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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Are 100 Ensemble Members Enough to Capture the Remote Atmospheric Response to +2°C Arctic Sea Ice Loss?

This study presents results from the Polar Amplification Multimodel Intercomparison Project (PAMIP) single-year time-slice experiments that aim to isolate the atmospheric response to Arctic sea ice loss at global warming levels of +2°C. Using two general circulation models (GCMs), the ensemble size is increased up to 300 ensemble members, beyond the recommended 100 members. After partitioning the response in groups of 100 ensemble members, the reproducibility of the results is evaluated, with a focus on the response of the midlatitude jet streams in the North Atlantic and North Pacific. Both atmosphere-only and coupled ocean–atmosphere PAMIP experiments are analyzed. Substantial differences in the midlatitude response are found among the different experiment subsets, suggesting that 100-member ensembles are still significantly influenced by internal variability, which can mislead conclusions. Despite an overall stronger response, the coupled ocean–atmosphere runs exhibit greater spread due to additional ENSO-related internal variability when the ocean is interactive. The lack of consistency in the response is true for anomalies that are statistically significant according to Student’s t and false discovery rate tests. This is problematic for the multimodel assessment of the response, as some of the spread may be attributed to different model sensitivities whereas it is due to internal variability. Here, we propose a method to overcome this consistency issue that allows for more robust conclusions when only 100 ensemble members are used.

58 GEOSCIENCES↗
DOE OSTI2024

Tropical Cyclone Wind Shear-Relative Asymmetry in Reanalyses

Abstract While tropical cyclones (TCs) are axisymmetric vortices to the first order, they often exhibit noteworthy structural asymmetries. These often result from environmental vertical wind shear, which tilts the vortex and induces a wavenumber 1 pattern in the circulation and precipitation fields. Reanalyses and climate models have improved in representing the TC structure and climatology, but their relatively coarse resolution and dependence on parameterized physics cast doubt on their ability to capture the asymmetric TC structure. We perform the most comprehensive process-oriented assessment of TC asymmetry to date in reanalyses. Specifically, we analyze the composite shear-relative TC structure in ERA5 and Climate Forecast System Reanalysis (CFSR), which vary in their resolutions, physical parameterization suites, and data assimilation techniques. These structures are compared with aircraft reconnaissance radar observations. In agreement with the observations, the strongest tangential winds are usually found left-of-shear, while inner core rainfall, ascent, vortex tilt, and low-level inflow are favored directly downshear or in the downshear-left quadrant. Outer rainband convection generally peaks in the downshear-right quadrant. Thermodynamic asymmetries are also apparent, with anomalous low-level moisture right-of-shear, midlevel warmth in the upshear-right quadrant (uptilt), and cloud properties suggestive of a realistic precipitation life cycle from growth to fallout. We also decompose rainfall contributions from the convective parameterization and large-scale cloud schemes and highlight the roles of vorticity advection, buoyancy advection, and diabatic processes in driving asymmetric vertical motions in the inner core and outer rainband regions. Our results suggest that process-level studies of TC asymmetry and TC–wind shear interaction under future warming are viable using climate models. Significance Statement Asymmetries are common in tropical cyclones (TCs), influencing their intensity, track, and hazards. Vertical wind shear often plays a leading-order role in causing these asymmetries. It is uncertain how well asymmetric structures and processes are captured in reanalyses and global climate models (GCMs) with grid spacings of 0.25° and coarser. In this study, we first evaluate TC asymmetry in reanalyses, which have the benefit of being forced by observations. This helps to assess whether the resolutions associated with GCMs sufficiently capture asymmetric structures and processes and motivates upcoming work with free-running GCMs to study how TC asymmetry may change in a warming climate.

