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DOE OSTI2022

Genotype–environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence

Abstract Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush ( Catharus guttatus ), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Eight Metagenome-Assembled Genomes Provide Evidence for Microbial Adaptation in 20,000- to 1,000,000-Year-Old Siberian Permafrost

Permafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly cored permafrost from the Siberian Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ~20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with <10% contamination and were taxonomically identified as Aminicenantes, Atribacteria, Chloroflexi, and Actinobacteria within bacteria and Thermoprofundales within archaea. MAGs from these taxa have been obtained previously from nonpermafrost environments and have been suggested to show adaptations to long-term energy starvation, but they have never been explored in ancient permafrost. The permafrost MAGs had greater proportions in the Clusters of Orthologous Groups (COGs) categories of energy production and conversion and carbohydrate transport and metabolism than did their nonpermafrost counterparts. They also contained genes for trehalose synthesis, thymine metabolism, mevalonate biosynthesis, and cellulose degradation, which were less prevalent in nonpermafrost genomes. Furthermore, many of these genes are involved in membrane stabilization and osmotic stress responses, consistent with adaptation to the anoxic, high-ionic-strength, cold environments of permafrost brine films. Our results suggest that this ancient permafrost contains DNA of high enough quality to assemble MAGs from microorganisms with adaptations to survive long-term freezing in this extreme environment.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Host-specific adaptation in Fusarium oxysporum correlates with distinct accessory chromosome content in human and plant pathogenic strains

ABSTRACT Fusarium oxysporumis a cross-kingdom pathogen. While some strains cause disseminated fusariosis and blinding corneal infections in humans, others are responsible for devastating vascular wilt diseases in plants. To better understand the distinct adaptations ofF. oxysporumto animal or plant hosts, we conducted a comparative phenotypic and genetic analysis of two strains: MRL8996 (isolated from a keratitis patient) and Fol4287 (isolated from a wilted tomato [Solanum lycopersicum]). Infection of mouse corneas and tomato plants revealed that, while both strains cause symptoms in both hosts, MRL8996 caused more severe corneal disease in mice, whereas Fol4287 induced more pronounced wilting symptoms in tomato plants.In vitroassays using abiotic stress treatments revealed that the human pathogen MRL8996 was better adapted to elevated temperatures, whereas the plant pathogen Fol4287 was more tolerant to osmotic and cell wall stresses. Both strains displayed broad resistance to antifungal treatment, with MRL8996 exhibiting the paradoxical effect of increased tolerance to higher concentrations of the antifungal caspofungin. We identified a set of accessory chromosomes (ACs) that encode genes with different functions and have distinct transposon profiles between MRL8996 and Fol4287. Interestingly, ACs from both genomes also encode proteins with shared functions, such as chromatin remodeling and post-translational protein modifications. Our phenotypic assays and comparative genomics analyses lay the foundation for future studies correlating genotypes with phenotype and for developing targeted antifungals for agricultural and clinical uses. IMPORTANCE Fusarium oxysporumis a cross-kingdom fungal pathogen that infects both plants and animals. In addition to causing many devastating wilt diseases, this group of organisms was recently recognized by the World Health Organization as a high-priority threat to human health. Climate change has increased the risk ofFusariuminfections, asFusariumstrains are highly adaptable to changing environments. Deciphering fungal adaptation mechanisms is crucial to developing appropriate control strategies. We performed a comparative analysis ofFusariumstrains using an animal (mouse) and plant (tomato) host andin vitroconditions that mimic abiotic stress. We also performed comparative genomics analyses to highlight the genetic differences between human and plant pathogens and correlate their phenotypic and genotypic variations. We uncovered important functional hubs shared by plant and human pathogens, such as chromatin modification, transcriptional regulation, and signal transduction, which could be used to identify novel antifungal targets.

