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DOE OSTI2025

LLM-Based Adaptive Distribution Voltage Regulation Under Frequent Topology Changes: An In-Context MPC Framework

This paper proposes a large language model (LLM) based adaptive inverter control for distribution voltage regulation under frequent topology changes. We leverage the ability of the LLM to perform in-context learning and create a topology-adaptive surrogate model for power flow calculation. The surrogate model is then integrated with a long short-term memory-based load forecaster and a model predictive control (MPC) scheme to achieve the optimal inverter control that adapts to frequent topology changes. Unlike many existing works that assume fixed-topology grids or require the knowledge of all possible topologies when training a model, the proposed in-context MPC method tackles the distribution voltage control problem under various topologies and adapts to unknown topologies with limited data requirement for fine-tuning. The effectiveness of our method is demonstrated on a modified IEEE 123-bus test system.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae

Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae , cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae . We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae , providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.

Conversion↗

DOE OSTI2020

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Coevolution of the Ess1-CTD axis in polar fungi suggests a role for phase separation in cold tolerance

Most of the world’s biodiversity lives in cold (-2° to 4°C) and hypersaline environments. To understand how cells adapt to such conditions, we isolated two key components of the transcription machinery from fungal species that live in extreme polar environments: the Ess1 prolyl isomerase and its target, the carboxy-terminal domain (CTD) of RNA polymerase II. Polar Ess1 enzymes are conserved and functional in the model yeast, Saccharomyces cerevisiae. By contrast, polar CTDs diverge from the consensus (YSPTSPS) 26 and are not fully functional in S. cerevisiae. These CTDs retain the critical Ess1 Ser-Pro target motifs, but substitutions at Y1, T4, and S7 profoundly affected their ability to undergo phase separation in vitro and localize in vivo. We propose that environmentally tuned phase separation by the CTD and other intrinsically disordered regions plays an adaptive role in cold tolerance by concentrating enzymes and substrates to overcome energetic barriers to metabolic activity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Reweighting Underlying Event and Colour Reconnection parameter variations in Sherpa

We propose and validate a new method to trace the impact of parameter variations in the simulation of multi-parton interactions and colour reconnections in the Sherpa event generator. They are reflected, at an event-by-event basis, through relative weights with respect to the central production parameters that give rise to the generated events and distributions. Our method facilitates the tuning of the Monte Carlo event generator at a dramatically reduced computational cost, alleviates parameter sensitivity studies, and enables robust quantification of parametric uncertainties on-the-fly, one of the missing ingredients for future simulations of high-energy particle collisions. The method can easily be adapted to and implemented in other event generators. To illustrate its potential, we here consider combined tunes of the multi-parton-interaction and colour-reconnection models in Sherpa using LHC proton-proton collision data at $\sqrt{s}=7\,\text{TeV}$. We furthermore calibrate the energy-scaling behaviour of dimensionful model parameters based on $\sqrt{s}=13\,\text{TeV}$ LHC data and Tevatron data taken at $\sqrt{s}=1.96\,\text{TeV}$.

Pabst, Moritz [Gottingen U.]↗

DOE OSTI2023

Leveraging the Polymer Glass Transition to Access Thermally Switchable Shear Jamming Suspensions

Suspensions of polymeric nano-and microparticles are fascinating stress-responsive material systems that, depending on their composition, can display a diverse range of flow properties under shear, such as drastic thinning, thickening, and even jamming (reversible solidification driven by shear). However, investigations to date have almost exclusively focused on nonresponsive particles, which do not allow in situ tuning of the flow properties. Polymeric materials possess rich phase transitions that can be directly tuned by their chemical structures, which has enabled researchers to engineer versatile adaptive materials that can respond to targeted external stimuli. Reported herein are suspensions of (readily prepared) micrometer-sized polymeric particles with accessible glass transition temperatures (T g ) designed to thermally control their non-Newtonian rheology. The underlying mechanical stiffness and interparticle friction between particles change dramatically near T g . Capitalizing on these properties, it is shown that, in contrast to conventional systems, a dramatic and nonmonotonic change in shear thickening occurs as the suspensions transition through the particles' T g . This straightforward strategy enables the in situ turning on (or off) of the system's ability to shear jam by varying the temperature relative to T g and lays the groundwork for other types of stimuli-responsive jamming systems through polymer chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Towards philosophical reasoning with agentic LLMs: Socratic method for scientific assistance

