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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Scale dependence in functional equivalence and difference in the soil microbiome

Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (Quercus rubra L.) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. Here, a similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Notably, for the site with pronounced local-scale functional legacies, there was much greater within-site variation in field-soil microsite moisture than at the site which did not exhibit functional legacies, suggesting that the extent of local-scale variation in microclimate may act as control on whether local-scale functional legacies are observed. Regardless of whether this mechanism does explain our findings, our observations do confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extend this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes are associated with microbial functional legacies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Integration of Large-Scale Electrical Imaging into Geological Framework Development and Refinement

Geologic framework models (GFMs) are critical to the construction of reliable simulation models of groundwater flow and contaminant transport. To support GFM development, direct information (e.g., core samples, fluid samples, hydraulic testing) tends to be sparse and separated by large distances relative to the spatial scales of aquifer heterogeneity. There are additional challenges associated with highly contaminated legacy waste sites, where drilling is particularly costly, and invasive sampling requires specialized handling and disposal of hazardous materials. At these sites in particular, non-invasive geophysical imaging can play an important role in filling spatial gaps between boreholes and reducing characterization costs by optimizing and minimizing the number of necessary boreholes. Here this paper presents a case study demonstrating the use of large-scale (> 30 km 2 ) electrical mapping to identify hydrostratigraphy and potential paleochannels at the Hanford Site, located in Washington State, USA. In two field campaigns, over 36 line-kilometers of electrical resistivity tomography (ERT) data were collected along 14 transects. ERT surveys were sited and performed to image critical aspects (e.g., paleochannels, stratigraphic contacts) of the subsurface, demonstrating a general workflow for integrating ERT with GFM development. Inconsistencies between the GFM and ERT were catalogued to provide a basis for future site characterization using complementary geophysical methods and (or) direct sampling.

58 GEOSCIENCES↗
DOE OSTI2025

Perspectives on Systematic Cloud Microphysics Scheme Development With Machine Learning

Cloud microphysics—the collection of processes that govern the small‐scale formation, evolution, and interactions of liquid droplets and ice crystals in clouds and precipitation—remains a major source of uncertainty in weather and climate models. Although too small in scale to be explicitly resolved in any large‐eddy simulation, weather, or climate model, the representation of cloud microphysical processes has significant impact at the climate scale. Current microphysical schemes are limited by both parametric uncertainty, linked to uncertainty in physical parameter values, and structural uncertainty, arising from incomplete physical understanding of the processes at play or approximations made for computational efficiency. Recent advances in the application of machine learning (ML) to the physical sciences show significant potential for minimizing these limitations by leveraging high‐fidelity simulations and observations. Here we outline the challenges that must be addressed to apply ML toward cloud microphysics scheme development. This perspectives paper synthesizes recent progress in using data‐driven methods, including ML, to improve cloud microphysics parameterizations and highlights opportunities to address key uncertainties. We discuss the roles of aleatoric (irreducible, or statistical) and epistemic (reducible, or systematic) errors in contributing to microphysics parameterization uncertainty. ML can leverage observations to improve microphysical schemes via bottom‐up and top‐down constraints. Methods such as differentiable programming and ML‐enhanced sampling strategies and the creation of large scale benchmark data sets promise to bridge the gap between observations and models and to improve the consistency of cloud microphysical representation across temporal and spatial scales.

Lamb, Kara D. [Columbia Univ., New York, NY (Unite↗
DOE OSTI2024

Pseudospectral Landau-Lifshitz description of magnetization dynamics

Magnetic materials host a wealth of nonlinear dynamics, textures, and topological defects. This is possible due to the competition between strong nonlinearity and dispersion, which act at the atomic scale, as well as long-range interactions. However, these features are difficult to study analytically and numerically because of the vastly different temporal and spatial scales involved. Here, in this work, we present a pseudospectral approach for the Landau-Lifshitz equation that invokes energy and momentum conservation embodied in the magnon dispersion relation to accurately describe both atomic and continuum limits. Furthermore, this approach enables analytical study at every scale. We show the applicability of this model in both the continuum and atomic limit by investigating modulational instability and ultrafast evolution of magnetization due to transient grating, respectively, in a one-dimensional ferromagnetic chain with perpendicular magnetic anisotropy. This model provides the possibility of grid-independent multiscale numerical approaches that will enable the description of singularities within a single framework.

