Search NASA⌕ Search

SEARCH · Search NASA

Results for “graphic user interface”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18

INSPIRED: Inelastic neutron scattering prediction for instantaneous results and experimental design

Inelastic neutron scattering (INS) has unique advantages in probing how atoms vibrate and how the vibrations propagate and interact. Such dynamic information is crucial in understanding various material properties, from heat capacity, thermal conductivity, phase transitions, and chemical reactions to more exotic quantum behavior. The analysis and interpretation of the INS spectra often start from a model structure of the sample, followed by a series of calculations to obtain the simulated spectra to compare with experiments. The conventional way to perform such calculations usually requires significant time, computing resources, and specialized expertise. Here, we present a new program named INSPIRED (Inelastic Neutron Scattering Prediction for Instantaneous Results and Experimental Design), which enables users to perform rapid INS simulations in several different ways on their personal computers in just a few clicks, with the crystal structure as the only input file. Specifically, the users can choose a pre-trained symmetry-aware neural network (coupled with an autoencoder) to predict the phonon density of states (DOS), 1D S(E) and 2D S(|Q|,E) spectra for any given structure. One can also choose an existing density functional theory (DFT) calculation from a database (containing over 12,000 crystals), and quickly obtain the simulated INS spectra for single crystals and powders. It is also possible to use pre-trained universal machine learning force fields to relax a given crystal structure, calculate the phonon dispersion and DOS, and, subsequently, the INS spectra. All these functions are implemented with a PyQt graphic user interface. Finally, we expect these new tools will benefit broad user communities and significantly improve the efficiency of experiment design, execution, and data analysis for INS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗

A Review of the Lawrence Livermore Nuclear Accident Dosimeter 1980s-present

A Nuclear Accident Dosimetry program is a federal requirement for all facilities that have the potential to have a criticality accident. Personnel Nuclear Accident Dosimeter (PNAD) theory and analytical procedures are driven by various scientific needs and interacting regulations. A brief history of the status of USA Department of Energy (DOE) nuclear accident dosimetry regulations, recommendations, and performance testing criteria are given. Then, the history of the Lawrence Livermore National Laboratory (LLNL) PNAD is explored, including changes in the physical dosimeter and adjustments of the analysis method through the last four decades. Finally, the performance of LLNL’s PNAD at criticality accident intercomparison training exercises since 2009 is explored. In general, reported neutron doses have been within or close to DOE-STD-1098 performance criteria while reported gamma doses have been outside of DOE-STD-1098 performance criteria. Reported total absorbed doses have varied in meeting ANSI/HPS N13.3 and ANSI/HPS N13.3 (R2019) performance criteria. Dosimetry staff retirement and turnover have left historical knowledge gaps, yet provided opportunities within the NAD program at LLNL. This review paper serves as an overview of the history and status of the NAD program. Brief technical, procedural and programmatic recommendations to improve LLNL’s NAD program are given. Technical recommendations include investigating orientation factors through modeling or empirical experimentation, investigating gamma dosimetry methods for high-dose scenarios, and exploring other dosimetric methods for simpler, quicker NAD analysis. Procedural recommendations include better documentation of conversion factor (activity-to-fluence and fluence-to-dose) derivations and spectrum uses, and updated analysis spreadsheets or simple Graphic User Interfaces for dose calculations. In conclusion, programmatic recommendations include formalized training for NAD analysts, and having multiple SMEs trained on the NAD program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

CDB-AP: An application for coincidence Doppler broadening spectroscopy analysis

Coincidence Doppler Broadening (CDB) Positron Annihilation Spectroscopy (PAS) is a material analysis technique that can be used to non-destructively measure characteristics of structural defects in samples. Analyzing and comparing large datasets obtained using this technique, however, can be complicated and time intensive. The Coincidence Doppler Broadening Analysis Program (CDB-AP) is a graphical user interface that facilitates rapid analysis of many data files while using transparent processes. It is already used in three laboratories at Idaho National Laboratory and can be used in laboratories worldwide.