Microbiology↗

DOE OSTI2025

SIDDA: SInkhorn Dynamic Domain Adaptation for Image Classification

SInkhorn Dynamic Domain Adaptation (SIDDA) supplements the experiments presented in 2501.14048, SIDDA: SInkhorn Dynamic Domain Adaptation for Image Classification with Equivariant Neural Networks. SIDDA introduces a semi-supervised, automatic domain adaptation method that leverages Sinkhorn divergences to dynamically adjust the regularization in the optimal transport plan and the weighting between classification and domain adaptation loss terms during training.

Pandya, Sneh [Fermi National Accelerator Laborator↗

DOE OSTI2025

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that anti- viral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

ComEd Climate Risk and Adaptation Outlook, Phase 1: Temperature, Heat Index, and Average Wind

This Climate Risk and Adaptation Outlook report presents the research and findings of a joint venture between Commonwealth Edison (ComEd) and Argonne National Laboratory (Argonne) to evaluate future climate risks to ComEd’s infrastructure and operations. ComEd recognizes that its position as the state of Illinois’ largest electric utility, serving roughly 70% of the state’s population, underscores the importance for communities across Illinois to consider climate risk as they plan for future conditions. Climate impacts, such as more severe heatwaves or more frequent flood events, can disrupt the generation, transmission, and distribution of electricity and create public health challenges. Taking a proactive approach to adapt to climate risks will help ensure that ComEd continues to serve its growing customer-base reliably and efficiently. This Climate Risk and Adaptation Outlook serves as an important first step to inform ComEd’s grid planning efforts, but Argonne and ComEd recognize that additional research beyond this report will be necessary to characterize future climate conditions more comprehensively throughout northern Illinois, to assess their impacts to grid assets and system operations, and to index effective adaptation options at an asset-level.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2023

Avoiding symmetry roadblocks and minimizing the measurement overhead of adaptive variational quantum eigensolvers

Quantum simulation of strongly correlated systems is potentially the most feasible useful application of near-term quantum computers. Minimizing quantum computational resources is crucial to achieving this goal. A promising class of algorithms for this purpose consists of variational quantum eigensolvers (VQEs). Among these, problem-tailored versions such as ADAPT-VQE that build variational ansätze step by step from a predefined operator pool perform particularly well in terms of circuit depths and variational parameter counts. However, this improved performance comes at the expense of an additional measurement overhead compared to standard VQEs. Here, we show that this overhead can be reduced to an amount that grows only linearly with the number n of qubits, instead of quartically as in the original ADAPT-VQE. We do this by proving that operator pools of size 2 n − 2 can represent any state in Hilbert space if chosen appropriately. We prove that this is the minimal size of such "complete" pools, discuss their algebraic properties, and present necessary and sufficient conditions for their completeness that allow us to find such pools efficiently. We further show that, if the simulated problem possesses symmetries, then complete pools can fail to yield convergent results, unless the pool is chosen to obey certain symmetry rules. We demonstrate the performance of such symmetry-adapted complete pools by using them in classical simulations of ADAPT-VQE for several strongly correlated molecules. Our findings are relevant for any VQE that uses an ansatz based on Pauli strings.

Shkolnikov, V. O.↗

DOE OSTI2021

Computational Fluid Dynamics Using the Adaptive Wavelet-Collocation Method

Advancements to the adaptive wavelet-collocation method over the last decade have opened up a number of new possible areas for active research. Volume penalization techniques allow complex immersed boundary conditions to be used with high efficiency for both internal and external flows. Anisotropic methods make it possible to use body-fitted meshes while still taking advantage of the dynamic adaptability properties wavelet-based methods provide. The parallelization of the approach has made it possible to perform large high-resolution simulations of detonation initiation and fluid instabilities to uncover new physical insights that would otherwise be difficult to discover. Other developments include space-time adaptive methods and nonreflecting boundary conditions. This article summarizes the work performed using the adaptive wavelet-collocation method developed by Vasilyev and coworkers over the past decade.