1-dimensional spin chains↗
DOE OSTI2021

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↗
DOE OSTI2021

Aquifer Monitoring Using Ambient Seismic Noise Recorded With Distributed Acoustic Sensing (DAS) Deployed on Dark Fiber

Abstract Groundwater is a critical resource for human activities worldwide, and a vital component of many natural ecosystems. However, the state and dynamics of water‐bearing aquifers remain uncertain, mostly due to the paucity of subsurface data at high spatial and temporal resolution. Here, we show that analysis of infrastructure‐generated ambient seismic noise acquired on distributed acoustic sensing (DAS) arrays has potential as a tool to track variations in seismic velocities (d v / v ) caused by groundwater level fluctuations. We analyze 5 months of ambient noise acquired along an unused, 23 km‐long telecommunication fiber‐optic cable in the Sacramento Valley, CA, a so‐called “dark fiber." Three array subsections, ∼6 km apart, are processed and the stretching technique is applied to retrieve daily d v / v beneath each location. Near the Sacramento river, d v / v variations in the order of 2%–3% correlate with precipitation events and fluctuations in river stage of ∼1.5 m. In contrast, regions away (2.5 km) from the river do not experience large d v / v variations. These observations reveal short‐scale spatial variability in aquifer dynamics captured by this approach. Dispersion analysis and surface wave inversion of noise gathers reveal that seismic velocity perturbations occur at depths of 10–30 m. Rock physics modeling confirms that observed d v / v are linked to pore pressure changes at these depths, caused by groundwater table fluctuations. Our results suggest that DAS combined with ambient noise interferometry provides a means of tracking aquifer dynamics at high spatial and temporal resolutions at local to regional scales, relevant for effective groundwater resource management.

58 GEOSCIENCES↗
DOE OSTI2023

On the Morphodynamics of a Wide Class of Large‐Scale Meandering Rivers: Insights Gained by Coupling LES With Sediment‐Dynamics

Abstract In meandering rivers, interactions between flow, sediment transport, and bed topography affect diverse processes, including bedform development and channel migration. Predicting how these interactions affect the spatial patterns and magnitudes of bed deformation in meandering rivers is essential for various river engineering and geoscience problems. Computational fluid dynamics simulations can predict river morphodynamics at fine temporal and spatial scales but have traditionally been challenged by the large scale of natural rivers. We conducted coupled large‐eddy simulation and bed morphodynamics simulations to create a unique database of hydro‐morphodynamic data sets for 42 meandering rivers with a variety of planform shapes and large‐scale geometrical features that mimic natural meanders. For each simulated river, the database includes (a) bed morphology, (b) three‐dimensional mean velocity field, and (c) bed shear stress distribution under bankfull flow conditions. The calculated morphodynamics results at dynamic equilibrium revealed the formation of scour and deposition patterns near the outer and inner banks, respectively, while the location of point bars and scour regions around the apexes of the meander bends is found to vary as a function of the radius of curvature of the bends to the width ratio. A new mechanism is proposed that explains this seemingly paradoxical finding. The high‐fidelity simulation results generated in this work provide researchers and scientists with a rich numerical database for morphodynamics and bed shear stress distributions in large‐scale meandering rivers to enable systematic investigation of the underlying phenomena and support a range of river engineering applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Scale-dependent enhancement of productivity and stability in xenic Nannochloropsis cultures

Although bacterial amendments can enhance algal productivity and stability, the development of algal-bacteria consortia for commercial-scale utilization is limited. Here, for this work, we used an established high-throughput approach to generate algal-bacteria consortia, and tested consortia performance at spatial scales from microplates to 320 L raceway ponds. We used both lab and field-reared strains of Nannochloropsis oceanica to build consortia. In some experiments, we imposed environmental perturbations to test the ability of bacteria to enhance algal culture stability. In repeated assays at the scale of well plates, flasks, and bioreactors, strong effects of bacterial amendments on N. oceanica were observed. These effects were most dramatic when cultures experienced stressors such as temperature perturbations or removal of CO 2 augmentation. Isolates that were advanced for field testing included species in the genera Algoriphagus, Oceanicaulis, and Marinobacter. When consortia were generated in the field, positive effects of bacterial amendments were not observed. The amended bacteria were outcompeted, and bacterial community composition across treatments converged after the first grow out. These results highlight the complexity of using consortia in open systems, where interactions between the existing bacterial community, inoculated bacteria, and changing environmental conditions are layered upon other differences in scale and cultivation regimes. Moreover, functionally redundant bacteria are likely present in the field. Following this work, we hypothesize that tight interactions (e.g., obligate relationships between partners) will scale more predictably to outdoor systems. We suggest relying on true synthetic ecological approaches in which the relationships between bacteria and algae partners are well understood, or synthetic ecological approaches coupled with high throughput approaches to design and test consortia. We also recommend future work to examine the effect of algae-bacteria inoculation ratios on productivity and stability, track dynamics of partners through time, and manage ponds to retain beneficial symbioses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Human-caused long-term changes in global aridity