As large language models (LLMs) become central tools in science, improving their reasoning capabilities is critical for meaningful and trustworthy applications. We introduce a Socratic agent for scientific reasoning, implemented through a structured system prompt that guides LLMs via classical principles of inquiry. Unlike typical prompt engineering or retrieval-based methods, our approach leverages definition, analogy, hypothesis elimination, and other Socratic techniques to generate more coherent, critical, and domain-aware responses. We evaluate the agent across diverse scientific domains and benchmark it on the abstraction and reasoning corpus challenge dataset, achieving 97.15% under a fixed prompting protocol and without fine-tuning or external tools. Expert evaluation shows improved reasoning depth, clarity, and adaptability over conventional LLM outputs, suggesting that structured prompting rooted in philosophical reasoning can improve the scientific utility of language models.

LLM reasoning↗

DOE OSTI2024

GalaxyFlow: upsampling hydrodynamical simulations for realistic mock stellar catalogues

ABSTRACT Cosmological N-body simulations of galaxies operate at the level of ‘star particles’ with a mass resolution on the scale of thousands of solar masses. Turning these simulations into stellar mock catalogues requires ‘upsampling’ the star particles into individual stars following the same phase-space density. In this paper, we introduce two new upsampling methods. First, we describe GalaxyFlow, a sophisticated upsampling method that utilizes normalizing flows to both estimate the stellar phase-space density and sample from it. Secondly, we improve on existing upsamplers based on adaptive kernel density estimation (KDE), using maximum likelihood estimation to fine-tune the bandwidth for such algorithms in a way that improves both the density estimation accuracy and upsampling results. We demonstrate our upsampling techniques on a neighbourhood of the Solar location in two simulated galaxies: Auriga 6 and h277. Both yield smooth stellar distributions that closely resemble the stellar densities seen in the Gaia DR3 catalogue. Furthermore, we introduce a novel multimodel classifier test to compare the accuracy of different upsampling methods quantitatively. This test confirms that GalaxyFlow more accurately estimates the density of the underlying star particles than methods based on KDE, at the cost of being more computationally intensive.

Lim, Sung Hak (ORCID:0000000330981092)↗

DOE OSTI2022

Reinforcement learning for online adaptation of model predictive controllers: Application to a selective catalytic reduction unit

Here we present a novel application of reinforcement learning (RL) for online dynamic tuning of model predictive controllers (MPC). Applying a state-action-reward-state-action (SARSA) algorithm for temporal difference learning with a control-specific reward function improves the error tracking performance of a standard MPC formulation. The proposed RL approach is also readily adaptable to other MPCs, or entirely different control approaches. Practical details for the implementation of the RL-MPC algorithm are also presented. The proposed algorithm is applied to a case study of controlling nitrogen oxide (NO x ) emissions in an industrial selective catalytic reduction (SCR) unit, a control problem characterized by significant nonlinearity and time delay. Along with an RL-MPC formulation for NOx control, another MPC is proposed to mitigate ammonia slip and decrease ammonia consumption in the SCR. Results showing the efficacy of the RL-MPC for NO x control through learning and implementation on the nonlinear SCR dynamic model are presented.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida

Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to segregate carbons from each substrate type into different metabolic pathways. However, the mechanisms of this metabolic segregation remain unresolved. Here, we investigate Pseudomonas putida KT2440 during processing of the sugar glucose through glycolysis versus the phenolic acid ferulate through gluconeogenesis. Metabolome profiling reveals up to twofold less tricarboxylic acid cycle metabolites but up to 10-fold higher metabolites of upper glycolysis, pentose-phosphate, and Entner–Doudoroff pathways in glucose-grown cells compared to ferulate-grown cells. After 13C-substrate switching, kinetic isotopic profiling captures rapid assimilation of new substrate carbons into initial catabolic pathways, but incorporation into downstream pathways is absent or incomplete. Proteomics identifies a 22-fold higher abundance of one homolog of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GapA) in cells fed on glucose relative to ferulate, while abundance of another homolog (GapB) remains unchanged. Growth phenotypes and quantitative metabolomics for single and double knockout mutants of these GAPDH homologs indicate only GapA involvement in glycolytic flux, which can be compensated by the Entner–Doudoroff pathway, and distinct preference of GapB with minimal role of GapA for gluconeogenic flux. Accordingly, growth of triple knockout mutant with deletion of gapA, gapB, and edd is possible only when glycolytic and gluconeogenic substrates are provided together to meet metabolic demands in a segregated fashion, but metabolic tradeoffs lead to slow growth. A mathematical, experimentally constrained, model of the GAPDH node shows that tuning of GapA and GapB concentrations enables transition between flux regimes for nutritional adaptability.

