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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Elasto-viscoplastic fast Fourier transform modeling framework for assessing microstructural effects on stress intensity factors characterizing fracture toughness

A large-strain elasto-viscoplastic fast Fourier transform (LS-EVPFFT) model with non-periodic (NP) velocity-based boundary conditions is adapted to simulate the sensitivity of stress intensity factors on microstructure for 304L stainless steel. The material was characterized via electron backscattered diffraction (EBSD) serial-sectioning to obtain a measured 3-D microstructural cell to perform simulations. The NP-LS-EVPFFT model, including the simulation setup and boundary conditions, was verified using a crystal plasticity finite element (CPFE) model. To this end, the generation of meshes of notched specimens was developed, which involved creating Python scripts for mesh “cutting” in Abaqus, and Sculpt scripts in Cubit for meshing of the measured microstructural cell processed with DREAM.3D. The complexity of the mesh preparation highlighted the advantages of the FFT-based model, which circumvents the mesh generation process. Given the efficiency of the FFT-based model, statistical distribution of stress intensity factors in function of crystal orientation at the crack tip, grain structure, and crystallographic texture surrounding the crack tip were predicted. Further, the distributions reveal about 10% variation of stress intensity factors with microstructure with the most significant sensitivity found to be the crystal orientation at the crack tip. The methodology developed in this work is discussed as a practical simulation tool for predicting the sensitivity of stress intensity factors on microstructural variability in metallic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

Alchemical free energy simulations have long been utilized to predict free energy changes for binding affinity and solubility of small molecules. However, while the theoretical foundation of these methods is well established, seamlessly handling many of the practical aspects regarding the preparation of the different thermodynamic end states of complex molecular systems and the numerous processing scripts often remains a burden for successful applications. Here, we present CHARMM-GUI Free Energy Calculator (http://www.charmm-gui.org/input/fec) that provides various alchemical free energy perturbation molecular dynamics (FEP/MD) systems with input and post-processing scripts for NAMD and GENESIS. Four submodules are available: Absolute Ligand Binder (for absolute ligand binding FEP/MD), Relative Ligand Binder (for relative ligand binding FEP/MD), Absolute Ligand Solvator (for absolute ligand solvation FEP/MD), and Relative Ligand Solvator (for relative ligand solvation FEP/MD). Each module is designed to build multiple systems of a set of selected ligands at once for high-throughput FEP/MD simulations. The capability of Free Energy Calculator is illustrated by absolute and relative solvation FEP/MD of a set of ligands and absolute and relative binding FEP/MD of a set of ligands for T4-lysozyme in solution and the adenosine A 2A receptor in a membrane. The calculated free energy values are overall consistent with the experimental and published free energy results (within ~1 kcal/mol). We hope that Free Energy Calculator is useful to carry out high-throughput FEP/MD simulations in the field of biomolecular sciences and drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

SNS Proton Beam Window Disposal

In order to support the disposal of the proton beam window assembly of the Spallation Neutron Source beamline to the target station, waste classification analyses are performed. The window has a limited life-time due to radiation-induced material damage. Here, analyses include calculation of the radionuclide inventory and shielding analyses for the transport package/container to ensure that the container is compliant with the transportation and waste management regulations. In order to automate this procedure and minimize manual work a script in Perl language was written.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

The neutrino gravitational memory from a core collapse supernova: phenomenology and physics potential

General Relativity predicts that the passage of matter or radiation from an asymmetrically-emitting source should cause a permanent change in the local space-time metric. This phenomenon, called the gravitational memory effect, has never been observed, however supernova neutrinos have long been considered a promising avenue for its detection in the future. With the advent of deci-Hertz gravitational wave interferometers, observing the supernova neutrino memory will be possible, with important implications for multimessenger astronomy and for tests of gravity. In this work, we develop a phenomenological (analytical) toy model for the supernova neutrino memory effect, which is overall consistent with the results of numerical simulations. This description is then generalized to several case studies of interest. We find that, for a galactic supernova, the dimensionless strain, h(t), is of order ~ 10 -22 - 10 -21 , and develops over a typical time scale that varies between ~ 0.1 - 10 s, depending on the time-evolution of the anisotropy of the neutrino emission. The characteristic strain, h c (f), has a maximum at a frequency f max ~ Script $\mathcal{O}$(10 -1 ) - Script $\mathcal{O}$(1) Hz. The detailed features of the time- and frequency-structure of the memory strain will inform us of the matter dynamics near the collapsed core, and allow to distinguish between different stellar collapse scenarios. Next generation gravitational wave detectors like DECIGO and BBO will be sensitive to the neutrino memory effect for supernovae at typical galactic distances and beyond; with Ultimate DECIGO exceeding a detectability distance of 10 Mpc

