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At least 523 records · Page 29

Integrated parameter and process learning for hydrologic and biogeochemical modules in Earth System Models

Focus area: Primary focal area #2; secondary focal area #3: Learning about parameters and processes of land surface hydrologic and biogeochemical models in Earth System models by integrating machine learning, physics, and big data. Science challenges: How do we maximally leverage big-data observations to improve hydrobiogeochemical process description and parameterization so that such modules more realistically capture hydrologic and vegetation responses and feedbacks under the future climate? For example, how can we leverage physics, limited observations of vegetation and streamflow to better estimate evapotranspiration, and, relatedly, net primary productivity, especially for drought areas? Vegetation plays a critical role in regional and global water cycles; however, existing vegetation models have failed to predict vegetation response to droughts (McDowell & Xu, 2017) , arctic greening (Keenan & Riley, 2018) , and critical transitions between forest and savanna (Hirota et al., 2011) . These studies suggest that when we build process-based models (PBM) parameterized from regional and global plant traits, we tend to poorly describe plant adaptation and local-scale competition processes. The models and their associated parameters assigned for different regions in the world are not capturing essential heterogeneity in vegetation responses at finer spatial scales. Many parameters of the land surface models control hydrology and vegetation dynamics at the same time. The heterogeneity in vegetation response is a function of (i) plant type, (ii) plant size, (iii) competition and succession, (iv) environmental controls, and (v) local variations due to the unique ecological community that are very difficult to describe (e.g., the size of gaps resulting from fire that facilitated the coexistence of pioneering species). In the demographic models, only factors (i) and (iv) were captured, and plant types were generally described only by leaf phenology and climate zones. With current demographic models, we generally consider more traits to define plant types (i) and calibrate these traits to consider factors (ii), (iii) and (iv); however, it is substantially challenging to scale to regional and global simulations due to trait variations across space (Ali et al., 2016). Moreover, it has been noted that hillslope processes, including ridge-to-valley flow and sunny vs. shady slopes are primary organizers of water, energy, and vegetation (Clark et al., 2015; Fan et al., 2019) . Although gradual improvements in the hydrologic model component in earth system models may reduce this error (at a remarkably slow pace), the long-term, gradual impact of hydrology on plant traits are not well captured. Recent work showed that the hydrologic controls exerted by groundwater and lateral flow are primary regulators of rooting depth (Fan et al., 2017) . Such hydrologic controls have seldom been reflected in vegetation model parameterizations.

54 ENVIRONMENTAL SCIENCES↗

HSR transition jump optics in the September 2022 layout

Transition is crossed during acceleration in the Hadron Storage Ring (HSR) for all species other than protons. A first-order transition jump scheme manipulates the value of the optical quantity γ T and distorts the optics of the HSR around the time that the beam energy γ beam crosses the nominal transition value γ T 0 . The jump scheme in the Relativistic Heavy Ion Collider (RHIC) uses 48 jump quads, driven by 12 bi-polar power supplies that each drive 4 quads in series. Ten of those 48 are eliminated in the preliminary September 2022 HSR layout (EIC-HSR-220921a) that was developed from RHIC with no initial regard for transition crossing. This note analyzes the performance of the 38-quad HSR scheme, by comparison with the 48-quad RHIC scheme. It is concerned only with optics – the manipulation and response of Twiss functions and related quantities – and not with beams. This evaluation is a necessary first step before enhancing the transition jump scheme to restore RHIC performance in the HSR. Eventually full beam simulations of transition crossing need to be performed.

