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At least 1,243 records · Page 69

UniKP: a unified framework for the prediction of enzyme kinetic parameters

Prediction of enzyme kinetic parameters is essential for designing and optimizing enzymes for various biotechnological and industrial applications, but the limited performance of current prediction tools on diverse tasks hinders their practical applications. Here, we introduce UniKP, a unified framework based on pretrained language models for the prediction of enzyme kinetic parameters, including enzyme turnover number (k cat ), Michaelis constant (K m ), and catalytic efficiency (k cat / K m ), from protein sequences and substrate structures. A two-layer framework derived from UniKP (EF-UniKP) has also been proposed to allow robust k cat prediction in considering environmental factors, including pH and temperature. In addition, four representative re-weighting methods are systematically explored to successfully reduce the prediction error in high-value prediction tasks. We have demonstrated the application of UniKP and EF-UniKP in several enzyme discovery and directed evolution tasks, leading to the identification of new enzymes and enzyme mutants with higher activity. UniKP is a valuable tool for deciphering the mechanisms of enzyme kinetics and enables novel insights into enzyme engineering and their industrial applications.

59 BASIC BIOLOGICAL SCIENCES↗

AI-based design of a nuclear reactor core

The authors developed an artificial intelligence (AI)-based algorithm for the design and optimization of a nuclear reactor core based on a flexible geometry and demonstrated a 3× improvement in the selected performance metric: temperature peaking factor. The rapid development of advanced, and specifically, additive manufacturing (3-D printing) and its introduction into advanced nuclear core design through the Transformational Challenge Reactor program have presented the opportunity to explore the arbitrary geometry design of nuclear-heated structures. The primary challenge is that the arbitrary geometry design space is vast and requires the computational evaluation of many candidate designs, and the multiphysics simulation of nuclear systems is very time-intensive. Therefore, the authors developed a machine learning-based multiphysics emulator and evaluated thousands of candidate geometries on Summit, Oak Ridge National Laboratory’s leadership class supercomputer. The results presented in this work demonstrate temperature distribution smoothing in a nuclear reactor core through the manipulation of the geometry, which is traditionally achieved in light water reactors through variable assembly loading in the axial direction and fuel shuffling during refueling in the radial direction. The conclusions discuss the future implications for nuclear systems design with arbitrary geometry and the potential for AI-based autonomous design algorithms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Preparing for the next pandemic via transfer learning from existing diseases with hierarchical multi-modal BERT: a study on COVID-19 outcome prediction

Abstract Developing prediction models for emerging infectious diseases from relatively small numbers of cases is a critical need for improving pandemic preparedness. Using COVID-19 as an exemplar, we propose a transfer learning methodology for developing predictive models from multi-modal electronic healthcare records by leveraging information from more prevalent diseases with shared clinical characteristics. Our novel hierarchical, multi-modal model ( $${\textsc {TransMED}}$$ T R A N S MED ) integrates baseline risk factors from the natural language processing of clinical notes at admission, time-series measurements of biomarkers obtained from laboratory tests, and discrete diagnostic, procedure and drug codes. We demonstrate the alignment of $${\textsc {TransMED}}$$ T R A N S MED ’s predictions with well-established clinical knowledge about COVID-19 through univariate and multivariate risk factor driven sub-cohort analysis. $${\textsc {TransMED}}$$ T R A N S MED ’s superior performance over state-of-the-art methods shows that leveraging patient data across modalities and transferring prior knowledge from similar disorders is critical for accurate prediction of patient outcomes, and this approach may serve as an important tool in the early response to future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

Extending deterministic transport capabilities for very-high and ultra-high energy electron beams