36 MATERIALS SCIENCE↗

Process design tools and techno-economic analysis for capacitive deionization

Capacitive deionization (CDI) devices use cyclical electrosorption on porous electrode surfaces to achieve water desalination. Process modeling and design of CDI systems requires accurate treatment of the coupling among input electrical forcing, input flow rates, and system responses including salt removal dynamics, water recovery, energy storage, and dissipation. Techno-economic analyses of CDI further require a method to calculate and compare between a produced commodity (e.g. desalted water) versus capital and operational costs of the system. In this work, we demonstrate a new modeling and analysis tool for CDI developed as an installable Matlab program that allows direct numerical simulation of CDI dynamics and calculation of key performance and cost parameters. The program is provided for free and is used to run open-source Simulink models. The Simulink environment sends information to the program and allows for a drag and drop design space where users can connect CDI cells to relevant periphery blocks such as grid energy, battery, solar panel, waste disposal, and maintenance/labor cost streams. The program allows for simulation of arbitrary current forcing and arbitrary flow rate forcing of one or more CDI cells. We employ validated well-mixed reactor formulations together with a non-linear circuit model formulation that can accommodate a variety of electric double layer sub-models (e.g. for charge efficiency). The program includes a graphical user interface (GUI) to specify CDI plant parameters, specify operating conditions, run individual tests or parameter batch-mode simulations, and plot relevant results. The techno-economic models convert among dimensional streams of species (e.g. feed, desalted water, and brine), energy, and cost and enable a variety of economic estimates including levelized water costs.

42 ENGINEERING↗

CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems

Membrane mimetics, such as detergent micelles, nanodiscs, and amphipol complexes, which can provide membrane-like environments while retaining small and soluble features, have been utilized to study membrane proteins. A bicelle, composed of varying lipids and detergents, is a useful membrane mimetic because the lipid-to-detergent ratio, the q-value, can be adjusted to alter the properties of the aggregate, including the thickness and size of the bicelle. However, building a bicelle model for modeling and simulation studies requires nontrivial efforts, even for experts. We introduce CHARMM-GUI Bicelle Builder, a web-based platform that can generate various all-atom bicelle systems via a graphical user interface with all available lipids and detergents in Membrane Builder. To illustrate and validate Bicelle Builder with practical systems, we have modeled and simulated pure bicelles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids with 1,2-dihexanoyl-sn-glycero-3-phosphocholine (C6DHPC) detergents and protein–bicelle complexes, composed of DMPC with C6DHPC, foscholine-10 (FOS10), and lysophosphatidylcholine-12 (LPC12) detergents. Our simulation results indicate that Bicelle Builder can generate reliable and robust bicelle models with and without proteins that retain DMPC bilayer characteristics. Bicelle Builder is expected to help researchers better understand not only bicelles themselves but also atomistic-level structures of protein–bicelle complexes that are often difficult to access through experimental approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗

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↗

SimELIT: A Novel GUI-Based Comprehensive Ion Trajectory Simulation Software for Mass Spectrometry

Ion trajectory simulation in mass spectrometry systems from injection to detection is technically challenging but very important for better understanding the ion dynamics in instrument development. Here, in this work, we present SimELIT (Simulator of Eulerian and Lagrangian Ion Trajectories), a novel ion trajectory simulation platform. SimELIT is built upon a suite of multiphysics solvers compiled into OpenFOAM (an open-source numerical solver library particularly used for computational mechanics), with a simple web-based graphical user interface (GUI) allowing users to define the details of OpenFOAM cases and run simulations. SimELIT is a modular program and can provide extensions of physics (e.g., gas flows, electrodynamic fields) and thus enable ion trajectory simulations from the ion source to detector. The current version (SimELIT) provides two numerical solvers for ion trajectory simulations–(1) a Lagrangian particle tracker in vacuum and (2) a Eulerian ion density solver in background gas in the presence of electric fields. Here, we describe the architecture of SimELIT, including its use of Docker and the React Framework, and demonstrate the computation of ion trajectories of multiple m/z values in a static/linear voltage drop in vacuum (across a 1 m long flight tube). Further, the drift motion of ions under 1 Torr pressure conditions in a static background (N 2 ) gas through a 20 V/cm static electric field is shown. The results produced from SimELIT were compared with SIMION and theoretical estimates. In addition, we report the computation of ion trajectories in electrodynamic fields within a planar FAIMS device operating at atmospheric pressure.

97 MATHEMATICS AND COMPUTING↗

Neutral Loss Mass Spectral Data Enhances Molecular Similarity Analysis in $\mathrm{METLIN}$

We report Neutral loss (NL) spectral data presents a mirror of MS 2 data and is a valuable yet largely untapped resource for molecular discovery and similarity analysis. Tandem mass spectrometry (MS 2 ) data is effective for the identification of known molecules and the putative identification of novel, previously uncharacterized molecules (unknowns). Yet, MS 2 data alone is limited in characterizing structurally related molecules. To facilitate unknown identification and complement the METLIN-MS 2 fragment ion database for characterizing structurally related molecules, we have created a MS 2 to NL converter as a part of the METLIN platform. The converter has been used to transform METLIN’s MS 2 data into a neutral loss database (METLIN-NL) on over 860 000 individual molecular standards. The platform includes both the MS 2 to NL converter and a graphical user interface enabling comparative analyses between MS 2 and NL data. Examples of NL spectral data are shown with oxylipin analogues and two structurally related statin molecules to demonstrate NL spectra and their ability to help characterize structural similarity. Mirroring MS 2 data to generate NL spectral data offers a unique dimension for chemical and metabolite structure characterization.