43 PARTICLE ACCELERATORS↗

Effects of hurricane disturbance and increased temperature on carbon cycling and storage of a Puerto Rican forest: a mechanistic investigation of above- and belowground processes (Final Technical Report)

The overall goal of the Tropical Responses for Altered Climate Experiment (TRACE) is to assess the effects of increasing temperature on tropical plant and soil carbon fluxes and storage as the forest recovers from major hurricane disturbance that occurred in September 2017. Ultimately, we aimed to reduce uncertainty and increase confidence with which tropical forests are represented in Earth System models to make more accurate global forecasts of future climate. We focused on both above- and belowground processes and explored temperature controls over critical aspects of carbon and nutrient cycling for tropical plants, soil, and microbes. TRACE is located in a wet tropical forest in the Luquillo Experimental Forest close to the USDA Forest Service Sabana Field Research Station in Luquillo, Puerto Rico. The warming treatment consists of six 4.7 m diameter plots. Three of the plots receive infrared warming and three have the same infrastructure but are not warmed (using ‘dummy’ heaters). Each plot was monitored from 2018-2023 to investigate two major questions: 1) Are there legacy effects of prior warming on forest recovery following hurricane disturbance? 2) Will the trajectory of forest recovery following disturbance be affected by warmer temperatures? Concurrent soil incubation experiments were conducted to enable more controlled mechanistic investigations of temperature response on microbial function. In sum, our goal was to use this novel climate manipulation experiment (the only of its kind in any tropical forest) and once-in-a-lifetime chance to assess how temperature and hurricane disturbance interact to affect coupled biogeochemical cycling in a tropical forest.

54 ENVIRONMENTAL SCIENCES↗

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses

Cytokines elicit pleiotropic and non-redundant activities despite strong overlap in their usage of receptors, JAKs and STATs molecules. We use IL-6 and IL-27 to ask how two cytokines activating the same signaling pathway have different biological roles. We found that IL-27 induces more sustained STAT1 phosphorylation than IL-6, with the two cytokines inducing comparable levels of STAT3 phosphorylation. Mathematical and statistical modeling of IL-6 and IL-27 signaling identified STAT3 binding to GP130, and STAT1 binding to IL-27Rα, as the main dynamical processes contributing to sustained pSTAT1 levels by IL-27. Mutation of Tyr613 on IL-27Rα decreased IL-27-induced STAT1 phosphorylation by 80% but had limited effect on STAT3 phosphorgylation. Strong receptor/STAT coupling by IL-27 initiated a unique gene expression program, which required sustained STAT1 phosphorylation and IRF1 expression and was enriched in classical Interferon Stimulated Genes. Interestingly, the STAT/receptor coupling exhibited by IL-6/IL-27 was altered in patients with systemic lupus erythematosus (SLE). IL-6/IL-27 induced a more potent STAT1 activation in SLE patients than in healthy controls, which correlated with higher STAT1 expression in these patients. Partial inhibition of JAK activation by sub-saturating doses of Tofacitinib specifically lowered the levels of STAT1 activation by IL-6. Our data show that receptor and STATs concentrations critically contribute to shape cytokine responses and generate functional pleiotropy in health and disease.

59 BASIC BIOLOGICAL SCIENCES↗

Pressure-temperature effects on knock with iso-octane and propane at various compression ratios and intake temperatures

Knock remains one of the main limitations for increased internal combustion engine efficiency. Recent trends in light-duty vehicles towards downsized, boosted engines increases the need for improving the understanding between fuel chemistry and thermodynamic effects contributing to knock. Previous studies have shown the importance of end-gas thermodynamic conditions on knock onset and behavior, with relationships to fuel chemistry illustrated. However, a complete understanding of how fuels allow access to higher engine loads and the governing physics behind end-gas knock under a wide range of thermodynamic conditions is still unclear. Experiments in this work improve this understanding with the use of three fuels (1) iso-octane, a low octane sensitivity (OS) fuel (2) a Co-Optima aromatic core fuel, which has similar research octane number (RON) yet significantly higher OS, and (3) propane, known for its knock resistance. Engine load sweeps are conducted with each fuel while maintaining a CA50 of 8 crank angle degrees after top dead center (°CA aTDCf). As load increases and knock onset is observed, spark is delayed to its knock limited spark advance (KLSA) allowing further increases in load until either one of two limits is reached; (1) CA50 retard limit (2) Peak cylinder pressure limit. Experiments are conducted at 40°C and 90°C intake temperature and at two distinct compression ratios (rc) 9.2:1 and 13.6:1. Two-zone zero-dimensional simulations were performed in Chemkin to extract end-gas pressure and temperature conditions through the combustion process for each experimental condition of interest. CA50 response as a function of engine load is compared for all experimental conditions and fuels, and a pressure-temperature (PT) trajectory analysis is conducted using constant volume ignition delay contours to explain the behavior of each fuel.

