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At least 235 records · Page 13

Computational tools and algorithms for ion mobility spectrometry-mass spectrometry

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.

59 BASIC BIOLOGICAL SCIENCES↗

MC3

MC3 is a model checking solver that provides a more efficient tool for a widely studied class of problems currently solved by other open-source software tools. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-4549 O

Rawlings, Blake↗

WaterTAP: Tool for analysis of water treatment systems

This presentation describes the Water treatment Technoeconomic Assessment Platform (WaterTAP), an open-source software tool to analyze water treatment trains. The presentation was provided to the NAWI Alliance Fall Meeting on November 29th 2023 and it includes an overview of the tool and a couple of analyses demonstrating its capabilities. The analyses include a technoeconomic assessment of a novel membrane-based technology called low salt rejection reverse osmosis and a brackish water desalination train with pretreatment.

Dudchenko, Alexander↗

LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MOOSE Reactor Module Meshing Enhancements to Support Reactor Physics Analysis

The U.S. Department of Energy Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) program develops an integrated suite of advanced reactor physics tools built upon the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. Each code generally requires an input finite element mesh on which the physics solution is calculated, reported, and transferred to other physics codes. The meshing process is often burdensome for the complex geometries present in reactors due to lack of easy-to-use, open-source meshing tools. To address the bottleneck associated with meshing complex geometries found in nuclear reactors, NEAMS initiated the development of the MOOSE Reactor Module starting in FY21. The Reactor Module builds off the existing MOOSE Mesh System to include targeted meshing capabilities such as the ability to generate hexagonal pin cells, assemblies with ducts, rotating control drums, cores, peripheral zones around a core, as well as the automatic labeling (“reporting IDs”) of pin, assembly, and planar zones to simplify post-processing of results. As a Physics Module in MOOSE, the Reactor Module is open-source, available with any MOOSE installation, directly compatible with MOOSE-based tools, and can be invoked from MOOSEbased applications to generate meshes. Functionality from the Reactor Module has been applied to several advanced reactor concepts to demonstrate user workflow improvements and accuracy. The primary objective of the Reactor Module is to improve useability of MOOSEbased tools by streamlining mesh generation and output inspection processes. During FY22, the functionality of the Reactor Module (and accompanying Mesh System) has been expanded based on user needs. First, the Reactor Geometry Mesh Builder capability developed primarily in FY21 has been refactored and merged to the public MOOSE repository. This capability wraps underlying Reactor Module mesh generators into a “Pin – Assembly – Core” workflow appropriate for conventional Cartesian and hexagonal geometries, and notably assigns material IDs during mesh generation stage and generates only the minimal number of blocks needed in order to reduce computational burden. Biasing and boundary layer options have been added to the base mesh generators as required by thermal hydraulics solvers. The reporting ID functionality has been expanded to differentiate ring-wise and azimuthal sectors within a pin for use with depletion algorithms, and VectorPostProcessor and Reporter objects are now available to integrate solution variables across zones based on ID combinations. Functionality to trim hexagonal meshes along the center or periphery has been developed so users may leverage symmetry and reflective boundary conditions to reduce the mesh size. A flexible and powerful tool to fill the space between two sidesets has been introduced to the framework and can be used for transition layers such as stitching two assemblies together with different numbers of pins, or for complex geometries which do not follow conventional Cartesian/hexagonal patterns. Finally, additional verification problems were performed with NEAMS physics tools in complement with existing NEAMS work.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Simulating Thermoelectric Devices Using the MOOSE Framework

Thermoelectric generators (TEG) are devices that generate energy by converting heat into electricity or provide cooling via the Peltier effect. This feature of thermoelectric devices originates from the Seebeck, Peltier, Thomson, and Joule heating effects. TEGs can be applied in energy and thermal management systems such as waste heat recovery and refrigeration, respectively. Thermoelectric device design is influenced by the material selection and the device's geometry operating conditions. Therefore, predicting, verifying, and validating thermoelectric device performance using simulations tools is essential to deploying thermoelectric devices in industry. The Multiphysics Object-Oriented Simulation Environment (MOOSE) Framework is an open-source simulation tool capable of modeling simple to complex systems. In this work, we demonstrate MOOSE's thermoelectric device modeling capabilities by simulating a unicouple, module, and exhaust gas recovery system. The Seebeck, Peltier, Thomson, and Joule heating physics are implemented into MOOSE. The MOOSE thermoelectric physics were thoroughly verified and validated using published COMSOL® results and experimental data. In addition, thermoelectric modules were integrated into an exhaust gas recovery system using the MOOSE MultiApp function as a demonstration of the model's ability. The verification and validation results and exhaust gas heat recovery system showcases MOOSE's capability to model thermoelectric devices and integrate these devices into practical energy systems.