59 BASIC BIOLOGICAL SCIENCES↗

BioRT‐HBV 1.0: A Biogeochemical Reactive Transport Model at the Watershed Scale

Abstract Reactive Transport Models (RTMs) are essential tools for understanding and predicting intertwined ecohydrological and biogeochemical processes on land and in rivers. While traditional RTMs have focused primarily on subsurface processes, recent watershed‐scale RTMs have integrated ecohydrological and biogeochemical interactions between surface and subsurface. These emergent, watershed‐scale RTMs are often spatially explicit and require extensive data, computational power, and computational expertise. There is however a pressing need to create parsimonious models that require minimal data and are accessible to scientists with limited computational background. To that end, we have developed BioRT‐HBV 1.0, a watershed‐scale, hydro‐biogeochemical RTM that builds upon the widely used, bucket‐type HBV model known for its simplicity and minimal data requirements. BioRT‐HBV uses the conceptual structure and hydrology output of HBV to simulate processes including advective solute transport and biogeochemical reactions that depend on reaction thermodynamics and kinetics. These reactions include, for example, chemical weathering, soil respiration, and nutrient transformation. The model uses time series of weather (air temperature, precipitation, and potential evapotranspiration) and initial biogeochemical conditions of subsurface water, soils, and rocks as input, and output times series of reaction rates and solute concentrations in subsurface waters and rivers. This paper presents the model structure and governing equations and demonstrates its utility with examples simulating carbon and nitrogen processes in a headwater catchment. As shown in the examples, BioRT‐HBV can be used to illuminate the dynamics of biogeochemical reactions in the invisible, arduous‐to‐measure subsurface, and their influence on the observed stream or river chemistry and solute export. With its parsimonious structure and easy‐to‐use graphical user interface, BioRT‐HBV can be a useful research tool for users without in‐depth computational training. It can additionally serve as an educational tool that promotes pollination of ideas across disciplines and foster a diverse, equal, and inclusive user community.

Sadayappan, Kayalvizhi↗

Real-time 3D analysis during electron tomography using tomviz

The demand for high-throughput electron tomography is rapidly increasing in biological and material sciences. However, this 3D imaging technique is computationally bottlenecked by alignment and reconstruction which runs from hours to days. We demonstrate real-time tomography with dynamic 3D tomographic visualization to enable rapid interpretation of specimen structure immediately as data is collected on an electron microscope. Using geometrically complex chiral nanoparticles, we show volumetric interpretation can begin in less than 10 minutes and a high-quality tomogram is available within 30 minutes. Real-time tomography is integrated into tomviz, an open-source and cross-platform 3D data analysis tool that contains intuitive graphical user interfaces (GUI), to enable any scientist to characterize biological and material structure in 3D.

36 MATERIALS SCIENCE↗

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

A database of battery materials auto-generated using ChemDataExtractor

A database of battery materials is presented which comprises a total of 292,313 data records, with 214,617 unique chemical-property data relations between 17,354 unique chemicals and up to five material properties: capacity, voltage, conductivity, Coulombic efficiency and energy. 117,403 data are multivariate on a property where it is the dependent variable in part of a data series. The database was auto-generated by mining text from 229,061 academic papers using the chemistry-aware natural language processing toolkit, ChemDataExtractor version 1.5, which was modified for the specific domain of batteries. The collected data can be used as a representative overview of battery material information that is contained within text of scientific papers. Public availability of these data will also enable battery materials design and prediction via data-science methods. To the best of our knowledge, this is the first auto-generated database of battery materials extracted from a relatively large number of scientific papers. We also provide a Graphical User Interface (GUI) to aid the use of this database.

25 ENERGY STORAGE↗

TEMImageNet training library and AtomSegNet deep-learning models for high-precision atom segmentation, localization, denoising, and deblurring of atomic-resolution images

Abstract Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional algorithms, such has thresholding, edge detection and clustering, can achieve reasonable performance in some predefined sceneries, they tend to fail when interferences from the background are strong and unpredictable. Particularly, for atomic-resolution STEM images, so far there is no well-established algorithm that is robust enough to segment or detect all atomic columns when there is large thickness variation in a recorded image. Herein, we report the development of a training library and a deep learning method that can perform robust and precise atom segmentation, localization, denoising, and super-resolution processing of experimental images. Despite using simulated images as training datasets, the deep-learning model can self-adapt to experimental STEM images and shows outstanding performance in atom detection and localization in challenging contrast conditions and the precision consistently outperforms the state-of-the-art two-dimensional Gaussian fit method. Taking a step further, we have deployed our deep-learning models to a desktop app with a graphical user interface and the app is free and open-source. We have also built a TEM ImageNet project website for easy browsing and downloading of the training data.