42 ENGINEERING↗

DOE OSTI2020

Interpreting Morphological Adaptations Associated with Viviparity in the Tsetse Fly Glossina morsitans (Westwood) by Three-Dimensional Analysis

Tsetse flies (genus Glossina), the sole vectors of African trypanosomiasis, are distinct from most other insects, due to dramatic morphological and physiological adaptations required to support their unique biology. These adaptations are driven by demands associated with obligate hematophagy and viviparous reproduction. Obligate viviparity entails intrauterine larval development and the provision of maternal nutrients for the developing larvae. The reduced reproductive capacity/rate associated with this biology results in increased inter- and intra-sexual competition. Here, we use phase contrast microcomputed tomography (pcMicroCT) to analyze morphological adaptations associated with viviparous biology. These include (1) modifications facilitating abdominal distention required during blood feeding and pregnancy, (2) abdominal and uterine musculature adaptations for gestation and parturition of developed larvae, (3) reduced ovarian structure and capacity, (4) structural features of the male-derived spermatophore optimizing semen/sperm delivery and inhibition of insemination by competing males and (5) structural features of the milk gland facilitating nutrient incorporation and transfer into the uterus. Three-dimensional analysis of these features provides unprecedented opportunities for examination and discovery of internal morphological features not possible with traditional microscopy techniques and provides new opportunities for comparative morphological analyses over time and between species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

CMIP7 data request: impacts and adaptation priorities and opportunities

The Coupled Model Intercomparison Project Phase 7 (CMIP7) undertook an extensive process to gather community input and refine data requests related to impacts and adaptation applications of Earth System Model (ESM) outputs. The Impacts and Adaptation (I&A) Data Request Team worked with CMIP7 leadership to distribute an open solicitation across many communities that use climate model outputs requesting inputs for new and existing variables, the most applicable temporal characteristics, and groupings of variables that together allow for specific application opportunities. This input was then collated and translated into CMIP7 standard templates for inclusion in the broader data request, leading to 13 I&A data request opportunities, 60 variable groups and 539 unique variables sought by vulnerability, impacts, adaptation, and climate services user communities. Here, we describe these opportunities and variable groups, as well as new insights into how ESM groups can prioritize outputs that set off a chain of further analyses, ultimately informing decisions impacting society and natural systems. These include an emphasis on high-resolution outputs to allow further modeling of climate impacts at regional and local scales, improved representation of extreme weather events, enhanced accuracy of downscaling and bias-adjustment techniques, and support for more detailed assessments for decision-making in adaptation and mitigation strategies. There is also broad interest in more extensive provisioning of two-dimensional variables at the Earth's surface, prioritizing experiments that enhance our understanding of both the recent past and future scenarios, and providing outputs that allow further downscaling and bias adjustment. We emphasize that variable groups are the fundamental level at which to engage with the I&A data request, matching the scale of input and the way output provision enables specific I&A applications. Given resource constraints, we applaud CMIP7 efforts to foster strong engagement and communication between ESM groups and the I&A team to build consensus around prudent compromises in priority variables, temporal resolutions, simulation experiments, time subsets, and ensemble members.

Ruane, Alex C. [NASA Goddard Inst. for Space Studi↗

DOE OSTI2025

Detecting flash drought events to inform adaptive water management

Abstract: Flash droughts are characterized by a rapid onset of drought conditions, a common feature among various indicators of these events. The lack of a standardized definition and indicator makes flash droughts particularly challenging to predict and manage. We test six state-of-the-art flash drought indicators using 41 years of daily data across all Hydrological Unit Code 4 (HUC4) regions in the contiguous United States. Our results show substantial disagreements among indicators, suggesting that the detection of a flash drought event strongly depends on the choice of indicator. From the perspective of informing management and operations, an open challenge remains: which flash drought indicator should be used to trigger operational adaptations? To this end, we propose a methodological framework that informs adaptive actions by regionally assessing the level of agreement between different indicators. The regional differences in hydroclimatic conditions are expected to be reflected in the level of agreement between indicators. To better inform adaptive actions, the framework will also consider the impacted sectoral water uses and their varying response times. The insights gained from this study improve the understanding of how these different flash drought indicators capture the different aspects of regional differences and impacted sectors. Furthermore, this information can support more targeted adaptive actions to mitigate adverse impacts through improved preparedness and response strategies.

