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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Optimal Efficiency and Operational Cost Savings: A Framework for Automated Rooftop PV Placement

Residential energy consumers are charged based on a utility rate structure, such as net metering or feed-in tariff. To lower consumers' electricity bills, expensive batteries are deployed to reduce the electricity fed from the grid during peak hours. However, strategic photovoltaic (PV) panel placement enables the reduction of operational energy cost while considering the spatial feasibility and efficiency for hosting rooftop PV. In this paper, we present a framework to automatically identify the optimal location of rooftop PV panels on residential buildings. Our framework integrates multiple workflows, including energy and environmental simulation, parametric modeling, and optimization to identify the ideal location of PV panels to balance the demand and supply at a building and community scale. These workflows are linked using the Grasshopper plug-in for Rhinoceros CAD software. The framework includes two different workflows, each satisfying a target for optimal PV placement: (a) maximizing PV panel efficiency, where users aim to maximize energy generation, and (b) minimizing operational energy cost, where "best'' panels are selected considering utility rates for operational energy cost. Our framework is demonstrated in a residential community in Fort Collins, Colorado, to generate the optimal PV placement for each of the two aforementioned targets. Results from the two workflows are compared to illustrate the effect of PV location and orientation on solar energy production efficiency and operational energy cost. The developed workflows are introduced as tools within the Grasshopper plug-in to investigate the solar potential of rooftop PV panels while taking into account factors such as contextual shading, utility rate structures, and buildings' energy demand profiles.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Micromobility Integrated Transit and Infrastructure for Efficiency (MITIE)

Nearly omnipresent in many cities of all sizes across the United States, micromobility vehicles-e-scooters, manual bicycles, e-bicycles, and larger seated electric scooters-are notably missing from SMART Mobility research. This project aims to expand the spectrum of modes currently being researched within SMART Mobility by exploring micromobility as an important tool toward meeting energy-efficient mobility goals. It expands on findings from SMART Mobility 1.0 that revealed preferences to reduce transportation-related expenses through use of a network of mobility-as-a-service (MaaS) and other shared mobility options, and builds on findings from a 2019 Vehicle Technology Analysis Program (VTAP) funded micromobility project conducted by our team. We will explore multiple facets of micromobility, including behavior and decision-making, the integration of micromobility within transportation infrastructure, energy estimates, and operations. Guiding research questions include: (1) What are the potential energy savings from low, medium, and high market penetration of micromobility (in passenger, multimodal, and freight domains)? (2) Which scenarios for micromobility use and related enablement of increased public transit use should be modeled/considered in the SMART 2.0 Workflow? (3) To what degree can micromobility supplement/complement transit system operations? (4) What are people's preferences towards micromobility? How do preferences vary across various sociodemographic segments? How can this knowledge inform operations? (5) What are optimal strategies to attain high user adoption and shift users toward more energy-efficient mode choices in terms of micromobility operation? How do these strategies affect energy savings, person-miles traveled, lifecycle energy use, and adoption rates? These questions will be addressed through applied research in five project emphasis areas: (1) Energy estimates of micromobility for Workflow scenarios: Expand and refine previous micromobility work to augment the Workflow approaches to modeling urban travel. (2) Multimodal connection with transit: Utilizing Mobility-Energy Productivity (MEP) tools to evaluate multimodal travel patterns enabled by micromobility, including assessing how to reduce barriers of inequity of access to mobility options and destinations. (3) Mode choice, induced demand, and infrastructure: Understanding the mode shift induced through micromobility to inform energy impact analysis. (4) Energy optimization of micromobility operations: Identification of micromobility operations parameters and development of operations scenarios to better understand present-day micromobility operations for integration into the Workflow, in partnership with BEAM and POLARIS modeling teams. (5) Micro-freight: Characterize the current state of micro-freight activities, including energy effects and geospatial analyses, to inform Workflow.

