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DOE OSTI2025

Roles for epigenetics in wood formation and stress response intrees–from basic biology to forest management

Annual model and crop species have been the subject of most epigenetic studies for plants. In contrast to annuals, forest trees persist on natural landscapes and experience environmental variation within and across seasons, years, and decades or even centuries. Most forest trees species are undomesticated and typically grown on variable landscapes with no irrigation or application of agricultural chemicals. Forest trees must thus rely on their inherent ability to alter growth and physiology to mitigate the effects of changing abiotic and biotic stressors. Like other plants, trees have mechanisms encoded in their genomic DNA sequence that can respond directly to stress events such as drought or heat. Hypothetically, it would be highly advantageous to join these mechanisms with a dynamic “memory” of past exposure to stress. It is now well established that annual model and crop plants can establish epigenetic-based memory of stress events that support more rapid and robust response to stress in the future. Here, evidence is discussed for epigenetic regulation and “memory” in two fundamental biological processes in trees, wood formation and abiotic stress response. Wood formation is an ideal trait for epigenetic research in trees, as wood formation is highly responsive to environmental conditions and includes multiple rapid developmental changes as cells adopt distinct fates within complex tissues. This is followed by a discussion of research needs that would provide the foundation for new epigenetic applications for forestry.

Groover, Andrew↗

DOE OSTI2025

Effect of Gamma Radiation on TaOₓ ECRAM

Electrochemical random access memory (ECRAM) is an emerging three-terminal nonvolatile memory (NVM) with highly controllable channel conductance which is promising for use as an analog memory (or synapse) in analog in-memory computing (IMC) systems. Energy-efficient analog IMC computing is particularly desirable for power-constrained, high-radiation environments such as satellites. However, little is known about the suitability of ECRAM for use in a total ionizing dose (TID) environment. Here, this work investigates the effect of Co-60 gamma radiation on the channel conductance and noise—two properties critical for analog IMC systems—of a TaO x -based ECRAM up to 17.3 Mrad(SiO 2 ) for both low- and high-channel-conductance state devices. A transient increase in conductance is observed in response to radiation which consists of two elements: an immediate increase in conductivity due to photocurrent and a secondary increase in conductivity, which has a slower rise and saturation and can persist for hours after exposure. This secondary, persistent photoconductivity is attributed to charging caused by hole trapping. These transient effects would not likely occur in a space environment due to the low dose rate compared with this experiment. No permanent change is found in the low conductance state (LCS) following exposure and the minor shift in the high conductance change would be less significant than the regular retention decay in this state. A permanent increase in the random telegraph noise is observed, possibly due to increased traps created in the channel. This work demonstrates that TaO x -based ECRAM is suitable for use in spaceborne analog IMC systems that are subject to significant TID.

ECRAM↗

DOE OSTI2025

Imaging Domain Walls in van der Waals Ferroelectrics Using Tip-Enhanced Second Harmonic Generation

van der Waals ferroelectrics have captured significant interest for applications in novel memory and neuromorphic computing devices. Within these materials, interfaces between regions of different ferroelectric polarizations (i.e., domain walls) exhibit distinctive behaviors. Characterization of these behaviors remains a challenge, as domain wall thickness resides at the nanoscale. Using tip-enhanced second harmonic generation (TESHG), we demonstrate nanoscale imaging of domain walls in 2D ferroelectric α-In 2 Se 3 . With a narrow-band near-IR laser, we take advantage of high-wavelength, off-resonant signal enhancement to generate robust and reproducible TESHG. In conclusion, a 16 nm spatial resolution is achieved, and we identify spectral features suggesting that nonlocal effects from domain walls persist nanometers into adjacent domains.

Mantilla, Alexander B. C. [Washington State Univ.,↗

DOE OSTI2024

Non-DNA radiosensitive targets that initiate persistent behavioral deficits in rats exposed to space radiation