Zhou, Nanqing [Northwestern University, Evanston]↗

DOE OSTI2026

HydraGNN_GFM_FineTuning4Materials v1.0

This repository enables fine-tuning of the HydraGNN Predictive GFM 2026 — an open-source ensemble of pre-trained graph foundation models for atomistic materials modeling, developed at Oak Ridge National Laboratory. The GFM 2026 is freely available and downloadable via Globus from the OLCF Data Constellation (DOI: 10.13139/OLCF/2562660). Starting from these pre-trained weights, this repository provides a complete transfer learning pipeline for adapting the GFM ensemble to domain-specific molecular and materials property prediction tasks. It includes: 1) Utilities for ensemble fine-tuning with task-specific output heads 2) Example pipelines for eight widely-used materials and molecular datasets 3) Tools for model adaptation and head configuration 4) Data preprocessing utilities for each supported dataset 5) Benchmarking and evaluation scripts

Ungerboeck, Linda↗

DOE OSTI2026

Disentangling interlayer confinement and pore surface adsorption in functionalized smectites for tunable ethylene gas capture

Smectite-based adsorbents are increasingly being studied as sustainable packaging materials for scavenging ethylene, a plant hormone that accelerates fruit ripening. However, the mechanisms governing their uptake and retention remain poorly understood. Here, to tackle this question we systematically investigate ethylene gas-solid interactions in pristine, acid-activated, and choline-functionalized montmorillonites using a complementary combination of structural, gravimetric, and spectroscopic techniques, including inelastic neutron scattering. We experimentally distinguish ethylene populations associated with interlayer confinement, mesopore, and external surface adsorption. We show that chemical functionalization distinctly controls adsorption pathways: acid activation enhances total uptake by generating mesoporous adsorption sites and promoting partial interlayer intercalation, yielding capacities comparable to those of leading smectite-based adsorbents, while choline functionalization promotes preferential confinement and stabilization of guest molecules within the interlayer galleries. Advanced spectroscopic analysis provides molecular-level insight into confinement environments and interaction strengths. We also establish clear structure-property relationships by correlating uptake values derived from independent techniques, linking chemical modification, accessible adsorption domains, and retention behavior. These findings provide general design principles for tuning gas-solid interactions in functionalized layered silicates and highlight their potential as adaptable platforms for sustainable ethylene gas capture and selective adsorption technologies.

Ethylene adsorption mechanism↗

DOE OSTI2026

PowerModelsGAT-AI: Physics-Informed Graph Attention for Multi-System Power Flow With Continual Learning

Solving the alternating current power flow equations in real time is essential for secure grid operation, yet classical Newton–Raphson solvers can be slow under stressed conditions. Existing graph neural networks for power flow are typically trained on a single system and often degrade on different systems. We present PowerModelsGAT-AI, a physics-informed graph attention network that predicts bus voltages and generator injections. The model uses bus-type-aware masking to handle different bus types and balances multiple loss terms, including a power-mismatch penalty, using learned weights. We evaluate the model on 14 benchmark systems (4 to 6,470 buses) and train a unified model on 13 of these under contingency conditions with up to two branch outages, achieving an average normalized mean absolute error of 0.89% for voltage magnitudes and R 2 >0.99 for voltage angles. We also show continual learning: when adapting a base model to a new 1,354-bus system, standard fine-tuning causes severe forgetting with error increases exceeding 1000% on base systems, while our experience replay and elastic weight consolidation strategy keeps error increases below 2% and in some cases improves base-system performance. Interpretability analysis shows that learned attention weights correlate with physical branch parameters (susceptance: r=0.38 ; thermal limits: r=0.22 ), and feature importance analysis supports that the model captures established power flow relationships.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Project Title: Adaptive Vertical Grid Enhancement for E3SM (Final Technical Report)