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Agentic artificial intelligence for multistage physics experiments at a large-scale user facility particle accelerator

We present a language-model-driven agentic artificial intelligence (AI) system to autonomously execute multistage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by 2 orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Accelerator/storage ring control systems↗
DOE OSTI2015

Porting Ordinary Applications to Blue Gene/Q Supercomputers

Efficiently porting ordinary applications to Blue Gene/Q supercomputers is a significant challenge. Codes are often originally developed without considering advanced architectures and related tool chains. Science needs frequently lead users to want to run large numbers of relatively small jobs (often called many-task computing, an ensemble, or a workflow), which can conflict with supercomputer configurations. In this paper, we discuss techniques developed to execute ordinary applications over leadership class supercomputers. We use the high-performance Swift parallel scripting framework and build two workflow execution techniques-sub-jobs and main-wrap. The sub-jobs technique, built on top of the IBM Blue Gene/Q resource manager Cobalt's sub-block jobs, lets users submit multiple, independent, repeated smaller jobs within a single larger resource block. The main-wrap technique is a scheme that enables C/C++ programs to be defined as functions that are wrapped by a high-performance Swift wrapper and that are invoked as a Swift script. We discuss the needs, benefits, technicalities, and current limitations of these techniques. We further discuss the real-world science enabled by these techniques and the results obtained.

Maheshwari, Ketan C.↗
DOE OSTI2025

Real-World Cyber Security Demonstration for Networked Electric Drives

In this article, we present the design and implementation of a cyber-physical security testbed for networked electric drive systems, aimed at conducting real-world security demonstrations. To our knowledge, this is one of the first security testbeds for networked electric drives, seamlessly integrating the domains of power electronics and computer science, and cybersecurity. By doing so, the testbed offers a comprehensive platform to explore and understand the intricate and often complex interactions between cyber and physical systems. The core of our testbed consists of four electric machine drives, meticulously configured to emulate small-scale but realistic information technology (IT) and operational technology (OT) networks. This setup both provides a controlled environment for simulating a wide array of cyber-attacks, and mirrors potential real-world attack scenarios with a high degree of fidelity. The testbed serves as an invaluable resource for the study of cyber-physical security, offering a practical and dynamic platform for testing and validating cybersecurity measures in the context of networked electric drive systems. As a concrete example of the testbed's capabilities, we have developed and implemented a Python-based script designed to execute step-stone attacks over a wireless local area network (WLAN). This script leverages a sequence of target IP addresses, simulating a real-world attack vector that could be exploited by adversaries. To counteract such threats, we demonstrate the efficacy of our developed cyber-attack detection algorithms, which are integral to our testbed's security framework. Furthermore, the testbed incorporates a real-time visualization system using InfluxDB and Grafana, providing a dynamic and interactive representation of networked electric drives and their associated security monitoring mechanisms. This visualization component not only enhances the testbed's usability but also offers insightful, real-time data for researchers and practitioners, thereby facilitating a deeper understanding of cyber-physical security dynamics in networked electric drive systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2018