Predicting future CNS risks for astronauts during deep-space missions will rely substantially on ground-based rodent data with space-relevant ions and behaviors. For rats, the accumulated evidence indicates that less densely ionizing radiation, such as 4 He and 12 C ions, induce behavior deficits at lower doses than densely ionizing ions, such as 48 Ti and 56 Fe. However, this observation conflicts with standard somatic radiobiology, in which densely ionizing ions are generally more effective than less densely ionizing ions, and where the DNA/nucleus is the accepted target for radiation-induced tumorigenesis, cytogenetic aberrations, genetic mutations, and reproductive cell death. To gain deeper insight into the subcellular nature of the radiation targets for behavior risks, we compared the effects of dose, fluence, and linear energy transfer (LET) of 4 He and 56 Fe particles using existing datasets for four distinct behavioral outcomes in rats: elevated plus maze (EPM-anxiety), novel object recognition (NOR-memory), operant responding (OR-response to environmental stimuli), and attentional set-shifting (ATSET-cognitive flexibility). We confirmed that less densely ionizing particles (except protons) showed ~100-fold lower threshold doses than densely ionizing particles for behavioral deficits (0.1–1 cGy for 4 He vs. 15–100 cGy for 56 Fe). However, when analyzed by fluence the behavioral responses converged, indicating that 4 He and 56 Fe were equally effective on a per-track basis. When analyzed by LET, there were ~100-fold differences in the LET for maximum effectiveness for behavioral deficits and DNA endpoints (~1 vs ~100 keV/μm, respectively). These unique features of radiation-induced behavioral deficits (high sensitivity to particles in the 1-keV/μm range, insensitivity to protons in the 0.2 keV/μm range, and isofluence dependence for particles with LET>1 keV/μm) provide evidence in support of a new hypothesis of sub-micron sized radiosensitive targets for behavioral effects consistent with the thickness of plasma membranes and/or small subcellular structures, smaller than a whole synapse. Like our behavior findings, mouse immature oocyte killing which is known to have a plasma membrane target was also better explained by fluence, rather than dose. In contrast, fluence analyses for DNA/nuclear endpoints in somatic cells (e.g., tumor induction, chromosome aberrations) showed opposite results, suggesting that behavior targets are not DNA. Our findings raise questions regarding the identity of subcellular targets and the multi-cellular functional unit for behavior risks, low-dose susceptibility, and generalizability from rat to other species and astronauts.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2021

A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies

HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

A Van der Waals Interface Hosting Two Groups of Magnetic Skyrmions

Multiple magnetic skyrmion phases add an additional degree of freedom for skyrmion-based ultrahigh-density spin memory devices. Extending the field to 2D van der Waals magnets is a rewarding challenge, where the realizable degree of freedoms (e.g., thickness, twist angle, and electrical gating) and high skyrmion density result in intriguing new properties and enhanced functionality. In this work, a van der Waals interface, formed by two 2D ferromagnets Cr 2 Ge 2 Te 6 and Fe 3 GeTe 2 with a Curie temperature of ≈65 and ≈205 K, respectively, hosting two groups of magnetic skyrmions, is reported. Two sets of topological Hall effect signals are observed below 6s0 K when Cr 2 Ge 2 Te 6 is magnetically ordered. These two groups of skyrmions are directly imaged using magnetic force microscopy, and supported by micromagnetic simulations. Interestingly, the magnetic skyrmions persist in the heterostructure with zero applied magnetic field. The results are promising for the realization of skyrmionic devices based on van der Waals heterostructures hosting multiple skyrmion phases.

2D magnetism↗

DOE OSTI2021

Short-term apartment-level load forecasting using a modified neural network with selected auto-regressive features

Residential electricity load profiles and their diversity have become increasingly important to realize the benefits of Smart or Transactive Energy Networks (TENs). An important element of TENs will be practical, accurate, and implementable residential load forecasting techniques. While there have been many approaches to short-term load forecasting, few have included forecasting for individual households, partly because the high volatility and idiosyncrasies present in individual household load data can pose significant challenges. In this study, we develop a Convolutional Long Short-Term Memory-based neural network with Selected Autoregressive Features (termed a CLSAF model) to improve short-term household electricity load forecasting accuracy by employing three strategies: autoregressive features selection, exogenous features selection, and a “default” state to avoid overfitting at times of high load volatility. We include aggregations of apartments to floor and building level, because utilities may favor transactive approaches that rely on aggregator models, e.g., a cluster of consumers as opposed to an individual. We demonstrate that the CLSAF model, by virtue of its enhanced feature representation and modest computational resources, can accomplish load forecasting in a multi-family residential building across three spatial granularities (individual apartment/household, floor, and building levels), with an accuracy improvement of up to 25% compared to a persistence model. We propose a data screening technique to characterize time-series electricity-load data. This technique is suitable for integration into a TEN ecosystem and allows one to estimate confidence levels of the load forecasts to optimize computational resources and the risks associated with uncertain forecasts.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Drought legacies mediated by trait trade‐offs in soil microbiomes