Dal Forno Chuahy, Flavio↗

Performance Evaluation of Multi-Vendor Grid-Forming Inverters for Grid-Connected Operation Through Hardware Experimentation

This paper presents the functional performance evaluation tests of multiple (three) commercial grid-forming (GFM) inverters when they operate in parallel with the grid through hardware experiments. The goal of these tests is to explore and benchmark the GFM inverters' functionalities and dynamic response when they are operated in parallel with power grids. Both steady-state (changing the inverter's frequency and voltage droop) and transient (adding step changes to grid's frequency/voltage) tests are performed for each GFM inverter with the same testing circuit and testing protocol. The key findings are summarized as follows: 1) The GFM inverters can be dispatched through frequency and voltage droop intercepts to output the target power; and 1) the GFM inverters automatically respond to system frequency and voltage events to output the needed power; 3) all the GFM inviters shows stability issues when absorbing reactive power from the grid.

frequency droop↗

Chemically controlled pattern formation in self-oscillating elastic shells

Significance Mechanochemical processes drive various biological functions including morphogenesis and morphological changes in responsive synthetic hydrogels. By allowing reactive components to function in an elastic closed shell, autonomous chemical reactions generate microcompartments capable of expanding or contracting or induce buckled patterns. This capability can drive specific functions such as enhancing the rate of diffusion of compartmentalized chemicals or releasing cargos at specific rates. Here, we demonstrate the coupling of mechanical response to autonomous chemical reactions in elastic shells which swell and deswell to generate specific dynamic patterns and morphologies. The reverse feedback from the mechanical input triggers the chemical reaction. Our work inspires the design of responsive shells to enhance the functionality of microcompartments and nanoreactors.

36 MATERIALS SCIENCE↗

Carbon source–driven metabolic and regulatory remodeling defines phenomic states in Lipomyces starkeyi

Lipomyces is a genus of oleaginous yeasts with potential for contributing to reliable biomanufacturing supply chains. However, progress in advanced strain designs and engineering efforts are still constrained by a lack of understanding of the underlying molecular drivers of Lipomyces phenotypes. To address this gap, we collected a suite of multi-omic data to dissect how carbon source availability reshapes the metabolic network, lipid allocation, and regulatory architecture of Lipomyces starkeyi. We observed that glucose promotes biosynthetic and proliferative processes supported by abundant energy and carbon intermediates, xylose enhances redox-balancing mechanisms centered on the pentose phosphate pathway, and glycerol activates respiratory metabolism, ß-oxidation, and the glyoxylate cycle. Lipid species distributions remained consistent in both nitrogen replete and depleted conditions across the carbon sources, indicating robust production mechanisms. Regulatory protein identification and network analysis revealed glycerol-driven respiratory growth favors regulatory programs integrating stress tolerance, redox balance, and lipid-associated metabolism, whereas xylose growth activates compensatory transcriptional responses aimed at maintaining mitochondrial function. Nitrogen limitation modulates the strength of these responses but does not fundamentally alter their direction, reinforcing carbon source as the dominant driver of regulatory architecture. Taken together, this data enhances the understanding of Lipomyces molecular rearrangements and provides a foundation for further development of predictive phenotypic tools in this genus.

