SEARCH · Search NASA

Results for “Replication”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Enhancing 2D hydrodynamic flood models through machine learning and urban drainage integration

Two-dimensional hydrodynamic flood models are commonly employed for simulating flood extent and inundation depth. However, the influence of urban drainage network (UDN) is frequently overlooked in these models, potentially compromising their accuracy. Furthermore, the expensive computational costs and longer processing times make them challenging for large-scale hydrodynamic simulation. To address these challenges, this paper develops a machine learning (ML)-driven emulator for an open-source flood model, the Two-dimensional Runoff Inundation Toolkit for Operational Needs (TRITON). A TRITON-ML Emulator (TR-Emulator) that utilizes Convolutional Long Short-Term Memory is developed to capture the spatiotemporal features of flood events based on the outputs from TRITON. We further enhance the emulator by integrating UDN parameters (TR-UDN), such as the flow capacity of drainage pipes, pipe size, and pipe length, via an ML stacking technique to improve the water surface elevation (WSE) simulation. Hurricane Harvey 2017 in Houston, TX is used as the case study. We compare WSE results from TRITON, TR-Emulator, TR-UDN, and the United States Geological Survey (USGS) observations to evaluate the performance of these models. The results indicate that the TR-Emulator effectively replicates the WSE simulated by TRITON. Additionally, TR-UDN performs well in capturing WSE patterns and peak flows, aligning more closely with USGS observations, except in areas with milder slopes where conveyance discrepancies are observed. We further test the generalizability of our ML-based models using another smaller event. This paper shows that the TR-Emulator is effective for users and engineers to emulate a 2D hydrodynamic model, and the enhanced version of the TR-Emulator, TR-UDN, can be an efficient tool for predicting WSEs during urban flooding.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Substituent size versus metal binding of inhibitors with variants of influenza endonuclease

The influenza virus causes a significant burden of illness each year. Although vaccination is the most effective method to prevent seasonal influenza infection, viral escape mechanisms make vaccine composition difficult to predict. Antivirals are crucial for decreasing rates of morbidity and mortality from influenza viral infection. The newest anti-influenza drugs target the RNA-dependent RNA polymerase acidic N-terminal (PA N ) endonuclease, a critical component of influenza viral replication machinery. This study examines the structure of inhibitors of PAN that utilize a hydroxypyridinone-based metal-binding pharmacophore (MBP). Specifically, this report explores how the size of substituent groups impacts the binding conformation and affinity of a series of compounds against both wild-type (WT) and resistance mutant strains, I38T and E23K. Co-crystal structures revealed that the distance between compounds and enzyme residue 38 was conserved to maintain strong interactions, resulting in deviations from ideal coordination geometries at the active site metal centers. This suggests the interactions with residue 38 with each compound is important and can impact inhibitor potency as a consequence of distortions in the metal binding geometry of the compounds.

Endonuclease↗

DOE OSTI2024

Comparison of hardening and microstructures of ferritic/martensitic steels irradiated with fast neutrons and dual ions

Ferritic/martensitic steels T91 and HT9 were irradiated with neutrons (BOR-60 reactor) and dual ions (9 MeV Fe 3+ and 3.42 MeV energy degraded He 2+ ) from 369 to 520 °C and damage levels of 16.6 to 72 dpa to quantify the possibility of using ion irradiation to simulate neutron irradiation in terms of microstructures and mechanical properties. Nanoindentation testing was performed to obtain the bulk equivalent hardness of the dual-ion irradiated samples. For the neutron irradiated samples, both nanoindentation and Vickers hardness testing were conducted. Transmission Electron Microscopy (TEM) characterizations of the cavities, dislocation loops and precipitates were conducted to account for the strengthening contribution of each microstructure element. The good agreement between the microstructure-predicted (dispersed barrier hardening) and measured strength of the irradiated specimens demonstrated the accuracy of the strengthening model and the nanoindentation tests. Furthermore, the comparison of mechanical property and microstructure changes in ion and neutron irradiated structural materials indicated that ion irradiation replicated many neutron irradiation features. However, a single 70 °C temperature shift is insufficient to match all complex microstructures of neutron vs. ion irradiation over the irradiation temperature range of 369–520 °C.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Discerning the effect of various irradiation modes on the corrosion of Zircaloy-4

