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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Ruddlesden–Popper Perovskites with Narrow Phase Distribution for Air-Stable Solar Cells

2D Ruddlesden-Popper perovskites have risen to prominence as stable and efficient photovoltaic materials because of their structural diversity, rich photophysics, and low moisture ingression. However, thin films processed from stoichiometric precursor solutions possess a broad phase distribution of different number of inorganic layers with random crystal orientation, crippling device performance. The effect of methylammonium chloride (MACI) and 3-amino4-phenolsulfonic acid (APSA) on the fabrication of perpendicularly oriented (PEA) 2 MA 4 Pb 5 I 16 films with narrow phase distribution using antisolvent and hot-casting processing techniques is investigated. MACI plays a critical role in suppressing parasitic n ≤ 2 and 3D-like phases. APSA performs the dual function of trap passivation and further narrowing phase polydispersity through strong coordination with Pb 2+ . Ex situ grazing-incident wide-angle X-Ray scattering (GIWAXS) and ultrafast spectroscopic characterization reveal uniformly mixed-phase distribution with disordered orientation in antisolvent treated films, while additive-assisted hot-casting treatment results in oriented, reverse-graded phase distribution, i.e., small-n on the film surface and large-n at the bottom. Arising thin films enable efficient p-i-n solar cells with an efficiency of 14.34%, and a V oc of 1.20 V, retaining 96% initial efficiency after 1440 h under ambient conditions (RH = 50-60%) without encapsulation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Interplay of structural fluctuations and charge carrier dynamics is key for high performance of hybrid lead halide perovskites

The ability of methylammonium lead triiodide (MAPbI 3 ) to achieve photoelectric conversion efficiency that is on par with crystalline silicon has led to a surge of interest in perovskite photovoltaics. However, an in-depth understanding of how the ubiquitous coupling between the fast rovibrational movements of the organic cations and the phonon vibrations of the inorganic framework affects the relaxation and recombination of hot carriers remains largely elusive. Access to such knowledge is critical to guide design and increase efficiency of new classes of perovskite solar cells. In this report, we report a time-domain ab initio investigation of temperature dependent excited state dynamics in MAPbI 3 , with particular emphasis on nuclear anharmonic effects. The observed strong anharmonicity is attributed to softness of the material and unusual dynamical coupling between the organic and inorganic components. At an elevated temperature, the hydrogen bonding between MA and iodines is weakened, enhancing rotation of MA cations, which become more dynamically disordered. As a result, thermal vibrations of the inorganic Pb–I sublattice are suppressed, and the lattice anharmonicity is decreased. Thermal fluctuations of the electronic energy levels are found to follow the trend of anharmonic motions of Pb and I atoms, with holes relaxing faster to the band edges than electrons, due to higher density of the hole states. While elevated temperature accelerates intraband carrier cooling, it slows nonradiative carrier recombination. The latter result is important for performance, since solar cells and other devices heat up during operation. The reported signatures of coupled structural dynamics of the organic cations and inorganic framework unravel the interplay between anomalous structural fluctuations and charge carrier dynamics, which is of particular importance for fundamental understanding of the structure–property relationships in hybrid metal halide perovskites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Data for Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production, a Process Model for Lipid-Producing Energy Crops

Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 °C and 180 °C for 10 minutes) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.

Conversion↗
DOE OSTI2024

X-ray Fluorescence Microscopy to Develop Elemental Classifiers and Investigate Elemental Signatures in BALB/c Mouse Intestine a Week after Exposure to 8 Gy of Gamma Rays

