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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 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

In Silico Screening of CO 2 –Dipeptide Interactions for Bioinspired Carbon Capture

Carbon capture, sequestration and utilization offers a viable solution for reducing the total amount of atmospheric CO 2 concentrations. On an industrial scale, amine-based solvents are extensively employed for CO 2 capture through chemisorption. Nevertheless, this method is marked by the high cost associated with solvent regeneration, high vapor pressure, and the corrosive and toxic attributes of by-products, such as nitrosamines. An alternative approach is the biomimicry of sustainable materials that have strong affinity and selectivity for CO 2 . Bioinspired approaches, such as those based on naturally occurring amino acids, have been proposed for direct air capture methodologies. In this study, we present a database consisting of 960 dipeptide molecular structures, composed of the 20 naturally occurring amino acids. Furthermore, those structures were analyzed with a novel computational workflow presented in this work that considers certain interaction sites that determine CO 2 affinity. Density functional theory (DFT) and symmetry-adapted perturbation theory (SAPT) computations were performed for the calculation of CO 2 interaction energies, which allowed to limit our search space to 400 unique dipeptide structures. Using this computational workflow, we provide statistical insights into dipeptides and their affinity for CO 2 binding, as well as design principles that can further enhance CO 2 capture through cooperative binding.

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

Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform

Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis, response to environmental perturbation, pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool to study plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This protocol describes a recently-developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, with ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant tissue harvest, tissue preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Risk-based area of review estimation in overpressured reservoirs to support injection well storage facility permit requirements for CO 2 storage projects

This paper by the Energy & Environmental Research Center presents a workflow and modeling approach for delineating a risk-based area of review (AOR) to support a U.S. Environmental Protection Agency (EPA) Class VI permit for a carbon dioxide (CO 2 ) storage project. The approach combines semianalytical solutions for estimating formation fluid leakage through a hypothetical leaky wellbore with the results of numerical reservoir simulations to define the AOR. The modeling utilizes 1) semianalytical solutions from the peer-reviewed literature for formation fluid leakage through abandoned wellbores by Raven (1990) and Avci (1994), 2) a FORTRAN model compiled and described in Cihan et al. (2011, 2012) called ASLMA (Analytical Solution for Leakage in Multilayered Aquifers), and 3) a computational framework for estimating a risk-based AOR first proposed by Oldenburg et al. (2014, 2016). Therefore, the approach builds upon well-established research and underlying hydrogeological principles that have been upheld for nearly three decades. Moreover, the ASLMA model has been broadly applied to an array of storage projects. The work presented herein extends these earlier works using a custom wrapper written in the software environment, R (R Core Team, 2020), which was developed to perform multiple runs of the ASLMA model using given ranges for one or more input parameters. In addition, the current work simulates the pressure buildup within the storage reservoir in response to CO 2 injection using a compositional simulator to better accommodate the temporospatial evolution of pressure buildup within the storage reservoir that is more accurately modeled using a heterogeneous geologic model and a compositional simulator that accounts for the multiphase interactions. The workflow is demonstrated using a case study for a 180,000-metric-ton-per-year storage project located in the PCOR (Plains CO 2 Reduction) Partnership region. For the storage project evaluated here, under the scenario where the leaky wellbore is open to a saline aquifer (thief zone) between the overlying seal (cap rock) and the underground sources of drinking water (USDW), the risk-based AOR essentially collapses to the areal extent of the CO 2 plume in the storage reservoir because the pressure buildup in the storage reservoir beyond the CO 2 plume is insufficient to drive formation fluids up a hypothetical leaky wellbore into the USDW. However, even under the conservative assumption that the leaky wellbore is not open to a thief zone, beyond the areal extent of the CO 2 plume, the incremental leakage is less than 400 m 3 over 20 years, which represents ~0.0001% or less of the total volume of water contained within the USDW rock volume. As discussed in the text, the threshold criterion for defining the risk-based AOR is site-specific and should be informed by the results of the sensitivity analysis and available site characterization data. The approach outlined in this paper is designed to be protective of USDWs and, therefore, comply with the Safe Drinking Water Act requirements and provisions for the U.S. EPA Class VI Underground Injection Control (UIC) Program (Class VI Rule) and North Dakota Administrative Code Chapter 43-05-01.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics

Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and applied it to screen 61eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functional competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deep Learning‐Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard‐to‐Transfect Cells

Abstract Genome engineering of cells using CRISPR/Cas systems has opened new avenues for pharmacological screening and investigating the molecular mechanisms of disease. A critical step in many such studies is the intracellular delivery of the gene editing machinery and the subsequent manipulation of cells. However, these workflows often involve processes such as bulk electroporation for intracellular delivery and fluorescence activated cell sorting for cell isolation that can be harsh to sensitive cell types such as human‐induced pluripotent stem cells (hiPSCs). This often leads to poor viability and low overall efficacy, requiring the use of large starting samples. In this work, a fully automated version of the nanofountain probe electroporation (NFP‐E) system, a nanopipette‐based single‐cell electroporation method is presented that provides superior cell viability and efficiency compared to traditional methods. The automated system utilizes a deep convolutional network to identify cell locations and a cell‐nanopipette contact algorithm to position the nanopipette over each cell for the application of electroporation pulses. The automated NFP‐E is combined with microconfinement arrays for cell isolation to demonstrate a workflow that can be used for CRISPR/Cas9 gene editing and cell tracking with potential applications in screening studies and isogenic cell line generation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Accelerating Discovery of Solid‐State Thin‐Film Metal Dealloying for 3D Nanoarchitecture Materials Design through Laser Thermal Gradient Treatment

Thin‐film solid‐state metal dealloying (thin‐film SSMD) is a promising method for fabricating nanostructures with controlled morphology and efficiency, offering advantages over conventional bulk materials processing methods for integration into practical applications. Although machine learning (ML) has facilitated the design of dealloying systems, the selection of key thermal treatment parameters for nanostructure formation remains largely unknown and dependent on experimental trial and error. To overcome this challenge, a workflow enabling high‐throughput characterization of thermal treatment parameters is demonstrated using a laser‐based thermal treatment to create temperature gradients on single thin‐film samples of Nb‐Al/Sc and Nb‐Al/Cu. This continuous thermal space enables observation of dealloying transitions and the resulting nanostructures of interest. Through synchrotron X‐ray multimodal and high‐throughput characterization, critical transitions and nanostructures can be rapidly captured and subsequently verified using electron microscopy. The key temperatures driving chemical reactions and morphological evolutions are clearly identified. While the oxidation may influence nanostructure formation during thin‐film treatment, the dealloying process at the dealloying front involves interactions solely between the dealloying elements, highlighting the availability and viability of the selected systems. Further, this approach enables efficient exploration of the dealloying process and validation of ML predictions, thereby accelerating the discovery of thin‐film SSMD systems with targeted nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Multipoint Aerostructural Optimization of Wind Turbine Rotors Using a Coupled Blade‐Resolved Aerostructural Solver

Physics‐based design optimization workflows thread the needle between computational cost limitations and simulation complexity, often compromising between modeling detail and the range of operating design conditions. Multipoint aerostructural optimization of wind turbine rotors has so far been confined to low‐fidelity analyses or to high‐fidelity studies with simplified structural models, leaving the most complex design trade‐offs unexplored. We close this gap by performing the first tightly coupled gradient‐based multipoint aerostructural rotor optimization using 3D aerodynamic and structural solvers with discrete coupled adjoints. The optimizer simultaneously varies blade planform, airfoil shapes, and structural thickness through more than 270 design variables, minimizing a weighted combination of rotor mass and power across multiple wind speeds. Applied to a modified DTU 10‐MW benchmark under conservative structural and aerodynamic constraints, our multipoint optimization reduces rotor mass by up to 36% and increases power by 12%–15% across the main operating conditions; biasing the objective toward power yields power gains up to 18% and a 17% mass reduction. For a nominal wind distribution, 3‐point rotor designs accounting for low RPM and high thrust conditions capture dominant trade‐offs and outperform single‐point designs. Adding two off‐design points changes individual‐condition power by less than 3% but leaves the weighted average within 0.5%, and the mass‐power bias has a stronger effect on the final design than the operating‐point weighting itself. Our framework extends naturally to richer load cases and site‐specific wind distributions, providing a basis for high‐fidelity multipoint design earlier in industrial workflows.