Using proton irradiation, this study investigates the individual influence of several factors on the corrosion kinetics of Zircaloy-4 in a hydrogenated water environment simulating a Pressurized Water Reactor (PWR). Using both simultaneous irradiation-corrosion and autoclave corrosion, we separately examine: (i) the effect of pre-irradiation on modifying the structure of the material, (ii) the impact of irradiation on creating defects in the growing oxide layer during corrosion, and (iii) the influence of irradiation on increasing the corrosion potential through radiolysis during corrosion. To replicate neutron-irradiated microstructure, two proton pre-irradiation schedules were employed: Schedule 1 (isothermal irradiation at 350 °C to 5 dpa) to simulate high-temperature PWR conditions, and Schedule 2 (two-step process: irradiation to 2.5 dpa at -10 °C followed by 2.5 dpa at 350 °C) to simulate lower temperature PWR and Boiling Water Reactor (BWR) conditions. Long-term autoclave corrosion testing over 360 days at 320 °C revealed no significant difference between unirradiated samples and those pre-irradiated according to either schedule, with all samples exhibiting sub-cubic kinetics within the pre-transition regime. Irradiated samples underwent Simultaneous Irradiation Corrosion (SIC) tests, corroding in 320 °C water while being irradiated with protons. Corrosion was found to accelerate in all SIC-tested samples relative to autoclave conditions, with the greatest increase observed in non-pre-irradiated samples. Pre-irradiation with either schedule resulted in a slower corrosion rate compared to non-pre-irradiated regions under SIC conditions. The degree of radiolysis observed in the SIC tests surpassed typical PWR conditions, approaching levels found in BWRs. Radiolysis products were identified as the primary contributors to accelerated corrosion, corroborated by radiolysis bar tests. Furthermore, these findings underscore the intricate interactions between irradiation, corrosion, and water chemistry in determining Zircaloy-4 corrosion kinetics within nuclear reactor environments.

Pressurized Water Reactor↗

DOE OSTI2026

Effect of spacer grids on high-burnup fuel fragmentation, relocation, and dispersal

Increasing the fuel burnup limit in light-water reactors to improve fuel cycle economics requires a strong technical foundation. Experimental observations from the Halden and Studsvik programs have revealed severe fuel fragmentation during loss-of-coolant accident (LOCA) conditions, highlighting the need for additional technical evaluation. Consequently, further LOCA test data are needed to complement existing findings and improve the understanding of fuel fragmentation, relocation, and dispersal (FFRD) behavior. Oak Ridge National Laboratory’s Severe Accident Test Station has played a significant role in advancing the understanding of high-burnup fuel fragmentation, relocation, and dispersal phenomena. One remaining gap in the available experimental database is the effect of fuel assembly structural features on cladding deformation behavior during a LOCA, and more specifically, their impact on the fuel’s ability to fragment, relocate, and disperse. Recent analyses using the BISON fuel performance code suggest that cladding deformation near grid spacers will remain below the 3% threshold that has been reported in the NRC Research Information Letter, indicating that the cladding could remain mechanically constrained during the LOCA event. This paper builds upon the BISON analyses to design and conduct a series of out-of-cell tests aimed at further evaluating cladding deformation in and around grid spacers. In addition, these tests were used to assess local cladding temperature conditions and compare them against analytical predictions in order to better replicate expected in-reactor behavior. Finally, an in-cell high-burnup LOCA test was designed and performed to evaluate the effects of a grid spacer, or cladding restraint, on fuel fragmentation, relocation, and dispersal susceptibility. The high-burnup test results differed from those of historical LOCA experiments, with a recorded rupture temperature of 861°C. Two ballooned regions and corresponding rupture openings were observed, with rupture widths of approximately 0.64 mm for both ruptures and rupture lengths of 4.8 mm and 5.6 mm, respectively.

Capps, Nathan [ORNL]↗

DOE OSTI2024

An in situ imaging investigation of the effect of gas flow rates on directed energy deposition

Gas flow rates in Directed Energy Deposition (DED) Additive Manufacturing (AM) can significantly affect the quality of built parts by altering melt pool geometry. Using a DED process replicator and in situ synchrotron radiography, together with analogous experiments in an industrial DED machine, we investigate the impact of carrier gas and shield gas flow rates on build quality. The results reveal that there is a critical shield gas flow rate above which melt pools are flattened, tracks widen, and thus layer thickness decreases. The reduction in layer thickness is most prominent in conditions with low carrier gas flow rate, as the highly turbulent shield gas flow may divert slow moving powder particles away from the melt pool, decreasing capture efficiency. Very high flow rates increase internal porosity, as fast-moving particles impacting the melt pool surface can entrain chamber gas behind them. High gas flow rates also cool the melt pool, creating shallower melt pools with increased thermal gradients near the solidification front, increasing pore entrapment in the solidified track.

