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At least 1,495 records · Page 83

Water-cooled Helmholtz coil for Ultra-low Magnetic Field Testing

Ultra-low magnetic field testing requires precise and finely calibrated instrumentation interacting with very marginal magnetic fields in highly controlled environments. We designed a large Helmholtz coil system for implementation around a 17.825-inch outer diameter Helium-3 Cryogenic fridge, to serve as both a field-zeroing device and to enable higher resolution on magnetic field sweeps during experiments. We present finite volume modeling and finite element analysis results which indicate the device could safely run at 20 [A] in perpetuity, producing a magnetic field of 65 [mT], without the surface facing the Cryogenic fridge exceeding 50°C. The overall system parts expense is $\$$4,882.76.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Remote Sensing Approach for Monitoring Tree Health Adjacent to Transmission Corridors

This study presents an initial proof-of-concept for a satellite-based remote sensing approach to identify and monitor potential areas of poor tree health across the entire BPA service territory on an annual basis. We tested three variants of “delta peak NDVI” ( ΔPN ) change detection metrics that express interannual variation in primary productivity relative to a baseline by comparing ΔPN values for known insect/disease disturbances and nearby reference locations. All three metrics showed promise for detecting poor tree health in the year during disturbance, but the metric based on the difference from the long-term (2016-2024) median ( Δ Med PN ) was preferred due to its responsiveness to change in the years during and after disturbance, resilience to interannual variation, and ease of interpretation as being above or below normal. Comparison of Δ Med PN grouped by relative severity of disturbance indicated it was not sensitive enough to detect “low” severity disturbances, as mapped by USGS’s LANDFIRE program, but could distinguish “moderate” and “high” severity disturbances from reference locations. These findings informed selection of a threshold for Δ Med PN , which was combined with areas exhibiting negative NDVI to map potential areas of concern. Visual inspection of before/after high-resolution imagery and NDVI time series showed that many areas of concern aligned with visible signs of defoliation and die-off as well as other types of disturbance (e.g., landslides, logging, road grading, flooding). Some areas of concern are thought to be false detections caused by persistent shadow, and some could not be explained with visual inspection due to spatiotemporal limitations of before/after imagery. In summary, our approach shows promise for large-scale monitoring of tree health adjacent to BPA transmission lines, but additional work is recommended to improve model sophistication and remove noise.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Hyperfine Splitting and Nuclear Spin Polarization in NdPd 5 Al 2 and Nd 3 Pd 20 Ge 6

Here the hyperfine splitting of Nd nuclei in NdPd 5 Al 2 was studied by means of high-resolution neutron spectroscopy. We observed inelastic peaks at ℏω = ±3 µeV and T = 0.3 K, originating from the hyperfine splitting in the magnetically ordered phase owing to the hyperfine interactions between Nd nuclei (I = 7/2) and the 4f electrons with the Γ 6 ground state composed of mainly |±9/2$\rangle$. At very low temperatures, the nuclear spin of Nd is polarized with an increasing occupation probability of low energy levels and contributes to the enhancement of the antiferromagnetic Bragg intensities; the elastic non-spin-flip channel is dominant. As an application of this phenomenon, we determined the Nd moment and hyperfine splitting from the temperature dependence of an antiferromagnetic Bragg intensity for Nd 3 Pd 20 Ge 6 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MIRC-X: A Highly Sensitive Six-telescope Interferometric Imager at the CHARA Array

