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All sources NASA NTRS DOE OSTI

DOE OSTI2025

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗

DOE OSTI2021

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Solvothermal Synthesis of [Cr 7 S 8 (en) 8 Cl 2 ]Cl 3 ⋅ 2H 2 O with Magnetically Frustrated [Cr 7 S 8 ] 5+ Double‐Cubes**

Abstract A novel transition metal chalcohalide [Cr 7 S 8 (en) 8 Cl 2 ]Cl 3 ⋅ 2H 2 O, with [Cr 7 S 8 ] 5+ dicubane cationic clusters, has been synthesized by a low temperature solvothermal method, using dimethyl sulfoxide (DMSO) and ethylenediamine ( en ) solvents. Ethylenediamine ligand exhibits bi‐ and monodentate coordination modes; in the latter case ethylenediamine coordinates to Cr atoms of adjacent clusters, giving rise to a 2D polymeric structure. Although magnetic susceptibility shows no magnetic ordering down to 1.8 K, a highly negative Weiss constant, θ =−224(2) K, obtained from Curie‐Weiss fit of inverse susceptibility, suggests strong antiferromagnetic (AFM) interactions between S =3/2 Cr(III) centers. Due to the complexity of the system with (2 S +1) 7 =16384 microstates from seven Cr 3+ centers, a simplified model with only two exchange constants was used for simulations. Density‐functional theory (DFT) calculations yielded the two exchange constants to be J 1 =−21.4 cm −1 and J 2 =−30.2 cm −1 , confirming competing AFM coupling between the shared Cr 3+ center and the peripheral Cr 3+ ions of the dicubane cluster. The best simulation of the experimental data was obtained with J 1 =−20.0 cm −1 and J 2 =−21.0 cm −1 , in agreement with the slightly stronger AFM exchange within the triangles of the peripheral Cr 3+ ions as compared to the AFM exchange between the central and peripheral Cr 3+ ions. This compound is proposed as a synthon towards magnetically frustrated systems assembled by linking dicubane transition metal‐chalcogenide clusters into polymeric networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

In-route inductive versus stationary conductive charging for shared automated electric vehicles: A university shuttle service

In-route inductive charging technology, as applied to automated electric vehicles, can help realize a fully automated system of both vehicles and chargers. This study presents a planning optimization analysis for fixed-route automated shuttles supported by in-route inductive charging technology. A techno-economic feasibility of inductive charging was assessed in comparison with stationary charging, including Level 2 AC chargers, and DC fast chargers (DCFCs). This analysis considered both present-day and future vehicle operations and overall system costs. A real project with two circulator Navya Arma shared automated electric vehicles (SAEVs) at the University of Michigan was investigated using real-world collected energy and travel data. The outcomes show that the proper design of quasi-dynamic inductive chargers at designated stops allows SAEVs to realize unlimited driving range and be cost-competitive to DCFC technology. Considering present-day costs and vehicles, low-speed SAEVs can realize charge-sustaining operation at a minimum cost either by implementing a 50-kW inductive charger at two stops with one segment per position and a 29-kWh onboard battery, or by installing a 100-kW inductive charger at one stop with one segment per position and a 28-kWh onboard battery. Overall, considering future costs and vehicles, either a 40-kW charger at one stop with a 29-kWh battery or a 50-kW charger at the north stop with a 14-kWh battery would enable charge-sustaining operation. In addition, quasi-dynamic inductive solution can reduce the onboard battery by about 15% while providing unlimited driving range, but stationary scenarios require about 112% additional battery capacity to support a 12-h driving range.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2022

Volcanology, Geochemistry, and Petrology Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science

This article is composed of a commentary about the state of Integrated, Coordinated, Open, and Networked (ICON) principles in Volcanology, Geochemistry, and Petrology (VGP), and discussion on the opportunities and challenges of adopting them. VGP encompasses a broad field that addresses volcanic, magmatic, hydrothermal, geomicrobial systems; process investigations that span the physical, geochemical and biological realms, including planetary geology; and one that is extensively supported by state-of-the-art research facilities. We suggest that an open, inclusive, collaborative and evolving model of an international coordinated network is critical to answering the most pressing challenges in VGP. In this commentary piece, we begin to discuss the elements of, challenges to, and path forward in developing such a model. For this team, ICON means collaboration, equitable access to data for the entire scientific community, and forging of partnerships that potentially contribute to more innovative ways of coordinating and sharing research. It also means bringing more equity to science, by implementing effective measures which consider access to funding, analytical equipment, resources, and mentors. More importantly, ICON to us means having important conversations around what we value in the advancement of science, perhaps exploring outside the idea of meritocracy and evaluating what individual traits can contribute to science outside what has traditionally been considered the norm.