Iron redistribution in the intestine after total body irradiation is an established phenomenon. However, in the literature, there are no reports about the use of X-ray fluorescence microscopy or equivalent techniques to generate semi-quantitative 2D maps of iron in sectioned intestine samples from irradiated mice. In this work, we used X-ray fluorescence microscopy (XFM) to map the elemental content of iron as well as phosphorus, sulfur, calcium, copper and zinc in tissue sections of the small intestine from eight-week-old BALB/c male mice that developed gastrointestinal acute radiation syndrome (GI-ARS) in response to exposure to 8 Gray of gamma rays. Seven days after irradiation, we found that the majority of the iron is localized as hot spots in the intercellular regions of the area surrounding crypts and stretching between the outer perimeter of the intestine and the surface cell layer of villi. In addition, this study represents our current efforts to develop elemental cell classifiers that could be used for the automated generation of regions of interest for analyses of X-ray fluorescence maps. Once developed, such a tool will be instrumental for studies of effects of radiation and other toxicants on the elemental content in cells and tissues. While XFM studies cannot be conducted on living organisms, it is possible to envision future scenarios where XFM imaging of single cells sloughed from the human (or rodent) intestine could be used to follow up on the progression of GI-ARS.

X-ray fluorescence microscopy↗
DOE OSTI2022

Coprocessing Corn Germ Meal for Oil Recovery and Ethanol Production: A Process Model for Lipid-Producing Energy Crops

Efforts to engineer high-productivity crops to accumulate oils in their vegetative tissue present the possibility of expanding biodiesel production. However, processing the new crops for lipid recovery and ethanol production from cell wall saccharides is challenging and expensive. In a previous study using corn germ meal as a model substrate, we reported that liquid hot water (LHW) pretreatment enriched the lipid concentration by 2.2 to 4.2 fold. This study investigated combining oil recovery with ethanol production by extracting oil following LHW and simultaneous saccharification and co-fermentation (SSCF) of the biomass. Corn germ meal was again used to model the oil-bearing energy crops. Pretreated germ meal hydrolysate or solids (160 and 180 °C for 10 min) were fermented, and lipids were extracted from both the spent fermentation whole broth and fermentation solids, which were recovered by centrifugation and convective drying. Lipid contents in spent fermentation solids increased 3.7 to 5.7 fold compared to the beginning germ meal. The highest lipid yield achieved after fermentation was 36.0 mg lipid g−1 raw biomass; the maximum relative amount of triacylglycerol (TAG) was 50.9% of extracted oil. Although the fermentation step increased the lipid concentration of the recovered solids, it did not improve the lipid yields of pretreated biomass and detrimentally affected oil compositions by increasing the relative concentrations of free fatty acids.

09 BIOMASS FUELS↗
DOE OSTI2020

Conductive Adhesives for Metallization of Interdigitated Back Contact Solar Cells

The metallization and interconnection of Si solar cells to form a module is usually a multi-step process: cells are metallized individually, soldered into strings, and subsequently assembled into a module. Furthermore, the metallization process for individual cells must be compatible with the doped surfaces being contacted, which creates additional challenges when moving from diffused junctions to heterojunctions and/or passivated contact structures. To mitigate these problems and streamline module manufacturing for the case of interdigitated back contact (IBC) cell modules, we developed an approach wherein unmetallized IBC cells are bonded directly to a circuitized backsheet using a conductive adhesive (CA) that only conducts out-of-plane. The metal/CA/silicon stack is bonded by hot-pressing at 100-200 degrees C.For a CA consisting of ethylene vinyl acetate (EVA) filled with Ag-coated spheres or indium powder we find that contact resistivities in the range of 1-10 Wcm 2 are obtained, regardless of which conductive filler and which hot pressing parameters are used. XPS revealed that about 1-2 nm EVA residue bonds to the Si in these samples, suggesting the formation of an insulating barrier that is responsible for the high contact resistance. Using indium powder alone, improved contact resistivities <0.6 Wcm 2 , high shunt resistances, and an implied open-circuit voltage loss below 10 mV were obtained. Furthermore, a cost estimate is presented, indicating that substantial cost savings of up to $10/m 2 , or about $0.05/W DC , are possible through CA-based IBC module manufacturing.