Abstract Soil microbiomes play a key role in driving biogeochemical cycles of the Earth system. As drought frequency and intensity increase due to climate change, soil microbes and the processes they control will be impacted. Even after a drought ends, microbiomes and other systems take time to recover and may display a memory of previous climate conditions. Still, the mechanisms involved in these legacy effects remain unclear, making it difficult to predict climate and biogeochemical rates in the future. Here, we used a trait‐based microbiome model (DEMENTpy) to implement trade‐off‐mediated mechanisms that may lead to drought legacy effects on litter decomposition. Trade‐offs were assumed to follow the Y‐A‐S framework that defines three primary life‐history strategies of microorganisms: high growth Yield, resource Acquisition, and Stress tolerance. We represented cellular trade‐offs between osmolytes required for drought tolerance and investment in enzymes involved in litter decomposition. Simulations were run under varying levels of drought severity and dispersal. With high levels of dispersal, no legacy effects were predicted by DEMENTpy following drought. With limited dispersal, severe drought resulted in a persistent legacy of altered community‐level traits and reduced litter decomposition. Moderate drought resulted in a transient legacy that disappeared after two years, consistent with recent empirical observations in Southern California ecosystems. These results imply that greater movement along the trade‐off between enzyme investment and osmolyte production resulted in stronger legacy effects. More generally, factors that shift the position of a microbiome in YAS space may alter the legacy outcome following drought. Our trait‐based modeling study motivates additional empirical measurements to quantify YAS traits and trade‐offs that are needed to make accurate predictions of soil microbiome resilience and functioning. Also, our study illustrates an emerging approach for representing trait trade‐offs in microbiomes and vegetation that dictate ecosystem responses to drought and other environmental perturbations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Adaptive Scalpel Scanning Probe Microscopy for Enhanced Volumetric Sensing in Tomographic Analysis

Controlling nanoscale tip‐induced material removal is crucial for achieving atomic‐level precision in tomographic sensing with atomic force microscopy (AFM). While advances have enabled volumetric probing of conductive features with nanometer accuracy in solid‐state devices, materials, and photovoltaics, limitations in spatial resolution and volumetric sensitivity persist. This work identifies and addresses in‐plane and vertical tip‐sample junction leakage as sources of parasitic contrast in tomographic AFM, hindering real‐space 3D reconstructions. Novel strategies are proposed to overcome these limitations. First, the contrast mechanisms analyzing nanosized conductive features are explored when confining current collection purely to in‐plane transport, thus allowing reconstruction with a reduction in the overestimation of the lateral dimensions. Furthermore, an adaptive tip‐sample biasing scheme is demonstrated for the mitigation of a class of artefacts induced by the high electric field inside the thin oxide when volumetrically reduced. This significantly enhances vertical sensitivity by approaching the intrinsic limits set by quantum tunneling processes, allowing detailed depth analysis in thin dielectrics. The effectiveness of these methods is showcased in tomographic reconstructions of conductive filaments in valence change memory, highlighting the potential for application in nanoelectronics devices and bulk materials and unlocking new limits for tomographic AFM.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Dual blockade of IL-10 and PD-1 leads to control of SIV viral rebound following analytical treatment interruption

Human immunodeficiency virus (HIV) persistence during antiretroviral therapy (ART) is associated with heightened plasma interleukin-10 (IL-10) levels and PD-1 expression. We hypothesized that IL-10 and PD-1 blockade would lead to control of viral rebound following analytical treatment interruption (ATI). Twenty-eight ART-treated, simian immunodeficiency virus (SIV)mac 239 -infected rhesus macaques (RMs) were treated with anti-IL-10, anti-IL-10 plus anti-PD-1 (combo) or vehicle. ART was interrupted 12 weeks after introduction of immunotherapy. Durable control of viral rebound was observed in nine out of ten combo-treated RMs for >24 weeks post-ATI. Induction of inflammatory cytokines, proliferation of effector CD8 + T cells in lymph nodes and reduced expression of BCL-2 in CD4 + T cells pre-ATI predicted control of viral rebound. Twenty-four weeks post-ATI, lower viral load was associated with higher frequencies of memory T cells expressing TCF-1 and of SIV-specific CD4 + and CD8 + T cells in blood and lymph nodes of combo-treated RMs. These results map a path to achieve long-lasting control of HIV and/or SIV following discontinuation of ART.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

LSTM-Based Data Integration to Improve Snow Water Equivalent Prediction and Diagnose Error Sources