58 GEOSCIENCES↗

DOE OSTI2025

Reduce Revenue Versus Increase Expenditure: Fires and Plant Invasion Drive Soil Carbon Loss With Different Mechanisms in a Mediterranean Shrubland

Fires and plant invasions threaten Mediterranean ecosystems substantially, particularly in the context of changing climate. Our study utilized a data-model integration approach to assess the response of soil organic carbon (SOC) to fires and plant invasion under three Shared Socio-Economic Pathway (SSP) scenarios (SSP1-26, SSP2-45, and SSP5-85). We parameterized the CLM-Microbe model and then investigated the individual and interactive impacts of fires and plant invasion on soil C by comparing factorial simulations of initialization (fire/no wildfire in 2021), fire module on/off, and with and without plant invasion during 2023–2100 in a Mediterranean ecosystem. The simulations indicated a marked C loss due to the 2021 wildfire, projected fires, and plant invasion across all future climate scenarios. Specifically, the 2021 wildfire, projected fires, and plant invasion reduced the SOC (0–30 cm) by 0.12, 0.26, and 0.15 kg C m −2 under SSP1-26, 0.12, 0.30, and 0.12 kg C m −2 under SSP2-45, and 0.12, 0.24, and 0.13 kg C m −2 under SSP5-85, respectively. However, fires and plant invasion decreased SOC through distinct mechanisms. The effects of the 2021 wildfire occurred due to its negative legacy on soil microbial community and, thus, litter accumulation, suppressing the formation of soil carbon via decomposition. Influences of projected fires happen via consuming fuel and suppressing carbon input to soils. In contrast, the impacts of plant invasions were due to enhanced microbial respiration, leading to C loss. In conclusion, these findings emphasize the need for tailored C sequestration strategies considering the disparate effects of fires and plant invasions in the Mediterranean climate.

microbe↗

DOE OSTI2021

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II

In this work, we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Graph Sparsification by Approximate matrix Multiplication

Graphs arising in statistical problems, signal processing, large networks, combinatorial optimization, and data analysis are often dense, which causes both computational and storage bottlenecks. One way of sparsifying a weighted graph, while sharing the same vertices as the original graph but reducing the number of edges, is through spectral sparsification. We study this problem through the perspective of RandNLA. Specifically, we utilize randomized matrix multiplication to give a clean and simple analysis of how sampling according to edge weights gives a spectral approximation to graph Laplacians, without requiring spectral information. Through the CR–MM algorithm, we attain a simple and computationally efficient sparsifier whose resulting Laplacian estimate is unbiased and of minimum variance. Here, we define a new notion of additive spectral sparsifiers, which has not been considered in the literature.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Downscaled Daily 1 km Climate Data (NEX-GDDP-CMIP6) for Southeast Texas. Full ensemble of downscaled CMIP6 climate projections at 1 km daily resolution.

For the SETx-UIFL, the daily NASA Earth Exchange Global Daily Downscaled Projections (NEX-GDDP-CMIP6) dataset climate projections were downscaled from approximately 27 km to 1 km. The SETx dataset provides very high-resolution climate data for the historical period (1950–2014) and future scenarios derived from CMIP6 global models under the four Tier 1 Shared Socioeconomic Pathways (SSPs 1.26, 2.45, 3.70, and 5.85), developed for the IPCC Sixth Assessment Report. A subset of ten NEX-GDDP-CMIP6 models was selected to represent a balance of model families, climate sensitivities, and availability across scenarios, ensuring a diverse and reliable ensemble for regional analysis. Selected models: BCC-CSM2-MR, CESM2, CMCC-ESM2, CNRM-ESM2-1, EC-Earth3, FGOALS-g3, GFDL-CM4, MPI-ESM1-2-HR, MRI-ESM2-0, NorESM2-MM. Daily variables downscaled include tasmax, tasmin, tas, pr, hurs, huss, rsds, rlds, and sfcWind.