25 ENERGY STORAGE↗

Resolving experimental biases in the interpretation of diffusion experiments with a user-friendly numerical reactive transport approach

The reactive transport code CrunchClay was used to derive effective diffusion coefficients (D e ), clay porosities (ε), and adsorption distribution coefficients (K D ) from through-diffusion data while considering accurately the influence of unavoidable experimental biases on the estimation of these diffusion parameters. These effects include the presence of filters holding the solid sample in place, the variations in concentration gradients across the diffusion cell due to sampling events, the impact of tubing/dead volumes on the estimation of diffusive fluxes and sample porosity, and the effects of O-ring-filter setups on the delivery of solutions to the clay packing. Doing so, the direct modeling of the measurements of (radio)tracer concentrations in reservoirs is more accurate than that of data converted directly into diffusive fluxes. While the above-mentioned effects have already been described individually in the literature, a consistent modeling approach addressing all these issues at the same time has never been described nor made easily available to the community. A graphical user interface, CrunchEase, was created, which supports the user by automating the creation of input files, the running of simulations, and the extraction and comparison of data and simulation results. While a classical model considering an effective diffusion coefficient, a porosity and a solid/solution distribution coefficient (D e –ε–K D ) may be implemented in any reactive transport code, the development of CrunchEase makes it easy to apply by experimentalists without a background in reactive transport modeling. CrunchEase makes it also possible to transition more easily from a D e –ε–K D modeling approach to a state-of-the-art process-based understanding modeling approach using the full capabilities of CrunchClay, which include surface complexation modeling and a multi-porosity description of the clay packing with charged diffuse layers.

58 GEOSCIENCES↗

A field programmable gate array-based timing and control system for the dynamic compression sector

A field programmable gate array (FPGA)-based timing and trigger control system has been developed for the Dynamic Compression Sector (DCS) user facility located at the Advanced Photon Source (APS) at Argonne National Laboratory. The DCS is a first-of-its-kind capability dedicated to dynamic compression science. All components of the DCS laser shock station—x-ray choppers, single-shot shutter, internal laser triggers, and shot diagnostics—must be synchronized with respect to the arrival of x rays in the hutch. An FPGA synchronized to the APS storage ring radio frequency clock (352 MHz) generates trigger signals for each stage of the laser and x-ray shutter system with low jitter. The developed FPGA-based control system was the first system used to control the laser and the shutter system since its commissioning, and it has been developing since then to improve the timing jitter. The system is composed of a Zynq FPGA, a debug card, line drivers, and a power supply. The delay and offsets of the trigger signals can be adjusted by using a user-friendly graphical user interface with high precision. Here, the details of the system architecture, timing requirements, firmware, and software implementation along with the performance evaluation are presented in this paper. The system offers low timing jitter (15.5 ps rms) with respect to the APS 352 MHz clock, suitable for the 100 ps (FWHM) x-ray bunch duration at the APS.

47 OTHER INSTRUMENTATION↗

An automated fast neutron computed tomography instrument with on-line focusing for non-destructive evaluation

A fast neutron tomography imaging instrument has been designed, built, and tested at The Ohio State University 500 kW Research Reactor on a fast neutron beamline with a peak neutron flux ≈5.4 × 107 n·cm−2·s−1 at 1.6 MeV median neutron energy. The instrument and beamline are also configurable for thermal neutron imaging. The imaging apparatus is composed of a lens coupled, water-cooled Electron Multiplying Charge Coupled Device camera, a front-surface mirror, and a high light yield plastic Polyvinyl toluene scintillator. The instrument sits on a mobile cart. A total of 5 motion-control stages are built into the system for XYZ and rotational degrees of freedom for sample positioning; the fifth stage fine tunes the focal distance between the camera and the scintillator to achieve on-line focusing. A Python code with a user-friendly graphical user interface controls the fully automated image acquisition, not requiring user interaction, yet facilitating tracking of the image acquisition. A complete fast neutron computed tomography dataset with 360 projections requires less than 3 h, with 30 s per projection. On-line focusing is accomplished with a commercial, off-the-shelf, dielectrically actuated liquid lens. Finally, tomographic reconstructions are visualized using the Livermore Tomography Tools software package. The effective pixel size (width and height) is ≈0.1058 mm, yielding a minimum voxel size of 0.1058 × 0.1058 × 0.1058 mm3, and produces a spatial resolution of 231 μm when calculated from knife-edge measurements.

Bisbee, M. G. (ORCID:0000000313466697)↗