Widespread aridification of the land surface causes substantial environmental challenges and is generally well documented. However, the mechanisms underlying increased aridity remain relatively underexplored. Here, we investigated the anthropogenic and natural factors affecting long-term global aridity changes using multisource observation-based aridity index, factorial simulations from the Coupled Model Intercomparison Project phase 6 (CMIP6), and rigorous detection and attribution (D&A) methods. Our study found that anthropogenic forcings, mainly rising greenhouse gas emissions (GHGE) and aerosols, caused the increased aridification of the globe and each hemisphere with high statistical confidence for 1965–2014; the GHGE contributed to drying trends, whereas the aerosol emissions led to wetting tendencies; moreover, the bias-corrected CMIP6 future aridity index based on the scaling factors from optimal D&A demonstrated greater aridification than the original simulations. These findings highlight the dominant role of human effects on increasing aridification at broad spatial scales, implying future reductions in aridity will rely primarily on the GHGE mitigation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Generating high-resolution total canopy SIF emission from TROPOMI data: Algorithm and application

Solar-induced chlorophyll fluorescence (SIF) is a rapidly advancing front in modeling global terrestrial gross primary production (GPP). Canopy total SIF emissions (SIF total ) are mechanistically linked to the plant photosynthesis, and can be estimated from satellite observed SIF (SIF obs ) through radiative transfer modeling. However, the current satellite SIF obs and thus SIF total are available only at coarse spatial resolutions from several kilometers to tens of kilometers, inhibiting the application at fine spatial scales. Here, in this work, we proposed an algorithm to generate both global high-resolution SIF total (HSIF total ) and high-resolution SIF obs (HSIF obs ) at 1 km from low-resolution SIF obs (LSIF obs ) from the TROPOspheric Monitoring Instrument (TROPOMI), which has a spatial resolution at nadir of 3.5 km by 5.6–7 km. Our statistical method is based on the law of energy conservation and uses satellite derived fraction of absorbed photosynthetically active radiation, fluorescence efficiency, and the escape probability of fluorescence. We evaluated the accuracy of our HSIF total using the Orbiting Carbon Observatory-2 SIF (R 2 = 0.78). We found that the spatial resolution had clear effects on the relationship between HSIF total and GPP. We also compared HSIF total to 8-day averaged tower GPP from 135 flux sites and found that they were better correlated when HSIF total was averaged over a 1-km radius around the tower than when averaged over a larger radius. Our study provided a unique high-resolution HSIF total product, which will advance the estimation of GPP by extrapolating site-level relationships to the global scale.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Spatio-temporal Fourier Transformer for Long-term Dynamics Prediction (StFT) v1.0

We propose a novel machine learning model spatio-temporal Fourier transformer (StFT) to emulate long-term dynamics of multi-scale and multi-physics systems. Our method StFT overcomes the limitations of rapid error accumulation, particularly in long-term forecasting of systems characterized by complex and coupled dynamics. StFT achieves outstanding accuracy and computational efficiency by effectively capturing multi-scale interactions, and quantify the uncertainties inherent in the predictions. Our model leverages a structured hierarchy of StFT blocks, and explicitly captures dynamics across both macro- and micro- spatial scales. Evaluations conducted on three benchmark datasets (plasma, fluid, and atmospheric dynamics) demonstrate the advantages of our approach over state-of-the-art ML methods.