Biotechnology↗

Dynamic response of 17-4 stainless steel as a function of manufacturing method and heat treatment

We present a series of plate-impact experiments on 17-4 stainless steel to study the effect of manufacturing method and heat treatment on the Hugoniot elastic limit (HEL), Hugoniot, phase transformation stress, and spallation strength. Two traditional manufacturing methods were considered, wrought processing and casting, as well as two additive manufacturing methods, laser powder-bed fusion (LPBF) and wire-fed electron beam (EBAM). For both LPBF and EBAM 17-4 stainless steel variants, two billets were printed, enabling the application of two unique heat treatments. The HEL stress depended heavily on the thermal history, with the HEL increasing after the formation of Cu-rich precipitates via heat treatment. The Hugoniot response both below and above the phase transition was unaffected by the manufacturing method or heat treatment. The phase transition stress depended heavily on the thermal history, with its variation being attributed to the presence of various microstructural features. This is supported by a marked increase in the phase transition stress after precipitation hardening. These results suggest that the notion of the phase transition stress being dictated by bulk composition is an oversimplification and the stress fields generated by the meso-scale structure are a dominant force. The spallation strength was lower in the cast material compared to all other 17-4 stainless steel variants due to the presence of brittle δ-ferrite inclusions. Additionally, a drop in the tensile strain-rate was observed in the spallation response above the phase transition stress, which was hypothesized to stem from the kinetics of the reversion to the low-pressure phase during spall.

Compressive stress↗

Natural Charge-Transfer Analysis: Eliminating Spurious Charge-Transfer States in Time-Dependent Density Functional Theory via Diabatization, with Application to Projection-Based Embedding

For many types of vertical excitation energies, linear-response time-dependent density functional theory (LR-TDDFT) offers a useful degree of accuracy combined with unrivaled computational efficiency, although charge-transfer excitation energies are often systematically and dramatically underestimated, especially for large systems and those that contain explicit solvent. As a result, low energy electronic spectra of solution-phase chromophores often contain tens to hundreds of spurious charge-transfer states, making LR-TDDFT needlessly expensive in bulk solution. More nefariously, intensity borrowing by the low-energy charge-transfer states can affect intensities of the valence excitations even if those excitation energies are accurate. At higher excitation energies, it is difficult to distinguish spurious CT states from genuine charge-transfer-to-solvent (CTTS) excitations. In this work, we introduce an automated diabatization scheme that enables fast and effective screening of the CTTS acceptor space in bulk solution. Our procedure introduces the concept of “natural charge-transfer orbitals”, which provide a means to isolate characteristic pairs of orbitals that are most likely to participate in a CTTS excitation. The projection of these orbitals onto solvent-centered virtual orbitals provides a criterion for defining the most important solvent molecules in a given excitation. We apply this method to analyze an ab initio molecular dynamics (MD) trajectory of I-(aq) and report the lowest-energy CTTS band in the absorption spectrum. Our results are in excellent agreement with experimental measurements for bulk I-(aq), and only one-third of the water molecules in the I-(H2O)96 simulation cell need to be described with LR-TDDFT in order to obtain excitation energies that are converged to < 0.1 eV. The tools introduced herein will improve the accuracy, efficiency, and usability of LR-TDDFT in solution-phase environments

Carter-Fenk, Kevin D.↗

Imposing correct jellium response is key to predict the density response by orbital-free DFT

Orbital-free density functional theory constitutes a computationally highly effective tool for modeling electronic structures of systems ranging from room-temperature materials to warm dense matter. Its accuracy critically depends on the employed kinetic energy (KE) density functional, which has to be supplied as an external input. In this work we consider several nonlocal and Laplacian-level KE functionals and use an external harmonic perturbation to compute the static density response at T = 0 K in the linear and beyond-linear response regimes. We test for the satisfaction of exact conditions in the limit of uniform densities and for how approximate KE functionals reproduce the density response of realistic materials (e.g., Al and Si) against the Kohn-Sham DFT reference, which employs the exact KE. The results illustrate that several functionals violate exact conditions in the uniform electron gas (UEG) limit. We find a strong correlation between the accuracy of the KE functionals in the UEG limit and in the strongly inhomogeneous case. This empirically demonstrates the importance of imposing the limit of UEG response for uniform densities and validates the use of the Lindhard function in the formulation of kernels for nonlocal functionals. This conclusion is substantiated by additional calculations for bulk aluminum (Al) with a face-centered cubic (fcc) lattice and silicon (Si) with an fcc lattice, body-centered cubic (bcc) lattice, and semiconducting crystal diamond state. The analysis of fcc Al, and fcc as well as bcc Si data follows closely the conclusions drawn for the UEG, allowing us to extend our conclusions to realistic systems that are subject to density inhomogeneities induced by ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sequence-defined structural transitions by calcium-responsive proteins