climate resilience↗

DOE OSTI2021

Optoelectronic system with a wedge-shaped adapter

Optoelectronic systems with an adapter and methods of manufacturing or assembling the same are provided. An example of an optoelectronic system according to the present disclosure includes a substrate, an interposer, an electronic component disposed on the interposer, and an optical component. The optoelectronic system includes a ferrule and an optical fiber coupled to the ferrule. The optoelectronic system also includes an optical socket configured to receive the ferrule therein. The optoelectronic system further includes an adapter positioned between the interposer and the optical socket. The adapter has a wedge-shaped configuration such that the ferrule is disposed at a non-zero angle relative to the interposer when the ferrule is received in the optical socket and the optical socket is coupled to the adapter.

Mathai, Sagi Varghese↗

DOE OSTI2021

Method and apparatus for controlling a vehicle including an adaptive cruise control system

Operating a subject vehicle equipped with an adaptive cruise control system includes setting initial states for control parameters, including setting a desired vehicle speed and determining a desired following gap range, wherein the desired following gap range is associated with a lead vehicle. Operation is controlled via the adaptive cruise control system based upon the initial states for the control parameters. Operation also includes monitoring for presence of the lead vehicle. Upon detecting presence of the lead vehicle, an actual following gap is determined between the subject vehicle and the lead vehicle, and the initial states of the control parameters associated with the adaptive cruise control system are adjusted based upon the actual following gap between the subject vehicle and the lead vehicle, and the desired following gap range. Operation is controlled via the adaptive cruise control system based upon the adjusted initial states of the control parameters.

Zhao, Junfeng↗

DOE OSTI2022

Adaptive Protective Relay Settings – A Vision to the Future

Adaptive relaying utilizes the continuously changing status of the power system as the basis for online adjustment of the power system relay settings. Fundamentally they are protection schemes that adjust settings and/or logic of operations based on the prevailing conditions of the system. These adjustments can include, but are not limited to, the logging of data for post-mortem analysis, communication throughout the system, as well as changing relay parameters. Adaptive relaying considers the fact that the status of a power system can change. These include system configuration changes, load effect, cold load pickup, end-of-line protection, transformer protection, and automatic reclosing. In this research, the author focus on the need for a secure, selective, and reliable system for adaptive overcurrent protection in T&D and Distributed Energy Systems. Various types of adaptive methods are presented and explained along with some pros and cons of each.

Mukherjee, Srijib↗

DOE OSTI2020

Panel Session 26: Risk-Based Approaches to Environmental Remediation and Adaptive Site Management

This panel discussed the needs and importance of developing risk-based approaches to environmental remediation that will enable complex sites to be adaptively managed by applying cost-effective remedies that are protective of human health and the environment. The discussion emphasized risk-based approaches within decision processes and subsequent incorporation into regulatory decision documents. Remedy approaches, remediation exit strategies, and long-term monitoring plans that support risk-based end-states for difficult-to-remediate sites were discussed Panelists with presentations: Risk-Informed Approaches to Environmental Remediation and Adaptive Site Management (Vicky Freedman); ITRC Adaptive Site Management Perspective (Michael Truex); Optimization During Operations and Maintenance Phase at the Hanford Site 200-ZP-1 Groundwater Operable Unit (Emerald Laija, Kate Amrhein, Michael Truex); Adaptive Management: EPA Overview (Benjamin Simes); Decommissioning and Environmental Remediation Section Division of Nuclear Fuel Cycle and Waste Technology (Horst Monken Fernandes)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Adaptive, Active Learning, and Multifidelity Monte Carlo Methods in the MOOSE Stochastic Tools Module

