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At least 1,117 records · Page 62

Coarse-Grained Modeling Elucidates Differential Metabolism of Saccharomyces cerevisiae under Varied Nutrient Limitations

Microorganisms such as Saccharomyces cerevisiae have a native ability to adapt their metabolism to varying nutrient conditions. Understanding their responses to nutrient limitations is critical for decoding cellular physiology and designing strategies for metabolic engineering. While the influence of carbon availability on yeast metabolism has been extensively studied, the role of nitrogen availability remains relatively underexplored. In this study, we utilized a coarse-grained kinetic model to systematically analyze and compare the effects of carbon and nitrogen limitations on yeast metabolism. Our model successfully revealed the differential metabolic characteristics of S. cerevisiae under carbon- and nitrogen-limited chemostat conditions. It also highlighted the significance of protein activity regulation at varying carbon-to-nitrogen ratios, and elucidated distinct strategies employed to maintain ATP homeostasis. Furthermore, this study provides a computational tool for investigating yeast physiology under nutrient limitations and offers quantitative and mechanistic insights into yeast metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Development of a Performance Portable Non-Equilibrium Plasma Fluid Solver on Adaptive Grids

This presentation will describe the numerical techniques, programming paradigms, verification, and performance of a non-equilibrium plasma fluid solver that can effectively utilize current and upcoming central processing and graphics processing unit (CPU+GPU) architectures. Our plasma fluid model solves the conservation equations for self-consistent electrostatic Poisson, electron and heavy species transport, and electron temperature on adaptive Cartesian grids. Our solver is written using performance portable adaptive mesh management library, AMReX (Zhang et al., JOSS, 4 (37) 1370, 2019), and can be built and run on widely available vendor specific GPU architectures (NVIDIA/AMD/Intel). We utilize a non-subcycled second order semi-implicit time-stepping method where all adaptive mesh refinement (AMR) levels are advanced with the same time step. The composite multi-level multigrid solver from within AMReX is used for each of the governing equations that are cast into a Helmholtz equation form. We have also developed a python based chemical mechanism parser framework that uses a similar format as CANTERA (Goodwin et al., Zenodo, 2018) yaml files as input. Our custom parser reads the yaml file and provides C++ files with transport and production rate functions that can be executed on both host (CPU) and device (GPU). We present verification of our solver using method of manufactured solutions that indicate formal second order accuracy with central diffusion and fifth order weighted-essentially-non-oscillatory (WENO) advection scheme. We also verify our solver with published literature on low-pressure capacitive and high-pressure streamer discharges. Our initial performance studies indicate 10X speed-up using 20 NVIDIA GPUs versus 200 CPUs for an atmospheric streamer discharge problem solved on a 512 x 1024 x 512 grid.

graphics processing units↗

Parameter extraction for a SPICE model of an hTron superconducting thermal switch

Efficiently simulating large circuits is crucial to the development of superconducting nanowire-based electronics. However, current simulation tools for this technology are not adapted to the scaling of circuit size and complexity. We focus on the multilayered heater-nanocryotron (hTron), a promising superconducting nanowire-based switch used in applications such as superconducting nanowire single-photon detector readout. Previously, the hTron was modeled using traditional finite-element methods, which fall short in simulating systems at a larger scale. An empirical-based method would be better adapted to this task, enhancing both simulation speed and agreement with experimental data. In this work, we perform switching current and activation delay measurements on 17 hTron devices. We then develop a method for extracting physical fitting parameters used to characterize the devices. We build a SPICE behavioral model that reproduces the static and transient device behavior using these parameters, and validate it by comparing its performance to a model developed in prior work, showing an improvement in simulation time by several orders of magnitude. Furthermore, our model provides circuit designers with a tool to help understand the hTron’s behavior during all design stages, thus enabling broader use of the hTron across various new areas of application.