17 WIND ENERGY↗
DOE OSTI2022

Discovery of unknown posttranslational modifications by top-down mass spectrometry

Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.

Wilson, Jesse W.↗
DOE OSTI2023

Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection

Early detection of solid tumors through a simple screening process, such as the proteomic analysis of biofluids, has the potential to significantly alter the management and outcomes of cancers. The application of advanced targeted proteomics measurements and data analysis strategies to uniformly collected serum or plasma samples would enable longitudinal studies of cancer risk, progression, and response to therapy that have the potential to significantly reduce cancer burden in general. In this article, we describe a generalizable workflow combining robust, multiplexed targeted proteomics measurements applied to longitudinal samples from the Department of Defense Serum Repository with a Random Forest machine learning method for developing and initially evaluating the performance of candidate biomarker panels for early detection of cancers. The effectiveness of this approach was demonstrated in a cohort of 175 head and neck squamous cell carcinoma patients. The outlined protocols include methods for sample preparation, instrument analysis, and data analysis and interpretation using this workflow.

Longitudinal analysis, machine learning, cancer, e↗
DOE OSTI2019

Exploratory Visual Analysis of Anomalous Runtime Behavior in Streaming High Performance Computing Applications

Online analysis of runtime behavior is essential for performance tuning in streaming scientific workflows. Integration of anomaly detection and visualization is necessary to support human-centered analysis, such as verification of candidate anomalies utilizing domain knowledge. In this work, we propose an efficient and scalable visual analytics system for online performance analysis of scientific workflows toward the exascale scenario. Here, our approach uses a call stack tree representation to encode the structural and temporal information of the function executions. Based on the call stack tree features (e.g., execution time of the root function or vector representation of the tree structure), we employ online anomaly detection approaches to identify candidate anomalous function executions. We also present a set of visualization tools for verification and exploration in a level-of-detailed manner. General information, such as distribution of execution times, are provided in an overview visualization. The detailed structure (e.g., function invocation relations) and the temporal information (e.g., message communication) of the execution call stack of interest are also visualized. The usability and efficiency of our methods are verified in a real-world HPC application.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Software Framework for Federated Science Instruments

There is an unprecedented promise of enhanced capabilities for federations of leadership computing systems and experimental science facilities by leveraging software technologies for fast and efficient operations. These federations seek to unify different science instruments, both computing and experimental, to effectively support science users and operators to execute complex workflows. The FedScI project addresses the software challenges associated with the formation and operation of federated environments by leveraging recent advances in containerization of software and softwarization of hardware. We propose a software framework to streamline the federation usage by science users and it’s provisioning and operations by facility providers. A distinguishing element of our work is the support for improved interaction between experimental devices, such as beam-line instruments, and more traditional high-performance computing resources, including compute, network, storage systems. We present guiding principles for the software framework and highlight portions of a current prototype implementation. We describe our science use case involving neutron imaging beam-lines (SNAP/BL-3, Imaging/CG-1D) at the Spallation Neutron Source and High Flux Isotope Reactor facilities at Oak Ridge National Laboratory. Additionally, we detail plans for a more direct instrument interaction within a federated environment, which could enable more advanced workflows with feedback loops to shorten the time to science.

Naughton III, Thomas↗
DOE OSTI2023

Scaling Optimal Allocation of Cloud Resources Using Lagrange Relaxation

The rapid growth of Cloud Computing (CC) has increased the variety of computing resources, storage, and communication services that pose significant new challenges for the efficient use of cloud resources. The cost-efficient allocation of cloud resources has become a decisive premise for the adoption of CC services. The cost-efficient selection and scheduling of these resources to meet the demands of a scientific workflow is a challenging problem that is exacerbated by the inclusion of multiple CC providers. In this paper, we present a novel strategy for the cost-efficient selection of CC resources using Lagrange relaxation. Our approach is based on preselection of resources and demand decomposition to create a series of smaller sub-problems, which allow the estimation of the best cost-structures and selection of CC service providers for a subset of the time period of the planning horizon. Decomposition of the demand is achieved through the boundary analysis of a continuous relaxation of the problem. Using the metrics defined in terms of the cost and time of completion, we demonstrate excellent performance in relation to optimal solutions. Our method reduced the computational time from hours to seconds for a representative 36-month problem and provided high-quality solutions (< 0.05% relative error). Given the importance of selecting resources and scheduling complex scientific workflows, we believe that this novel strategy will be beneficial for many researchers and users of cloud computing resources.