Focused Very-High Energy Electron (VHEE, 50–300 MeV) and Ultra-High Energy Electron (UHEE, > 300 MeV) beams can accurately target both large and deeply seated human tumors with high sparing properties, while avoiding the spatial requirements and cost of proton and heavy ion facilities. Advanced testing phases are underway at the CLEAR facilities at CERN (Switzerland), NLCTA at Stanford (USA), and SPARC at INFN (Italy), aiming to accelerate the transition to clinical application. Currently, Monte Carlo (MC) transport is the sole paradigm supporting preclinical trials and imminent clinical deployment. In this paper, we propose an alternative: the first extension of the nuclear-reactor deterministic chain Njoy-Dragon for VHEE and UHEE applications. We have extended the Boltzmann-Fokker-Planck (BFP) multigroup formalism and validated it using standard radio-oncology benchmarks, complex assemblies with a wide range of atomic numbers, and comprehensive irradiation of the entire periodic table. We report that 99% of water voxels exhibit a BFP-MC deviation below 2% for electron energies under 1.5 GeV. Additionally, we demonstrate that at least 97% of voxels of bone, lung, adipose tissue, muscle, soft tissue, tumor, steel, and aluminum meet the same criterion between 50 MeV and 1.5 GeV. For water, the thorax, and the breast intra-operative benchmark, typical average BFP-MC deviations of 0.3% and 0.4% were observed at 300 MeV and 1 GeV, respectively. By irradiating the entire periodic table, we observed similar performance between lithium (Z = 3) and cerium (Z = 58). Deficiencies observed between praseodymium (Z = 59) and einsteinium (Z = 99) have been reported, analyzed, and quantified, offering critical insights for the ongoing development of the Evaluated Nuclear Data File mode in NJOY.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Deep learning with mixup augmentation for improved pore detection during additive manufacturing

In additive manufacturing (AM), process defects such as keyhole pores are difficult to anticipate, affecting the quality and integrity of the AM-produced materials. Hence, considerable efforts have aimed to predict these process defects by training machine learning (ML) models using passive measurements such as acoustic emissions. This work considered a dataset in which keyhole pores of a laser powder bed fusion (LPBF) experiment were identified using X-ray radiography and then registered both in space and time to acoustic measurements recorded during the LPBF experiment. Due to AM’s intrinsic process controls, where a pore-forming event is relatively rare, the acoustic datasets collected during monitoring include more non-pores than pores. In other words, the dataset for ML model development is imbalanced. Moreover, this imbalanced and sparse data phenomenon remains ubiquitous across many AM monitoring schemes since training data is nontrivial to collect. Hence, we propose a machine learning approach to improve this dataset imbalance and enhance the prediction accuracy of pore-labeled data. Specifically, we investigate how data augmentation helps predict pores and non-pores better. This imbalance is improved using recent advances in data augmentation called Mixup, a weak-supervised learning method. Convolutional neural networks (CNNs) are trained on original and augmented datasets, and an appreciable increase in performance is reported when testing on five different experimental trials. When ML models are trained on original and augmented datasets, they achieve an accuracy of 95% and 99% on test datasets, respectively. We also provide information on how dataset size affects model performance. Lastly, we investigate the optimal Mixup parameters for augmentation in the context of CNN performance.

36 MATERIALS SCIENCE↗

BeeSwarm: Enabling Parallel Scaling Performance Measurement in Continuous Integration for HPC Applications

Testing is one of the most important steps in software development–it ensures the quality of software. Continuous Integration (CI) is a widely used testing standard that can report software quality to the developer in a timely manner during development progress. Performance, especially scalability, is another key factor for High Performance Computing (HPC) applications. There are many existing profiling and performance tools for HPC applications, but none of these are integrated into CI tools. In this work, we propose BeeSwarm, an HPC container based parallel scaling performance system that can be easily applied to the current CI test environments. BeeSwarm is mainly designed for HPC application developers who need to monitor how their applications can scale on different compute resources. We demonstrate BeeSwarm using a multi-physics HPC application with Travis CI, GitLab CI and GitHub Actions while using ChameleonCloud and Google Compute Engine as the compute backends. Finally, our results show that BeeSwarm can be used for scalability and performance testing of HPC applications.

97 MATHEMATICS AND COMPUTING↗

Converged Computing: A Best of Both Worlds of High-Performance Computing and Cloud

Collaboration between Cloud and High Performance Computing (HPC) communities has accelerated in the last half decade. A common goal to run batch workloads combined with a desire for reproducibility, automation, and optimization has led to successful projects that range from container technologies to workload management and security. This span of current and future work defines a novel “Converged Computing” paradigm that aims to combine the best of both worlds, both from a technological and cultural standpoint. Furthermore, in this Special Issue, we review common themes in the space, showcasing current work and encouraging a continued effort toward innovative ideas that will enable the next generations of scientific discovery.