Caloritronics↗

Implementing Ordinary Differential Equation Solvers in Rust Programming Language for Modeling Vehicle Powertrain Systems: Preprint

Efficient and accurate ordinary differential equation (ODE) solvers are necessary for powertrain and vehicle dynamics modeling. However, current commercial ODE solvers can be financially prohibitive, leading to a need for accessible, effective, open-source ODE solvers designed for powertrain modeling. Rust is a compiled programming language that has the potential to be used for fast and easy-to-use powertrain models, given its exceptional computational performance, robust package ecosystem, and short time required for modelers to become proficient. However, of the three commonly used (>3,000 downloads) packages in Rust with ODE solver capabilities, only one has more than four numerical methods implemented, and none are designed specifically for modeling physical systems. Therefore, the goal of the Differential Equation System Solver (DESS) was to implement accurate ODE solvers in Rust designed for the component-based problems often seen in powertrain modeling. DESS is a text-based software package that provides a flexible framework for building and solving systems of ODEs. This allows DESS to be included as a dependency for automotive powertrain models that require a variety of solvers and solver configurations. Seven explicit ODE solver methods have been implemented in DESS: Euler’s, Heun’s, midpoint, Ralston’s, classic Runge-Kutta, Bogacki-Shampine, and Cash-Karp. These represent five fixed-step methods and two adaptive-step methods. This paper shows that the solver implementations increase accuracy and computational efficiency compared to Euler's method when modeling a system of three thermal masses in Rust. DESS also includes features designed for modeling component-based physical systems. Users can define relationships between nodes in their system, which the package then translates into a system of equations, leading to simpler and more intuitive code. In the case of a three-thermal-mass system, the user can specify node thermal properties (e.g., thermal capacitance), how nodes are interconnected, and thermal conductance between nodes rather than providing a system of equations. The core contribution from this work is an open-source, text-based Rust package with ODE solvers for automotive powertrain modeling to support cost-free, fast, and accurate simulation.

ADVANCED PROPULSION SYSTEMS↗

Quantum-classical embedding via ghost Gutzwiller approximation for enhanced simulations of correlated electron systems

Simulating correlated materials on present-day quantum hardware remains challenging due to limited quantum resources. Quantum embedding methods offer a promising route by reducing computational complexity through the mapping of bulk systems onto effective impurity models, allowing more feasible simulations on pre- and early-fault-tolerant quantum devices. Here, this work develops a quantum-classical embedding framework based on the ghost Gutzwiller approximation to enable quantum-enhanced simulations of ground-state properties and spectral functions of correlated electron systems. Circuit complexity is analyzed using an adaptive variational quantum algorithm on a statevector simulator, applied to the infinite-dimensional Hubbard model with increasing ghost mode numbers from 3 to 5, resulting in circuit depths growing from 16 to 104. Noise effects are examined using a realistic error model, revealing significant impact on the spectral weight of the Hubbard bands. To mitigate these effects, the Iceberg quantum error detection code is employed, achieving up to 40% error reduction in simulations. Finally, the accuracy of the density matrix estimation and the derived spectral function is benchmarked on IBM and Quantinuum quantum hardware, featuring distinct qubit-connectivity and employing multiple levels of error mitigation techniques.

Chen, I-Chi [Ames Laboratory (AMES), Ames, IA (Uni↗

Toward the application of the Risk-Based Maintenance approach to a hydrogen-fueled manufacturing plant

Safety, reliability, and maintenance of hydrogen-based equipment, including Risk-Based Maintenance (RBM), have recently gained increasing attention, as hydrogen, while key to decarbonizing hard-to-abate sectors, raises safety concerns. However, two literature gaps limit the development of risk-based strategies for hydrogen technologies. First, existing RBM methodologies do not account for hydrogen-specific components, such as electrolyzers, which differ from conventional equipment. Second, available studies on electrolyzer reliability remain largely qualitative or laboratory-scale. This study addresses these gaps by proposing an adapted RBM methodology tailored to hydrogen-fueled manufacturing facilities. Integrating qualitative tools (e.g., FMEA) with probabilistic models (e.g., Bayesian Networks) enables comprehensive hazardous scenarios identification and likelihood estimation. A conceptual layout of a glass furnace supplied by a 3 MW PEM electrolyzer is considered as a case study to demonstrate the feasibility of the adapted RBM framework in identifying high-risk components and enabling maintenance prioritization, potentially improving plant safety.