Regression-Based Analytics for Response Dynamics of SDN Solutions and Components

We consider Software-Defined Network (SDN) solutions that dynamically setup and teardown connections, and also their response dynamics of connectivity and TCP throughput. There is a wide variety of choices for controllers, switches, andsoftware modules, and objective analytics of measurements are needed to compare the response dynamics of solutions based on their combinations. Throughput and ping measurements during connection changes contain significant statistical variations due to the complexities of controllers, northbound scripts, and network devices. We propose analytical methods to estimate response regression functions, which provide a rigorous and objective comparison of different SDN solutions and their components, namely, controllers, switches, and OpenFlow versions. We apply this approach in two scenarios: (a) switching of long-haul connections emulated in hardware by ANUE devices over a testbed consisting of HP and Cisco switches, and (b) multi-site science infrastructure emulated using VMs and Mininet. The results provide useful practical insights including: (i) the dpctl method responds seconds faster than the OpenDayLight (ODL) method on average under OpenFlow 1.0, but performs similar to ODL under OpenFlow 1.3, and (ii) the ping response of dpctl is about 0.6 sec faster than ODL for the second scenario.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Same Data, Different Audiences: Using Personas to Scope a Supercomputing Job Queue Visualization

Domain-specific visualizations sometimes focus on narrow, albeit important, tasks for one group of users. This focus limits the utility of a visualization to other groups working with the same data. While tasks elicited from other groups can present a design pitfall if not disambiguated, they also present a design opportunity—namely, the development of visualizations that support multiple groups. This development choice presents a trade-off of broadening the scope but limiting support for the more narrow tasks of any one group, which in some cases can enhance the overall utility of the visualization. We investigate this scenario through a design study where we develop Guidepost, a notebook-embedded visualization of data that helps scientists assess compute wait times, machine learning researchers understand prediction accuracy, and system maintainers analyze usage trends. We adapt the use of personas for visualization design from existing literature in the HCI and design domains, applying them to categorize tasks based on their uniqueness across stakeholder personas. Under this model, tasks shared between all groups should be supported by interactive visualizations and tasks unique to each group can be deferred to scripting with notebook-embedded visualization design. We evaluate our visualization through real-world case studies and a task-focused evaluation with nine participants. We observe that together, Guidepost's visual encodings, interactions, and export capabilities support the tasks of our differing personas.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Efficient species identification for Pacific salmon genetic monitoring programs

Abstract Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs.

Robinson, Zachary L.↗
DOE OSTI2024

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves

The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model pho-tosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosyn-thetic parameters using concurrent gas exchange and chlorophyll fluorescence mea-surements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, Km, that is, Michaelis constant for CO2 by Rubisco, prefixed. Additionally, we show that including detailed low CO2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement proto-cols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided.

Bayesian statistics, leaf photosynthesis, mesophyl↗
DOE OSTI2018

Connectivity and functional verification for the LSST science raft towers

The LSST Camera focal plane will be constructed with 21 144-Mpixel modules (\Raft Tower Module", RTM). An extensive operational test is performed to confirm the integrity of all connections and to verify the basic functionality. Each RTM undergoes at least four connectivity tests. A python script communicates with Java- based control software and performs the test. A python script parses the test data and generates a PDF report. The report includes a summary PASS/FAIL table, several hundred current, voltage and temperature parameters, and images taken with the CCD array at room temperature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

SU-F-T-94: Plan2pdf - a Software Tool for Automatic Plan Report for Philips Pinnacle TPS

Purpose: To implement an automatic electronic PDF plan reporting tool for Philips Pinnacle treatment planning system (TPS) Methods: An electronic treatment plan reporting software is developed by us to enable fully automatic PDF report from Pinnacle TPS to external EMR programs such as MOSAIQ. The tool is named “plan2pdf”. plan2pdf is implemented using Pinnacle scripts, Java and UNIX shell scripts, without any external program needed. plan2pdf supports full auto-mode and manual mode reporting. In full auto-mode, with a single mouse click, plan2pdf will generate a detailed Pinnacle plan report in PDF format, which includes customizable cover page, Pinnacle plan summary, orthogonal views through each plan POI and maximum dose point, DRR for each beam, serial transverse views captured throughout the dose grid at a user specified interval, DVH and scorecard windows. The final PDF report is also automatically bookmarked for each section above for convenient plan review. The final PDF report can either be saved on a user specified folder on Pinnacle, or it can be automatically exported to an EMR import folder via a user configured FTP service. In manual capture mode, plan2pdf allows users to capture any Pinnacle plan by full screen, individual window or rectangular ROI drawn on screen. Furthermore, to avoid possible patients’ plan mix-up during auto-mode reporting, a user conflict check feature is included in plan2pdf: it prompts user to wait if another patient is being exported by plan2pdf by another user. Results: plan2pdf is tested extensively and successfully at our institution consists of 5 centers, 15 dosimetrists and 10 physicists, running Pinnacle version 9.10 on Enterprise servers. Conclusion: plan2pdf provides a highly efficient, user friendly and clinical proven platform for all Philips Pinnacle users, to generate a detailed plan report in PDF format for external EMR systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-167: Measurement of Proton Beam Spot Size Using a 2D Ion Chamber Array for Daily QA