ADVANCED PROPULSION SYSTEMS,POWER TRANSMISSION AND↗
DOE OSTI2023

Micromobility Integrated Transit and Infrastructure for Efficiency (MITIE)

Nearly omnipresent in many cities of all sizes across the United States, micromobility vehicles-e-scooters, manual bicycles, e-bicycles, and larger seated electric scooters-are notably missing from SMART Mobility research. This project aims to expand the spectrum of modes currently being researched within SMART Mobility by exploring micromobility as an important tool toward meeting energy-efficient mobility goals. It expands on findings from SMART Mobility 1.0 that revealed preferences to reduce transportation-related expenses through use of a network of mobility-as-a-service (MaaS) and other shared mobility options, and builds on findings from a 2019 Vehicle Technology Analysis Program (VTAP) funded micromobility project conducted by our team. We will explore multiple facets of micromobility, including behavior and decision-making, the integration of micromobility within transportation infrastructure, energy estimates, and operations. Guiding research questions include: 1) what are the potential energy savings from low, medium, and high market penetration of micromobility (in passenger, multimodal, and freight domains)? 2) which scenarios for micromobility use and related enablement of increased public transit use should be modeled/considered in the SMART 2.0 Workflow? 3) to what degree can micromobility supplement/complement transit system operations? 4) what are people's preferences towards micromobility? How do preferences vary across various sociodemographic segments? How can this knowledge inform operations? 5) what are optimal strategies to attain high user adoption and shift users toward more energy-efficient mode choices in terms of micromobility operation? How do these strategies affect energy savings, person-miles traveled, lifecycle energy use, and adoption rates? These questions will be addressed through applied research in five project emphasis areas: 1) energy estimates of micromobility for Workflow scenarios: Expand and refine previous micromobility work to augment the Workflow approaches to modeling urban travel; 2) multimodal connection with transit: Utilizing Mobility-Energy Productivity (MEP) tools to evaluate multimodal travel patterns enabled by micromobility, including assessing how to reduce barriers of inequity of access to mobility options and destinations; 3) mode choice, induced demand, and infrastructure: Understanding the mode shift induced through micromobility to inform energy impact analysis; 4) energy optimization of micromobility operations: Identification of micromobility operations parameters and development of operations scenarios to better understand present-day micromobility operations for integration into the Workflow, in partnership with BEAM and POLARIS modeling teams; 5) micro-freight: Characterize the current state of micro-freight activities, including energy effects and geospatial analyses, to inform Workflow.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2024

Enabling the broader adoption of fusion simulation on complex geometry

This project addressed a key barrier to advanced fusion and nuclear simulation: the difficulty of performing high-fidelity Monte Carlo neutronics directly on complex, real-world CAD geometry. Traditional workflows require engineers to rebuild CAD models as simplified constructive solid geometry, a time-consuming and error-prone process that limits design iteration and broader adoption of simulation tools. The goal of this Phase I SBIR was to make CAD-based neutronics practical, accessible, and robust for industrial and research users. During the project, Coreform significantly enhanced the Direct Accelerated Geometry Monte Carlo (DAGMC) workflow and fully integrated it into Coreform Cubit as a first-class capability. Major achievements include optimized material assignment and surface meshing workflows, substantial performance improvements to geometry imprinting and preparation, native export of DAGMC models, and new visualization tools to support OpenMC source definition and lost-particle debugging. Coreform also expanded Cubit’s capabilities as a full OpenMC preprocessor, including the ability to convert OpenMC constructive solid geometry models back into CAD for visualization, multiphysics coupling, and debugging. In collaboration with Argonne National Laboratory, the project delivered comprehensive new DAGMC documentation and training materials, transforming DAGMC from a research-oriented tool into a production-ready workflow. Results were disseminated through tutorials, conference training, and multiple well-attended webinars demonstrating integrated CAD-based neutronics and multiphysics workflows. Overall, this project demonstrated that high-fidelity Monte Carlo simulations can be performed directly on complex CAD geometry, reducing setup time, improving usability, and enabling faster, more informed design decisions for fusion and nuclear energy systems.

