Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “learning rate”

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.

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

At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Cost of Offshore Wind Energy in the United States From 2025 to 2050

This study presents estimates of the levelized cost of energy (LCOE) of offshore wind energy throughout major U.S. coastal regions between a time frame of 2025 - 2050. The LCOE modeling accounts for impacts of supply chain shocks, inflation, and rising interest rates on cost. Given the near-term uncertainty in these factors, we present three possible scenarios driven by how uncertainty in costs, technology, and deployment may evolve over time. The cost increases reported by industry in recent years will likely be felt over next several years, but we expect long-term cost reductions enabled by growing offshore wind deployment and industry learning. This study helps inform decision-makers about the potential role that offshore wind energy can play in future clean energy strategies.

17 WIND ENERGY↗
DOE OSTI2021

Machine learning enables national assessment of wind plant controls with implications for land use

Summary As deployment of wind energy continues to expand, computationally efficient tools for predicting wind plant performance over a wide range of layout designs, technology innovations, and spatial locations are increasingly important for policy and investment decisions. We demonstrate two approaches to training a surrogate model to predict annual energy production (AEP) of parameterized wind plant layouts: one using a Gaussian process (GP) and the other using a fully convolutional neural network (FCNN). We leverage the powerful FCNN architecture by encoding wind plant design parameters and output response surface as an image. The FCNN produces more accurate results than the GP with mean absolute errors equivalent to 1% and 1.9% of plant rated power, respectively, although the GP performs well under limited training data and provides useful uncertainty information. We also evaluate a surrogate model for wake steering, enabling a nationwide assessment of the impact of plant control strategies and plant layout decisions. Across two million locations, we find that wake steering strategies boost AEP with relative gains upwards of 3%. Gains are most pronounced at sites without a dominant wind direction and where layout optimization is less fruitful. Additionally, we perform a nationwide sensitivity analysis showing that wake steering can mitigate wake losses from higher density plant layouts. Our results suggest that regions which have not been previously viable for wind deployment due to moderate wind resources are especially well enhanced by wake steering strategies that could help overcome land constraints and inflexible layout options, potentially identifying new deployment opportunities.

17 WIND ENERGY↗
DOE OSTI2021

Lessons Learned in Employing Data Analytics to Predict Oxidation Kinetics and Spallation Behavior of High-Temperature NiCr-Based Alloys

Machine learning (ML) can offer many advantages in predicting material properties over traditional materials development methods based solely on limited experimental investigations or physical-based simulations with the capability to reduce development cost, risk, and time. However, so far, limited efforts have been made to predict alloy oxidation kinetics and spallation behavior via ML due to the lack of consistently measured and sufficient experimental data and the inherent complexity in oxidation behavior of multicomponent high-temperature alloys. A previous study reported the ability of ML to predict oxidation kinetics of NiCr-based alloys as a function of alloy composition and operating conditions. Here, the performance of a ML model in predicting rate constants and spallation probability was evaluated in light of the roles of the data distribution of the experimental dataset (data analytics), the alloy composition, the exposure environment and the chosen oxidation approach to extracting kinetic values from the measured mass changes (but using either a simple parabolic law or a statistical cyclic oxidation model). Potential strategies to improve the predictions and enhance the extrapolative capability of the previously trained model will be discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Real-time optimization of multi-cell industrial evaporative cooling towers using machine learning and particle swarm optimization

Existing electrical generating stations must operate with greater flexibility due to increasing renewable energy penetration on the electrical grid, and many coal-fired power stations have transitioned away from baseload operation to load-following operation to aid in grid stability. In cases where multiple independently controlled cooling tower cells are used in parallel for the cooling purposes of such stations, there is an opportunity to increase plant efficiency through data-driven optimization across their full load ranges. This work presents a novel application of real-time optimization using machine learning and particle swarm optimization on a multi-cell induced-draft cooling tower servicing a coal-fired power station under variable load. This is the first work to demonstrate simultaneous optimization of a multi-cell cooling tower, in addition to using machine learning for closed-loop control on a cooling tower. A novel control configuration is presented that ensures original control logic is not adversely affected and that the overall plant process is not disrupted using only existing hardware and operational data. To verify this methodology, the 12 independent cooling tower cells are simulated in parallel using historic operating data to demonstrate the effectiveness of real-time optimization compared to current practice. An artificial neural network is trained to predict overall cooling tower power consumption using only operational data and ambient conditions with an R2 value of greater than 0.96. The real-time optimization using particle swarm yields 6.7% annual energy usage savings compared to current practices, although the extent of the real-time savings varies greatly with both plant load and environmental conditions. This is particularly significant for a variable load situation because frequent ramping typically results in reduced overall efficiency. Furthermore, this proposed AI-based solution presents an opportunity to improve the overall heat rate of a load-following coal-fired power plant without the need to perform extensive first-principles modeling or add additional hardware to the cooling tower, resulting in more resources conserved and less overall emissions per unit of electricity generated.