Purpose: To develop an algorithm which can calculate the Full Width Half Maximum (FWHM) of a Proton Pencil Beam from a 2D dimensional ion chamber array (IBA Matrixx) with limited spatial resolution ( 7.6 mm inter chamber distance). The algorithm would allow beam FWHM measurements to be taken during daily QA without an appreciable time increase. Methods: Combinations of 147 MeV single spot beams were delivered onto an IBA Matrixx and concurrently on EBT3 films for a standard. Data were collected around the Bragg Peak region and evaluated by a custom MATLAB script based on our algorithm using a least squared analysis. A set of artificial data, modified with random noise, was also processed to test for robustness. Results: The Matlab script processed Matixx data shows acceptable agreement (within 5%) with film measurements with no single measurement differing by more than 1.8 mm. In cases where the spots show some degree of asymmetry, the algorithm is able to resolve the differences. The algorithm was able to process artificial data with noise up to 15% of the maximum value. Time assays of each measurement took less than 3 minutes to perform, indicating that such measurements may be efficiently added to daily QA treatment. Conclusion: The developed algorithm can be implemented in daily QA program for Proton Pencil Beam scanning beams (PBS) with Matrixx to extract spot size and position information. The developed algorithm may be extended to small field sizes in photon clinic.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

SU-F-T-531: Determination of Site-Specific Dynamic-Jaw Versus Static-Jaw RapidArc Delivery

Purpose: Dynamic-jaw tracking maximizes the area blocked by both jaw and MLC in RapidArc. We developed a method to quantify jaw tracking. Methods: An Eclipse Scripting API (ESAPI) was used to export beam parameters for each arc’s control points. The specific beam parameters extracted were: gantry angle, control point number, meterset, x-jaw positions, y-jaw positions, MLC bank-number, MLC leaf-number, and MLC leaf-position. Each arc contained 178 control points with 120 MLC positions. MATLAB routines were written to process these parameters in order to calculate both the beam aperture (unblocked) size for each control point. An average aperture size was weighted by meterset. Jaw factor was defined as the ratio between dynamic-jaw to static-jaw aperture size. Jaw factor was determined for forty retrospectively replanned patients treated with static-jaw delivery sites including lung, brain, prostate, H&N, rectum, and bladder. Results: Most patients had multiple arcs and reduced-field boosts, resulting in 151 fields. Of these, the lowest (0.4722) and highest (0.9622) jaw factor was observed in prostate and rectal cases, respectively. The median jaw factor was 0.7917 meaning there is the potential unincreased blocking by 20%. Clinically, the dynamic-jaw tracking represents an area surrounding the target which would receive MLC-only leakage transmission of 1.68% versus 0.1% with jaws. Jaw-tracking was more pronounced at areas farther from the target. In prostate patients, the rectum and bladder had 5.5% and 6.3% lower mean dose, respectively; the structures closer to the prostate such as the rectum and bladder both had 1.4% lower mean dose. Conclusion: A custom ESAPI script was coupled with a MATLAB routine in order to extract beam parameters from static-jaw plans and their replanned dynamic-jaw deliveries. The effects were quantified using jaw factor which is the ratio between the meterset weighted aperture size for dynamic-jaw fields versus static-jaw fields.

60 APPLIED LIFE SCIENCES↗