42 ENGINEERING↗
DOE OSTI2024

GDSA framework, a computational framework for complex modeling problems in radioactive waste management

This paper details a computational framework to produce automated, graphical workflows, and how this framework can be deployed to support complex modeling problems like those in nuclear engineering. Key benefits of the framework include: automating previously manual workflows; intuitive construction and communication of workflows through a graphical interface; and automated file transfer and handling for workflows deployed across heterogeneous computing resources. This paper demonstrates the framework's application to probabilistic post-closure performance assessment of systems for deep geologic disposal of nuclear waste. However, the framework is a general capability that can help users running a variety of computational studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Enabling machine learning-ready HPC ensembles with Merlin

With the growing complexity of computational and experimental facilities, many scientific researchers are turning to machine learning (ML) techniques to analyze large scale ensemble data. With complexities such as multi-component workflows, heterogeneous machine architectures, parallel file systems, and batch scheduling, care must be taken to facilitate this analysis in a high performance computing (HPC) environment. Here, we present Merlin, a workflow framework to enable large ML-friendly ensembles of scientific HPC simulations. By augmenting traditional HPC with distributed compute technologies, Merlin aims to lower the barrier for scientific subject matter experts to incorporate ML into their analysis. As a producer–consumer workflow model, Merlin enables multi-machine, cross-batch job, dynamically allocated yet persistent workflows capable of utilizing surge-compute resources. Key features of Merlin are a flexible HPC-centric interface, low per-task overhead, multi-tiered fault recovery, and a hierarchical sampling algorithm that allows for $\mathscr{O}$(N) task execution and $\mathscr{O}$(N ln N) task queuing to ensembles of millions of tasks. In addition to Merlin’s design, we test the algorithm’s performance in an HPC center and demonstrate the ability to enqueue 40 million simulations in 100 s, with a 30 millisecond per-task overhead that is independent of ensemble size. Finally, we describe some example applications that Merlin has enabled on leadership-class HPC resources, such as the ML-augmented optimization of nuclear fusion experiments and the calibration of infectious disease models to study the progression of and possible mitigation strategies for COVID-19.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The Exascale Framework for High Fidelity coupled Simulations (EFFIS): Enabling whole device modeling in fusion science

We present the Exascale Framework for High Fidelity coupled Simulations (EFFIS), a workflow and code coupling framework developed as part of the Whole Device Modeling Application (WDMApp) in the Exascale Computing Project. EFFIS consists of a library, command line utilities, and a collection of run-time daemons. Together, these software products enable users to easily compose and execute workflows that include: strong or weak coupling, in situ (or offline) analysis/visualization/monitoring, command-and-control actions, remote dashboard integration, and more. We describe WDMApp physics coupling cases and computer science requirements that motivate the design of the EFFIS framework. Furthermore, we explain the essential enabling technology that EFFIS leverages: ADIOS for performant data movement, PerfStubs/TAU for performance monitoring, and an advanced COUPLER for transforming coupling data from its native format to the representation needed by another application. Finally, we demonstrate EFFIS using coupled multi-simulation WDMApp workflows and exemplify how the framework supports the project’s needs. We show that EFFIS and its associated services for data movement, visualization, and performance collection does not introduce appreciable overhead to the WDMApp workflow and that the resource-dominant application’s idle time while waiting for data is minimal.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

AToM: Advanced Tokamak Modeling Environment

Stability constraints play an important role in integrated modeling. The global plasma stability and macro-instabilities such as internal kink modes, neoclassical tearing modes, and edge localized perturbations limit the plasma performance and can result in large-scale transient events and plasma disruptions. These macro-instabilities can be also beneficial to the plasma performance. For example, the peeling models often lead to the edge localized modes (ELMs). However, the formation of stationary edge harmonic oscillations (EHOs) due to nonlinear interaction of peeling modes can result in a transition to the Quiescent H-mode (QH-mode) without ELMs. The profiles predicted with transport models need to be refined using the MHD stability constraints. This is important especially for transient and nonlinear stages of discharges such as ramp-up access to hybrid and steady state operation, and L- to H-mode transition as well as transition to the QH-mode. Several stability and MHD codes are already included in the OMFIT framework. These codes include BALOO, ELITE, GATO, M3DC1, MARS, and NIMROD. However, the verifications of stability constraints are currently mostly excluded from transport modeling workflows. The only exception is the EPED module which includes the ELITE predictions to limit the pedestal height. Here, we improved the OMFIT workflow to include stability calculations. Including the stability conditions to the integrated modeling workflow improved the robustness of the predictive modeling discharges. Being implemented in the workflow, the stability conditions can be also used for the stability analysis of experimental data. This improved the physics understanding of various discharge scenarios and can be used in experiment planning.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