Michigan InfraRed Combiner-eXeter (MIRC-X) is a new highly sensitive six-telescope interferometric imager installed at the CHARA Array that provides an angular resolution equivalent of up to a 330 m diameter baseline telescope in J- and H-band wavelengths ((λ/(2B))∼0.6 mas). We upgraded the original Michigan InfraRed Combiner (MIRC) instrument to improve sensitivity and wavelength coverage in two phases. First, a revolutionary sub-electron noise and fast-frame-rate C-RED ONE camera based on an SAPHIRA detector was installed. Second, a new-generation beam combiner was designed and commissioned to (i) maximize sensitivity, (ii) extend the wavelength coverage to J band, and (iii) enable polarization observations. A low-latency and fast-frame-rate control software enables high-efficiency observations and fringe tracking for the forthcoming instruments of the CHARA Array. Since mid-2017, MIRC-X has been offered to the community and has demonstrated best-case H-band sensitivity down to 8.2 correlated magnitude. MIRC-X uses single-mode fibers to coherently combine the light from six telescopes simultaneously with an image-plane combination scheme and delivers a visibility precision better than 1%, and closure phase precision better than 1°. MIRC-X aims at (i) imaging protoplanetary disks, (ii) detecting exoplanets with precise astrometry, and (iii) imaging stellar surfaces and starspots at an unprecedented angular resolution in the near-infrared. In this paper, we present the instrument design, installation, operation, and on-sky results, and demonstrate the imaging capability of MIRC-X on the binary system ι Peg. The purpose of this paper is to provide a solid reference for studies based on MIRC-X data and to inspire future instruments in optical interferometry.

79 ASTRONOMY AND ASTROPHYSICS↗

Bias Correcting NOAA's High-Resolution Rapid Refresh (HRRR) Wind Resource Data for Grid Integration Applications [Slides]

Many weather years of high-quality wind data are widely accepted in the grid integration community to be important for studying wind energy technical potential, energy system operations, and grid resilience. NREL makes high-quality wind and solar resource data available. NREL's Grid-Atmosphere workshop (March 2024) identified NREL National Solar Radiation Database as widely used in grid integration modeling, but there is less agreement on commonly used wind datasets. One important factor identified by ESIG's 2023 report 'Weather Dataset Needs for Planning and Analyzing Modern Power Systems' for gold standard wind data is regular updates. To address the need for regular updates, NREL's team can now process all currently available and regularly updated High-Resolution Rapid Refresh (HRRR) outputs. HRRR is an hourly-updated operational forecast product produced by the National Oceanic and Atmospheric Administration (NOAA) (Dowell et al., 2022). One barrier to NREL using HRRR is systematic bias and consistency with NREL's existing wind datasets (e.g. WIND Toolkit, 'WTK') across weather years. To address this barrier, we show that the HRRR can be interpolated and bias-corrected to be consistent with NRE's existing datasets. We call the new dataset BC-HRRR (bias-corrected HRRR). As with historical datasets like the WTK, BC-HRRR is intended for use in grid integration modeling (e.g., capacity expansion, production cost, and resource adequacy modeling). BC-HRRR's (2015-present) consistency with WTK (2007-2013) allows NREL to extend internal grid integration tooling with 15+ weather years of wind data with low-overhead extensibility to future years as they are made available by NOAA. The rest of this slide deck documents the BC-HRRR processing methods, validation, and its implications for intended use.

17 WIND ENERGY↗

Multifidelity deep operator networks for data-driven and physics-informed problems

Operator learning for complex nonlinear systems is increasingly common in modeling multi-physics and multi-scale systems. However, training such high-dimensional operators requires a large amount of expensive, high-fidelity data, either from experiments or simulations. In this work, we present a composite Deep Operator Network (DeepONet) for learning using two datasets with different levels of fidelity to accurately learn complex operators when sufficient high-fidelity data is not available. Additionally, we demonstrate that the presence of low-fidelity data can improve the predictions of physics-informed learning with DeepONets. We demonstrate the new multi-fidelity training in diverse examples, including modeling of the ice-sheet dynamics of the Humboldt glacier, Greenland, using two different fidelity models and also using the same physical model at two different resolutions.