Additive manufacturing↗

DOE OSTI2025

Development of a high-throughput method for processing sponge-stick samples to detect viable Bacillus anthracis spores

Since the national validation of the sponge-stick based method for detection of Bacillus anthracis spores in environmental samples, there have not been focused efforts to address the low throughput nature of the method, which processes only one sample at one time. Sample processing remains a serious bottleneck for rapidly analyzing large numbers of samples expected from a biological warfare attack. Therefore, we developed a high-throughput method to simultaneously process multiple sponge-stick samples to be better prepared for rapid response and recovery after wide area anthrax incidents. In this method, sponges are placed in 50 mL tubes containing 25 mL extraction buffer and shaken to release spores, after which the suspension is recovered for analysis. Here, we determined that an additional extraction step, conducted in the same tubes with 10 mL buffer, further increased spore recovery from sponge-stick by approximately 10 %. We determined that orbital shaking and multi-tube vortexing were both more effective than reciprocating shaking for recovering spores. We conducted simultaneous processing of up to 12 sponge-stick samples and demonstrated comparable spore recovery efficiencies to the traditional low-throughput stomacher-based method (approximately 60 % recovery at 10 2 -spore level and 75 % recovery at 10 4 -spore level for both methods in three replicate experiments, P > 0.05 for two-tailed t-tests for each experiment and spore level). We also demonstrated that our high-throughput method could be integrated with Rapid Viability-Polymerase Chain Reaction (RV-PCR) analysis and could detect levels as low as 40 spores per sponge even when challenged by a PCR particulate contaminant.

Anthrax↗

DOE OSTI2024

Neural network interatomic potential-driven analysis of phase stability in Ti–V alloys at the atomistic scale

The evolution of the ω phase in titanium–vanadium (Ti–V) alloys is critical for their mechanical properties, particularly in aerospace and biomedical applications. Here, this study employs a Rapid Artificial Neural Network (RANN) potential to model the ω phase evolution at the atomistic level, demonstrating a high degree of consistency with experimental observations, unlike the Modified Embedded Atom Method (MEAM), which fails to capture this phase transformation accurately. RANN simulations replicate key phenomena such as the nucleation of α precipitates at ω/β interfaces and accurate lattice orientations, enhancing our understanding of phase stability and transformation kinetics. The findings affirm that RANN potentials can significantly improve the prediction accuracy of complex material behaviors, offering a powerful tool for designing advanced materials with tailored properties such as solute effect in various stacking fault energies. This approach not only bridges the gap between theoretical predictions and empirical data but also sets a new direction for future research in materials science, emphasizing the integration of machine learning techniques in the development and optimization of new alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Vascular endothelial growth factor receptor-1 (FLT1) interactions with amyloid-beta in Alzheimer’s disease: A putative biomarker of amyloid-induced vascular damage

We have identified FLT1 as a protein that changes during Alzheimer's disease (AD) whereby higher brain protein levels are associated with more amyloid, more tau, and faster longitudinal cognitive decline. Given FLT1's role in angiogenesis and immune activation, we hypothesized that FLT1 is upregulated in response to amyloid pathology, driving a vascular-immune cascade resulting in neurodegeneration and cognitive decline. We sought to determine (1) if in vivo FLT1 levels (CSF and plasma) associate with biomarkers of AD neuropathology or differ between diagnostic staging in an aged cohort enriched for early disease, and (2) whether FLT1 expression interacts with amyloid on downstream outcomes, such as phosphorylated tau levels and cognitive performance. Additionally, we sought to replicate FLT1 interactions in the brain. The results showed that higher levels of FLT1 in CSF and post-mortem brain tissue related to increased tau, particularly among amyloid positive individuals. These analyses help clarify the potential utility of FLT1 as a biomarker among individuals with evidence of brain amyloidosis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Evaluation of neutron dosimetry capabilities with the MC-15 portable multiplicity counter

