Results for “Advanced Workflow” — Page 10

DOE OSTI2019

Supporting Simulation Families in Nuclear Reactor Workflows SBIR Phase I. Final Scientific/Technical Report

The US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) Toolkit has accelerated both the solutions to existing problems and deployment of new designs for current and advanced reactors. Within the toolkit, there exist various families of simulation tools that target specific aspects of a multi-physics simulation for a nuclear reactor. Tools within a specific family vary in both complexity and fidelity as well as the types of resources they require. To complement the NEAMS effort, the Computational Model Builder (CMB) has been designed to provide a graphical user interface to design and execute nuclear reactor workflows. Previously, we had designed a workflow in CMB to design and prepare for execution a neutronics simulation using DIF3D, a diffusion and transport solver developed at Argonne National Laboratory. For this Phase I effort, we extended CMB’s reactor modeling tools to design and execute a workflow using Proteus-SN, a higher-fidelity transport solver developed at Argonne with more preparatory requirements from the workflow. Furthermore, this workflow was designed to maximize the common features of the two workflows, describing the analogous tasks between the workflows as belonging to a “simulation family”. This perspective facilitates the abstraction of the neutronics simulations to a single bifurcated workflow, allowing the engineer to design a reactor and then choose the appropriate simulation according to his or her needs for fidelity and computational cost.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Scalable Multi-Facility Workflows for Artificial Intelligence Applications in Climate Research

Earth observation satellites and earth system models are sources of vast, multi-modal datasets that are invaluable for advancing climate and environmental research. However, their scale and complexity pose significant challenges for processing and analysis. In this paper we discuss our experiences in developing and using a scientific research application using an automated multi-facility workflow that orchestrates data collection, preprocessing, artificial intelligence (AI) inferencing, and data movement across diverse computational resources, leveraging the Advanced Computing Ecosystem Testbed at the Oak Ridge Leadership Computing Facility (OLCF). We demonstrate that our workflow can be seamlessly integrated and orchestrated across research facilities managed by different federal agencies, thus allowing users to extract new scientific insights from climate datasets. The experimental results indicate that the multi-facility workflow significantly reduces processing time, enhances scalability, and maintains high efficiency across varying workloads. Notably, our workflow processes 12,000 high-resolution satellite images in just 44 seconds using 80 workers distributed across 10 nodes on the OLCF systems. Such high throughput is essential for dynamic tokenization and sharding of petascale satellite data for distributed AI model training and inferencing at scale across thousands of GPUs.

Kurihana, Takuya [ORNL] (ORCID:0000000156698565)↗

DOE OSTI2019

Modern data analytics approach to predict creep of high-temperature alloys

A breakthrough in alloy design often requires comprehensive understanding in complex multi-component/multi-phase systems to generate novel material hypotheses. We introduce a modern data analytics workflow that leverages high-quality experimental data augmented with advanced features obtained from high-fidelity models. Herein, we use an example of a consistently-measured creep dataset of developmental high-temperature alloy combined with scientific alloy features populated from a high-throughput computational thermodynamic approach. Extensive correlation analyses provide ranking insights for most impactful alloy features for creep resistance, evaluated from a large set of candidate features suggested by domain experts. We also show that we can accurately train machine learning models by integrating high-ranking features obtained from correlation analyses. Consequently, the demonstrated approach can be extended beyond incorporating thermodynamic features, with input from domain experts used to compile lists of features from other alloy physics, such as diffusion kinetics and microstructure evolution.

36 MATERIALS SCIENCE↗

DOE OSTI2026

BL7011 v1.0.0

This is a software package tailored to the needs of beam line 7.0.1.1 at the Advanced Light Source. It use open source packages to increase workflow efficiency around the beam line. This software package provides analysis code to deal with tasks connected to coherent x-ray measurements at the Cosmic Scattering end station.