Bai, Zhe [Lawrence Berkeley National Laboratory (L↗
DOE OSTI2022

Revised monthly energy generation estimates for 1,500 hydroelectric power plants in the United States

Abstract The U.S. Energy Information Administration (EIA) conducts a regular survey (form EIA-923) to collect annual and monthly net generation for more than ten thousand U.S. power plants. Approximately 90% of the ~1,500 hydroelectric plants included in this data release are surveyed at annual resolution only and thus lack actual observations of monthly generation. For each of these plants, EIA imputes monthly generation values using the combined monthly generating pattern of other hydropower plants within the corresponding census division. The imputation method neglects local hydrology and reservoir operations, rendering the monthly data unsuitable for various research applications. Here we present an alternative approach to disaggregate each unobserved plant’s reported annual generation using proxies of monthly generation—namely historical monthly reservoir releases and average river discharge rates recorded downstream of each dam. Evaluation of the new dataset demonstrates substantial and robust improvement over the current imputation method, particularly if reservoir release data are available. The new dataset—named RectifHyd—provides an alternative to EIA-923 for U.S. scale, plant-level, monthly hydropower net generation (2001–2020). RectifHyd may be used to support power system studies or analyze within-year hydropower generation behavior at various spatial scales.

13 HYDRO ENERGY↗
DOE OSTI2023

Single molecule insights into interfacial molecular recognition for model electrochemical DNA biosensors

Electrochemical sensors that use surface-immobilized DNA to bind analytes and transduce the binding into electrochemical signals, have the potential for rapid, specific, and sensitive detection of bioanalytes via a compact and portable platform. However, accessing the structure of these surfaces/interfaces at the relevant spatial scale (< 10 nm), which determines the interfacial interactions and ultimately sensing performance, remains an unsolved challenge. Here, we review studies that have used high resolution atomic force microscope imaging and spatial statistical analysis tools to understand crowding interactions between thiolated DNA probes immobilized on gold electrodes and how such interactions impact target binding. We also review related studies that attempt to control the nanoscale spatial arrangement of the immobilized recognition elements to optimize sensing performance. Furthermore, these efforts have led to new advances in understanding of the structure-function relationships of DNA-based electrochemical biosensors to move the field toward rational engineering of these biosensing interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The impact of capillary heterogeneity on CO 2 flow and trapping across scales

Capillary heterogeneity has been identified over the last decade as a key control on subsurface CO 2 flow behavior during geological CO 2 sequestration. These heterogeneities can be formed in all sedimentary rocks, ranging from slight variations in the sand grain sizes to extensive sequences of interbedded sands, shales, and limestones. Capillary heterogeneity has been largely, although not entirely, overlooked in subsurface flow modeling because it is assumed to only directly influence fluid redistribution over scales of centimeters to meters. However, even small-scale fluid movements can result in dramatic impacts on the mobility and trapping of the CO 2 over kilometers. Therefore, neglecting capillary heterogeneity at multiple scales could potentially lead to errors in modeling and predicting field-scale plume migration. In this review paper, we aim to provide a consistent overview to (1) establish that capillary heterogeneity can have a major impact on CO 2 plume migration, (2) establish the respective length scales at which capillary heterogeneity matters, and (3) provide guidance for numerical modeling. This review covers pertinent literature and extracts key observations from the core to the field scales. Experimental studies have shown that millimeter-decimeter scale capillary heterogeneity can cause the so-called capillary heterogeneity trapping in addition to pore-scale residual trapping. Even at such a small scale, capillary heterogeneity can already lead to complex upscaled constitutive relationships, such as flow-rate dependent and anisotropic relative permeability, which affects field-scale CO 2 migration even when field-scale heterogeneities are present. Under gravity-dominated flow regimes, centimeter-meter scale capillary heterogeneity can entrap a significant amount of CO 2 at field scale, not just after imbibition but also during drainage. In certain cases, the presence of capillary heterogeneity can even completely stop the vertical movement of the CO 2 plume, hence greatly reducing leakage risks. At meter-kilometer scale, the influence of capillary heterogeneity is more pronounced and can hinder or redirect CO 2 migration in both lateral and vertical directions. The impact of capillary heterogeneity across multiple spatial scales poses a great challenge in modeling CO 2 migration at field scale, because it is practically impossible to build a field-scale earth model with grid blocks at millimeter scale. We recommend a hierarchical modeling approach to address this challenge. At field scale, earth models are built to capture geological features and heterogeneities in high but still practical grid resolutions. For each facies or rock type of the field-scale model, high- resolution meter-scale “conceptual” models are built with millimeter-scale grid blocks to capture representative fine-scale bedding geometries and heterogeneities in various environments of deposition, bridging the gap from subcore scale to the size of a field-scale simulation grid block. Upscaling is then used to preserve the smaller-scale flow dynamics of various rock types in field-scale simulations. Here, future work is needed to (1) refine, improve, and validate the hierarchical modeling approach; (2) build libraries of fine-scale bedding models for facies in various environments of deposition; (3) quantify multiscale capillary heterogeneity effects under subsurface uncertainties; (4) gain learning from different storage formations; and (5) establish best practices that balance accuracy and computational speed.

