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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Sub-Sampled Imaging for STEM: Maximising Image Speed, Resolution and Precision Through Reconstruction Parameter Refinement

Sub-sampling during image acquisition in scanning transmission electron microscopy (STEM) has been shown to provide a means to increase the overall speed of acquisition while at the same time providing an efficient means to control the dose, dose rate and dose overlap delivered to the sample. In this paper, we discuss specifically the parameters used to reconstruct sub-sampled images and highlight their effect on inpainting using the beta-process factor analysis (BPFA) methodology. The selection of the main control parameters can have a significant effect on the resolution, precision and sensitivity of the final inpainted images, and here we demonstrate a method by which these parameters can be optimised for any image in STEM. As part of this paper, we also provide a link to open source code and a tutorial on its use, whereby these parameters can be tested for any datasets. When coupled with the hardware necessary to rapidly sub-sample images in STEM, this approach can have significant implications for imaging beam sensitive materials and dynamic processes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction

Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R

Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing) is available for easy local installation.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2025

Tutorial: Machine-Learning-Based CREASE-2D Analysis of 2D SAXS Profiles to Characterize Anisotropic Nanostructures in Soft Materials

We present a tutorial to guide users on how to extend the Computational Reverse Engineering Analysis of Scattering Experiments-2D (CREASE-2D) framework to interpret their experimental two-dimensional small-angle scattering (SAS) data from soft materials (e.g., polymers, peptide amphiphiles, biomolecular fibrils). Unlike most traditional SAS analysis approaches, which typically rely on azimuthally averaged onedimensional (1D) profiles, CREASE-2D utilizes the complete 2D scattering profile to reveal information about anisotropy in the structure. In past applications, CREASE has provided insights into complex structural features, including the cross-sectional shapes of assembled nanostructures and dispersity in these features, which are difficult to discern with existing analytical models. While (1D- ) CREASE has been applied to SANS and SAXS data, this tutorial shares the steps for implementing CREASE-2D using an example of a dipeptide solution system, for which we have SAXS data. We present details for these steps involved in using CREASE-2D to interpret SAXS profiles: how to preprocess SAXS data, define relevant structural features, generate three-dimensional real-space structures for specific values of these features, train a machine learning (ML) surrogate model to predict scattering profiles for given structural features, and optimize these features using genetic algorithms (GA). Then, we use these steps to interpret complex 2DSAXS data collected from dipeptide solutions that, in microscopy images, exhibit nanoscale structures that could be elliptical tubes/ flat tapes/cylinders or a combination of these cross sections. Open-source codes, computational hardware, and software requirements, as well as the strengths and limitations of this protocol, are also presented. We expect researchers working with (soft) biomaterials, peptide amphiphiles, amphiphilic polymer solutions, polymer nanocomposites, and blends of particles/polymers will find this CREASE-2D method and this tutorial of use.

CREASE↗
DOE OSTI2026

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗
DOE OSTI2020

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Effects of MOF linker rotation and functionalization on methane uptake and diffusion

The flexible degrees of freedom in metal–organic frameworks (MOFs) can have significant effects on guest molecule behavior. However, in the majority of studies applying molecular simulations to MOFs, the framework is assumed to be rigid in order to minimize computational cost. Here, in this work, we assess the significance of this assumption on a representative example of methane uptake and diffusion in UiO-66. We introduce an open-source code to modify MOFs through functionalization and linker rotation and we perform Grand Canonical Monte Carlo and molecular dynamics simulations of methane in each of the functionalized and linker-rotated derivatives of UiO-66. We find that linker rotation moderately influences methane uptake and significantly influences methane diffusion. Our assessment provides ranges of property values that serve as measures of uncertainty of these two properties associated with linker rotation. We further determine that void volume fraction and minimum pore size are the features that govern methane uptake and diffusion, respectively. These findings illustrate the impact of linker rotation on MOFs and provide design principles to guide future investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Effects of surface diffusion in electrocatalytic CO 2 reduction on Cu revealed by kinetic Monte Carlo simulations