Morley, Sophie [Lawrence Berkeley National Laborat↗

DOE OSTI2016

Warthog: Progress on Coupling BISON and PROTEUS

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program from the Office of Nuclear Energy at the Department of Energy (DOE) provides a robust toolkit for modeling and simulation of current and future advanced nuclear reactor designs. This toolkit provides these technologies organized across product lines, with two divisions targeted at fuels and end-to-end reactor modeling, and a third for integration, coupling, and high-level workflow management. The Fuels Product Line (FPL) and the Reactor Product Line (RPL) provide advanced computational technologies that serve each respective field effectively. There is currently a lack of integration between the product lines, impeding future improvements of simulation solution fidelity. In order to mix and match tools across the product lines, a new application called Warthog was produced. Warthog is built on the Multi-physics Object-Oriented Simulation Environment (MOOSE) framework developed at Idaho National Laboratory (INL). This report details the continuing efforts to provide the Integration Product Line (IPL) with interoperability using the Warthog code. Currently, this application strives to couple the BISON fuel performance application from the FPL using the PROTEUS Core Neutronics application from the RPL. Warthog leverages as much prior work from the NEAMS program as possible, enabling interoperability between the independently developed MOOSE and SHARP frameworks, and the libMesh and MOAB mesh data formats. Previous work performed on Warthog allowed it to couple a pin cell between the two codes. However, as the temperature changed due to the BISON calculation, the cross sections were not recalculated, leading to errors as the temperature got further away from the initial conditions. XSProc from the SCALE code suite was used to calculate the cross sections as needed. The remainder of this report discusses the changes to Warthog to allow for the implementation of XSProc as an external code. It also discusses the changes made to Warthog to allow it to fit more cleanly into the MultiApp syntax of the MOOSE framework. The capabilities, design, and limitations of Warthog will be described, in addition to some of the test cases that were used to demonstrate the code. Future plans for Warthog will be discussed, including continuation of the modifications to the input and coupling to other SHARP codes such as Nek5000.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2017

Advances in microscale separations towards nanoproteomics applications

Microscale separations (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. While significant advances have been achieved in MS-based proteomics, the current platforms still face a significant challenge in overall sensitivity towards nanoproteomics (i.e., with less than 1 g total amount of proteins available) applications such as cellular heterogeneity in tissue pathologies. Herein, we review recent advances in microscale separation techniques and integrated sample processing systems that improve the overall sensitivity and coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2023

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a “user guide” for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure–property relationships in soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency

Many workflows in high-energy-physics (HEP) stand to benefit from recent advances in transformer-based large language models (LLMs). While early applications of LLMs focused on text generation and code completion, modern LLMs now support orchestrated agency: the coordinated execution of complex, multi-step tasks through tool use, structured context, and iterative reasoning. We introduce the HEP Toolkit for Agentic Planning, Orchestration, and Deployment (HEPTAPOD), an orchestration framework designed to bring this emerging paradigm to HEP pipelines. The framework enables LLMs to interface with domain-specific tools, construct and manage simulation workflows, and assist in common utility and data analysis tasks through schema-validated operations and run-card-driven configuration. To demonstrate these capabilities, we consider a representative Beyond the Standard Model (BSM) Monte Carlo validation pipeline that spans model generation, event simulation, and downstream analysis within a unified, reproducible workflow. HEPTAPOD provides a structured and auditable layer between human researchers, LLMs, and computational infrastructure, establishing a foundation for transparent, human-in-the-loop systems.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

DOE OSTI2025

New approaches to secondary metabolite discovery from anaerobic gut microbes

The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme & Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

SU-F-T-351: Establishing a Workflow for IMRT Pre-Treatment Reviews for NRG-GY006 Clinical Trial

Purpose: To establish a workflow for NRG-GY006 IMRT pre-treatment reviews, incorporating advanced radiotherapy technologies being evaluated as part of the clinical trial. Methods: Pre-Treatment reviews are required for every IMRT case as part of NRG-GY006 (a randomized phase II trial of radiation therapy and cisplatin alone or in combination with intravenous triapine in women with newly diagnosed bulky stage I B2, stage II, IIIB, or IVA cancer of the uterine cervix or stage II-IVA vaginal cancer. The pretreatment review process includes structures review and generating an active bone marrow(ABM)- to be used as an avoidance structure during IMRT optimization- and evaluating initial IMRT plan quality using knowledgeengineering based planning (KBP). Institutions will initially submit their simulation CT scan, structures file and PET/CT to IROC QA center for generating ABM. The ABM will be returned to the institution for use in planning. Institutions will then submit an initial IMRT plan for review and will receive information back following implementation of a KBP algorithm, for use in re-optimization, before submitting the final IMRT used for treatment. Results: ABM structure is generated using MIM vista software (Version 6.5, MIM corporation, Inc.). Here, the planning CT and the diagnostic PET/CT are fused and a sub threshold structure is auto segmented above the mean value of the SUV of the bone marrow. The generated ABM were compared with those generated with other software system (e.g. Velocity, Varian) and Dice coefficient (reflects the overlap of structures) ranged between 80 – 90% was achieved. A KBP model was built in Varian Eclipse TPS using the RapidPlan KBP software to perform plan quality assurance. Conclusion: The workflow for IMRT pretreatment reviews has been established. It represents a major improvement of NRG Oncology clinical trial quality assurance and incorporates the latest radiotherapy technologies as part of NCI clinical trials. This project was supported by grants U24CA180803 (IROC), UG1CA189867 (NCORP), U10CA180868 (NRG Oncology Operations), U10CA180822 (NRG Oncology SDMC) from the National Cancer Institute (NCI) and PA CURE grant.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