Biopolymer sequences dictate their functions, and protein-based polymers are a promising platform to establish sequence–function relationships for novel biopolymers. To efficiently explore vast sequence spaces of natural proteins, sequence repetition is a common strategy to tune and amplify specific functions. This strategy is applied to repeats-in-toxin (RTX) proteins with calcium-responsive folding behavior, which stems from tandem repeats of the nonapeptide GGXGXDXUX in which X can be any amino acid and U is a hydrophobic amino acid. To determine the functional range of this nonapeptide, we modified a naturally occurring RTX protein that forms β-roll structures in the presence of calcium. Sequence modifications focused on calcium-binding turns within the repetitive region, including either global substitution of nonconserved residues or complete replacement with tandem repeats of a consensus nonapeptide GGAGXDTLY. Some sequence modifications disrupted the typical transition from intrinsically disordered random coils to folded β rolls, despite conservation of the underlying nonapeptide sequence. Proteins enriched with smaller, hydrophobic amino acids adopted secondary structures in the absence of calcium and underwent structural rearrangements in calcium-rich environments. In contrast, proteins with bulkier, hydrophilic amino acids maintained intrinsic disorder in the absence of calcium. In conclusion, these results indicate a significant role of nonconserved amino acids in calcium-responsive folding, thereby revealing a strategy to leverage sequences in the design of tunable, calcium-responsive biopolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nuclear moonlighting of cytosolic glyceraldehyde-3-phosphate dehydrogenase regulates Arabidopsis response to heat stress

Abstract Various stress conditions induce the nuclear translocation of cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC), but its nuclear function in plant stress responses remains elusive. Here we show that GAPC interacts with a transcription factor to promote the expression of heat-inducible genes and heat tolerance in Arabidopsis. GAPC accumulates in the nucleus under heat stress. Overexpression of GAPC enhances heat tolerance of seedlings and the expression of heat-inducible genes whereas knockout of GAPCs has opposite effects. Screening of Arabidopsis transcription factors identifies nuclear factor Y subunit C10 (NF-YC10) as a GAPC-binding protein. The effects of GAPC overexpression are abolished when NF-YC10 is deficient, the heat-induced nuclear accumulation of GAPC is suppressed, or the GAPC-NF-YC10 interaction is disrupted. GAPC overexpression also enhances the binding ability of NF-YC10 to its target promoter. The results reveal a cellular and molecular mechanism for the nuclear moonlighting of a glycolytic enzyme in plant response to environmental changes.

59 BASIC BIOLOGICAL SCIENCES↗

A variational phase-field model For ductile fracture with coalescence dissipation

A novel phase-field model for ductile fracture is presented. The model is developed within a consistent variational framework in the context of finite-deformation kinematics. A novel coalescence dissipation introduces a new coupling mechanism between plasticity and fracture by degrading the fracture toughness as the equivalent plastic strain increases. The proposed model is compared with a recent alternative where plasticity and fracture are strongly coupled. Several representative numerical examples motivate specific modeling choices. In particular, a linear crack geometric function provides an “unperturbed” ductile response prior to crack initiation, and Lorentz-type degradation functions ensure that the critical fracture strength remains independent of the phase-field regularization length. In addition, the response of the model is demonstrated to converge with a vanishing phase-field regularization length. Additionally, the model is then applied to calibrate and simulate a three-point bending experiment of an aluminum alloy specimen with a complex geometry. The effect of the proposed coalescence dissipation coupling on simulations of the experiment is first investigated in a two-dimensional plane strain setting. The calibrated model is then applied to a three-dimensional calculation, where the calculated load-deflection curves and the crack trajectory show excellent agreement with experimental observations. Finally, the model is applied to simulate crack nucleation and growth in a specimen from a recent Sandia Fracture Challenge.