We report Kinetic Monte Carlo (KMC) methods are frequently used for mechanistic studies of thermally driven heterogeneous catalysis systems but are underused for electrocatalysis. Here, we develop a lattice KMC approach for electrocatalytic CO 2 reduction. The work is motivated by a prior experimental report that performed electroreduction of a mixed feed of 12 CO 2 and 13 CO on Cu; differences in the 13 C content of C2 products ethylene and ethanol (Δ 13 C) were interpreted as evidence of site selectivity. The lattice KMC model considers the effect of surface diffusion on this system. In the limit of infinitely fast diffusion (mean-field approximation), the key intermediates 12 CO* and 13 CO* would be well mixed on the surface and no evidence of site selectivity could have been observed. Using a simple two-site model and adapting a previously reported microkinetic model, we assess the effects of diffusion on the relative isotope fractions in the products using the estimated surface diffusion rate of CO* from literature reports. We find that the size of the active sites and the total surface adsorbate coverage can have a large influence on the values of Δ 13 C that can be observed. Δ 13 C is less sensitive to the CO* diffusion rate as long as it is within the estimated range. We further offer possible methods to estimate surface distribution of intermediates and to predict intrinsic selectivity of active sites based on experimental observations. This work illustrates the importance of considering surface diffusion in the study of electrochemical CO 2 reduction to multi-carbon products. Our approach is entirely based on a freely available open-source code, so will be readily adaptable to other electrocatalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cost- and Risk-Based Seismic Design Optimization of Nuclear Power Plant Safety Systems

Seismic analysis, design, and qualification of systems, structures, and components (SSCs) is a significant contributor to the capital cost of a nuclear power plant. To reduce capital costs of advanced nuclear power plants and make commercial nuclear energy more competitive, innovations are needed in their structural design and construction, and not just in the reactor core and associated systems. Seismic isolation has been identified as an important cost-cutting technology that enables standardization of equipment across various sites. This paper develops and demonstrates a cost- and risk-based seismic design optimization of a representative safety system in a nuclear power plant with the dual goals of minimizing overnight capital cost and meeting safety goals. The design optimization can also include component seismic isolation, in which case, the optimized design includes a set of equipment that needs to be seismically isolated to minimize capital cost. The open-source codes MASTODON and Dakota are used for seismic probabilistic risk assessment and design optimization, respectively. A generic nuclear facility with a safety system comprising SSCs that are common to nuclear power plants is considered for the demonstration of the design optimization and is assumed to be located at the Idaho National Laboratory site. Generic costs and seismic design cost functions are assumed for the SSCs of the safety system. The sum of the costs of the SSCs is minimized in the optimization process, while the risk of failure of the safety system is provided as a constraint. Furthermore, results show that the optimization process reduces capital costs significantly while automatically prioritizing the safety of SSCs that contribute most to the risk of the safety system.

42 ENGINEERING↗
DOE OSTI2023

Visualizing the NIOSH Pocket Guide: Open-source web application for accessing and exploring the NIOSH Pocket Guide to Chemical Hazards

The NIOSH Pocket Guide to Chemical Hazards is a trusted resource that displays key information for a collection of chemicals commonly encountered in the workplace. Entries contain chemical structures—occupational exposure limit information ranging from limits based on full-shift time-weighted averages to acute limits such as short-term exposure limits and immediately dangerous to life or health values, as well as a variety of other data such as chemical-physical properties and symptoms of exposure. The NIOSH Pocket Guide (NPG) is available as a printed, hardcopy book, a PDF version, an electronic database, and a downloadable application for mobile phones. All formats of the NIOSH Pocket Guide allow users to access the data for each chemical separately, however, the guide does not support data analytics or visualization across chemicals. This project reformatted existing data in the NPG to make it searchable and compatible with exploration and analysis using a web application. The resulting application allows users to investigate the relationships between occupational exposure limits, the range and distribution of occupational exposure limits, and the specialized sorting of chemicals by health endpoint or to summarize information of particular interest. These tasks would have previously required manual extraction of the data and analysis. The usability of this application was evaluated among industrial hygienists and researchers and while the existing application seems most relevant to researchers, the open-source code and data are amenable to modification by users to increase customization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Multiphysics modelling in PyLith: poroelasticity

SUMMARY PyLith, a community, open-source code for modelling quasi-static and dynamic crustal deformation with an emphasis on earthquake faulting, has recently been updated with a flexible multiphysics implementation. We demonstrate the versatility of the multiphysics implementation by extending the code to model fully coupled continuum poromechanics. We verify the newly incorporated physics using standard benchmarks for a porous medium saturated with a slightly compressible fluid. The benchmarks include the 1-D consolidation problem as outlined by Terzaghi, Mandel’s problem for the 2-D case, and Cryer’s problem for the 3-D case. All three benchmarks have been added to the PyLith continuous integration test suite. We compare the closed form analytical solution for each benchmark against solutions generated by our updated code, and lastly, demonstrate that the poroelastic material formulation may be used alongside the existing fault implementation in PyLith.