This work proposes a preliminary neutron dose rate estimation method for a neutron multiplicity detector through measurement- and simulation-based analyses. Uncharacterized neutron-emitting sources may be encountered in situations such as nuclear emergency response, safeguards, and treaty verification. These circumstances may present irradiation risk to personnel conducting field assay, search, and characterization measurements. It is therefore of interest to provide a field neutron dosimetry capability with the existing neutron multiplicity counting (NMC) capabilities. To date, no commercially-available neutron detection systems are capable of both accurate NMC and real-time neutron dosimetry. This work will focus on estimating dose rate using input from a single fielded NMC called the MC-15. The energy-dependent neutron detection efficiency response of the MC-15 was quantified in monoenergetic neutron simulations and evaluated in response to two neutron-emitting sources and to a polyethylene-moderated source. The results were compared to existing neutron dosimeters and established the proof of concept for further investigation of the MC-15 for dose estimation. Measurement results were also replicated in simulations; additional simulations were then conducted to expand upon the limited empirical data. The initial empirical results provided a conversion factor appropriate for use when measuring 252 Cf neutrons that is independent of polyethylene shielding presence and thickness. The simulated data sets were then used to evaluate a fit equation allowing estimation of the neutron dose rate for less restricted geometric configurations and dependent only on the distance between the source and the detector. Additionally, the energy dependence of the efficiency response indicates that further empirical evaluations could provide energy-dependent conversion factors for broader neutron dosimetry capabilities with a wider range of neutron-emitting sources.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Scalability analysis of heavy-duty gas turbines using data-driven machine learning

With the increasing integration of variable renewable energy sources into power systems, the role of flexible power generation technologies like gas turbines (GT) in rapid grid balancing remains crucial. This sustained importance underscores the need for scaled and precise modeling of GT to ensure effective integration within evolving energy frameworks. While physics-driven GT models integrate thermodynamics, fluid dynamics, and combustion principles, they often rely on approximate mathematical representations to accommodate scaling that may not capture the actual complex dynamics for GTs and inertial effects associated to GTs with different ratings. In this study, a data-driven model is proposed using machine learning (ML) techniques to conduct GT scalability analysis and performance evaluation with high accuracy. The ML model, trained on data from various operating conditions and performance parameters, aims to uncover intricate relationships and patterns, resembling GT characteristics at different scales (ratings). The model is developed to capture complex system interaction and to adapt to changing operational scenarios at different capacities, providing valuable insights of power system dynamics. In this study, the real-time digital simulator platform was employed to generate training data for the ML model and assess its dynamic characteristics. The ultimate objective was to develop a detailed modeling framework based on governing equations and data-driven ML capable of predicting key performance indicators, in thermal systems such as GTs, including power output, speed, fuel consumption, and exhaust temperature under diverse operating conditions at different scales. The developed ML framework demonstrated high accuracy, with mean relative errors for GT power prediction, reference speed, exhaust temperature, and compressor pressure ratio (CPR) parameters consistently below 0.1% across typical load fluctuation scenarios. Maximum deviations were limited to approximately 0.5 K for exhaust temperature and 0.009 for CPR, underscoring the model’s ability to replicating dynamic GT behavior with high precision. The adaptability of the ML model enables its application across diverse operational conditions and its extension to other thermal systems. By leveraging advanced ML techniques, this study presents a robust and scalable modeling framework that enhances GT simulation precision, facilitating improved integration into evolving power systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Measurement of top-quark pair production in association with charm quarks in proton–proton collisions at √s = 13 TeV with the ATLAS detector

Inclusive cross-sections or top-quark pair production in association with charm quarks are measured with proton-proton collision data at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 140 fb -1 , collected with the ATLAS experiment at LHC between 2015 and 2018. The measurements are performed by requiring one or two charged leptons (electrons and muons), two b-tagged jets, and at least one additional jet in the final state. A custom flavor-tagging algorithm is employed for the simultaneous identification of b-jets and c-jets. In a fiducial phase space that replicates the acceptance of the ATLAS detector, the cross-sections for $t\bar{t}$ + ≥ 2c and $t\bar{t}$ + 1c production are measured to be $1.28^{+0.27}_{-0.24}$ pb and $6.4^{+1.0}_{-0.9}$ pb, respectively. The measurements are primarily limited by uncertainties in the modeling of inclusive $t\bar{t}$ and $t\bar{t}$ + $b\bar{b}$ production, in the calibration of the flavor-tagging algorithm, and by data statistics. Cross-section predictions from various $t\bar{t}$ simulations are largely consistent with the measured cross-section values, though all underpredict the observed values by 0.5 to 2.0 standard deviations. In a phase-space volume without requirements on the $t\bar{t}$ decay products and the jet multiplicity, the cross-section ratios of $t\bar{t}$ + ≥ 2c and $t\bar{t}$ + 1c to total $t\bar{t}$ + jets production are determined to be (1.23 ± 0.25)% and (8.8 ± 1.3)%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Visualization of post-detonation fireball flowfields and comparison to CFD modeling