14 SOLAR ENERGY↗
DOE OSTI2024

A kinetic study of fusion burn waves in compressed deuterium–tritium and proton–boron plasmas

We present particle-in-cell simulations with Monte Carlo collisions of fusion burn waves in compressed deuterium–tritium and proton–boron plasmas. We study the energy balance in the one-dimensional expansion of a hot-spot by simulating Coulomb collisions, fusion reactions, and bremsstrahlung emission with a Monte Carlo model and inverse bremsstrahlung absorption using a new PIC model. This allows us to self-consistently capture the alpha particle heating and radiative losses in the expanding hot-spot and surrounding cold fuel. After verifying our model in a code-to-code comparison with both kinetic and fluid codes for the case of a deuterium–tritium hot-spot, we simulate the expansion of a proton–boron hot-spot initialized at 200 keV and 1,000 g/cm 3 . Our model predicts that energy radiated by the hot-spot is recaptured by the surrounding high-density opaque fuel reducing the expansion work done by the propagating burn wave. As a result, we find the net fusion energy produced over the course of $20$~ps is twice the initial hot-spot energy independent of whether radiation physics is included.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Shock Ignition Laser-Plasma Interactions in Ignition-Scale Plasmas

Here, we use a subignition scale laser, the 30 kJ Omega, and a novel shallow-cone target to study laser-plasma interactions at the ablation-plasma density scale lengths and laser intensities anticipated for direct drive shock-ignition implosions at National Ignition Facility scale. Our results show that, under these conditions, the dominant instability is convective stimulated Raman scatter with experimental evidence of two plasmon decay (TPD) only when the density scale length is reduced. Particle-in-cell simulations indicate this is due to TPD being shifted to lower densities, removing the experimental back-scatter signature and reducing the hot-electron temperature. The experimental laser energy-coupling to hot electrons was found to be 1%–2.5%, with electron temperatures between 35 and 45 keV. Radiation-hydrodynamics simulations employing these hot-electron characteristics indicate that they should not preheat the fuel in MJ-scale shock ignition experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Evidence for Lignin–Carbohydrate Complexes from Studies of Transgenic Switchgrass and a Model Lignin–Pectin Composite

Lignin–carbohydrate complexes (LCCs) form through interactions of lignin with plant cell wall polysaccharides and are thought to be a significant source of biomass recalcitrance. In this work, we investigated LCCs formed between lignin and pectin homogalacturonan (HG). The structural changes in HG deficient transgenic switchgrass (GAUT4-knockdown, GAUT4-KD) after hot water pretreatment were compared to wild-type plants using small-angle neutron scattering (SANS), which showed that there were ~2.2-fold more lignin aggregates in GAUT4-KD biomass compared to the wild type. This demonstrated that decreased pectin resulted in more lignin redistribution and suggested that interactions between lignin and HG restrict lignin mobility in plant cell walls. To better understand the types of interactions between lignin and pectin, a model composite was prepared by polymerizing either protiated or partially deuterated coniferyl alcohol to form a dehydrogenation polymer (DHP) in the presence of HG. Small-angle X-ray scattering (SAXS) showed that the DHP and HG form a highly interconnected network structure that is not observed in a physical mixture of the individual polymers. Contrast matching SANS revealed the structure of DHP and HG in the composite and showed that the HG forms a swollen interconnected polymer network (power-law exponent, P = 1.5) interspersed with DHP particles (radius of gyration, Rg, 264 Å) that are composed of solvent-accessible DHP polymers (P = 2.3). Fourier transform infrared spectroscopy showed a unique ester absorption band in the DHP/HG composites. Solid-state nuclear magnetic resonance (NMR) analysis also supports interactions between DHP and HG. Overall, this study provides new insights into the relationship between primary and secondary cell wall polymers during cell wall synthesis and how LCCs formed between pectin and lignin could represent a previously unrecognized source of biomass recalcitrance. This knowledge may help develop new approaches to modulate cell wall properties to improve biofuel and bioproduct production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

FY2022 Progress Report for Advanced Re-fabrication/Re-instrumentation Capability Development