Geochemistry & Geophysics↗
DOE OSTI2024

Measuring stomatal and guard cell metrics for plant physiology and growth using StoManager1

Abstract Automated guard cell detection and measurement are vital for understanding plant physiological performance and ecological functioning in global water and carbon cycles. Most current methods for measuring guard cells and stomata are laborious, time-consuming, prone to bias, and limited in scale. We developed StoManager1, a high-throughput tool utilizing geometrical, mathematical algorithms, and convolutional neural networks to automatically detect, count, and measure over 30 guard cell and stomatal metrics, including guard cell and stomatal area, length, width, stomatal aperture area/guard cell area, orientation, stomatal evenness, divergence, and aggregation index. Combined with leaf functional traits, some of these StoManager1-measured guard cell and stomatal metrics explained 90% and 82% of tree biomass and intrinsic water use efficiency (iWUE) variances in hardwoods, making them substantial factors in leaf physiology and tree growth. StoManager1 demonstrated exceptional precision and recall (mAP@0.5 over 0.96), effectively capturing diverse stomatal properties across over 100 species. StoManager1 facilitates the automation of measuring leaf stomatal and guard cells, enabling broader exploration of stomatal control in plant growth and adaptation to environmental stress and climate change. This has implications for global gross primary productivity (GPP) modeling and estimation, as integrating stomatal metrics can enhance predictions of plant growth and resource usage worldwide. Easily accessible open-source code and standalone Windows executable applications are available on a GitHub repository (https://github.com/JiaxinWang123/StoManager1) and Zenodo (https://doi.org/10.5281/zenodo.7686022).

Wang, Jiaxin (ORCID:0000000348085085)↗
DOE OSTI2025

Heavy quark mass effects in charged-current deep-inelastic scattering at approximate NNLO in the Aivazis-Collins-Olness-Tung scheme

The approximate SACOT-𝜒 scheme for heavy quark production in deep-inelastic scattering was initially formulated for the neutral current structure functions 𝐹 2 and 𝐹 𝐿 . We extend this approach to the charged current case (also including 𝐹 3 ), and thereby complete the definitions for the most relevant inclusive structure functions. Furthermore, we implement these structure functions in the open-source code APFEL++ which provides fast numerical evaluations over a wide kinematic range; this addition to the APFEL++ code is publicly available, with details provided in the Appendix. This SACOT-𝜒 implementation enables detailed numerical insights on the mass dependence of the structure functions and cross sections in the (𝑥,𝑄 2 )-plane for both neutral and charged current processes. We consider kinematic regions relevant for the experimental measurements from fixed-target 𝜈⁢ DIS experiments (NuTeV, CCFR, and Chorus) and HERA, and also projections for the upcoming EIC. In particular, the 𝜈⁢ DIS experiments reveal a surprisingly strong dependence on the mass effects, offering valuable insights that may help resolve long-standing challenges in accurately describing these datasets.

Risse, P. [Westfälische Wilhelms-Universität Münst↗
DOE OSTI2024

Structural complexity of snapshots of two-dimensional Fermi-Hubbard systems

The development of quantum gas microscopy for two-dimensional optical lattices has provided an unparalleled tool to study the Fermi-Hubbard model (FHM) with ultracold atoms. Spin-resolved projective measurements, or snapshots, have played a significant role in quantifying correlation functions, theory verification, and thus the uncovering of underlying physical phenomena such as antiferromagnetism at commensurate filling on bipartite lattices and other charge and spin correlations, as well as dynamical properties at various densities. Here we employ a recent concept, the multiscale structural complexity, and show that when computed for the snapshots (of single spin species, local moments, or total density) it can provide a theory-free property, immediately accessible to experiments. Specifically, after benchmarking results for Ising and $XY$ models, we study the structural complexity of snapshots of the repulsive FHM in the two-dimensional square lattice as a function of doping and temperature. We generate projective measurements using determinant quantum Monte Carlo and compare their complexities against those from the experiment. We demonstrate that these complexities are linked to relevant physical observables such as the entropy and double occupancy. Their behaviors capture the development of correlations and relevant length scales in the system. Furthermore, we provide an open-source code in python which can be implemented into data analysis routines in experimental settings for the square lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