Visualization of flow structures within post-detonation fireballs has been performed for benchmark validation of numerical simulations. Custom pressed PETN explosives with a 12-mm diameter hemispherical form factor were used to produce a spherically symmetric post-detonation flow with low soot yield. Hydroxyl-radical planar laser induce fluorescence (OH-PLIF) was employed to visualize the structure ranging from approximately 10 μs to 35 μs after shock breakout from the explosive pellet. Fireball simulations were performed using the HyBurn Computational Fluid Dynamics (CFD) package. Experimental OH-PLIF results were compared to synthetic OH-PLIF from post-processing of CFD simulations. From the comparison of experimental and synthetic OH-PLIF images, CFD is shown to replicate much of the flow structure observed in the experiments, revealing potential differences in turbulent length scales and OH kinetics. Furthermore, results provide significant advancement in experimental resolution of these harsh turbulent combustion environments and validate physical models thereof.

Detonator↗

DOE OSTI2026

Filling the cellulosic bio-economy gap by utilizing a wedge approach combined with stakeholder collaboration

The price gap between the market and breakeven prices of cellulosic biomass for farmers represents a significant barrier to the development of a low-carbon cellulosic bioeconomy. Using a bottom-up, agent-based modeling tool that replicates the behaviors and interactions of key stakeholders, this study analyzes the emergence of a cellulosic bioeconomy at the local scale through a wedge approach that examines an integrated portfolio of multiple policy options, including subsidies for small-scale bioproducts and environmental credits. Here, the role of collaboration among multiple stakeholders, such as biomass producers (farmers), bio-refinery industry, government, and society, is assessed for filling the price gap. Using the Sangamon River Basin as a case study site, we evaluate the effectiveness of the wedge approach by comparing simulation results from multiple scenarios, each incorporating different combinations of bioeconomy wedges, with and without stakeholder collaboration. Results underscore that active collaboration among stakeholders acts as a catalyst enlarging the effectiveness of bioeconomy wedges. Including the carbon credits and environmental value in the policy portfolio is found to bridge the price gap through collective contributions from diverse stakeholders, where the cellulosic biofuel and bioproduct industry plays a pivotal role. Although this study is conducted at the local watershed scale, the methodology and findings offer valuable insights for market development in other watersheds and the potential scaling of local markets to regional and national levels.

09 BIOMASS FUELS↗

DOE OSTI2025

Beneath the surface: Unsolved questions in soil virus ecology

Soil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research studies, many fundamental questions remain unanswered, and a range of technical and bioinformatic challenges need to be overcome. In this perspective article, we present a series of key questions that highlight fruitful research areas for ongoing and future efforts. These include describing the challenges involved in understanding soil viral abundance and activity, spatiotemporal dynamics, life strategy prevalence, virus-mediated biogeochemical impacts, viral protein function, host prediction, and soil RNA virus discovery. In the near term, combining approaches (e.g., cultivation-based, meta-omics, biogeochemical, experimental, and bioinformatic) will be key to assessing the ecological and biogeochemical impacts of soil viruses from the microscopic to the field and global scales. Still, we stress that results must be tempered by current methodological limitations and highlight knowledge gaps that are most pressing to fill via new methods or measurements, such as the prevalence of different viral replication strategies across soils, the fate of microbial necromass carbon after viral lysis, the frequency of virus-host encounters that do not lead to successful infections yet could be bioinformatically mistaken as infections, and the diversity and ecological impacts of RNA viruses in soil.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Phosphate amendment drives bloom of RNA viruses after soil wet-up