AI-Driven Detector Design for the EIC (Final Technical Report)

We developed an optimization workflow based on DNN-based fast-simulation and reconstruction algorithms. We used these methods to advance the design of calorimeter systems for the Electron-Ion Collider (EIC). This DNN-driven optimization provides a blueprint for integrating gradient-based methods into detector-design workflows. All software pipelines and methods have been released publicly and incorporated into the EIC collaboration’s physics studies, broadening their impact. Three journal articles detailing the methods developed here serve as a reference for the design and optimal use of next generation high-granularity calorimeter systems in nuclear and particle physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2014

TH-C-17A-07: Visualizing and Quantifying Radiation Therapy in Real-Time Using a Novel Beam Imaging Technique

Purpose: Radiation therapy uses invisible high energy X-rays to treat an invisible tumor. Proper positioning of the treatment beam relative to the patient's anatomy during dose delivery is critically important to the success of treatment. We develop and characterize a novel radiation therapy beam visualization technique for real-time monitoring of patient treatment. Methods: Custom made flexible scintillator sheets were fabricated from gadolinium oxysulfide (GOS) particles that had been doped with terbium within a silicone elastomer matrix. Sheets of several thicknesses ranging from 0.3 to 1mm were prepared and tested. Sheets were exposed to megavoltage X-ray and electron beams from a Varian linac and the resulting optical signal was collected by multiple CMOS cameras placed in the treatment room. Real-time images were collected for different beam energies and dose rates. Signal intensity and SNR were calculated by processing the acquired images. Results: All signals were detectable in the presence of full room lighting and at an integration time of 45ms. Average signal intensity and SNR increased with both sheet thickness and dose rate and decreased with beam energy and incident light. For a given sheet thickness and beam energy the correlation between dose rate and signal intensity was highly linear. Increased sheet thickness or dose rate results in a linear increase in the detected signal. All results are consistent with analytical approximations. Conclusion: The technique offers a means of accurately visualizing a radiation therapy beam shape and fluence in real time. The effects of salient parameters have been characterized and will enable further optimization of the technique as it is implemented into the clinical workflow. The project described was supported by the National Center for Advancing Translational Sciences of the National Institutes of Health through UL1 TR001085.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

WE-D-BRD-00: New Developments in Hybrid MR-Treatment: Technology

The advantages that make MR highly desirable for in-room treatment guidance, i.e. soft-tissue visualization and physiological assessment of healthy/tumor tissues, are largely recognized in the research community. However, the MR absorption in practical clinical workflows is still hindered by lack of sufficient technological infrastructure. Recent advances have been made towards filling that gap such as the development of integrated therapy systems relying on an MR scanner and a radiation source (linac, Co-60) and/or brachytherapy. The session is intended to present new efforts and methods aimed at facilitating the adoption of MR guidance for treatment delivery. Specifically, the discussion will focus on a) linac designs for reduced footprint and seamless integration with MR/linac systems, b) tracking coils for brachytherapy applications, and c) procedures for the commissioning and monitoring of MR and MR/linac performance. Learning Objectives: Understand limitations and proposed solutions for linac designs and associated integration with MR/linac systems; Understand current issues with MR-guided brachytherapy procedures Understand the issues and needs for new MR commissioning and QC. License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image distortions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