Persad, Geeta↗

DOE OSTI2025

If We Build Them, They Will Run: Automated HPC Apps Deployment and Profiling with eBPF in Cloud

The high performance computing (HPC) community is in a period of transition. The rise of AI/ML coupled with a changing landscape of resources deems portability a new metric of performance, and methods to move between on-premises and cloud environments and assess compatibility are paramount. Here we design and test a strategy for bridging the gap between traditional HPC and Kubernetes environments – first containerizing applications, providing automated orchestration to run studies, and packaging the setup with automated means to assess performance using low overhead eXtended Berkeley Packet Filter (eBPF) programs. We first assess different designs for eBPF collection, demonstrating a tradeoff between number of programs deployed on a node and overhead added. We develop 5 low overhead eBPF programs that combine with streaming ML models to assess CPU, futex, TCP, shared memory, and file access across four different builds of an HPC application for CPU and GPU. We use eBPF data to generate insights into the possible underlying etiology of scaling issues. We then assess compatibility of a well-known benchmark, HPCG, across matrices of micro-architectures and optimization levels (217 containers across 24 instance types and over 7500 runs). We provide to the community 30 applications to deploy in our automated setup and perform a scaling study from 4 to a maximum of 256 nodes for both CPU and GPU applications. Finally, we use our gained knowledge about performance to generate compatibility artifacts that are used by a newly developed Kubernetes controller to intelligently select instance type based on optimizing a figure of merit. Along with insights to scaling in this environment with a collection of applications and templates to work from, we provide an overall strategy for approaching HPC application deployment and image selection based on compatibility in cloud.

Computer science↗

DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Characterization of U Isotope Ratios by Laser Ablation MC-ICP-MS for IAEA Safeguards

This project will develop methodology to identify and analyze U and Pu containing particles using laser ablation MC-ICP-MS. The proposed work will involve: i) setup and optimization of the LA-MC-ICP-MS system, ii) testing and validation by analysis of QC standards, iii) designing analytical protocols for single particles, and iv) developing a data processing system. Ultimately, this project will output a detailed operating procedure documenting the experimental techniques and data processing routines required to perform particle identification and analysis by laser ablation MC-ICP-MS, that can be shared with IAEANWAL laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

The ABCs of On-Demand Transit (ODT)

On-demand mobility - also referred to as on-demand transit (ODT) - is a form of public mobility that is flexible with respect to where and when service is provided, and ODT deployments have increased significantly in recent years. Transit agencies are becoming increasingly interested in ODT, and due to differing definitions and various service design and business model options, it can be difficult to learn about the emerging industry. This work provides an overview of the definitions of ODT, recent trends internationally and in the U.S., ODT's benefits and challenges (particularly compared to fixed-route transit), three primary service design options, system costs and funding considerations, and a metrics framework for evaluating ODT systems to ensure continued successful performance. Identified benefits include increased service areas, short ride and wait times, increased user flexibility, potential to reduce energy consumption and emissions through shared trips and smaller, right-sized vehicles, increased safety and comfort through door-to-door service, and rich data streams including granular spatio-temporal data that can be analyzed to continuously improve the service. Challenges include scaling ODT service up as small increases in ridership require additional supply to keep service quality high, serving peak times including keeping low wait times, the lack of fixed schedule being challenging for commuters, integrating ODT services with nearby transit systems, and equity for riders without smartphones who cannot track the vehicle in a mobile app. Finally, an overview of seven ODT case studies (in Texas, Missouri, New York, and Ontario, Canada) performed by NREL and related analysis of travel time, energy and emissions, costs, and equity are presented. Initial key findings include: ODT can be cost- and energy-effective compared to fixed-route transit, ODT serves more people than other transit options, and ODT system deployments can be followed by rapid growth.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

U.S. Distribution Transformer Demand Phase III - Key Drivers and Managing Demand [Slides]

This presentation demonstrates a significant analysis, on forecasting the demand for distribution transformers. The analysis is conducted for the United States, estimating the initial in-service capacity of these assets, and forecasting demand for these assets through 2050 with several sensitivities conducted. It examines not only demand for these assets, but importantly, how utility planning practices can impact the demand for theses assets in time. Under load growth scenarios, whether utilities practice like-for-like replacement strategies as failures occur, or whether they practice proactive up-sizing, anticipating electric load growth, can have major impacts on future demand. It also examines several other growth factors, such as the increasing demand for step-up transformers, which share many of the same characteristics as distribution transformers, and the demand for specific transformers for large project growth from data centers.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Transportation Energy Data Book: Edition 38