42 ENGINEERING↗
DOE OSTI2023

Generating Co-expression Networks for Three Cyanobacteria: Synechococcus sp. PCC 7942, Synechococcus sp. PCC 7002, Synechocystis sp. PCC 6803

Cyanobacteria are photosynthetic organisms capable of high growth rate and represent a promising bioplatform for harnessing the sun’s energy to make biofuel. Additionally, the process of photosynthesis absorbs CO2 from the environment. Understanding the metabolic processes involved in photosynthesis could lead to solutions to the recent rise of CO2 concentration in Earth’s atmosphere and the associated climate change. More research on the transcriptional regulation of these cells is needed to learn how to harness the untapped potential of cyanobacteria for these applications. Transcriptional analysis via RNA-seq provides an understanding of how gene expression changes at the mRNA level under diverse growing conditions. I systematically collected and analyzed RNA-Seq data obtained under a variety of conditions and available on the NCBI database for three cyanobacteria model organisms: Synechococcus elongatus sp. PCC 7942, Synechococcus sp. PCC 7002, and Synechocystis sp. PCC 6803. For each organism, the data was mapped to a reference genome to characterize the RNA expression profile. Samples were checked for quality based on the number of reads and the correlation of the expression profile between labeled replicates. All samples were transformed into transcripts per million reads, followed by a log transformation to account for the wide range of sample sizes. Gene co-expression networks were generated and analyzed for each species using Cytoscape. These networks provide a base level of gene expression for each species. The network topology and high-betweeness nodes of these networks need to be analyzed further to provide insight on potential ways to harness cyanobacteria genetics. Additionally, these datasets can be used together to form a core genome network analysis- one that includes only the genes that are homologous between the three species. This project has prepared the way for a more in-depth study on photosynthetic microbes on a genetic level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Deep learning models for interpretation of point of care ultrasound in military working dogs

Introduction: Military working dogs (MWDs) are essential for military operations in a wide range of missions. With this pivotal role, MWDs can become casualties requiring specialized veterinary care that may not always be available far forward on the battlefield. Some injuries such as pneumothorax, hemothorax, or abdominal hemorrhage can be diagnosed using point of care ultrasound (POCUS) such as the Global FAST® exam. This presents a unique opportunity for artificial intelligence (AI) to aid in the interpretation of ultrasound images. In this article, deep learning classification neural networks were developed for POCUS assessment in MWDs. Methods: Images were collected in five MWDs under general anesthesia or deep sedation for all scan points in the Global FAST® exam. For representative injuries, a cadaver model was used from which positive and negative injury images were captured. A total of 327 ultrasound clips were captured and split across scan points for training three different AI network architectures: MobileNetV2, DarkNet-19, and ShrapML. Gradient class activation mapping (GradCAM) overlays were generated for representative images to better explain AI predictions. Results: Performance of AI models reached over 82% accuracy for all scan points. The model with the highest performance was trained with the MobileNetV2 network for the cystocolic scan point achieving 99.8% accuracy. Across all trained networks the diaphragmatic hepatorenal scan point had the best overall performance. However, GradCAM overlays showed that the models with highest accuracy, like MobileNetV2, were not always identifying relevant features. Conversely, the GradCAM heatmaps for ShrapML show general agreement with regions most indicative of fluid accumulation. Discussion: Overall, the AI models developed can automate POCUS predictions in MWDs. Preliminarily, ShrapML had the strongest performance and prediction rate paired with accurately tracking fluid accumulation sites, making it the most suitable option for eventual real-time deployment with ultrasound systems. Further integration of this technology with imaging technologies will expand use of POCUS-based triage of MWDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Beyond Point Estimates: Benchmarking Uncertainty Quantification Methods on the AION-1 Astronomical Foundation Model