42 ENGINEERING↗

Evaluation of simulated soil carbon dynamics in Arctic-Boreal ecosystems

Given the magnitude of soil carbon stocks in northern ecosystems, and the vulnerability of these stocks to climate warming, land surface models must accurately represent soil carbon dynamics in these regions. We evaluate soil carbon stocks and turnover rates, and the relationship between soil carbon loss with soil temperature and moisture, from an ensemble of eleven global land surface models. We focus on the region of NASA's Arctic-Boreal vulnerability experiment (ABoVE) in North America to inform data collection and model development efforts. Models exhibit an order of magnitude difference in estimates of current total soil carbon stocks, generally under- or overestimating the size of current soil carbon stocks by greater than 50 PgC. We find that a model's soil carbon stock at steady-state in 1901 is the prime driver of its soil carbon stock a hundred years later—overwhelming the effect of environmental forcing factors like climate. The greatest divergence between modeled and observed soil carbon stocks is in regions dominated by peat and permafrost soils, suggesting that models are failing to capture the frozen soil carbon dynamics of permafrost regions. Using a set of functional benchmarks to test the simulated relationship of soil respiration to both soil temperature and moisture, we find that although models capture the observed shape of the soil moisture response of respiration, almost half of the models examined show temperature sensitivities, or Q10 values, that are half of observed. Significantly, models that perform better against observational constraints of respiration or carbon stock size do not necessarily perform well in terms of their functional response to key climatic factors like changing temperature. This suggests that models may be arriving at the right result, but for the wrong reason. The results of this work can help to bridge the gap between data and models by both pointing to the need to constrain initial carbon pool sizes, as well as highlighting the importance of incorporating functional benchmarks into ongoing, mechanistic modeling activities such as those included in ABoVE.

54 ENVIRONMENTAL SCIENCES↗

Autonomous hydrogel locomotion regulated by light and electric fields

Autonomous robotic functions in materials beyond simple stimulus-response actuation require the development of functional soft matter that can complete well-organized tasks without step-by-step control. We report the design of photo- and electroactivated hydrogels that can capture and deliver cargo, avoid obstacles, and return without external, stepwise control. By incorporating two spiropyran monomers with different chemical substituents in the hydrogel, we created chemically random networks that enabled photoregulated charge reversal and autonomous behaviors under a constant electric field. In addition, using perturbations in the electric field induced by a dielectric inhomogeneity, the hydrogel could be attracted to high dielectric constant materials and autonomously bypasses the low dielectric constant materials under the guidance of the electric field vector. The photo- and electroactive hydrogels investigated here can autonomously perform tasks using constant external stimuli, an encouraging observation for the potential development of molecularly designed intelligent robotic materials.

42 ENGINEERING↗

Waning immunity and IgG4 responses following bivalent mRNA boosting

Messenger RNA (mRNA) vaccines were highly effective against the ancestral SARS-CoV-2 strain, but the efficacy of bivalent mRNA boosters against XBB variants was substantially lower. Here, we show limited durability of neutralizing antibody (NAb) responses against XBB variants and isotype switching to immunoglobulin G4 (IgG4) responses following bivalent mRNA boosting. Bivalent mRNA boosting elicited modest XBB.1-, XBB.1.5-, and XBB.1.16-specific NAbs that waned rapidly within 3 months. In contrast, bivalent mRNA boosting induced more robust and sustained NAbs against the ancestral WA1/2020 strain, suggesting immune imprinting. Following bivalent mRNA boosting, serum antibody responses were primarily IgG2 and IgG4 responses with poor Fc functional activity. In contrast, a third monovalent mRNA immunization boosted all isotypes including IgG1 and IgG3 with robust Fc functional activity. These data show substantial immune imprinting for the ancestral spike and isotype switching to IgG4 responses following bivalent mRNA boosting, with important implications for future booster designs and boosting strategies.

Science & Technology - Other Topics↗