The Transportation Energy Data Book: Edition 38 is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Designed for use as a desk-top reference, the Data Book represents an assembly and display of statistics and information that characterize transportation activity, and presents data on other factors that influence transportation energy use. The purpose of this document is to present relevant statistical data in the form of tables and graphs. The latest edition of the Data Book is available via the Internet. This edition of the Data Book has 13 chapters which focus on various aspects of the transportation industry. Chapter 1 - focuses on petroleum; Chapter 2 - energy; Chapter 3 - highway vehicles; Chapter 4 - light vehicles; Chapter 5 - heavy vehicles; Chapter 6 - alternative fuel vehicles; Chapter 7 - transit and shared mobility; Chapter 8 - fleet vehicles; Chapter 9 - household vehicles; Chapter 10 - nonhighway modes; Chapter 11 - transportation and the economy; Chapter 12 - greenhouse gas emissions; and Chapter 13 - criteria pollutant emissions. The sources used represent the latest available data. There are also three appendices which include detailed source information for some tables, measures of conversion, and energy tables and figures with electricity generation and distribution taken into account. A glossary of terms is also included for the reader’s convenience.

02 PETROLEUM↗

DOE OSTI2026

Detector Characterization for SuperCDMS Commissioning

Super Cryogenic Dark Matter Search (SuperCDMS) SNOLAB is a next generation direct detection experiment search ing for low mass dark matter using cryogenic germanium and silicon detectors operated at millikelvin temperatures. As the experiment begins its first commissioning data taking, establishing that the detectors respond to energy deposits in a stable, predictable way is a prerequisite for any future physics analysis. This work presents a study of detector stability for four SuperCDMS SNOLAB detectors, det 7 and det 15 (germanium), and det 11 and det 14 (silicon), using two data sets taken during early commissioning: dedicated Barium-133 calibration runs, which provide a known gamma ray energy reference at 356 keV, and low background runs, which record whatever background radiation the detectors see with no external source present. The Ba-133 data do not show a distinct, well localized line at the expected energy, and the low background data show a baseline that drifts and oscillates over time rather than remaining flat. This baseline instability appears consistently across multiple channels rather than being confined to one, suggesting a shared, detector wide cause rather than a single faulty channel. Together, these observations point to the detectors’ cryogenic support system as the likely source of the instability, since small temperature fluctuations introduced during normal operation of the cooling system could plausibly couple into the exquisitely temperature sensitive detectors. These results inform the ongoing commissioning effort by narrowing down where instability in the current data is originating from.

O'Hanlon, Viktoria M. [Skidmore Coll.; Fermilab]↗

DOE OSTI2026

Detector Characterization for SuperCDMS Commissioning

O'Hanlon, Viktoria M. [Skidmore Coll.; Fermilab]↗

DOE OSTI2022

IM3 SELECT Urbanization Data

IM3 SELECT Urbanization Data Urban fraction is provided in TIF files projected on the WGS84 datum at coarse (1/8 degree) and downscaled (1km) resolutions across the globe for each of three Shared Socioeconomic Pathway (SSP) scenarios corresponding to SSP2, SSP3, and SSP5; and each of two population scenarios corresponding to the default population scenario and an updated population scenario with more detailed projections for the United States. The population projections are provided as CSV files. Folder structure: default_population population urban_fraction coarse SSP2 SSP3 SSP5 downscaled SSP2 SSP3 SSP5united_states_updated_population population urban_fraction coarse SSP2 SSP3 SSP5 downscaled SSP2 SSP3 SSP5 Urban fraction data was produced using the SELECT model v1.0.0 (Gao, J. & O'Neill, B.C. 2019). Default population data derived from Gao, J. & O'Neill, B.C. 2020. Original model outputs produced using the default population data are available from Gao, J. 2020. Updated United States population data derived from Zoraghein, H. & O'Neill, B.C. 2020. Other SELECT input files available at Gao, J. & O'Neill, B.C. 2022.

McManamay, Ryan↗