42 - ENGINEERING↗

NREL's Tools for AgriPV Modeling

As part of the Tools and Apps for Agrivoltaics session, NREL presents their tools that have capabilities for modeling PV and agricultural dual use sites. These include the System Advisor Model (SAM), bifacial_radiance open-source raytracing tool, and a simplified agriPV calculator available in the InSPIRE website.

agriculture↗

A Flang Plugin for Fortran Feature Characterization

As new compute systems are developed, there is still a need to compile and execute codes authored in Fortran on these leading edge systems. In order to achieve this, development of compilers that support the latest hardware is continuously under development. Though the specification of Fortran is extensive, it is helpful to compiler authors to be able to prioritize the development of key features in order to get certain codes deemed important, e.g., applications of interest to leadership computing facilities, executable on leading edge compute systems. Identifying key features though is largely done through querying software experts or users of the Fortran applications of interest, who then manually report what features are and are not present. This exercise can both time consuming and error prone. To automate this process, we present a compiler plugin to Flang, the Fortran frontend for LLVM. This plugin is a tool that operates on the parse tree representation generated by Flang and detects key features based on walking parse tree nodes that correspond to features of interest. We show the result of our tool on four applications, three of which were manually profiled by software experts. We show the discrepancies between our tool and the manual characterization of the three applications, as well as generate a characterization for an application not yet profiled. We intend to open-source our tool in order to invite the community to benefit from the tool and make contributions for other features.

Cabrera, Anthony [ORNL]↗

Wind Turbine Airfoil Design Tools

SAND2025-11738O Wind Turbine Airfoil Design Tools is a software tool that connects existing open-source airfoil analysis tools with optimization software to produce modern airfoil design for wind turbine applications. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Maniaci, David↗

Using Facebook to Recruit Urban Participants for Smartphone-Based Travel Surveys

Social media has become an integral part of everyday life for many individuals, serving as a platform to express opinions, share memories and lifestyles, follow news, and adapt to social trends and norms. The wealth of user information and analytics on these platforms has facilitated the development and sale of tailored products and services, benefiting advertisers and researchers seeking survey participants. Social media advertising has demonstrated its effectiveness in reaching hard-to-reach populations. However, transport researchers have yet to capitalise on this potential fully. This paper presents our experience using social media to recruit participants for two smartphone travel surveys conducted in Australia. We demonstrate that social media recruitment and smartphone-based travel surveys are highly effective, adaptable, and can be rapidly deployed in response to research opportunities, such as during the early phase of the COVID-19 pandemic when traditional methods may be less suitable. This approach also holds great potential for travel surveys targeting the general population. This paper shares several lessons from this experiment, including our administrative approach and detailed technical instructions to utilise open-source software tools for conducting smartphone travel surveys like ours. This approach significantly reduces study costs compared to most commercial solutions.

97 MATHEMATICS AND COMPUTING↗

NASA's Aviary Takes Flight: A Public Software for Aircraft Design

Aviary, developed by NASA, is an open-source software tool for modeling and optimizing traditional and next-generation aircraft designs. It modernizes legacy design tools and integrates disciplines together more tightly to evaluate new vehicles, like X-66, open-rotor electric aircraft, and blended wing body. Aviary has the potential to revolutionize aircraft analysis by leveraging the complex interactions between disciplines to make aircraft conceptual designs more efficient.

Carl Recine↗

Development of Waypoint Planning Tool in Response to NASA Field Campaign Challenges

Airborne real time observations are a major component of NASA 's Earth Science research and satellite ground validation studies. Multiple aircraft are involved in most NASA field campaigns. The coordination of the aircraft with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. Planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. A flight planning tools is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama ]Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point -and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin on web platform, and to the rising open source GIS tools with New Java Script frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientist reach their mission objectives.