Carstens, Jacob D.↗
DOE OSTI2020

The Impact of Parameterized Lateral Mixing on the Antarctic Circumpolar Current in a Coupled Climate Model

This study examines the impact of changing the lateral diffusion coefficient ARedi on the transport of the Antarctic Circumpolar Current (ACC). The lateral diffusion coefficient ARedi is poorly constrained, with values ranging across an order of magnitude in climate models. The ACC is difficult to accurately simulate, and there is a large spread in eastward transport in the Southern Ocean (SO) in these models. This paper examines how much of that spread can be attributed to different eddy parameterization coefficients. A coarse-resolution, fully coupled model suite was run with A Redi = 400, 800, 1200, and 2400 m 2 s -1 . Additionally, two simulations were run with two-dimensional representations of the mixing coefficient based on satellite altimetry. Relative to the 400 m 2 s -1 case, the 2400 m 2 s -1 case exhibits 1) an 11% decrease in average wind stress from 50° to 65°S, 2) a 20% decrease in zonally averaged eastward transport in the SO, and 3) a 14% weaker transport through the Drake Passage. The decrease in transport is well explained by changes in the thermal current shear, largely due to increases in ocean density occurring on the northern side of the ACC. In intermediate waters these increases are associated with changes in the formation of intermediate waters in the North Pacific. We hypothesize that the deep increases are associated with changes in the wind stress curl allowing Antarctic Bottom Water to escape and flow northward.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Identifying Meteorological Drivers for Errors in Modeled Winds along the Northern California Coast

Abstract An accurate wind resource dataset is required for assessing the potential energy yield of floating offshore wind farms that are expected along the California outer continental shelf. The National Renewable Energy Laboratory has developed and disseminated an updated wind resource dataset offshore of California, using the Weather Research and Forecasting Model, referred to as the CA20 dataset. As compared to buoy lidar measurements that have become available recently, the CA20 dataset showed significant positive biases for 100-m wind speeds along Northern California wind energy lease areas. To investigate the meteorological drivers for the model errors, we first consider two 1-yr simulations run with two different planetary boundary layer (PBL) parameterizations: the Mellor–Yamada–Nakanishi–Niino (MYNN) PBL scheme (the chosen configuration in the CA20 dataset) and the Yonsei University PBL scheme (which significantly reduces the bias in modeled winds). By comparing the 1-yr simulations to the concurrent lidar buoy observations, we find that errors are larger with the MYNN PBL scheme in warm seasons. We then dive deeper into the analysis by running simulations for short-term (3-day) case studies to evaluate the sensitivity of initial/boundary condition forcings on model results. By analyzing the short-term simulations, we find that during synoptic-scale northerly flows driven by the North Pacific high and inland thermal low, a coastal warm bias in the MYNN simulation is mainly responsible for the modeled wind speed bias by altering the boundary layer thermodynamics. The results of our analysis will help guide the creation of an updated version of the CA20 dataset.

17 WIND ENERGY↗
DOE OSTI2024

A Case Study Investigating the Low Summertime CAPE Behavior in the Global Forecast System

Convective available potential energy (CAPE) is an important index for storm forecasting. Recent versions (v15.2 and v16) of the Global Forecast System (GFS) predict lower values of CAPE during summertime in the continental United States than analysis and observation. We conducted an evaluation of the GFS in simulating summertime CAPE using an example from the Unified Forecast System Case Study collection to investigate the factors that lead to the low CAPE bias in GFS. Specifically, we investigated the surface energy budget, soil properties, and near-surface and upper-level meteorological fields. Results show that the GFS simulates smaller surface latent heat flux and larger surface sensible heat flux than the observations. This can be attributed to the slightly drier-than-observed soil moisture in the GFS that comes from an offline global land data assimilation system. The lower simulated CAPE in GFS v16 is related to the early drop of surface net radiation with excessive boundary layer cloud after midday when compared with GFS v15.2. A moisture-budget analysis indicates that errors in the large-scale advection of water vapor does not contribute to the dry bias in the GFS at low levels. Common Community Physics Package single-column model (SCM) experiments suggest that with realistic initial vertical profiles, SCM simulations generate a larger CAPE than runs with GFS IC. SCM runs with an active LSM tend to produce smaller CAPE than that with prescribed surface fluxes. Note that the findings are only applicable to this case study. Including more warm-season cases would enhance the generalizability of our findings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Evaluating Ensemble Predictions of South Asian Monsoon Low Pressure System Genesis