Soil rewetting after a dry period results in a surge of activity and succession in both microbial and DNA virus communities. Less is known about the response of RNA viruses to soil rewetting—while they are highly diverse and widely distributed in soil, they remain understudied. We hypothesized that RNA viruses would show temporal succession following rewetting and that phosphate amendment would influence their trajectory, as viral proliferation may cause phosphorus limitation. Using 39 time-resolved metatranscriptomes and amplicon data, 2190 RNA viral populations were identified across five phyla, with 26 % of these predicted to infect bacteria, and 11 % fungi. Only 1.2 % of viral populations had annotated capsid genes, suggesting most persist via intracellular replication without a free virion phase. Phosphate amendment altered RNA viral community composition within the first week and amended vs. unamended communities remained distinguishable for up to three weeks. While the overall host community remained stable, certain bacterial populations showed reduced abundance in phosphate-amended soils, likely due to increased viral lysis, as RNA bacteriophages proliferated significantly. Notably, 60 % of the viruses with increased abundance under phosphate amendment belonged to basal Lenarviricota clades rather than well-known groups like Leviviricetes. We estimate RNA bacteriophage infections may affect 10 7 –10 9 bacteria per gram of soil, aligning with the total bacterial population (10 7 –10 10 g -1 soil), suggesting that RNA phages significantly influence bacterial communities post-wet-up, with phosphorus availability modulating this effect.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

A consumer-centric approach to quantify efficiency of receiving goods purchased via online

Virtual participation in shopping activities has increased exponentially in the past four years compared to the last couple of decades. E-tailing or online shopping offers the convenience of goods reaching a consumer instead of a consumer traveling to a store, but it has downsides like geographical service variability and negative social externalities such as increased energy consumption and emissions. This study proposes a novel approach to quantify e-tailing efficiency from the consumers’ viewpoint. The methodology is innovative in its integration of accessibility theory with energy and cost impedance factors and consideration of delivering and picking up goods purchased via online. The methodology is implemented for the San Francisco Bay Area and is subject to scenarios that see enhancements to various facets of online shopping delivery. Results demonstrate that increasing the frequency of e-commerce deliveries helps improve e-tailing efficiency in rural locations, while improvements in energy and cost aspects of delivery modes are seen to improve e-tailing efficiencies in the central parts of the region. The approach proposed can provide valuable insights on where people have limited benefits from online shopping and how emerging delivery mechanisms can change the quality of the e-commerce experience within a city. This research offers a replicable framework for assessing e-commerce systems in diverse geographic contexts, contributing to the development of equitable and environmentally sustainable urban freight systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

PET-FBA: A lightweight enzyme allocation and thermodynamics-constrained flux analysis approach to explore Escherichia coli metabolic adaptation to intracellular acidification

Escherichia coli employs diverse strategies to adapt to acidic environments that disrupt enzyme activity and the thermodynamic feasibility of essential reactions. To understand the impact of pH stress on cell metabolism, we present the PET-FBA (pH-, Enzyme protein allocation-, and Thermodynamics-constrained Flux Balance Analysis) framework. PET-FBA extends genome-scale modeling by integrating enzyme protein costs and reaction Gibbs free energy changes. Additionally, by incorporating pH-dependent enzyme kinetics in response to intracellular acidification, this framework enables the simulation of E. coli's metabolic adjustments across varying external pH levels. The model's accuracy is validated by comparing in silico growth simulations with experimental measurements under both anaerobic and aerobic conditions, as well as in silico gene knockouts of essential genes. By explicitly incorporating pH effects, our model accurately replicates the metabolic shift towards lactate production as the primary fermentation product at low pH in anaerobic conditions. This shift is only predicted when enzyme kinetics are dynamically adjusted as a function of pH. Further analysis revealed that this shift can be attributed to the reduced protein efficiency of the acetyl-CoA branch compared to lactate dehydrogenase under acidic stress, which then becomes crucial for maintaining NAD regeneration and cell growth at low pH. Furthermore, we identified strategies for enhancing cell growth under acidic anaerobic conditions by improving the enzyme activity of lactate dehydrogenase and pyruvate formate lyase, which increases NAD production efficiency and reduces enzyme protein allocation costs. Designed as a lightweight yet versatile framework, PET-FBA enables efficient genome-scale metabolic analysis. Using E. coli as a model system, our framework provides a systematic approach to understanding metabolic responses to environmental stress, pinpointing key metabolic bottlenecks, and identifying potential targets for strain optimization.

42 ENGINEERING↗