Foundation models for astronomical surveys offer powerful learned representations that can be transferred to downstream regression tasks such as galaxy property estimation. However, point predictions alone are insufficient for scientific inference; reliable uncertainty quantification (UQ) is essential. We compare seven UQ methods on galaxy property regression using frozen AION-1 foundation-model embeddings, predicting redshift, stellar mass, stellar-population age, gas-phase metallicity, and specific star-formation rate, from Legacy Survey photometry/imaging and DESI spectra, with PROVABGS-derived labels. Distribution-free conformal methods achieve marginal coverage within $\sim$1 pp of the nominal 90% across all properties, while non-conformal baselines (Deep Ensembles, MC~Dropout) fail to calibrate reliably. Among conformal approaches, Conformalized Quantile Regression (CQR) delivers the best coverage in the bin with the poorest model predictions. More importantly, only the Locally Valid and Discriminative (LVD) framework -- particularly when operating on AION-1 embeddings -- also provides finite-sample \emph{local validity}, producing intervals that adapt to each galaxy's local prediction difficulty rather than relying on marginal guarantees alone. These results establish conformal prediction, and LVD in particular, as the preferred UQ framework for uncertainty-aware inference on foundation-model embeddings in astrophysics.

Tame-Narvaez, Karla [Fermilab] (ORCID:000000022249↗
DOE OSTI2024

Bayesian Conavigation: Dynamic Designing of the Material Digital Twins via Active Learning

Scientific advancement is universally based on the dynamic interplay between theoretical insights, modeling, and experimental discoveries. However, this feedback loop is often slow, including delayed community interactions and the gradual integration of experimental data into theoretical frameworks. This challenge is particularly exacerbated in domains dealing with high-dimensional object spaces, such as molecules and complex microstructures. Hence, the integration of theory within automated and autonomous experimental setups, or theory in the loop-automated experiment, is emerging as a crucial objective for accelerating scientific research. The critical aspect is to use not only theory but also on-the-fly theory updates during the experiment. Furthermore, we introduce a method for integrating theory into the loop through Bayesian conavigation of theoretical model space and experimentation. Our approach leverages the concurrent development of surrogate models for both simulation and experimental domains at the rates determined by latencies and costs of experiments and computation, alongside the adjustment of control parameters within theoretical models to minimize epistemic uncertainty over the experimental object spaces. This methodology facilitates the creation of digital twins of material structures, encompassing both the surrogate model of behavior that includes the correlative part and the theoretical model itself. While being demonstrated here within the context of functional responses in ferroelectric materials, our approach holds promise for broader applications, such as the exploration of optical properties in nanoclusters, microstructure-dependent properties in complex materials, and properties of molecular systems.

Microscopy↗
DOE OSTI2020

Interpreting and Stabilizing Machine-Learning Parametrizations of Convection

Neural networks are a promising technique for parameterizing subgrid-scale physics (e.g., moist atmospheric convection) in coarse-resolution climate models, but their lack of interpretability and reliability prevents widespread adoption. For instance, it is not fully understood why neural network parameterizations often cause dramatic instability when coupled to atmospheric fluid dynamics. This paper introduces tools for interpreting their behavior that are customized to the parameterization task. First, we assess the nonlinear sensitivity of a neural network to lower-tropospheric stability and the midtropospheric moisture, two widely studied controls of moist convection. Second, we couple the linearized response functions of these neural networks to simplified gravity wave dynamics, and analytically diagnose the corresponding phase speeds, growth rates, wavelengths, and spatial structures. To demonstrate their versatility, these techniques are tested on two sets of neural networks, one trained with a super-parameterized version of the Community Atmosphere Model (SPCAM) and the second with a near-global cloud-resolving model (GCRM). Additionally, even though the SPCAM simulation has a warmer climate than the cloud-resolving model, both neural networks predict stronger heating/drying in moist and unstable environments, which is consistent with observations. Moreover, the spectral analysis can predict that instability occurs when GCMs are coupled to networks that support gravity waves that are unstable and have phase speeds larger than 5 m s -1 . In contrast, standing unstable modes do not cause catastrophic instability. Using these tools, differences between the SPCAM-trained versus GCRM-trained neural networks are analyzed, and strategies to incrementally improve both of their coupled online performance unveiled.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Multi-fidelity Bayesian neural networks: Algorithms and applications