$\mathrm{RADICAL}$-Pilot and $\mathrm{PMIx}$/$\mathrm{PRRTE}$: Executing Heterogeneous Workloads at Large Scale on Partitioned $\mathrm{HPC}$ Resources

Execution of heterogeneous workflows on high-performance computing (HPC) platforms present unprecedented resource management and execution coordination challenges for runtime systems. Task heterogeneity increases the complexity of resource and execution management, limiting the scalability and efficiency of workflow execution. Re-source partitioning and distribution of tasks execution over portioned re-sources promises to address those problems but we lack an experimental evaluation of its performance at scale. Here this paper provides a performance evaluation of the Process Management Interface for Exascale (PMIx) and its reference implementation PRRTE on the leadership-class HPC plat-form Summit, when integrated into a pilot-based runtime system called RADICAL-Pilot. We partition resources across multiple PRRTE Distributed Virtual Machine (DVM) environments, responsible for launching tasks via the PMIx interface. We experimentally measure the work-load execution performance in terms of task scheduling/launching rate and distribution of DVM task placement times, DVM startup and termination overheads on the Summit leadership-class HPC platform. Integrated solution with PMIx/PRRTE enables using an abstracted, standardized set of interfaces for orchestrating the launch process, dynamic process management and monitoring capabilities. It extends scaling capabilities allowing to overcome a limitation of other launching mechanisms (e.g., JSM/LSF). Explored different DVM setup configurations provide insights on DVM performance and a layout to leverage it. Our experimental results show that heterogeneous workload of 65,500 tasks on 2048 nodes, and partitioned across 32 DVMs, runs steady with resource utilization not lower than 52%. While having less concurrently executed tasks resource utilization is able to reach up to 85%, based on results of heterogeneous workload of 8200 tasks on 256 nodes and 2 DVMs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Optimizing inference of segmentation on high-resolution images in MLExchange

MLExchange is a machine learning (ML) operations platform providing web user-interfaces (UIs) for data visualization and analysis pipelines at synchrotron facilities. Among these UIs is the segmentation app which helps synchrotron users utilize ML algorithms to automatically segment high-resolution scientific images with minimal manual annotation effort. In this work, we share code optimizations that significantly speed up the segmentation inference workflow of large data in short time. By optimizing the sequence of CPU-GPU data transfers and introducing CPU parallelization to key operations, we improve the per-device, per-image frame computational efficiency and observe close to 3×$$\times$$ speedup over the original segmentation inference workflow run time when utilizing a single GPU. Further adaptations enabling multi-GPU inference yield more than 40×$$\times$$ speedup with 100 GPUs compared to the optimized single GPU inference workflow. This acceleration of the segmentation inference workflow will provide MLExchange users with easy access to segmentation results with little wait time.

Lu, Shizhao↗
DOE OSTI2023

The use of gas chromatography – high resolution mass spectrometry for suspect screening and non-targeted analysis of per- and polyfluoroalkyl substances

