thermal management systems in electric vehicles at extreme weather conditions: Case study on Nissan Leaf 2019 Plus, Chevrolet Bolt 2020 and Tesla Model 3 2020

With the surge in electric vehicle (EV) adoption and the need for extended driving ranges, optimizing energy efficiency, particularly through thermal management, is critical, especially in extreme weather. Managing the substantial energy needed for cabin climate control and battery temperature regulation can increase energy demands by over 50 %, severely limiting range. This study conducts a comparative analysis of thermal management systems (TMS) in three popular EV vehicles, 2020 Chevrolet Bolt, 2019 Nissan Leaf Plus, and 2020 Tesla Model 3, evaluating their distinct TMS configurations and performance under varied weather conditions. Using both numerical simulations and experimental data collected on a controlled test bench at Argonne National Laboratory, we assess how TMS architecture and operational modes influence energy consumption and range. A comprehensive TMS model was developed, integrating cabin and battery thermal sub-models in the Autonomie software platform, to simulate temperature fluctuations and range impacts. Cabin climate was modeled using a mono-zonal approach, while battery cell temperature distribution was estimated through a 2D nodal structure. Each vehicle's distinct TMS setup was evaluated: the Chevrolet Bolt and Tesla Model 3 use a dual evaporator vapor compression cycle with a PTC heater for the cabin and a coolant loop for battery thermal management; the Nissan Leaf Plus employs a heat pump with a PTC heater for the cabin and air-cooling for the battery. Tests conducted at ambient temperatures of 35°C, 22°C, -7°C, and -18°C reveal significant differences in energy use and range reduction across both configurations and conditions. At 35°C, the Tesla Model 3, Chevrolet Bolt, and Nissan Leaf Plus have a range reduction of 8%, 9%, and 13%, respectively, due to air conditioning. In winter, heating technology is paramount; at -7°C, the Nissan Leaf's heat pump configuration achieves a lower range reduction (19.3%) compared to the Tesla and Chevrolet Bolt PTC heaters, which reduce range by 28.3% and 31%, respectively. Further, this study provides valuable insights for automotive engineers, EV technology researchers, and thermal management system designers aiming to enhance electric vehicle performance by understanding how different weather conditions and TMS architectures impact energy consumption and driving range.

33 ADVANCED PROPULSION SYSTEMS↗

Modeling fission product diffusion in TRISO fuel particles with BISON

Diffusion of fission products in intact TRISO particles depends on particle geometry, fission product source rates, time, temperature, and temperature-dependent diffusion coefficients. Simulating this diffusion process requires models for source rates and diffusion coefficients, plus computation of the temperature field if not prescribed. In addition, simulation quality depends on discretization of the geometry, appropriate time stepping, and the accuracy of the solution method. In this paper, we explore the simulation of fission product diffusion in TRISO fuel particles using the finite element method via the fuel performance code Bison. Recent material model development has occurred in Bison for each material present in tri-structural isotropic (TRISO) fuel particles: the buffer, inner pyrolytic carbon, silicon carbide, and outer pyrolytic carbon layers, as well as the fuel kernel. Also, new mesh generation and fission product release fraction capabilities have been added. Diffusion capabilities are shown to converge to the correct solution via formal verification tests. A large number of code benchmarking problems are also given, with good results, showing that Bison’s computed release fractions closely match those of other software tools. Finally, a significant validation effort is detailed in which fission product release, measured as part of the AGR-1 capsule experiments, is compared to Bison outputs. Bison outputs compare very well to the experimental data and to PARFUME results.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