Here we propose a new class of Bayesian neural networks (BNNs) that can be trained using noisy data of variable fidelity, and we apply them to learn function approximations as well as to solve inverse problems based on partial differential equations (PDEs). These multi-fidelity BNNs consist of three neural networks: The first is a fully connected neural network, which is trained following the maximum a posteriori probability (MAP) method to fit the low-fidelity data; the second is a Bayesian neural network employed to capture the cross-correlation with uncertainty quantification between the low- and high-fidelity data; and the last one is the physics-informed neural network, which encodes the physical laws described by PDEs. For the training of the last two neural networks, we first employ the mean-field variational inference (VI) to maximize the evidence lower bound (ELBO) to obtain informative prior distributions for the hyperparameters in the BNNs, and subsequently we use the Hamiltonian Monte Carlo (HMC) method to estimate accurately the posterior distributions for the corresponding hyperparameters. We demonstrate the accuracy of the present method using synthetic data as well as real measurements. Specifically, we first approximate a one- and four-dimensional function, and then infer the reaction rates in one- and two-dimensional diffusion-reaction systems. Moreover, we infer the sea surface temperature (SST) in the Massachusetts and Cape Cod Bays using satellite images and in-situ measurements. Taken together, our results demonstrate that the present method can capture both linear and nonlinear correlation between the low- and high-fidelity data adaptively, identify unknown parameters in PDEs, and quantify uncertainties in predictions, given a few scattered noisy high-fidelity data. Finally, we demonstrate that we can effectively and efficiently reduce the uncertainties and hence enhance the prediction accuracy with an active learning approach, using as examples a specific one-dimensional function approximation and an inverse PDE problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Exploring the Feasibility of INCONEL® ALLOY 740H® for Power Plant Headers: Integrating Machine Learning with Computational Fluid Dynamics (CFD)

This keynote presentation explores the behavior of headers—essential components of pipeline systems—using ANSYS simulation software and machine learning techniques. The study aims to predict the thermal and mechanical performance of headers under diverse conditions through both steady-state and transient simulations. We investigate critical parameters such as heat transfer coefficient, fluid velocity, and temperature to optimize header design. Conducted as part of a DOE project led by NCAT in collaboration with UNC Charlotte, this research encompasses multiple key topics. The initial section focuses on the behavior of header systems under steady-state conditions using ANSYS simulation. It underscores the importance of headers in industrial infrastructure, especially in the energy sector, and examines the implications of material selection and flow direction on heat transfer dynamics. Methodologically, we employ Computational Fluid Dynamics (CFD) analysis through ANSYS, detailing the development of models, material properties, geometry specifications, boundary conditions, and meshing strategies. Our simulations explore various operational parameters, including temperature and mass flow rates, crucial for predicting heat transfer coefficients and enhancing header design. Results from the study include parametric investigations into mesh sensitivity, viscosity model evaluations, and the effects of heat transfer locations, all validated against theoretical calculations. We conclude with insights on mesh optimization, the suitability of viscosity models, and recommendations for future research aimed at improving header system efficiency and sustainability in industrial applications.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2023

Analysis of an optical imaging system prototype for autonomously monitoring zooplankton in an aquaculture facility

Traditional approaches to biomonitoring in aquatic systems, such as sample collection, sorting, and identification, require significant time and effort, thereby limiting the spatiotemporal resolution of sample collection. Additionally, collection and preservation of samples for subsequent taxonomic identification and enumeration leads to mortality of organisms. Recent advances in technologies that utilize optical imaging and machine learning have provided new opportunities to expedite biomonitoring and lead to significant cost savings. These technologies can be advantageous to scientists or managers that conduct routine biomonitoring to inform operations, as in the case of aquaculture facilities. The Small Aquatic Organism optical imaging system (SAO) is a high-throughput optical imaging and classification prototype system that relies on computer vision and machine learning (Support Vector Machines, or SVMs) to autonomously identify and enumerate aquatic organisms. The SAO provides a more sustainable method of collecting large volumes of data and has the benefit of being used in situ. In this study, we tested the performance of the SAO in providing comparable results to manual zooplankton community monitoring in ten ponds at an aquaculture facility. We performed a side-by-side study comparing the sampling methods of plankton tow nets, where major zooplankton taxonomic classes were manually identified and enumerated, to sampling with the SAO. Vouchered samples were used to develop a training library for the SAO, where classes consisted of water boatman and zooplankton groups: cladocerans, copepod adults, copepod nauplii, and rotifers. SAO imagery was manually classified and compared with predicted results for validation. Accuracy for the SVM classifier of the SAO was 37.4 %. Convolutional Neural Networks (CNN) and Random Forest classifiers were also applied to SAO imagery and image features for comparison. The best CNN model and our Random Forest model had accuracies of 80.4 % and 46.6 % respectively. Challenges faced included the small size of copepod nauplii and rotifers and the limited resolution of the imaging camera, although there are tradeoffs between imaging resolution and the sample processing rate. Furthermore, our comparison shows that advancement in both optical imaging and ML are needed in order for the SAO prototype to yield comparable results to manual community monitoring in an aquaculture facility.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Deep learning-enabled probing of irradiation-induced defects in time-series micrographs