De La Torre, Luis↗
DOE OSTI2024

CI/CD Efforts for Validation, Verification and Benchmarking OpenMP Implementations

Software developers must adapt to keep up with the changing capabilities of platforms so that they can utilize the power of High-Performance Computers (HPC), including exascale systems. OpenMP, a directive-based parallel programming model, allows developers to include directives to existing C, C++, or Fortran code to allow node level parallelism without compromising performance. This paper describes our CI/CD efforts to provide easy evaluation of the support of OpenMP across different compilers using existing testsuites and benchmark suites on HPC platforms. Our main contributions include (1) the set of a Continuous Integration (CI) and Continuous Development (CD) workflow that captures bugs and provides faster feedback to compiler developers, (2) an evaluation of OpenMP (offloading) implementations supported by AMD, HPE, GNU, LLVM, and Intel, and (3) evaluation of the quality of compilers across different heterogeneous HPC platforms. With the comprehensive testing through the CI/CD workflow, we aim to provide a comprehensive understanding of the current state of OpenMP (offloading) support in different compilers and heterogeneous platforms consisting of CPUs and GPUs from NVIDIA, AMD, and Intel.

Jarmusch, Aaron↗
DOE OSTI2025

A2SD: Accelerating Scientific Innovation Through Autonomous Discovery Systems

The 2025 Advancing Autonomous Scientific Discovery (A2SD) workshop convened researchers from academia, national laboratories, and industry to explore the transformative role of autonomy in scientific discovery. The workshop highlighted a convergence of artificial intelligence, robotics, and computational workflows into autonomous systems capable of accelerating the scientific process. Presentations and discussions spanned autonomous experimentation, intelligent workflow orchestration, digital twins, and agent-based systems for managing complex research ecosystems. Key challenges discussed included interoperability across heterogeneous infrastructures, near real-time data management under FAIR principles, reproducibility, and the integration of human oversight. The workshop also emphasized the need for modular software interfaces, federated learning models, and education initiatives to support a next-generation scientific workforce.

Taufer, Michela [University of Tennessee, Knoxvill↗
DOE OSTI2022

An Adaptive Geometry-Free Thermo-Mechanical Model for Directed Energy Deposition Process Modeling

This presentation describes a novel, geometry-free thermo-mechanical model with adaptive subdomain con- struction to accurately predict the thermal conditions, distortions, and residual stresses throughout the directed energy deposition (DED) process. A novel finite element workflow is designed to con- duct the numerical analysis, based on the multi-app and data transfer capabilities in the open-source Multiphysics Object-Oriented Simulation Environment (MOOSE). Unlike with traditional methods, the part geometry in this model is not predefined. Instead, it is a combined effect of the processing parameters and material properties. At each time step, the model utilizes a subdomain construction paradigm to model the material deposition. A specialized mesh adaptivity scheme is incorporated to provide an accurate prediction while reducing the overall computational cost. The results generated by the proposed model show general agreement with the experimental measurements for the single track scan with varying processing parameters and demonstrate reasonable predictions for higher material buildups.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Standard Lexicons, Coding Systems and Ontologies for Interoperability and Semantic Computation in Imaging

Standard clinical terms, codes, and ontologies promote clarity and interoperability. Within radiology, there is a variety of relevant content resources, tools and technologies. These provide the basis for fundamental imaging workflows such as reporting and billing, and also facilitate a range of applications in quality improvement and research. This article reviews the key characteristics of lexicons, coding systems, and ontologies. A number of standards are described, including International Classification of Diseases-10-Clinical Modification (ICD-10-CM), Current Procedural Terminology (CPT), Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT), Logical Observation Identifiers Names and Codes (LOINC), and RadLex. Tools for accessing this material are reviewed, such as the National Center for Biomedical Ontology BioPortal system. Web services are discussed as a mechanism for semantic application development. Several example systems, workflows, and research applications using semantic technology are also surveyed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