Abstract Synoptic-scale vortices known as monsoon low pressure systems (LPSs) frequently produce intense precipitation and hydrological disasters in South Asia, so accurately forecasting LPS genesis is crucial for improving disaster preparedness and response. However, the accuracy of LPS genesis forecasts by numerical weather prediction models has remained unknown. Here, we evaluate the performance of two global ensemble models—the U.S. Global Ensemble Forecast System (GEFS) and the Ensemble Prediction System of the European Centre for Medium-Range Weather Forecasts (ECMWF)—in predicting LPS genesis during the years 2021–22. The GEFS successfully predicted about half the observed LPS genesis events 1–2 days in advance; the ECMWF model captured an additional 10% of observed genesis events. Both models had a false alarm ratio (FAR) of around 50% for 1–2-day lead times. In both ensembles, the control run typically exhibited a higher probability of detection (POD) of observed events and a lower FAR compared to the perturbed ensemble members. However, a consensus forecast, in which genesis is predicted when at least 20% of ensemble members forecast LPS formation, had POD values surpassing those of the control run for all lead times. Moreover, probabilistic predictions of genesis over the Bay of Bengal, where most LPSs form, were skillful, with the fraction of ensemble members predicting LPS formation over a 5-day lead time approximating the observed frequency of genesis, without any adjustment or bias correction.

Suhas, D. L.↗
DOE OSTI2025

Demographic Microsimulator for Integrated Urban Systems: Adapting Panel Survey of Income Dynamics to Capture the Continuum of Life

Agent-based models (ABMs) in transportation modeling simulate activity and travel decisions at the disaggregate level of households and individuals. To do this, ABMs require detailed and realistic information on agents’ socioeconomic and demographic characteristics. Various synthetic population generators have been proposed to address this need. However, most of those currently in practice are cross-sectional in nature and do not account for the dynamics within households and individuals as they progress through life events over time. This is a major shortcoming, as literature has shown that transportation decisions are affected by the transition between and co-occurrence of life cycle events. While some demographic evolution simulators have been proposed to address this issue, they are developed using cross-sectional data and capture only a small set of life cycle events and their interdependence. Addressing these drawbacks, we propose a demographic microsimulator (DEMOS) that captures the “continuum of life” by considering a range of household- and individual-level life cycle events. DEMOS is developed using the Panel Survey of Income Dynamics, one of the world’s longest-running longitudinal surveys. The DEMOS submodels consider key life cycle events that are influenced by agents’ demographic variables. DEMOS is applied to evolve the population of the San Francisco Bay Area over a 9-year horizon. Results demonstrate how DEMOS generates life trajectories and how DEMOS outputs match the observed demographic trends. DEMOS is expected to enable longitudinal analysis in the context of ABMs and expand ABMs analyses relating to dynamic processes such as household-level vehicle transactions.

Demographic evolution↗
DOE OSTI2020

Understanding performance variability in standard and pipelined parallel Krylov solvers

In this work, we collect data from runs of Krylov subspace methods and pipelined Krylov algorithms in an effort to understand and model the impact of machine noise and other sources of variability on performance. We find large variability of Krylov iterations between compute nodes for standard methods that is reduced in pipelined algorithms, directly supporting conjecture, as well as large variation between statistical distributions of runtimes across iterations. Based on these results, we improve upon a previously introduced nondeterministic performance model by allowing iterations to fluctuate over time. We present our data from runs of various Krylov algorithms across multiple platforms as well as our updated non-stationary model that provides good agreement with observations. We also suggest how it can be used as a predictive tool.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Online data analysis and reduction: An important co-design motif for extreme-scale computers