In support of performing follow-on irradiation experiments with previously irradiated materials, the Halden Reactor Project developed unique and state of the art capabilities to refabricate and re-instrument previously irradiated materials. Such materials were used in in-pile tests at the Halden reactor, and out-of-pile tests for example using furnaces as a heat source. The decision to close the Halden Reactor Project results in the loss of this refabrication and re-instrumentation capability. As a result, the United States (U.S.) Department of Energy (DOE) has determined to develop refabrication and re-instrumentation capability at the unique shielded facilities at Idaho National Laboratory (INL). The development of refabrication capability has been completed and demonstrated. This report focuses on the complementary aspects of reinstrumentation and the progress to-date. Halden spent nearly 30 years developing both refabrication and re-instrumentation. Collaboration with Halden is allowing Idaho National Laboratory (INL) to develop this capability much more rapidly. In FY-21 the results include development of the capability to drill annular center holes in ceramic UO2 fuel pellets, development of fuel rod end caps with feedthroughs for centerline instrumentation inside the rodlet, The procurement of both fuel drilling and welding demonstration equipment from Halden, evaluation of surface thermocouple attachments to support better understanding of temperature measurement uncertainties, and finally, the conceptual design of a new shielded enclosure where advanced refabrication and re-instrumentation equipment can be housed. In FY-22, the results include; Completing set up of the drilling and welding modules procured from Halden, and early experimental trials using that equipment.; Completing set up of an out-of-cell circumferential weld system to allow for further weld development to take place and support fabrication of fuel for fresh fuel experiments.; Evaluation of the Hot Fuel Examination Facility (HFEF) infrastructure to support future installation of advanced re-fabrication/re-instrumentation equipment, specifically related to necessary infrastructure for cryo-drilling.; Developments in dry-drilling alternative. Including experimental studies showing cordierite is the most suitable surrogate for UO 2 for performing drilling studies. That drilling performance is enhanced when a fuel-clad bonding condition is simulated.; Conceptual design completed for attaching surface thermocouples to irradiated fuel in support of TWIST capsule experiments. The authors would like to thank the numerous colleagues at INL and Halden who provided support in accomplishing this work. Their support both material and intellectual is invaluable in advancing the state of the art and establishing the capabilities for refabrication and re-instrumentation at INL.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Laser wavelength dependence of particle acceleration mechanisms in high intensity laser–solid density plasma interactions

We investigate the generation of relativistic electrons and the subsequent ion acceleration due to target-normal sheath acceleration when ultra-intense (⁠ I > 10 18 W/cm 2 ⁠) short pulse (⁠ τ L < 10ps⁠) lasers are incident onto solid density targets as laser wavelength is varied. Scaling laws for the hot electron temperature, T hot ⁠, and the maximum ion energy, E max ⁠, are recast as a function of laser wavelength. These predictions are compared to results from particle-in-cell computer simulations in a variety of geometries, including cases where realistic plasma density profiles as determined by a radiation hydrodynamics code are used. It is found that the wavelength dependence observed in simulation is less pronounced than what is predicted from the well-established scaling laws. An assessment of how switching to longer laser wavelengths, specifically 2 μm Tm:YLF technology, would impact current high energy density science applications and diagnostics is made.

Electromagnetism↗
DOE OSTI2025

Symplectic neural network and its application to charged particle dynamics in electromagnetic fields

Recently, machine learning models have shown many successes in various applications in science and technology. In this work, we focus on the charged particle dynamics, with the development of a class of symplectic neural networks, including a linear version, SympMat, and a nonlinear version, HénonNet. Both are designed to preserve the structure of Hamiltonian systems. We show that they can be used to model relevant Hamiltonian systems of interest in plasma physics and astrophysics, for linear and nonlinear charged particle dynamics, with the potential to bridge multi-scale simulations. These symplectic neural networks are adapted to the applications in plasma simulations and particle-wave interaction with parametric dependence and periodicity, where we have investigated their performance and accuracy. In particular, SympMat is shown to outperform the traditional Boris particle pusher down to the sub-gyroperiod scale in the case of charged particles in uniform magnetic fields. HénonNet successfully predicts the hot electron distribution, which is validated against theoretical results. These results highlight the potential of symplectic neural networks as a trajectory integrator for particle-in-cell simulations or a fast surrogate to replace conventional numerical schemes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Microstructure Scale Lithium-Ion Battery Modeling: Part III. When and Where Lithium Plating Occurs and its Correlation with the Electrode Microstructure