Modeling time-series data with convolutional neural networks (CNNs) requires building a model to learn in batches as opposed to training sequentially. Coupling CNNs with in situ or operando techniques opens the possibility of accurately segmenting dynamic reactions and mass transport phenomena to understand how materials behave under the conditions in which they are used. In this article, in situ ion irradiation transmission electron microscopy (TEM) images are used as inputs into the CNN to assess the defect generation rate, defect cluster density, and saturation of defects. We then use the output segmentation maps to correlate with conventional TEM micrographs to assess the model’s ability to detail nanoscale interactions. Next, we discuss the implications of preprocessing and hyperparameters on model variability, accuracy when expanded to other datasets, and the role of regularization when controlling model variance. Ultimately, we eliminate human bias when extrapolating physical metrics, speed up analysis time, decouple reactions that happen at 100 ms intervals, and deploy models that are both accurate and transferable to similar experiments.

Burns, Kory (ORCID:0000000158019909)↗
DOE OSTI2020

A Proposed Common Model of Multi-phase Strength and Equation of State for a Tri-laboratory Collaboration (Working Draft 1.1)

The proposed simple common model for multiphase strength and EoS (CMMP) is meant to be sufficiently simple that each of the collaborating labs can share in a common starting point. Another objective is to start with relatively simple assumptions, which will not necessarily capture details of the physical processes, and incrementally add complexity in order to identify the minimal-needed technical detail. Through this co-evolution of model and experiment, we will better learn the importance of various theoretical approximations and where to invest future resources in experiment and model development. This simple framework is based on pressure and temperature equilibrium of all co-existing phases combined with deviatoric stress averaging through a volume fraction weighted ow stress and a volume fraction weighted shear modulus. Implementations of the framework based on equilibrium phase fractions (i.e. instantaneous kinetic rate) and for finite rate transition kinetics are proposed.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Extending Component Lifetime And Improving Inverter Reliability (ECLAIIR)

Inverter reliability remains one of the most persistent challenges limiting the performance, availability, and economic viability of utility‑scale photovoltaic (PV) plants. Industry data consistently show that inverters account for the highest share of corrective maintenance events and unplanned outages across PV fleets. These failures result in energy losses, increased O&M costs, and reduced confidence in long‑term solar asset performance. Motivated by these challenges, this project—Extending Component Lifetime and Improving Inverter Reliability (ECLAIIR)—was undertaken to systematically investigate inverter degradation and failure mechanisms, develop predictive maintenance capabilities, and establish data‑driven pathways to improve service life and reduce the Levelized Cost of Energy (LCOE) for large‑scale PV systems. The primary goal of the project was to identify pre‑failure signatures in string inverters using both lab‑based accelerated lifetime testing and field‑based data and to develop predictive maintenance algorithms that can anticipate inverter faults before they occur. Through collaboration with inverter testing laboratory, solar PV plant owner, and failure‑analysis experts, the project advanced the technical understanding of inverter reliability. By instrumenting inverters with thermistors, humidity sensors, power‑quality meters, and acoustic sensors, the research established how multiple sensing modalities can reliably detect deviations from normal behavior hours to days before failure. These findings substantially enhance scientific understanding of inverter failure kinetics and provide the PV industry with the most comprehensive cross‑OEM characterization of early‑stage failure indicators reported to date. Technically, the project demonstrated the effectiveness of predictive maintenance by developing and validating the PreDICT (Predictive Diagnostics of PV Inverters Using Condition Monitoring and Trend Analysis) framework—a multi‑layer diagnostic architecture combining peer‑to‑peer analytics, historical trend modeling, and advanced machine‑learning techniques such as the Sequential Conditional Variational Autoencoder (SCVAE). This predictive model achieved more than 90% accuracy in detecting pre‑failure conditions and provided up to four days of lead time before inverter failure in field scenarios. Economically, the project’s LCOE analysis showed that predictive maintenance can reduce lifetime energy losses and minimize corrective maintenance interventions. Modeling indicated that, depending on inverter failure rates and replacement timelines, predictive maintenance can significantly reduce LCOE impacts associated with inverter downtime: from as high as 19.4% under conventional maintenance strategies to 0.1%–10.17% when predictive analytics are adopted. These results confirm that predictive maintenance is both technically feasible and economically advantageous for utilities and plant operators. The project’s findings also have broad public benefit. By improving inverter reliability and reducing downtime, predictive maintenance directly increases electricity generation from existing PV assets. Enhanced reliability lowers operational costs for utilities, which can translate over time into lower energy costs for consumers. Furthermore, the project’s technical publications, conference presentations, and industry workshops ensure that knowledge gained is shared broadly across the solar industry, supporting workforce development and enabling utilities of all sizes to adopt modern asset‑health monitoring practices. The retrofitting case study and service‑life prediction framework further support informed decision‑making for aging PV fleets, helping operators extend system life and reduce electronic waste. In summary, the ECLAIIR project significantly advanced the state of knowledge on inverter degradation, demonstrated the technical and economic value of predictive maintenance, and delivered actionable tools and insights that support more reliable, cost‑effective, and sustainable PV plant operation. The outcomes of this project will continue to inform utility practices, guide inverter design improvements, and strengthen the long‑term performance of solar assets nationwide.