08 HYDROGEN↗

Advanced Turbulence Models for Large-Scale Atmospheric Boundary Layer Flows

We present high-fidelity large-eddy-simulation (LES) modeling approaches for the turbulent atmospheric boundary layer (ABL) flows. Wind energy is a prime example of an application driven by ABL. Generation of electrical energy from farms of wind turbines at night in the stable ABL is a particularly interesting situation. In this report, we consider the well-known GEWEX (Global Energy and Water Cycle Experiment) Atmospheric Boundary Layer Study (GABLS) stably stratified benchmark LES case. We use a high-order spectral element code Nek5000/RS, which is supported under the DOE's Exascale Computing Project (ECP) Center for Efficient Exascale Discretizations (CEED) project, targeting application simulations on various acceleration-device based exascale computing platforms. In our earlier ANL report, we demonstrated our newly developed subgrid-scale (SGS) models based on high-pass filter (HPF), mean-field eddy viscosity (MFEV), and Smagorinsky (SMG) with no-slip and traction boundary conditions, provided with low-order statistics, convergence and turbulent structure analysis. In this report, we extend the range of our SGS modeling approaches in the context of the mean-field eddy viscosity (MFEV), to include the solution of an SGS turbulent kinetic energy equation (TKE). We demonstrate the model fidelity of Nek5000/RS in comparison to that of AMR-Wind, a block-structured second-order finite-volume code with adaptive-mesh-refinement capabilities, with which we studied scaling performance for both codes in comparison on DOE's leadership computing platforms.

17 WIND ENERGY↗

Reinforcement Learning for Intentional Islanding in Resilient Power Transmission Systems

Intentional islanding is the process of identifying and deliberately decomposing the transmission network to form self-sustained islands from an endangered network during disruptions to improve resilience and security. Most existing intentional islanding models are offline resilience decision tools and hence do not provide outage responses in a timely manner. In this paper, a reinforcement learning (RL) based model for intentional islanding is developed, which offers real-time switching control, online deployability, and adaptability to varying system conditions. The intentional islanding process is formulated as a Markov decision process, where the optimal transmission switching policy is learned using the RL approach. The control policy is learned over an environment that encompasses a Power System Simulator for Engineering (PSS/E) model of the transmission network, facilitated by an interface to the standard openAI Gym framework. The proposed RL-based methodology aims to form stable and self-sustainable islands by ensuring voltage stability while reducing the power mismatch in the formed islands. A proximal policy optimization algorithm is designed, which is suitable for controlling the on/off status of the switches with multi-layer perceptron as value and actor networks. The effectiveness of the proposed framework in the self-recovery of the grid by island formation is applied on the modified IEEE 39-bus test network and validated by dynamic simulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model

Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.

AI agent↗

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗

Model Predictive Fault-Tolerant Tracking Control for PDF Control Systems With Packet Losses

In this article, a fault-tolerant tracking control strategy is investigated for nonlinear probability density function (PDF) control systems with the actuator fault, uncertainties, unknown disturbance, and random packet losses. The control input signal dropout and measurement signal dropouts are described as the independent Bernoulli distribution. An adaptive fault diagnosis (FD) observer based on the Lyapunov function is given to simultaneously estimate the fault, disturbance, and state with packet losses. Furthermore, different from the traditional robust fault-tolerant control (FTC), a new active fault-tolerant tracking controller is designed based on the model predictive control framework, which has better adaptive fault-tolerant performance. Finally, the validity of the proposed FTC method has been proved by a simulation study of a papermaking process.

42 ENGINEERING↗

Automated classification of big X-ray diffraction data using deep learning models

Abstract In current in situ X-ray diffraction (XRD) techniques, data generation surpasses human analytical capabilities, potentially leading to the loss of insights. Automated techniques require human intervention, and lack the performance and adaptability required for material exploration. Given the critical need for high-throughput automated XRD pattern analysis, we present a generalized deep learning model to classify a diverse set of materials’ crystal systems and space groups. In our approach, we generate training data with a holistic representation of patterns that emerge from varying experimental conditions and crystal properties. We also employ an expedited learning technique to refine our model’s expertise to experimental conditions. In addition, we optimize model architecture to elicit classification based on Bragg’s Law and use evaluation data to interpret our model’s decision-making. We evaluate our models using experimental data, materials unseen in training, and altered cubic crystals, where we observe state-of-the-art performance and even greater advances in space group classification.