This study is a workflow development for the analysis, identification, and categorization of per- and polyfluoroalkyl substances (PFAS) using gas chromatography-high resolution mass spectrometry (GC-HRMS) with non-targeted analysis (NTA) and suspect screening techniques. The behavior of various PFAS in a GC-HRMS was studied with regards to retention indices, ionization susceptibility, fragmentation patterns, etc. A custom PFAS database was constructed from 141 diverse PFAS. The database contains mass spectra from electron ionization (EI) mode, as well as MS and MS/MS spectra from positive and negative chemical ionization (PCI and NCI, respectively) modes. Common fragments of PFAS were identified across a diverse set of 141 PFAS analyzed. A workflow for suspect screening of PFAS and partially fluorinated products of incomplete combustion/destruction (PICs/PIDs) was developed which utilized both the custom PFAS database and external databases. PFAS and other fluorinated compounds were identified in both a challenge sample (designed to test the identification workflow) and incineration samples suspected to contain PFAS and fluorinated PICs/PIDs. The challenge sample resulted in a 100% true positive rate (TPR) for PFAS which were present in the custom PFAS database. In conclusion, several fluorinated species were tentatively identified in the incineration samples using the developed workflow.

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

Full spectrum optical constant interface to the Materials Project

Optical constants characterize the interaction of materials with light and are important properties in material design. Here we present a Python-based Corvus workflow for simulations of full spectrum optical constants from the visible and ultraviolet to hard x-ray wavelengths based on the real-space Green’s function code FEFF10 and structural data from the Materials Project (MP). The Corvus workflow manager and its associated tools provide an interface to FEFF10 and the MP database. The workflow parallelizes the FEFF computations of optical constants over all absorption edges for each material in the MP database specified by a unique MP-ID. The workflow tools determine the distribution of computational resources needed for that case. Similarly, the optical constants for selected sets of materials can be computed in a single-shot. Additionally, to illustrate the approach, we present results for several elemental solids in the periodic table, as well as a sample compound, and compare our predictions with experimental results. In addition, we provide a database of calculated results for all elements for which there is a stable elemental solid at standard conditions available in the Materials Project database. As in x-ray absorption spectra, these results are interpreted in terms of an atomic-like background and fine-structure contributions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗
DOE OSTI2022

Field validation of data-driven BSDF and peak extraction models for light-scattering fabric shades

Shading and daylighting systems affect cooling, heating, and lighting energy use by modulating solar radiation through the building façade. Characterizing shading systems holistically and accurately helps designers and engineers evaluate shading systems to achieve energy and non-energy performance goals. These complex fenestration systems can be modeled using Bidirectional Scattering Distribution Functions (BSDF), which map incident radiation to hemispherical distributions of outgoing radiation. Data-driven, tabulated BSDFs are derived from interpolated goniophotometer measured data, then sampled during the raytracing calculation. A peak extraction (PE) algorithm was developed to circumvent limits in BSDF angular resolution, where the specular peak is extracted during simulation by evaluating the BSDF in the through direction and surrounding region. The objective of this study was to validate this measurement and modeling workflow using field monitored data from a full scale testbed with eleven installed fabrics of different weaves, openness factors, and colors and assess the accuracy of the workflow under different adaptation and contrast conditions. Test conditions were limited to clear sky conditions with the sun in the field of view. Results showed that, for tensor tree datasets, vertical illuminance, solar luminance (2.5° apex), and daylight glare probability (DGP) were predicted to within a mean bias error (MBE) error of -456 lx (-12.3%), -3.46e5 (-38.4%), and -0.042 (-7.8%) when full PE occurred. With a binary classification of glare/ no glare, DGP was predicted accurately with a true positive rate of 0.98 and true negative rate of 1.0 using tensor tree data and less accurately with Klems BSDF data, particularly for cases of no glare. The workflow may be of insufficient accuracy to distinguish borderline performance between fabrics using the four-point glare scale, particularly under low adaptation, high contrast daylit conditions. Errors were due to reductions in peak shape and intensity across the BSDF interpolation and data reduction workflow. Future work is needed to better preserve measurement fidelity during interpolation and sampling, which in turn will improve PE performance.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Surrogate models for development of unconventional shale reservoirs by an integrated numerical approach of hydraulic fracturing, flow and geomechanics, and machine learning