Li-ion battery performance and degradation are closely related to the cell’s underlying electrode microstructure. Electrode microstructures are typically characterized with volume-averaged properties that neglect the impact of local heterogeneities. However, local heterogeneities create hot spots that can trigger degradation onset. Herein, a microstructure scale electrochemical model is used to investigate the impact of microstructure heterogeneity on lithium plating. The model predicts lithium plating is not uniform, even when considering a relatively small portion of the electrode (a cross-sectional area of 154×144 µm 2 ), preferring to plate on larger particles as compared to smaller particles. While local heterogeneities control where plating occurs, the model predicts that volume-averaged properties control when plating occurs. Additionally, the model predicts that the active material specific surface area has a linear relationship with the plating onset. However, the linear relationship between increased active material surface area and delayed plating response appears to be sensitive to the microstructure feature used to increase the active interface area. Here, a comparative case-study is explored where the specific surface area is increased by either reducing the active material particle diameter, adding open-porosity cracks, or increasing the active material surface roughness. The model predicts that increasing the specific surface area by reducing the active material particle diameter is the most effective strategy for delaying lithium plating. At 6C, reducing particle size is shown to be 3 and 20 times more effective than, respectively, adding open-porosity cracks and increasing surface roughness. A dual-layer electrode architecture combining gradations both for average properties and uniformities is eventually proposed to improve homogeneous material utilization and reduce degradation at high charge rates.

25 ENERGY STORAGE↗
DOE OSTI2026

Scalings of laser-driven MeV electron sources with relativistic multi-picosecond laser pulses

We investigate the generation of MeV electrons in relativistic multi-picosecond laser–solid interactions, using two-dimensional particle-in-cell simulations. Scanning a parameter space of intensities from 10 18 to 10 20 W/cm 2 and pulse durations between 100 fs and 10 ps, we discuss scalings of the effective hot electron temperature and MeV electron dose relevant to applications, as well as the direct laser acceleration mechanism that drives electrons to energies much higher than the ponderomotive potential of the laser pulse.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Fabrication of high-performance gas-diffusion-electrode based membrane-electrode assemblies

This paper demonstrates the fabrication and processing steps required to produce high performance fuel cell membrane electrode assemblies (MEAs) based on spray-coated gas-diffusion electrodes (GDEs). It is demonstrated that coating the catalyst layer with a thin layer of ionomer and then hot pressing the GDEs to the membrane is required to achieve comparable catalyst activity and air performance to catalyst-coated-membrane MEAs. We show that there is a critical amount of ionomer required to achieve maximized performance. Using electron microscopy, we show that the combination of the ionomer overlayer and hot-pressing bonds the catalyst layer to the membrane, increasing the interfacial contact area and quality of this interface. We also find that the ionomer overlayer smooths the surface of the GDE and provides increased contact area between the GDE and the membrane. Additionally, we demonstrate that much less ionomer is required for high-performance than has been previously reported. Through model fitting of electrochemical impedance spectroscopy, we show that this improvement in the catalyst layer - membrane interface reduces the effective catalyst layer resistance, which reduces Ohmic losses and increases catalyst utilization.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2026