During the first phase of the project (2018/05-2021/05), we proved the hypothesis that, without tuning, high vertical resolution improves the representation of unresolved, parameterized low altitude clouds such as stratocumulus clouds in global climate models. We evaluated the effectiveness of the newly developed computational framework, Framework for Improvement by Vertical Enhancement (FIVE) by implementing it into E3SM. FIVE aims to improve representation of the target cloud, low level cloud for this project, with use of a locally high vertical resolution for computation of selected processes. FIVE was assessed via direct comparison among E3SM, E3SM-FIVE, and satellite data as well as a newly developed ensemble artificial neural network methodology. We demonstrated that E3SM-FIVE remarkably improves marine stratocumulus representation. To advance the FIVE methodology, we took a first step toward the adaptive vertical grid in the FIVE method by modifying the E3SM single column model. For future application of FIVE to the global storm resolving model with a few km horizontal grid resolution, we developed the vertical-meridional two-dimensional (2D) Hadley circulation model, which allows one to run simulations with much higher vertical resolution and significantly longer duration than current three-dimensional global storm resolving model. During the second phase of the project (2021/05-2023/11; period for this technical report), we sought a way to appropriately transform FIVE to a regionalized version of FIVE, which allows one to select locations with/without FIVE. In parallel, we demonstrated that E3SM-FIVE with a 25-km mesh significantly reduced the bias associated with coastal stratocumulus. Furthermore, we showed that the same improvement was able to be obtained with the use of both the Regional Refined Model (RRM) targeted to one of the stratocumulus regions with 25-km resolution and FIVE. We explored a new implementation strategy of FIVE with our 2D Hadley circulation model. In parallel we applied the 2D Hadley circulation model to study the double intertropical convergence zone bias with storm resolving model resolution and aerosol-cloud interactions within the Hadley circulation with near large eddy simulation resolution. Last, we have been investigating Arctic mixed-phase stratocumulus clouds with large eddy simulations in order to improve their representation in global models. During the course of the entire project, 6 journal articles were published, and 3 manuscripts are currently in preparation. We gave a total of 30 presentations at various domestic and international conferences. In addition we gave 6 seminar talks at universities and a national laboratory. E3SM- FIVE is available as a branch of E3SM.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Adaptive Data-Driven Model Predictive Control for Heat Pipe Microreactors

To establish a technical basis for self-regulating microreactors, a model predictive control (MPC) system is investigated to proactively respond to anomalies and disturbances in anticipation of potential deviations from operating setpoints. Due to the difficulty of developing a physics-based surrogate model that can accurately match plant data in various operating conditions, machine learning algorithms are used in MPC, which allow for learning from both simulation and operation data, thus efficiently describing the targeted transient with arbitrary accuracy. However, one of the biggest concerns in applying ML algorithms like artificial neural networks (ANNs) is that the predictive capabilities of ANN are limited by training data. If there are gaps between the training and target domain, the accuracy of an ANN can degrade significantly when it is used to predict unseen data. To improve the predictive capability of ANN and enable a confident use of data-driven MPCs outside the training data, this study proposes an adaptive data-driven MPC framework. The system will monitor the discrepancy between plant responses and surrogate predictions, fine-tune the ANN-based surrogate when a large discrepancy is detected, and continue MPC operation with updated surrogates. The framework is demonstrated on a point kinetic model for microreactors. The hyperparameters of the update strategy, including layers to update, error thresholds, learning rate discount, and number of data points used for fine-tuning, are optimized so the simulated microreactor is able to follow changes in setpoint with the smallest of deviations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Adaptable Data Driven Model Predictive Control for Heat Pipe Microreactors

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Bezerra, Ana Rita (ORCID:0000000346131711)↗

DOE OSTI2024

Controlling cantilevered adaptive X-ray mirrors

Modeling the behavior of a prototype cantilevered X-ray adaptive mirror (held from one end) demonstrates its potential for use on high-performance X-ray beamlines. Similar adaptive mirrors are used on X-ray beamlines to compensate optical aberrations, control wavefronts and tune mirror focal distances at will. Controlled by 1D arrays of piezoceramic actuators, these glancing-incidence mirrors can provide nanometre-scale surface shape adjustment capabilities. However, significant engineering challenges remain for mounting them with low distortion and low environmental sensitivity. Finite-element analysis is used to predict the micron-scale full actuation surface shape from each channel and then linear modeling is applied to investigate the mirrors' ability to reach target profiles. Using either uniform or arbitrary spatial weighting, actuator voltages are optimized using a Moore–Penrose matrix inverse, or pseudoinverse, revealing a spatial dependence on the shape fitting with increasing fidelity farther from the mount.

47 OTHER INSTRUMENTATION↗