A growing disparity between supercomputer computation speeds and I/O rates means that it is rapidly becoming infeasible to analyze supercomputer application output only after that output has been written to a file system. Instead, data-generating applications must run concurrently with data reduction and/or analysis operations, with which they exchange information via high-speed methods such as interprocess communications. The resulting parallel computing motif, online data analysis and reduction (ODAR), has important implications for both application and HPC systems design. Here we introduce the ODAR motif and its co-design concerns, describe a co-design process for identifying and addressing those concerns, present tools that assist in the co-design process, and present case studies to illustrate the use of the process and tools in practical settings.

Data Analysis↗
DOE OSTI2024

Ginkgo - A math library designed to accelerate Exascale Computing Project science applications

Large-scale simulations require efficient computation across the entire computing hierarchy. A challenge of the Exascale Computing Project (ECP) was to reconcile highly heterogeneous hardware with the myriad of applications that were required to run on these supercomputers. Mathematical software forms the backbone of almost all scientific applications, providing efficient abstractions and operations that are crucial to harness the performance of computing systems. Ginkgo is one such mathematical software library, nurtured by ECP, providing high-performance, user-friendly, and performance portable interfaces for applications in ECP and beyond. In this paper, we elaborate on Ginkgo’s philosophy of high-performance software that is sustainable, reproducible, and easy to use. We showcase the wide feature set of solvers and preconditioners available in Ginkgo and the central concepts involved in their design. We elaborate on four different ECP software integrations: MFEM, PeleLM + SUNDIALS, XGC, and ExaSGD that use Ginkgo to accelerate their science runs. Performance studies of different problems from these applications highlight the effectiveness of Ginkgo and the benefits incurred by these ECP applications.

Cojean, Terry↗
DOE OSTI2024

The ECP ALPINE project: In situ and post hoc visualization infrastructure and analysis capabilities for exascale

A significant challenge on an exascale computer is the speed at which we compute results exceeds by many orders of magnitude the speed at which we save these results. Therefore the Exascale Computing Project (ECP) ALPINE project focuses on providing exascale-ready visualization solutions including in situ processing. In situ visualization and analysis runs as the simulation is run, on simulations results are they are generated avoiding the need to save entire simulations to storage for later analysis. The ALPINE project made post hoc visualization tools, ParaView and VisIt, exascale ready and developed in situ algorithms and infrastructures. The suite of ALPINE algorithms developed under ECP includes novel approaches to enable automated data analysis and visualization to focus on the most important aspects of the simulation. Many of the algorithms also provide data reduction benefits to meet the I/O challenges at exascale. ALPINE developed a new lightweight in situ infrastructure, Ascent.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Portable, heterogeneous ensemble workflows at scale using libEnsemble

libEnsemble is a Python-based toolkit for running dynamic ensembles, developed as part of the DOE Exascale Computing Project. The toolkit utilizes a unique generator–simulator–allocator paradigm, where generators produce input for simulators, simulators evaluate those inputs, and allocators decide whether and when a simulator or generator should be called. The generator steers the ensemble based on simulation results. Generators may, for example, apply methods for numerical optimization, machine learning, or statistical calibration. libEnsemble communicates between a manager and workers. Flexibility is provided through multiple manager–worker communication substrates each of which has different benefits. These include Python’s multiprocessing, mpi4py, and TCP. Multisite ensembles are supported using Balsam or Globus Compute. We overview the unique characteristics of libEnsemble as well as current and potential interoperability with other packages in the workflow ecosystem. We highlight libEnsemble’s dynamic resource features: libEnsemble can detect system resources, such as available nodes, cores, and GPUs, and assign these in a portable way. These features allow users to specify the number of processors and GPUs required for each simulation; and resources will be automatically assigned on a wide range of systems, including Frontier, Aurora, and Perlmutter. Such ensembles can include multiple simulation types, some using GPUs and others using only CPUs, sharing nodes for maximum efficiency. We also describe the benefits of libEnsemble’s generator–simulator coupling, which easily exposes to the user the ability to cancel, and portably kill, running simulations based on models that are updated with intermediate simulation output. We demonstrate libEnsemble’s capabilities, scalability, and scientific impact via a Gaussian process surrogate training problem for the longitudinal density profile at the exit of a plasma accelerator stage. In conclusion, the study uses gpCAM for the surrogate model and employs either Wake-T or WarpX simulations, highlighting efficient use of resources that can easily extend to exascale.