Mark-18A Target Material Recovery Program: Initial Hot Startup

The Savannah River National Laboratory (SRNL) has been tasked by the National Nuclear Security Administration to recover highly valued isotopes from irradiated Mark-18A (Mk-18A) targets. The Savannah River Site (SRS) has sixty-five Mk-18A targets available for the recovery of the high valued materials. The Mk-18A targets were manufactured with Pu-242 then irradiated under high neutron flux in K-Reactor at the SRS from 1968 to 1978. The sixty-five Mk-18A targets are currently stored in the SRS L-Area Basin and will be removed one at a time and individually transported to SRNL. Upon receipt at SRNL, the Mk-18A target material will be removed from the confinement, dissolved, chemically separated, and calcined to a stable oxide. The flowsheet is designed to recover the plutonium as well as the trivalent actinides. The original targets were manufactured with varying quantities of Pu-242, ranging from 5.2 grams to 121.5 grams. Taking a graded approach to process start up, the lowest loaded target (FT-80-03) was selected as the first target to be received and processed at SRNL. As operational experience and knowledge is gained from processing targets, higher loaded targets will be selected for processing to increase the quantities of valuable isotopes recovered. Due to dose concerns, the receipt and processing of the Mk-18A targets is performed in the SRNL Shielded Cells Facility. The targets are stored in a double J-can confinement in the L-Area Basin. A specially designed cask was procured for transport of the targets from L-Area to SRNL. Once received at SRNL, the targets are loaded into the back of Cell 7 and resized as they enter the cell. The resized targets (1/4 length) are then processed one at a time through the following processes: caustic dissolution and filtration, acidic dissolution and filtration, elutable Reillex anion exchange, diglycolamide (DGA) resin extraction, and DGA calcination. This processing results in two product streams. The first is an aqueous plutonium solution which is removed from the shielded cells and taken to a glovebox for further purification and conversion to an oxide. The second is a calcined oxide product containing the Am and Cm as well as other lanthanide fission products which is removed from the shielded cells using a bagless transfer system. Both materials are packaged for shipment to Oak Ridge National Laboratory (ORNL). This paper will discuss the operating experience, lessons learned, and results from initial process hot startup.

Armstrong, Christopher [Savannah River National La↗
DOE OSTI2020

Colloidal Quantum Dot Photovoltaics: Current Progress and Path to Gigawatt Scale Enabled by Smart Manufacturing

Colloidal quantum dots (QDs) have lately been pursued with intense vigor for optoelectronic applications such as photovoltaics (PV), flexible electronics, displays, mid-infrared photodetectors, lasers, and single-photon emitters. These nanometer-sized semiconducting crystals can be suitably mass-produced and size-tuned via cost-effective solution-based synthetic routes to operate in the quantum size confinement regime, endowing them with a wide array of exotic optical and electronic properties. While the first potential market entry could be in displays and in niche applications such as “internet-of-things”, ultimately, the technology has the potential to influence large-scale terrestrial power generation, because it is amenable to high-throughput synthesis from Earth-abundant materials and large-area solution-based coating techniques and can be air-stable. In this Review, we chronicle the recent advances that have propelled QD PV toward commercialization and highlight potential areas for further progress. We present an account of the material compositions being explored as QDs and their various benefits, major chemical passivation and doping strategies that have been developed to allay QD surface traps, and advanced device designs deployed to maximize charge extraction. We also discuss pathways to >20% efficient QD PV and describe recent advances in high-precision and autonomous synthesis of such materials. With recent demonstrations of scalable synthesis of high-quality QDs, smart manufacturing of QDs and QD solids, and fabrication of stable solar cells under ambient conditions, we suggest that the technology is on the road to achieving maturity and technological relevance and that gigawatt per year distributed panel production sites may be within reach.

14 SOLAR ENERGY↗
DOE OSTI2024

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here, we present the culmination of the efforts of the modENCODE (model organism Encyclopedia of DNA Elements) and modERN (model organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms,Drosophila melanogaster(fly) andCaenorhabditis elegans(worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites in the worm, and represent the majority of the regulatory space in each genome. We demonstrate that TFs associate with chromatin in clusters termed “metapeaks,” that larger metapeaks have characteristics of high-occupancy target (HOT) regions, and that the importance of consensus sequence motifs bound by TFs depends on metapeak size and complexity. Combining ChIP-seq data with single-cell RNA-seq data in a machine-learning model identifies TFs with a prominent role in promoting target gene expression in specific cell types, even differentiating between parent–daughter cells during embryogenesis. These data are a rich resource for the community that should fuel and guide future investigations into TF function. To facilitate data accessibility and utility, all strains expressing green fluorescent protein (GFP)-tagged TFs are available at the stock centers for each organism. The chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center, GEO, and through a direct interface that provides rapid access to processed data sets and summary analyses, as well as widgets to probe the cell-type-specific TF–target relationships.

Biochemistry & Molecular Biology↗