97 MATHEMATICS AND COMPUTING↗

Tetragonal BaCoO 3 : A Co 4+ Ferromagnetic Mott Insulator

We report the stabilization of the metastable body-centered tetragonal (BCT) phase of BaCoO 3 (BCT-BaCoO 3 ) under high-pressure (15 GPa) and hightemperature (1200 °C) conditions using a mixture precursor. This double perovskite adopts the EuTiO 3 -type structure (space group I4/mcm), as confirmed by powder Xray diffraction and high-resolution STEM. X-ray photoelectron spectroscopy indicates a predominant Co 4+ oxidation state without detectable oxygen vacancies. Magnetization and heat capacity measurements reveal ferromagnetic ordering at T C ∼ 107 K, attributable to the BCT-BaCoO 3 phase. Above this temperature, the mixed-phase sample exhibits Curie−Weiss paramagnetism, a low-spin to high-spin crossover upon cooling, and a possible intermediate-spin state at elevated temperatures. Resistivity data indicates insulating behavior with weak magnetoresistance. DFT and DFT + DMFT calculations suggest that the insulating state originates from an orbitally selective transition sensitive to the nominal valence of the Co-d shell. The metastable BCT-BaCoO 3 phase cannot be retained in pure form at ambient pressure but can be stabilized by embedding it in a disordered mixture, offering a potential route to discover and preserve other high-pressure phases under ambient conditions.

Magnetic properties↗

Hydrogen isotope analysis in W-tiles using fs-LIBS

Abstract Laser-Induced Breakdown Spectroscopy (LIBS) is a promising technology for in-situ analysis of Plasma-Facing Components in magnetic confinement fusion facilities. It is of major interest to monitor the hydrogen isotope retention i.e. tritium and deuterium over many operation hours to guarantee safety and availability of the future reactor. In our studies we use ultraviolet femtosecond laser pulses to analyze tungsten (W) tiles that were exposed to a deuterium plasma in the linear plasma device PSI-2, which mimics conditions at the first wall. A high-resolution spectrometer is used to detect the Balmer- $$\alpha$$ α transition of the surface from implanted hydrogen isotopes (H and D). We use Calibration Free CF-LIBS to quantify the amount of deuterium stored in W. This proof-of-principle study shows the applicability of femtosecond lasers for the detection of low deuterium concentration as present in first wall material of prevailing fusion experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Using millimeter-sized carbon–deuterium foils for high-precision deuterium–tritium neutron spectrum measurements in direct-drive inertial confinement fusion at the OMEGA laser facility

Millimeter-sized CD foils fielded close (order mm) to inertial confinement fusion (ICF) implosions have been proposed as a game-changer for improving energy resolution and allowing time-resolution in neutron spectrum measurements using the magnetic recoil technique. This paper presents results from initial experiments testing this concept for direct drive ICF at the OMEGA Laser Facility. Additionally, while the foils are shown to produce reasonable signals, inferred spectral broadening is seen to be high (~5 keV) and signal levels are low (by ~20%) compared to expectation. Before this type of foil is used for precision experiments, the foil mount must be improved, oxygen uptake in the foils must be better characterized, and impact of uncontrolled foil motion prior to detection must be investigated.

47 OTHER INSTRUMENTATION↗

Spectroscopy of states in 136 Ba using the 138 Ba(p,t) reaction

Background: The 136 Ba isotope is the daughter nucleus in 136 Xe $ββ$ decay. It also lies in a shape transitional region of the nuclear chart, making it a suitable candidate to test a variety of nuclear models. Purpose: To obtain spectroscopic information on states in 136 Ba, which will allow a better understanding of its low-lying structure. These data may prove useful to constrain future 136 Xe → 136 Ba neutrinoless $ββ$ decay matrix element calculations. Methods: Here, a 138 Ba(p, t) reaction was used to populate states in 136 Ba up to approximately 4.6 MeV in excitation energy. The tritons were detected using a high-resolution Q3D magnetic spectrograph. A distorted wave Born approximation analysis was performed for the measured triton angular distributions. Results: 102 excited states in 136 Ba were observed, out of which 52 are reported for the first time. Definite spin-parity assignments are made for 26 newly observed states, while previously ambiguous assignments for ten other states are resolved. Together with other available data, the results are used to determine level densities in 136 Ba. These were compared with theory predictions, obtained using shell model calculations with Hamiltonians previously used for 136 Xe neutrinoless $ββ$ decay matrix element evaluations. Conclusions: The shell model predicted level densities agree reasonably well for the two Hamiltonians. However the results for theory and experiment are found to agree only at lower energies, diverging from one another for the higher lying states, with the discrepancy increasing with energy. This is presumably because of lower production cross sections for a majority of the higher-lying predicted states and the experimental limitations in resolving a large number of nearly degenerate states predicted by the theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Early arrival waveform inversion using data uncertainties and matching filters with application to near-surface seismic refraction data