Dynamic ensembles↗
DOE OSTI2022

Experimental study of the impact of scavenging efficiency on diesel combustion in an opposed-piston two-stroke engine

The opposed-piston two-stroke (OP2S) engine is a promising alternative powertrain technology that can offer thermal and brake efficiency improvements over conventional four-stroke engines. In recent years, many of the technical barriers of the OP2S engine architecture have been overcome. However, there is still a need for fundamental studies to provide insight into the scavenging and combustion processes of the OP2S engine to help design and operate the most efficient combustion systems using this engine architecture. This work aims to provide such insights by analyzing experimental data collected on a 3-cylinder, 4.9 L OP2S engine. Specifically, a scavenging efficiency sweep, an engine speed sweep with a constant scavenging efficiency, and an engine speed with a constant pressure differential across the engine were studied in detail. It was found that in diesel combustion, as the scavenging efficiency decreased, the increase in temperature of the hot, internal residuals resulted in a significant increase in heat transfer. Despite lowering pumping losses, this resulted in an overall decrease in brake efficiency. When the bulk thermodynamic conditions of two different scavenging efficiency cases (67% and 72%) were matched at port closing, the lower scavenging efficiency case still displayed a 0.7 percentage point penalty in net thermal efficiency and an increase in engine-out indicated specific emissions of NOx of 18% due to residual stratification in the cylinder. The results presented in this work show that the optimal breathing strategy in diesel combustion on an OP2S engine architecture is one that results in a slightly under-scavenged environment at port closing. However, the results did show potential system-level efficiency benefits of decreasing scavenging efficiency, meaning that alternative fuels and combustion strategies without the constraints of diesel combustion could achieve system-level efficiency gains by running significantly under-scavenged.

Engineering↗
DOE OSTI2024

An evaluation of GPT models for phenotype concept recognition

Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. The best run, using in-context learning, achieved 0.58 document-level F1 score on publication abstracts and 0.75 document-level F1 score on clinical observations, as well as a mention-level F1 score of 0.7, which surpasses the current best in class tool. Without in-context learning, however, performance is significantly below the existing approaches. Our experiments show that gpt-4.0 surpasses the state of the art performance if the task is constrained to a subset of the target ontology where there is prior knowledge of the terms that are expected to be matched. While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Male Runners With Lower Energy Availability Have Impaired Skeletal Integrity Compared to Nonathletes