Accurate prediction of snow water equivalent (SWE) can be valuable for water resource managers. Recently, deep learning methods such as long short-term memory (LSTM) have exhibited high accuracy in simulating hydrologic variables and can integrate lagged observations to improve prediction, but their benefits were not clear for SWE simulations. Here we tested an LSTM network with data integration (DI) for SWE in the western United States to integrate 30-day-lagged or 7-day-lagged observations of either SWE or satellite-observed snow cover fraction (SCF) to improve future predictions. SCF proved beneficial only for shallow-snow sites during snowmelt, while lagged SWE integration significantly improved prediction accuracy for both shallow- and deep-snow sites. The median Nash–Sutcliffe model efficiency coefficient (NSE) in temporal testing improved from 0.92 to 0.97 with 30-day-lagged SWE integration, and root-mean-square error (RMSE) and the difference between estimated and observed peak SWE values d max were reduced by 41% and 57%, respectively. DI effectively mitigated accumulated model and forcing errors that would otherwise be persistent. Moreover, by applying DI to different observations (30-day-lagged, 7-day-lagged), we revealed the spatial distribution of errors with different persistent lengths. For example, integrating 30-day-lagged SWE was ineffective for ephemeral snow sites in the southwestern United States, but significantly reduced monthly-scale biases for regions with stable seasonal snowpack such as high-elevation sites in California. These biases are likely attributable to large interannual variability in snowfall or site-specific snow redistribution patterns that can accumulate to impactful levels over time for nonephemeral sites. These results set up benchmark levels and provide guidance for future model improvement strategies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Intranasal Nanoparticle Vaccination Elicits a Persistent, Polyfunctional CD4 T Cell Response in the Murine Lung Specific for a Highly Conserved Influenza Virus Antigen That Is Sufficient To Mediate Protection from Influenza Virus Challenge

We report lung-localized CD4 T cells play a critical role in the control of influenza virus infection and can provide broadly protective immunity. However, current influenza vaccination strategies primarily target influenza hemagglutinin (HA) and are administered peripherally to induce neutralizing antibodies. We have used an intranasal vaccination strategy targeting the highly conserved influenza nucleoprotein (NP) to elicit broadly protective lung-localized CD4 T cell responses. The vaccine platform consists of a self-assembling nanolipoprotein particle (NLP) linked to NP with an adjuvant. We have evaluated the functionality, in vivo localization, and persistence of the T cells elicited. Our study revealed that intranasal vaccination elicits a polyfunctional subset of lung-localized CD4 T cells that persist long term. A subset of these lung CD4 T cells localize to the airway, where they can act as early responders following encounter with cognate antigen. Polyfunctional CD4 T cells isolated from airway and lung tissue produce significantly more effector cytokines IFN-γ and TNF-α, as well as cytotoxic functionality. When adoptively transferred to naive recipients, CD4 T cells from NLP:NP-immunized lung were sufficient to mediate 100% survival from lethal challenge with H1N1 influenza virus.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Minimal cyclic behavior in sheared amorphous solids

Although jammed packings of soft spheres exist in potential energy landscapes with a vast number of minima, when subjected to cyclic shear they may revisit the same configurations repeatedly. Simple hysteretic spin models, in which particle rearrangements are represented by interacting spin flips called hysterons, capture many features of this periodic behavior. Yet it has been unclear to what extent individual rearrangements can be described by such binary objects and how such objects interact with one another. Using a particularly sensitive algorithm, we identify rearrangements in simulated jammed packings and select pairs of rearrangements that undo one another to create periodic cyclic behavior. We find that the rearrangement pairs surprisingly persist down to the smallest increments in strain, even in the smallest systems we can study. We explore the statistics of these rearrangement pairs and find that there is a relation between the amount of hysteresis and the energy drop and mean-square displacement of the particles; these results are inconsistent with the scaling found in models that treat rearrangements as localized buckling events. Finally, our analysis shows that there is no clean distinction between the particle motions that represent the identity of a single, individual rearrangement and the particle motions that lead to interactions between separated rearrangements or hysterons. These results offer insight into how complex systems such as amorphous solids can reach a limit cycle.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Probing Cretaceous-Paleogene crustal thickness in southern Tibet using quartz-zircon chronobarometry

Knowledge of the crustal thickness history of southern Tibet during the India-Asia collision is key to understanding what deformation mechanisms accommodated northward propagating crustal shortening. Thermoisotopic models suggest that a relatively thin margin of southern Asia persisted from ca. 200 to 45 Ma whereas trace element paleodepth proxies are interpreted to indicate a thinning phase from ca. 100 to 65 Ma when the crust reached ∼30 km-thickness. As neither of these methods directly measures crustal thickness, resolution of this conflict awaits development of a method that can. Here, in this study, we place bounds on the thickening history of southern Tibet using coupled quartz-zircon thermobarometry and U-Pb geochronology of granitoid plutons in the Gangdese batholith. We find that crustal thicknesses were as high (or higher) as 60–75 km at 65 Ma, or 10–15 Ma prior to the onset of hard continental collision. Magmatic inflation in the lower crust likely contributed to crustal thickening and thermal weakening of the lower crust, suggesting that pure shear in the lower crust was likely the primary accommodation mechanism for N-S shortening during collision. These data are in partial agreement with results of thermoisotopic models of crustal thickness but contradict thickness histories derived from empirical trace element proxies.

Chronobarometry↗