He, Matt↗

Development of Waypoint Planning Tool in Response to NASA Field Campaign Challenges

Airborne real time observations are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientists, planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircrafts are often involved in NASA field campaigns. The coordination of the aircrafts with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama-Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point -and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin and Java Web Start/Applet on web platform, and to the rising open source GIS tools with new JavaScript frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. The newly innovated, cross ]platform, modular designed JavaScript ]controlled Way Point Tool is planned to be integrated with NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientists reach their mission objectives. This presentation will discuss the development processes of the Waypoint Planning Tool in responding to field campaign challenges, identify new information technologies, and describe the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

He, Matt↗

OPET Hardware (Open PV Electrical Tool Hardware) [SWR-25-42]

OPET (Open-source Photovoltaic Electrical Tool) is used for performance measurements of solar photovoltaic (PV) devices in the field under natural sunlight or in the lab under artificial light. Its primary use is in research and development of solar cells and modules, specifically in reliability and durability research of PV devices. Some features and functions include: -IV curve measurements with linear or cosine distributed measurement points -PV device active loading at open circuit voltage (Voc), short circuit current (Isc) and maximum power point (Pmp) -Bias power supply to overcome series resistance in contact wires for Isc measurements and loading -PV voltage input in five ranges from 1V to 100V -PV current input ranges -Low current version, six current ranges from 1.1mA to 340mA -High current version, six current ranges from 50mA to 15A -IO ports for I2C and SPI temperature sensor Arduino extension boards -Integrated fan control This repository contains everything relating to the hardware of the OPET device. If you are looking for the firmware or software repositories, links are below: https://github.com/NREL/opet-firmware https://github.com/NREL/opet-control

McDanold, Byron [National Renewable Energy Laborat↗

The Way Point Planning Tool: Real Time Flight Planning for Airborne Science

Airborne real time observation are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientist, planning a research aircraft mission within the context of meeting the science objective is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircraft are often involved in the NASA field campaigns the coordination of the aircraft with satellite overpasses, other airplanes and the constantly evolving dynamic weather conditions often determine the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientist and help them plan and modify the flight tracks successfully. Scientists at the University of Alabama Huntsville and the NASA Marshal Space Flight Center developed the Waypoint Planning Tool (WPT), an interactive software tool that enables scientist to develop their own flight plans (also known as waypoints), with point and click mouse capabilities on a digital map filled with time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analyses during and after each campaign helped identify both issues and new requirements, initiating the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities to the Google Earth Plugin and Java Web Start/Applet on web platform, as well as to the rising open source GIS tools with new JavaScript frameworks, the Waypoint planning Tool has entered its third phase of technology advancement. The newly innovated, cross-platform, modular designed JavaScript-controled Waypoint tool is planned to be integrated with the NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientist reach their mission objectives. This presentation will discuss the development process of the Waypoint Planning Tool in responding to field campaign challenges, identifying new information technologies, and describing the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

He, Yubin↗

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↗

The Origins of the ParaView and VisIt Scientific Visualization Tools

ParaView and VisIt play a key role in the visual understanding of scientific simulation data. These tools are open source, designed to handle extremely large datasets, and can run on supercomputers and large-scale display walls. They are in daily use by scientists, practitioners, and students at supercomputing centers, in industry, and at universities. In conclusion, this article gives personal accounts of the origins of these visualization tools.

Ahrens, James [Los Alamos National Laboratory (LAN↗

Floating Wind Array Ontology and Modeling Framework

While there are many tools for designing and modeling a single floating turbine, array level design and modeling has much more to consider. Designing floating wind arrays requires a coupled approach considering many variables, from bathymetry to installation and maintenance to failure and risk analysis. With all of these considerations, an array-level modeling tool is needed to quickly evaluate array designs. The Floating Array Model (FAModel) tool developed at the National Renewable Energy Laboratory was created to fill this gap in low-fidelity array modeling. FAModel is a python framework created to streamline holistic low-fidelity floating wind modeling for array-level analysis. FAModel integrates site data and models with a variety of open-source modeling tools developed by NREL, including FLORIS, RAFT, MoorPy, and anchor capacity models. The integration of these tools allows users to quickly and holistically design an array by considering forces, area analysis, visualization, annual energy production, failure modeling, and component costs.

17 WIND ENERGY↗