We develop well-completion surrogate models by taking an integrated workflow of hydraulic fracturing, flow, geomechanics, and machine learning simulation. There are three steps in the proposed workflow. First, history-matching processes are conducted with the field data including pumping and production data for characterization. Second, full-physics simulation is performed with various parameters of the field development (e.g., cluster spacing, clusters per stage, pumping rates and times, amount of proppant, and well spacing) to generate multiple simulation results by changing the parameters of the completion design with well-known hydraulic fracturing, reservoir, geomechanics simulators to calculate fracture geometry, reservoir depressurization, induced stress changes. The workflow is demonstrated over a field in the Southern Midland Basin. Here, we take two completion scenarios: a single well case followed by a multi-well case. Finally, a Long Short-Term Memory (LSTM) machine learning algorithm is employed to create surrogate models that can replicate the full-physics simulation results. Furthermore, results show that the trained models applied in the single well and multi-well cases for a particular geological system can provide good accuracy close to those provided by full-physics simulations. Specifically, the site-specific surrogate models can predict fracture parameters (length, height, and surface area) and cumulative production accurately with computational efficiency, suggesting our proposed workflow can be used as a pragmatic tool for expediting the well completion optimization process.

Geomechanics↗
DOE OSTI2020

Visualization of hydraulic fracture using physics-informed clustering to process ultrasonic shear waves

Ultrasonic transmission is sensitive to the spatial variation in mechanical properties of materials due to the presence of cracks/fractures. Wave propagation through fractured media introduces changes in the frequency content, travel time and transmission coefficient of the wave. A workflow based on physics-informed unsupervised learning is developed to process the transmitted ultrasonic-shear waveforms to non-invasively visualize the geomechanical alterations due to hydraulic fracturing. Novelty of the work involves the assignment of both statistically consistent and physically consistent clusters to the measurements of shear waveforms acquired across the one axial and two frontal planes. Physically consistent/relevant information is incorporated by considering the travel time of the peak of spectral energy and transmission coefficient of the transmitted waveform. The proposed workflow generates maps of geomechanical alterations across the frontal and axial planes of the sample. The outputs of the workflow are in good agreement with independent techniques viz. acoustic emission and X-ray computed tomography. Finally, the proposed workflow can be adapted for improved fracture characterization in the subsurface when processing sonic-logging, cross-wellbore seismic or surface seismic waveform data.

42 ENGINEERING↗
DOE OSTI2023

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

Generating top-down tandem mass spectra (MS/MS) for complex mixtures of proteoforms has become possible through improvements in fractionation, on-line separation, dissociation, and mass analysis. The algorithms to match tandem mass spectra to sequences have undergone a parallel evolution, with both spectral alignment and peak matching being paired with diverse methods for scoring proteoform-spectral matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification through three distinct challenges. The first is identifying a large yield of PrSMs while controlling false discovery rate (FDR) in identifying thousands of proteoforms from complex cell lysates via four software workflows: ProSight Proteome Discoverer, TopPIC, Informed Proteomics, and pTop. The second is the deconvolution of data from both Thermo Orbitrap-class and Bruker maXis Q-TOF instruments to produce consistent precursor charge and mass determinations while generating fragment mass lists to optimize identification. The third attempts to detect diverse post-translational modifications (PTMs) in proteoforms from cow milk and human ovarian tissue. The data demonstrate that existing software suites produce admirable sensitivity, in some cases identifying a third of collected tandem mass spectra with FDR controlled below 2%; the overlap in these PrSMs, however, illustrates real value in searching data with multiple search engines. Differences among identification workflows seem to result from each search algorithm incorporating its own deconvolution algorithm. By transmitting deconvolution data from multiple deconvolution routes (Thermo Xtract, Bruker Auto MSn, Mascot Distiller, TopFD, and FLASHDeconv) to the downstream TopPIC search algorithm, we were able to detect common causes of deconvolution disagreement. The detection of PTMs was very inconsistent among search algorithms, with some workflows suggesting as little as 1% of PrSMs from cow’s milk were singly-phosphorylated while other workflows found that 18% of PrSMs were singly-phosphorylated. Taken together, these results make a strong argument for top-down researchers to adopt a standard practice of analyzing each MS/MS experiment with at least two different search engines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