14 SOLAR ENERGY↗
DOE OSTI2022

Modeling Combustion Reaction ODEs with Neural Networks

The chemistry of combustion reactions is complex as it involves many species and reactions. In practice, such a system is often modeled computationally using an empirically derived chemical mechanism. Given the large range of reaction rates, the system is then time evolved using a stiff ODE solver. However, even when reduced chemical mechanisms are employed, the system can become computationally expensive for two-dimensional or three-dimensional systems. Such systems can also face problems with instability. As such, it is desirable to find a cheaper, stable alternative to solving the reaction system. Neural networks offer the potential to learn these reaction ODEs and time evolve a combustion reaction in a more cost-efficient manner than stiff ODE solvers. In this study, a variety of neural networks are trained on zero-dimensional Cantera simulations of methane combustion with varying initial conditions. Several predictive approaches as well as several neural network architectures (artificial neural network with dropout, ResNet, and Neural ODE) are compared in their ability to predict combustion trajectories. Promising models are then identified.

combustion kinetics↗
DOE OSTI2020

Enzyme activities predicted by metabolite concentrations and solvent capacity in the cell

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we use two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization–reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. As previously hypothesized, regulation is herein shown to control the concentrations of both immediate and downstream product concentrations at physiological levels. Model predictions provide the following two novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; and (2) the minimal regulation needed to maintain metabolite levels at physiological concentrations maximizes the free energy dissipation rate instead of preserving a specific energy charge. The resulting energy dissipation rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism of E. coli (gluconeogenesis, glycolysis-tricarboxylic acid (TCA) and pentose phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Multidimensional quantitative phenotypic and molecular analysis reveals neomorphic behaviors of p53 missense mutants

Abstract Mutations in the TP53 tumor suppressor gene occur in >80% of the triple-negative or basal-like breast cancer. To test whether neomorphic functions of specific TP53 missense mutations contribute to phenotypic heterogeneity, we characterized phenotypes of non-transformed MCF10A-derived cell lines expressing the ten most common missense mutant p53 proteins and observed a wide spectrum of phenotypic changes in cell survival, resistance to apoptosis and anoikis, cell migration, invasion and 3D mammosphere architecture. The p53 mutants R248W, R273C, R248Q, and Y220C are the most aggressive while G245S and Y234C are the least, which correlates with survival rates of basal-like breast cancer patients. Interestingly, a crucial amino acid difference at one position—R273C vs. R273H—has drastic changes on cellular phenotype. RNA-Seq and ChIP-Seq analyses show distinct DNA binding properties of different p53 mutants, yielding heterogeneous transcriptomics profiles, and MD simulation provided structural basis of differential DNA binding of different p53 mutants. Integrative statistical and machine-learning-based pathway analysis on gene expression profiles with phenotype vectors across the mutant cell lines identifies quantitative association of multiple pathways including the Hippo/YAP/TAZ pathway with phenotypic aggressiveness. Further, comparative analyses of large transcriptomics datasets on breast cancer cell lines and tumors suggest that dysregulation of the Hippo/YAP/TAZ pathway plays a key role in driving the cellular phenotypes towards basal-like in the presence of more aggressive p53 mutants. Overall, our study describes distinct gain-of-function impacts on protein functions, transcriptional profiles, and cellular behaviors of different p53 missense mutants, which contribute to clinical phenotypic heterogeneity of triple-negative breast tumors.

60 APPLIED LIFE SCIENCES↗