We develop an early arrival waveform inversion (EAWI) technique for high-resolution near-surface velocity estimation by iteratively updating the P-wave velocity model to minimize the difference between the observed and calculated seismic refraction data. Traditional EAWI uses a least-squares penalty function and an acoustic forward-modeling engine. Conventional least-squares error is sensitive to data with low signal-to-noise ratio (S/N) and iterations of EAWI stop at a local-minimum data misfit or at the preassigned maximum number of iterations. These stopping criteria can result in overfitting the data. In addition, fitting the elastic field data with an acoustic modeling engine can introduce artifacts in velocity estimation, especially in land data with significant elastic effects. To overcome these challenges, we develop a robust EAWI (REAWI) method by (1) incorporating the data uncertainties into the penalty function and (2) mitigating the elastic effects using a matching filter workflow. The data uncertainties are estimated from waveform reciprocal errors. When full-waveform reciprocity is not available, trace interpolation is applied. The proposed method prevents closely fitting data with low S/N, avoids overall overfitting by stopping the iterations when a normalized chi-square ([Formula: see text]) waveform misfit of one is achieved, and is less affected by elastic effects. Numerical examples and application to near-surface refraction data at a groundwater contamination site suggest that the final REAWI models are more accurate than the corresponding EAWI models, at the same level of misfit. This is the first known application of a matching filter workflow to real land data. The final REAWI models satisfy an appropriate misfit between the real data and predicted elastic P-wave data, making this approach in this respect equivalent to elastic waveform inversion. We also develop a method to analyze model constraint by examining the energy of the wavefield Fréchet derivative thereby avoiding the influence of the data residuals in traditional Fréchet kernels.

Geochemistry & Geophysics↗

Mountain Basin Controls on the Snow-to-Streamflow Signal: An AIC-Weighted Multiple Linear Regression Framework

A regression-based analysis quantifies how basin characteristics modulate the snow-to-streamflow signal. First, we use the ERA5-Land reanalysis gridded product (European Centre for Medium Range Weather Forecasts reanalysis 5 -Land component) for 4,655 hydrologic unit code - 10 (HUC10) mountain basins across the western United States (US) for water years 1987–2024. Linear regressions are performed for peak snow water equivalent (SWE) and annual streamflow for each mountain basin. Models use ordinary least squares in Python’s statsmodels package. After which, an Akaike Information Criterion (AIC)–weighted ensemble multiple linear regression (MLR) framework with 47 watershed traits is used to predict the linear regression coefficient of determination (r-squared) defining the ability of peak SWE to predict annual streamflow across all mountain basin. Predictor sets are constrained to avoid multicollinearity by excluding models with variance inflation factors (VIF) greater than 5. Mountain basin traits included in the MLR include seasonal climate, topography, vegetation type and structure, and bedrock geology. Accepted models are considered if their AIC is within 2.0 of the model with the minimum AIC, or best model. To compare predictor influence across acceptable models, we computed standardized regression coefficients. To evaluate structural redundancy among models, we constructed binary inclusion vectors for each acceptable model, denoting whether a predictor was present (1) or absent (0). Core predictor variables are defined as occurring in at least 67% of the acceptable models. For this regional analysis, only one model was found acceptable, with higher snow-to-streamflow translation (higher r-squared) occurring in colder mountain basins with higher relative winter precipitation, more snow accumulation and a lower fraction of annual precipitation that falls in the spring and summer. The second component of the data package uses previously published, high-resolution output from an integrated hydrological model of the East River watershed using the U.S. Geological Survey Groundwater and Surface water Flow model (GSFLOW, doi:10.15485/1998576). East River MLR expands upon the approach described above to explore the response of five streamflow metrics—annual streamflow, runoff efficiency, 7-day minimum flow, low-flow duration, and non-perennial stream fraction to snow system indicators including peak SWE, snow-covered area, snow disappearance date, and the fraction of basin area characterized by low-to-no snow, as well as seasonal precipitation and temperature, and annual hydrologic variables representing soil moisture, evapotranspiration (ET), the partitioning of incoming precipitation to evapotranspiration (ET/P), groundwater storage, and groundwater inflow to streams. MLR was done on all water years (P0: 1987-2024) and for each period as determined in the split analysis using pooled regression techniques (P1: 1987-2011 and P2: 2012-2024) to evaluate shifting predictor variable emphasis on streamflow generation. Results indicate that since 2012, peak SWE has lost statistical strength in its prediction of annual streamflow and runoff efficiency, and the indirect influence of spring temperature has emerged as critically important. Low-flow metrics remain largely influenced by soil moisture, vegetation water use and groundwater inflows with summer precipitation becoming a direct influence on minimum summer flow. Together, these data and Python-based analysis tools provide a framework for identifying the key watershed characteristics that control how streamflow responds to snow from year to year. The package also helps quantify uncertainty in statistical models and assess how snow–streamflow relationships vary across regions and over time. This dataset contains comma-separated values files (.csv), text files (.txt), python code files (.py), figure files (.png), and shapefiles (.cpg, .dbf, .prj, .sbn, .sbx, .shp, .xml). Further details on file contents and MLR execution can be found in the readme file and the FLMD files. Work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗

Machine Learning Inference of Random Medium Properties

Earth materials are heterogeneous across a range of spatial scales, but the resolvability of small structures is limited by sparse data coverage, noise, bandlimitedness, and other difficulties. In practice, heterogeneities below a certain size cannot be recovered from seismic data except through statistical medium descriptions, which even then can be difficult to uniquely determine. To improve the characterization of such heterogeneities, we develop a novel supervised machine learning (ML) model that provides insight about the recoverability of statistical medium properties from elastic waveform data and succeeds despite cycle-skipping and other challenges well known from elastic waveform inversion. We demonstrate the approach using random media generated by superimposing self-affine random variations on homogeneous and layered background structures. After training on sparsely-recorded, high-frequency waveforms from hundreds of different random medium realizations, we show the ability of our ML model to recover correlation lengths and other statistical properties of interest to near-surface and crustal seismology, among other fields. For frequency passbands and spatial offsets encountered in seismology, Gaussian correlation lengths and the amplitude of the random variations relative to the background model are recovered even in challenging scenarios involving unknown medium parameters, complex crustal structures, and low signal-to-noise ratio. In comparison, von Kármán correlation lengths, which are related to larger-wavelength variations of the medium than Gaussian correlation lengths, are not as well recovered. These results provide one of the first and most systematic investigations of the recoverability of statistical properties of heterogeneities below the resolution limit of deterministic seismic tomography, and suggest practical ML strategies for high-frequency waveform seismology.

58 GEOSCIENCES↗

Low Mass Straw Tube Tracker for the Mu2e Experiment

The Mu2e Tracker is a state of the art low mass straw tube detector that will look for charged lepton flavor violation (CLFV) by measuring the position and the momentum of the monochromatic 105 MeV/c electron from the $\mu^- N\rightarrow e^- N$ neutrinoless electron conversion in the presence of aluminum nucleus. To achieve this goal, the tracker needs to have momentum resolution of less than 180 keV/c \cite{TDR} for the conversion electron spectrum. The tracker is still under construction with the joint effort of several institutes. This paper will detail technical information about the Mu2e tracker and show early cosmics data taken with a production tracker plane.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effects of Co doping on the structure and physicochemical properties of hausmannite (Mn 3 O 4 ) and its transformation during aging

Hausmannite is a common low-valence manganese oxide mineral with a distorted spinel structure in surficial sediments. Although natural Mn oxides often contain various transition metal (TM) impurities, few studies have addressed the substitution mechanisms of TMs, such as cobalt (Co), with hausmannite and induced changes in the mineral physicochemical properties. In this study, Co-doped hausmannites with final Co/Mn molar ratios of 0.05 and 0.11 were synthesized and characterized by wet chemical analysis, powder X-ray diffraction (XRD), Fourier transformed infrared spectra (FTIR), high resolution transmission electron microscope (HRTEM), X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure spectroscopy (XAFS). Co-doped samples have larger crystallite sizes and smaller specific surface areas than those of the hausmannite without Co. The Co cations exist in a mixed-valence of +3 and + 2. Powder XRD and acid dissolution experiments indicate that Co incorporates into the mineral structures, and increases the mineral structural stability. Co K-edge extended X-ray adsorption fine structure (EXAFS) analysis demonstrates that Co likely substitutes for lattice Mn(III). After aging at room temperature for three years, 14.1 ± 1.9% of pure hausmannite is transformed to manganite while only 2.6 ± 0.7% of manganite appears in the aged Co-doped sample with an initial Co/Mn molar ratio of 0.10. Finally, these results provide new insights into the incorporation mechanisms of TMs into low valence Mn oxides, and the stability of these minerals in natural environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