WE-D-BRD-01: New Linac Designs for MR-Guided Therapy Systems

The advantages that make MR highly desirable for in-room treatment guidance, i.e. soft-tissue visualization and physiological assessment of healthy/tumor tissues, are largely recognized in the research community. However, the MR absorption in practical clinical workflows is still hindered by lack of sufficient technological infrastructure. Recent advances have been made towards filling that gap such as the development of integrated therapy systems relying on an MR scanner and a radiation source (linac, Co-60) and/or brachytherapy. The session is intended to present new efforts and methods aimed at facilitating the adoption of MR guidance for treatment delivery. Specifically, the discussion will focus on a) linac designs for reduced footprint and seamless integration with MR/linac systems, b) tracking coils for brachytherapy applications, and c) procedures for the commissioning and monitoring of MR and MR/linac performance. Learning Objectives: Understand limitations and proposed solutions for linac designs and associated integration with MR/linac systems; Understand current issues with MR-guided brachytherapy procedures Understand the issues and needs for new MR commissioning and QC. License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image distortions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

WE-D-BRD-02: Tracking Coils for Brachy MR Guidance

The advantages that make MR highly desirable for in-room treatment guidance, i.e. soft-tissue visualization and physiological assessment of healthy/tumor tissues, are largely recognized in the research community. However, the MR absorption in practical clinical workflows is still hindered by lack of sufficient technological infrastructure. Recent advances have been made towards filling that gap such as the development of integrated therapy systems relying on an MR scanner and a radiation source (linac, Co-60) and/or brachytherapy. The session is intended to present new efforts and methods aimed at facilitating the adoption of MR guidance for treatment delivery. Specifically, the discussion will focus on a) linac designs for reduced footprint and seamless integration with MR/linac systems, b) tracking coils for brachytherapy applications, and c) procedures for the commissioning and monitoring of MR and MR/linac performance. Learning Objectives: Understand limitations and proposed solutions for linac designs and associated integration with MR/linac systems; Understand current issues with MR-guided brachytherapy procedures Understand the issues and needs for new MR commissioning and QC. License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image distortions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

WE-D-BRD-03: Novel Methods and Tools for MR Commissioning and QC

The advantages that make MR highly desirable for in-room treatment guidance, i.e. soft-tissue visualization and physiological assessment of healthy/tumor tissues, are largely recognized in the research community. However, the MR absorption in practical clinical workflows is still hindered by lack of sufficient technological infrastructure. Recent advances have been made towards filling that gap such as the development of integrated therapy systems relying on an MR scanner and a radiation source (linac, Co-60) and/or brachytherapy. The session is intended to present new efforts and methods aimed at facilitating the adoption of MR guidance for treatment delivery. Specifically, the discussion will focus on a) linac designs for reduced footprint and seamless integration with MR/linac systems, b) tracking coils for brachytherapy applications, and c) procedures for the commissioning and monitoring of MR and MR/linac performance. Learning Objectives: Understand limitations and proposed solutions for linac designs and associated integration with MR/linac systems; Understand current issues with MR-guided brachytherapy procedures Understand the issues and needs for new MR commissioning and QC. License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image distortions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

Knowledge about the role of genes under a particular growth condition is required for a holistic understanding of a bacterial cell and has implications for health, agriculture, and biotechnology. We developed the Tn-seq analysis software (TSAS) package to provide a flexible and statistically rigorous workflow for the high-throughput analysis of insertion mutant libraries, advanced the knowledge of gene essentiality in R. sphaeroides , and illustrated how Tn-seq data can be used to more accurately identify genes that play important roles in metabolism and other processes that are essential for cellular survival.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

The FabrIc for Frontier Experiments Project at Fermilab: Computing for Experiments

The FabrIc for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientific Computing Division designed to steer the computing model for non-LHC experiments at Fermilab. The FIFE project enables close collaboration between experimenters and computing professionals to serve high-energy physics experiments of differing scope and physics area of study. The project also tracks and provides feedback on the development of common tools for job submission, identity management, software and data distribution, job monitoring, and databases for project tracking. The computing needs of the experiments under the FIFE umbrella continue to increase, and present a complex list of requirements to their service providers. To meet these requirements, recent advances in the FIFE toolset include a new identity management infrastructure, significantly upgraded job monitoring tools, and a workflow management system. We have also upgraded existing tools to access remote computing resources such as GPU clusters and sites outside the United States. We will present these recent advances, highlight the nature of collaboration between the diverse set of experimenters and service providers, and discuss the project's future directions.

43 PARTICLE ACCELERATORS↗