Chemistry↗

Effects of non-thermal termolecular reactions on wedge-induced oblique detonation waves

The shock-induced combustion ramjet (Shcramjet) based on oblique detonation waves (ODWs) is among the promising choices for hypersonic propulsion systems. An understanding of the ignition, propagation, and stability of ODWs is critical to harnessing their propulsive potential. In such high speed reacting flows, there is a high probability of occurrence of non-thermal reactions due to the presence of non-trivial amounts of highly reactive radicals including H, O and OH apart from O 2 as demonstrated recently [M. P. Burke, S. J. Klippenstein, Nat. Chem. 9 (2017) 1078–1082, Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515–522]. The present work focuses on examining the initiation, propagation and structure of oblique detonation waves in stoichiometric H 2 -air mixtures through numerical simulations with and without non-thermal reactivity on a two-dimensional adaptive grid. Non-thermal reactions were included in the macroscopic kinetic model as chemically termolecular reactions facilitated by the H + OH radical-radical recombination and the H + O 2 radical-molecule association reactions. Since, the non-thermal reactions result in a corresponding decrease in the reaction fluxes of the incipient recombination/association reactions, an additional simulation was performed by applying corrections to the respective incipient recombination/association rate constants using the methodology demonstrated by Tao et al. [Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515–522]. Results show that, under ODWE relevant conditions, non-thermal reactivity fundamentally alters the induction length, intensity as well as the structure of the ODW. Specifically, it is found that non-thermal reactivity leads to a noticeable reduction in initiation length and a simultaneous increase in instantaneous peak heat release rate and the degree of unsteadiness of the ODW. Finally, statistical analysis of key thermo-chemical variables is performed to elucidate the important species as well as reactions responsible for the observed variations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Are Remote Sensing Evapotranspiration Models Reliable Across South American Ecoregions?

Many remote sensing-based evapotranspiration (RSBET) algorithms have been proposed in the past decades and evaluated using flux tower data, mainly over North America and Europe. Model evaluation across South America has been done locally or using only a single algorithm at a time. Here, in this work, we provide the first evaluation of multiple RSBET models, at a daily scale, across a wide variety of biomes, climate zones, and land uses in South America. We used meteorological data from 25 flux towers to force four RSBET models: Priestley–Taylor Jet Propulsion Laboratory (PT-JPL), Global Land Evaporation Amsterdam Model (GLEAM), Penman–Monteith Mu model (PM-MOD), and Penman–Monteith Nagler model (PM-VI). ET was predicted satisfactorily by all four models, with correlations consistently higher (R 2 > 6) for GLEAM and PT-JPL, and PM-MOD and PM-VI presenting overall better responses in terms of percent bias (-10 < PBIAS < 10%). As for PM-VI, this outcome is expected, given that the model requires calibration with local data. Model skill seems to be unrelated to land-use but instead presented some dependency on biome and climate, with the models producing the best results for wet to moderately wet environments. Our findings show the suitability of individual models for a number of combinations of land cover types, biomes, and climates. At the same time, no model outperformed the others for all conditions, which emphasizes the need for adapting individual algorithms to take into account intrinsic characteristics of climates and ecosystems in South America.

54 ENVIRONMENTAL SCIENCES↗

MultiSector Dynamics: Advancing the Science of Complex Adaptive Human-Earth Systems

The field of MultiSector Dynamics (MSD) explores the dynamics and co-evolutionary pathways of human and Earth systems with a focus on critical goods, services, and amenities delivered to people through interdependent sectors. This commentary lays out core definitions and concepts, identifies MSD science questions in the context of the current state of knowledge, and describes ongoing activities to expand capacities for open science, leverage revolutions in data and computing, and grow and diversify the MSD workforce. Central to our vision is the ambition of advancing the next generation of complex adaptive human-Earth systems science to better address interconnected risks, increase resilience, and improve sustainability. This will require convergent research and the integration of ideas and methods from multiple disciplines. Understanding the tradeoffs, synergies, and complexities that exist in coupled human-Earth systems is particularly important in the context of energy transitions and increased future shocks.