First-principles residual resistivity using a locally self-consistent multiple scattering method

The locally self-consistent multiple scattering (LSMS) method can perform efficient first-principles calculations of systems with a large number of atoms. Here, in this paper, we combine the Kubo-Greenwood equation with LSMS, enabling us to calculate the first-principles residual resistivity of large systems. This has been implemented in the open-source code LSMS . We apply this method to selected pure elements and binary random alloys. The results compare well with experiment, and with values obtained from a first-principles effective medium technique (the Korringa-Kohn-Rostoker coherent potential approximation). We discuss future applications of this method to complex systems where other methods are not applicable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Framework for X-ray mirror surface shape fitting

For accurate characterization of grazing-incidence X-ray mirrors, we present a comprehensive framework to fit measured surface shapes (either slope or height) of X-ray mirrors used in synchrotron radiation and free-electron laser facilities. We summarize the closed-form expressions of some typical surface shapes of X-ray mirrors including elliptic cylinders, hyperbolic cylinders, ellipsoids, hyperboloids, and diaboloids. This framework is composed of four layers: definition of standard shapes with closed-form expressions, generation of theoretical surface with pose parameters (six degrees of freedom defining an object's position and orientation relative to a coordinate system), parameter optimization with the ability to select which parameters are fit and which are held constant, and the development of user-friendly fitting function wrappers for particular fitting tasks. A few practical fitting examples are demonstrated to verify the effectiveness of the proposed fitting framework. We discuss the physical meanings of the fitting parameters, and provide several examples using the elliptic cylinder and ellipsoid shapes to highlight some features of the framework. Moreover, we provide the presented framework as open-source codes (MATLAB and Python codes available at https://github.com/nsls2omf/xmf) to the community to encourage academic collaboration and further improvements.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Pulsar Movement Animation and its Corresponding Signal Visualization for Timing Source

The global positioning system, widely used for synchronization in energy systems, faces vulnerabilities, while Pulsars—natural cosmic clocks—offer long-term stability as potential backup timing sources. Existing research lacks sufficient exploration of Pulsar signal animation under astrophysical factors, limiting practical applications. This study establishes a mathematical model based on the rotation dynamics of dual-beam Pulsars and implements dynamic signal visualization through MATLAB. The model dynamically illustrates the relative motion between Pulsar beams and observers via timeline calculations, beam intensity modeling, and rotation matrix derivation. A case study on the millisecond Pulsar J1939+2134 reveals that observer angles influence signal peak timing, while beam widths determine signal duration, highlighting the critical role of parameter calibration for timing accuracy. Open-source code and animation results are publicly shared, providing tools for interdisciplinary research. This study validates the feasibility of Pulsar-based timing in energy systems, offering new insights to enhance synchronization robustness.

Wu, Ori [ORNL] (ORCID:0000000326723410)↗
DOE OSTI2022

Investigating the Origins of Cyclic Variability in Internal Combustion Engines Using Wall-Resolved Large Eddy Simulations

Modern internal combustion engines (ICE) operate at the ragged edge of stable operation characterized by high cycle-to-cycle variations (CCV). A key scientific challenge for ICE is the understanding, modeling, and control of CCV in engine performance, which can contribute to partial burns, misfire, and knock. The objective of this study is to use high-fidelity numerical simulations to improve the understanding of the causes of CCV. Nek5000, a leading high-order spectral element, open source code, is used to simulate the turbulent flow in the engine combustion chamber. Multicycle, wall-resolved large-eddy simulations (LESs) are performed for the General Motors (GM), Transparent Combustion Chamber (TCC-III) optical engine under motored operating conditions. The mean and root-mean-square (rms) of the in-cylinder flow fields at various piston positions are validated using particle image velocimetry (PIV) measurements during the intake and compression strokes. The large-scale flow structures, including the swirl and tumble flow patterns, are analyzed in detail and the causes for cyclic variabilities in these flow features are explained. The energy distribution across the different scales of the flow are quantified using one-dimensional (1D) energy spectra, and the effect of the tumble breakdown process on the energy distribution is examined. Finally, the insights from this study can help us develop improved engine designs with reduced cyclic variabilities in the in-cylinder flow leading to enhanced engine performance.

33 ADVANCED PROPULSION SYSTEMS↗