Abstract Context Female athletes, particularly runners, with insufficient caloric intake for their energy expenditure [low energy availability (EA) or relative energy deficiency] are at risk for impaired skeletal integrity. Data are lacking in male runners. Objective To determine whether male runners at risk for energy deficit have impaired bone mineral density (BMD), microarchitecture, and estimated strength. Design Cross-sectional. Setting Clinical research center. Participants 39 men (20 runners, 19 controls), ages 16–30 years. Main Outcome Measures Areal BMD (dual-energy x-ray absorptiometry); tibia and radius volumetric BMD and microarchitecture (high-resolution peripheral quantitative computed tomography); failure load (microfinite element analysis); serum testosterone, estradiol, leptin; energy availability. Results Mean age (24.5 ± 3.8 y), lean mass, testosterone, and estradiol levels were similar; body mass index, percent fat mass, leptin, and lumbar spine BMD Z-score (−1.4 ± 0.8 vs −0.8 ± 0.8) lower (P < .05); and calcium intake and running mileage higher (P ≤ .01) in runners vs controls. Runners with EA <median had lower lumbar spine (−1.5 ± 0.7, P = .028), while runners with EA ≥median had higher hip (0.3 ± 0.7 vs −0.4 ± 0.5, P = .002), BMD Z-scores vs controls. After adjusting for calcium intake and running mileage, runners with EA <median had lower mean tibial total and trabecular volumetric BMD, trabecular bone volume fraction, cortical porosity, and apparent modulus vs controls (P < .05). Appendicular lean mass and serum estradiol (R ≥ 0.45, P ≤ .046), but not testosterone, were positively associated with tibial failure load among runners. Conclusions Despite weight-bearing activity, skeletal integrity is impaired in male runners with lower caloric intake relative to exercise energy expenditure, which may increase bone stress injury risk. Lower estradiol and lean mass are associated with lower tibial strength in runners.

Haines, Melanie S. (ORCID:0000000310024754)↗
DOE OSTI2023

Endurance Exercise Performance Is Reduced after 6-h Dives at 1.35 ATA When Breathing 100% Oxygen Compared with Air

ABSTRACT Introduction Long-duration dives on consecutive days reduces muscular performance, potentially affecting military personnel. However, a paucity of data exists on how breathing gases affect endurance performance. This study examined the influence of long-duration diving with different breathing gases on aerobic endurance and handgrip performance. Methods Twenty-three military divers completed a single 6-h dive (single dive [SD]) and five 6-h dives over consecutive days (dive week [DW]) with 30-min cycling intervals using air (AIR,n= 13) or 100% oxygen (OXY,n= 10). Before and after SD and DW, subjects completed a maximum handgrip strength test, a handgrip endurance test at 40% maximal strength, and a time to exhaustion run. Results Handgrip endurance decreased after DW in OXY (SD, 1.9 ± 0.0 vs 1.4 ± 0.3 min) compared with AIR (1.8 ± 0.0 vs 1.8 ± 0.2 min) (P< 0.001). Run time decreased after SD (Pre, 20.7 ± 10.4 min; Post, 16.6 ± 7.6 min;P= 0.039) and DW (Pre, 21.6 ± 9.0 min; Post, 11.2 ± 4.0 min;P< 0.001) in OXY and after overall diving in AIR (Pre, 26.5 ± 10.2 min; Post, 22.3 ± 7.5 min;P= 0.025). V̇O 2 decreased after diving only in AIR (Pre, 42.6 ± 3.4 mL·kg −1 ⋅min −1 ; Post, 40.4 ± 3.7 mL·kg −1 ⋅min −1 ;P= 0.010). There were no other significant effects. Conclusions Breathing 100% oxygen during long-duration dives on consecutive days may exacerbate decreases in aerobic endurance and impairs handgrip endurance compared with air. Additional research is needed to elucidate mechanisms of action and possible mitigation strategies.

Sport Sciences↗
DOE OSTI2026

Data for "Quantifying the Propagation of Parametric Uncertainty on Flux Balance Analysis"

In the repository are example scripts that perform uncertainty injection and propagation to flux balance analysis with outputs for a small sample size (for demonstration purpose only). For proper analysis, user should download the scripts and run for a large sample size (e.g., 10,000 samples). If you use the scripts, please cite the following Metabolic Engineering article: “Quantifying the propagation of parametric uncertainty on flux balance analysis” (https://doi.org/10.1016/j.ymben.2021.10.012) There are two subdirectories: /uncFBA/uncBiom: injection of normally distributed noise to biomass precursor coeffcients and ATP maintenance (growth-associated ATP maintenance (GAM) and non-growth associated ATP maintenance (NGAM)) /uncFBA/uncRHS: departure from steady-state by adding noise drawn from normal distribution to the RHS terms of mass balance constraints

Metabolomics↗