Reed, Patrick↗

The Climatic Impact‐Driver Framework for Assessment of Risk‐Relevant Climate Information

Abstract The climate science and applications communities need a broad and demand‐driven concept to assess physical climate conditions that are relevant for impacts on human and natural systems. Here, we augment the description of the “climatic impact‐driver” (CID) approach adopted in the Working Group I (WGI) contribution to the Intergovernmental Panel on Climate Change (IPCC) Sixth Assessment Report. CIDs are broadly defined as “physical climate system conditions (e.g., means, events, and extremes) that affect an element of society or ecosystems. Depending on system tolerance, CIDs and their changes can be detrimental, beneficial, neutral, or a mixture of each across interacting system elements and regions.” We give background information on the IPCC Report process that led to the development of the 7 CID types (heat and cold, wet and dry, wind, snow and ice, coastal, open ocean, and other) and 33 distinct CID categories, each of which may be evaluated using a variety of CID indices. This inventory of CIDs was co‐developed with WGII to provide a useful collaboration point between physical climate scientists and impacts/risk experts to assess the specific climatic phenomena driving sectoral responses and identify relevant CID indices within each sector. The CID Framework ensures that a comprehensive set of climatic conditions informs adaptation planning and risk management and may also help prioritize improvements in modeling sectoral dynamics that depend on climatic conditions. CIDs contribute to climate services by increasing coherence and neutrality when identifying and communicating relevant findings from physical climate research to risk assessment and planning activities.

54 ENVIRONMENTAL SCIENCES↗

Emergent Constrained Projections of Mean and Extreme Warming in China

Reliable regional temperature projections including heat extremes are essential for climate change adaptation and mitigation. Taking China as an example, simple averages from Coupled Model Intercomparison Project Phase 6 (CMIP6) models project high warming due to sampling many high climate sensitivities in the ensemble. Here, we develop an emergent constraint (EC) framework to obtain constrained mean and daily maximum temperature (TXx) warming over China by using observed global warming and local residual warming. The constrained annual mean and TXx warming over China (2.33°C [1.61–3.05°C] and 2.31°C [1.21–2.99°C]) are 0.65°C [0.04–1.76°C] and 0.63°C [–0.50–2.39°C], respectively, lower than raw projections (2.98°C [1.85–4.22°C] and 2.94°C [2.04–4.39°C]) for 2080–2099 under the intermediate-emission scenario. Approximately half model uncertainty is reduced after constraint. The land area (population) experiencing temperature extremes in our metric is 78% (85%) of the raw projections. Our results imply a lower impact of extreme heat than implied by current raw CMIP6 projections.

54 ENVIRONMENTAL SCIENCES↗

Machine learning-based observation-constrained projections reveal elevated global socioeconomic risks from wildfire

Reliable projections of wildfire and associated socioeconomic risks are crucial for the development of efficient and effective adaptation and mitigation strategies. The lack of or limited observational constraints for modeling outputs impairs the credibility of wildfire projections. Here, we present a machine learning framework to constrain the future fire carbon emissions simulated by 13 Earth system models from the Coupled Model Intercomparison Project phase 6 (CMIP6), using historical, observed joint states of fire-relevant variables. During the twenty-first century, the observation-constrained ensemble indicates a weaker increase in global fire carbon emissions but higher increase in global wildfire exposure in population, gross domestic production, and agricultural area, compared with the default ensemble. Such elevated socioeconomic risks are primarily caused by the compound regional enhancement of future wildfire activity and socioeconomic development in the western and central African countries, necessitating an emergent strategic preparedness to wildfires in these countries.

54 ENVIRONMENTAL SCIENCES↗