FTR for: Reducing plug-load electricity footprint of residential buildings through low-cost, non-intrusive sub-metering and personalized feedback technology

The project started in October 2016 and ended in December 2022. The project's principal goals and achievements were: (i) Measure real and reactive electric power consumption in ~400 apartments in multifamily settings of varying size and vintage and publish the data; data was published according to New York State's recommended 15x15 rule continuously from Jan 2019 through December 2022 (10 second time resolution); with the combination of large number of apartments, real and reactive power, as well as high time resolution (10-seconds), the dataset is first of its kind worldwide; because the dataset New York City apartment consumption pre, during, and post pandemic, it further offers unique insights into changes in residential electricity consumption during lockdowns and after modified work from home schedules. (ii) Measure effectiveness of different feedback types to prompt residents to lower their electricity consumption; achieved 11% (kWh-weighted) reduction versus baseline consumption; confirmed previous studies that social comparisons elicit above average responses; showed, for the first time, that the so called boomerang effect in power consumption feedback projects can be explained by a previously hypothesized norm-conforming "magnet effect" (rather than a non-conforming defiance effect), thus substantially advancing the research in the field. (iii) Disaggregate apartment-level consumption to appliance level; because the hardware for electricity consumption unexpectedly allowed only for 10-second time resolution (rather than the 1-second resolution we had planned on), the disaggregation algorithms we developed on sample data could not be applied to the actual field data we collected. The project has yielded high visibility, with a total of 17 publications, from peer reviewed journals, published data sets (free access), blog posts, NY Times, National Public Radio, and CNN.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Regional-Scale 3D Ground-Motion Simulations of M w 7 Earthquakes on the Hayward Fault, Northern California Resolving Frequencies 0–10 Hz and Including Site-Response Corrections

Large earthquake ground-motion simulations in 3D Earth models provide constraints on site-specific shaking intensities but have suffered from limited frequency resolution and ignored site response in soft soils. In this work we report new regional-scale 3D simulations for moment magnitude 7.0 scenario earthquakes on the Hayward Fault, northern California with SW4. Simulations resolved significantly broader band frequencies (0–10 Hz) than previous studies and represent the highest resolution simulations for any such earthquake to date. Seismic waves were excited by a kinematic rupture following Graves and Pitarka (2016) and obeyed wave propagation in a 3D Earth model with topography from the U.S. Geological Survey (USGS) assuming a minimum shear wavespeed, VSmin, of 500 m/s. We corrected motions for linear and nonlinear site response for the shear wavespeed, VS, from the USGS 3D model, using a recently developed ground-motion model (GMM) for Fourier amplitude spectra . At soft soil locations subjected to strong shaking, the site-corrected intensities reflect the competing effects of linear amplification by low V S material, reduction of stiffness during nonlinear deformation, and damping of high frequencies. Sites with near-surface V S of 500 m/s or greater require no linear site correction but can experience amplitude reduction due to nonlinear response. Averaged over all sites, we obtained reasonable agreement with empirical ergodic median GMMs currently used for seismic hazard and design ground motions (epsilon less than 1), with marked improvement at soft sedimentary sites. At specific locations, the simulated shaking intensities show systematic differences from the GMMs that reveal path and site effects not captured in these ergodic models. Results suggest how next generation regional-scale earthquake simulations can provide higher spatial and frequency resolution while including effects of soft soils that are commonly ignored in scenario earthquake ground-motion simulations.

58 GEOSCIENCES↗

Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.

59 BASIC BIOLOGICAL SCIENCES↗