MOOSE is an open-source computational platform for constructing multi-physics models and executing them in a massively parallel fashion. It has a stochastic tools module (STM) for forward/inverse uncertainty quantification (UQ) and surrogate modeling. This presentation details some recent developments to the STM with respect to the implementation of adaptive, active learning, and multifidelity Monte Carlo methods for forward UQ of computational models. Specifically, the adaptive Monte Carlo methods include Markov Chain Monte Carlo (MCMC)-driven algorithms like adaptive importance sampling and parallelized subset simulation for statistical QoI estimation, rare events analysis, and stochastic gradient-free optimization. The active learning methods include Gaussian Process (GP) surrogates and their training via Adam optimization, design of acquisition functions, and integration with samplers like Monte Carlo, adaptive importance, and parallelized subset simulation. These active learning methods are also designed to work in a batch mode, wherein, the required calls to the full computational model are executed in parallel whenever a user-specified batch size is met. The multifidelity methods in STM are broadly divided into two categories: hierarchical, where a defined hierarchy exists among the low-fidelity models, and peer, where all the low-fidelity models are treated equally. A GP surrogate is used to learn the differences between the low- and high-fidelity models in both multifidelity categories, and acquisition functions from the active learning classes are used to decide whether to rely on a low-fidelity model or call the expensive high-fidelity model. Alongside the software description and usage, applications are also presented to nuclear engineering computational models including a TRISO nuclear fuel particle, a reactor pressure vessel, and a heat-pipe microreactor.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Adaptive Model-Free Vehicle Path-Tracking via Fast-Converging Prescribed-Time Newton-Based Extremum-Seeking Control

Model-free control (MFC) offers a simple and effective approach to automated vehicle path-tracking without requiring an explicit plant model for control law design. However, gain tuning in MFC is typically carried out through trial-and-error, which can be time-consuming and may lead to suboptimal performance. To address this limitation, extremum-seeking-based adaptive MFC has shown promise by enabling real-time adaptation of control gains, without relying on a predefined vehicle model. Nonetheless, existing ESC approaches often suffer from slow convergence. This paper integrates MFC, employing longitudinal and lateral ultra-local models of a rear-wheel-drive vehicle, with a novel prescribed-time (PT) Newton-based extremum-seeking control (ESC) strategy that ensures rapid convergence of control gains within the prescribed time. Unlike conventional gradient-based ESC methods, the PT Newton-based ESC leverages artificial delays and time-periodic gains, not only to guarantee convergence within the specified time, but also to compensate for feedback delays. Simulation results demonstrate that the proposed approach significantly improves gain adaptation speed and tracking accuracy. This work advances adaptive model-free vehicle control by offering a high-performance, delay-resilient alternative to existing ESCMFC frameworks.

Waleed khan, Muhammad [The University of Texas at ↗

DOE OSTI2025

Self-adaptive weights based on balanced residual decay rate for physics-informed neural networks and deep operator networks

Physics-informed deep learning has emerged as a promising alternative for solving partial differential equations. However, for complex problems, training these networks can still be challenging, often resulting in unsatisfactory accuracy and efficiency. In this work, we demonstrate that the failure of plain physics-informed neural networks arises from the significant discrepancy in the convergence rate of residuals at different training points, where the slowest convergence rate dominates the overall solution convergence. Based on these observations, we propose a pointwise adaptive weighting method that balances the residual decay rate across different training points. The performance of our proposed adaptive weighting method is compared with current state-of-the-art adaptive weighting methods on benchmark problems for both physics-informed neural networks and physics-informed deep operator networks. In conclusion, through extensive numerical results we demonstrate that our proposed approach of balanced residual decay rates offers several advantages, including bounded weights, high prediction accuracy, fast convergence rate, low training uncertainty, low computational cost, and ease of hyperparameter tuning.

Balanced convergence rate↗