97 MATHEMATICS AND COMPUTING↗

GEOS: A performance portable multi-physics simulation framework for subsurface applications

GEOS is a simulation framework focused on solving tightly coupled multi-physics problems with an initial emphasis on subsurface reservoir applications. Currently, GEOS supports capabilities for studying carbon sequestration, geothermal energy, hydrogen storage, and related subsurface applications. The unique aspect of GEOS that differentiates it from existing reservoir simulators is the ability to simulate tightly coupled compositional flow, poromechanics, fault slip, fracture propagation, and thermal effects, etc. Extensive documentation is available on the GEOS documentation pages (GEOS Documentation, 2024). Note that GEOS, as presented here, is a complete rewrite of the previous incarnation of the GEOS referred to in (Settgast et al., 2017).

58 GEOSCIENCES↗

White Paper: Scalable Digital Twin Capabilities for Aging and Surveillance of Engineered Systems

This white paper presents a multi-year initiative to develop practical, secure, and scalable digital twin capabilities for engineered systems in aging and surveillance contexts—an approach pioneered at the National Nuclear Security Administration (NNSA) Lawrence Livermore National Laboratory (LLNL) that maps directly onto the needs and ambitions of the Navy for ship- and fleet-level digital twins. LLNL’s work in building part- and process-level digital twins for advanced manufacturing, with a vision to scale up to entire factory floors and, ultimately, enterprise-wide digital twins, offers an adaptable pathway for the Navy as it seeks to modernize lifecycle management, readiness, and predictive maintenance across ships and fleets. For our application, we integrate physics-based modeling with automated data ingestion, processing, and AI-driven calibration, creating hybrid models that are both interpretable and data responsive. We modernized legacy workflows, established centralized data infrastructure, automated experimental pipelines, and demonstrated end-to-end coupling of accelerated aging data with finite element simulations via optimization and surrogate modeling. The result is a generalizable framework that supports part-level digital twins today and lays the groundwork for future system-level twins suitable for Navy applications.

36 MATERIALS SCIENCE↗

NASA Tech Briefs, March 1996

Topics: Computer-Aided Design and Engineering; Electronic Components and Cicuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Machinery/Automation; Manufacturing/Fabrication; Mathematics and Information; Books and Reports.

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NASA Tech Briefs, April 1996

Topics covered include: Advanced Composites and Plastics; Computer-Aided Design and Engineering; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Machinery/Automation; Manufacturing/Fabrication; Mathematics and Information; Books and Reports.

Source record↗

NASA Tech Briefs, April 2000

Topics covered include: Imaging/Video/Display Technology; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Bio-Medical; Test and Measurement; Mathematics and Information Sciences; Books and Reports.

Source record↗

NASA Tech Briefs, February 1988

Topics covered include: New Product Ideas; NASA TU Services; Electronic Components and Circuits; Electronic Systems; Physical Sciences; Materials; Computer Programs; Mechanics; Machinery; Fabrication Technology; Mathematics and Information Systems; and Life Sciences.

Source record↗

Characterization of Aerodynamic Interactions with the Mars Science Laboratory Reaction Control System Using Computation and Experiment

On August 5 , 2012, the Mars Science Laboratory (MSL) entry capsule successfully entered Mars' atmosphere and landed the Curiosity rover in Gale Crater. The capsule used a reaction control system (RCS) consisting of four pairs of hydrazine thrusters to fly a guided entry. The RCS provided bank control to fly along a flight path commanded by an onboard computer and also damped unwanted rates due to atmospheric disturbances and any dynamic instabilities of the capsule. A preliminary assessment of the MSL's flight data from entry showed that the capsule flew much as predicted. This paper will describe how the MSL aerodynamics team used engineering analyses, computational codes and wind tunnel testing in concert to develop the RCS system and certify it for flight. Over the course of MSL's development, the RCS configuration underwent a number of design iterations to accommodate mechanical constraints, aeroheating concerns and excessive aero/RCS interactions. A brief overview of the MSL RCS configuration design evolution is provided. Then, a brief description is presented of how the computational predictions of RCS jet interactions were validated. The primary work to certify that the RCS interactions were acceptable for flight was centered on validating computational predictions at hypersonic speeds. A comparison of computational fluid dynamics (CFD) predictions to wind tunnel force and moment data gathered in the NASA Langley 31-Inch Mach 10 Tunnel was the lynch pin to validating the CFD codes used to predict aero/RCS interactions. Using the CFD predictions and experimental data, an interaction model was developed for Monte Carlo analyses using 6-degree-of-freedom trajectory simulation. The interaction model used in the flight simulation is presented.

Schoenenberger, Mark↗