Capillary heterogeneity↗
DOE OSTI2022

Dissecting Nearby Galaxies with piXedfit. I. Spatially Resolved Properties of Stars, Dust, and Gas as Revealed by Panchromatic SED Fitting

We study spatially resolved properties (on spatial scales of ~1–2 kpc out to at least 3 effective radii) of the stars, dust, and gas in 10 nearby spiral galaxies. The properties of the stellar population and dust are derived by fitting the spatially resolved spectral energy distribution (SED) with more than 20 photometric bands ranging from far-ultraviolet to far-infrared. Our newly developed software piXedfit performs point-spread function matching of images, pixel binning, and models the stellar light, dust attenuation, dust emission, and emission from a dusty torus heated by an active galactic nucleus simultaneously through the energy-balance approach. With this self-consistent analysis, we present the spatially resolved version of the IRX–βrelation, finding that it is consistent with the relationship from the integrated photometry. We show that the old stellar populations contribute to the dust heating, which causes an overestimation of the star formation rate (SFR) derived from the total ultraviolet and infrared luminosities on kiloparsec scales. With archival high-resolution maps of atomic and molecular gas, we study the radial variation of the properties of the stellar populations (including stellar mass, age, metallicity, and SFR), dust (including dust mass, dust temperature, and abundance of polycyclic aromatic hydrocarbon), and gas, as well as dust-to-stellar mass and dust-to-gas mass ratios. We observe a depletion of the molecular gas mass fraction in the central region of the majority of the galaxies, suggesting that the lack of available fuel is an important factor in suppressing the specific SFR at the center.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

How does urbanization affect CO 2 emissions of central heating systems in China? An assessment of natural gas transition policy based on nighttime light data

Understanding the different impacts of urbanization on sectorial carbon dioxide (CO 2 ) emissions at different spatial scales is of great importance for the evaluation of energy transition policies and reduction of environmental inequality. However, how urbanization affects the CO 2 emissions of central heating systems at high spatial resolution in China has not been fully studied before. Based on satellite-observed NPP-VIIRS nighttime light (NTL) data, we develop a 5 km x 5 km annual CO 2 emission inventory for coal boilers, thermal power plants (TPPs), and natural gas boilers in China's central heating systems for the period 2012-2017 by using the geographical and temporally weighted regression (GTWR) model. It is observed that nonurban areas generated 2-4 times the CO 2 emissions of coal boilers in urban areas. The largest increments of CO 2 emissions of gas boilers are observed in urban areas of the eastern (6.80 times) and central regions (2.86 times) in 2013-2014, due to the clean heating policy in the "2 + 26" cities in China. The effects of urbanization on CO 2 emissions from natural gas boilers are approximately 2-3 times those of coal boilers, and the differences are largest in western cities with only minor differences in northeastern cities. Overall, our results will aid in designing low-carbon development goals and provide micro-level information on central heating facilities in urbanized and less developed regions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗
DOE OSTI2024

GAMPix: a novel fine-grained, low-noise and ultra-low power pixelated charge readout for TPCs

Here, we report on the development of a novel pixel charge readout system, Grid Activated Multi-scale pixel readout (GAMPix), which is under development for use in the GammaTPC gamma ray instrument concept. GammaTPC is being developed to optimize the use of liquid argon time projection chamber technology for gamma ray astrophysics, for which a fine grained low power charge readout is essential. GAMPix uses a new architecture with coarse and fine scale instrumented electrodes to solve the twin problems of loss of measured charge after diffusion, and high readout power. Fundamentally, it enables low noise and ultra low power charge readout at the spatial scale limited by diffusion in a time projection chamber, and has other possibly applications, including future DUNE modules.

Shutt, Tom↗