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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Range extender mediates long-distance enhancer activity

Although most mammalian transcriptional enhancers regulate their cognate promoters over distances of tens of kilobases, some enhancers act over distances in the megabase range1. The sequence features that enable such long-distance enhancer–promoter interactions remain unclear. Here we used in vivo enhancer-replacement experiments at the mouse Shh locus to show that short- and medium-range limb enhancers cannot initiate gene expression at long-distance range. We identify a cis-acting element, range extender (REX), that confers long-distance regulatory activity and is located next to a long-range limb enhancer of Sall1. The REX element has no endogenous enhancer activity. However, addition of the REX to other short- and mid-range limb enhancers substantially increases their genomic interaction range. In the most extreme example observed, addition of REX increased the range of an enhancer by an order of magnitude from its native 73 kb to 848 kb. The REX element contains highly conserved [C/T]AATTA homeodomain motifs that are critical for its activity. These motifs are enriched in long-range limb enhancers genome-wide, including the ZRS (zone of polarizing activity (ZPA) regulatory sequence), a benchmark long-range limb enhancer of Shh2. The ZRS enhancer with mutated [C/T]AATTA motifs maintains limb activity at short range, but loses its long-range activity, resulting in severe limb reduction in knock-in mice. In summary, we identify a sequence signature associated with long-range enhancer–promoter interactions and describe a prototypical REX element that is necessary and sufficient to confer long-distance activation by remote enhancers.

Bower, Grace↗
DOE OSTI2024

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, in this study, we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson–Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Oral microbiome and mycobiome dynamics in cancer therapy-induced oral mucositis

Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral mucositis commonly occurs 7–10 days after initiation of therapy; it is a dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and a rise of infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, and the oral microbiome. Our longitudinal study analysed the dynamics of the oral microbiome (bacteria and fungi) in nineteen patients undergoing chemo-radiation therapy for oral and oropharyngeal squamous cell carcinoma as compared to healthy volunteers. The microbiome was characterized in multiple oral sample types using rRNA and ITS sequence amplicons and followed the treatment regimens. Microbial taxonomic diversity and relative abundance may be correlated with disease state, type of treatment and responses. Identification of microbial-host interactions could lead to further therapeutic interventions of mucositis to re-establish normal flora and promote patients’ health. Data presented here could enhance, complement and diversify other studies that link microbiomes to oral disease, prophylactics, treatments, and outcome.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

X-ray diffraction of metastable structures from supercooled liquid hydrogen

We report time resolved observations of the crystallization from liquid hydrogen, supercooled to temperatures below the melting point, using 11.2 keV X-ray diffraction from the Linac Coherent Light Source (LCLS). Changes to the metastable solid and liquid structure factors have been dynamically measured. This allows for a direct determination of the lowest energy crystal polymorphs, the stacking probabilities, as well as the liquid and solid densities and temperatures. Such measurements provide experimental evidence of an Arrhenius-like growth kinetics along the stacking direction during supercooling.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A multi model ensemble reveals net climate benefits from regenerative practices in US Midwest croplands

Process-based cropping systems models (CSMs) are key components of measurement, monitoring, reporting, and verification frameworks of carbon markets, but model-specific differences limit their applicability across diverse pedo-climatic conditions and agronomic practices. Multi-model ensemble (MME) provides an opportunity to better estimate changes in soil organic carbon (SOC) and nitrous oxide (N 2 O) emissions from agronomic practices at scale. We used an MME across 46 million hectares of US Midwest cropland at a resolution of 4-km 2 to assess the aggregate ability of different regenerative practices to sequester SOC and N 2 O emissions compared to their counterfactual dynamic baselines. MME was validated against long-term trials and compared to its constituent CSMs, showing greater accuracy and lower uncertainty. The results show that adopting no-till combined with cover crops increased SOC stocks by 0.36 ± 0.12 Mg ha -1 yr -1 , corresponding to a net regional SOC gain of 16.4 Tg C yr -1 compared to business-as-usual baselines. These benefits are halved when each management is practiced individually, and the SOC gains are only fully realized with low initial carbon stock. By including N 2 O emissions, we can assess the overall climate mitigation potential, specifically, the extent to which carbon sequestration can offset direct N 2 O emissions. The magnitude of this potential varies depending on management practices and geographic location with net climate benefits on average ranging from 0 to 3 Mg CO 2 -eq ha -1 yr -1 . High-resolution MME results allow for robust estimates of climate mitigation, reducing barriers to carbon market participation and supporting regenerative agriculture initiatives at scale.

carbon credits↗
DOE OSTI2025

High-energy ion beams generated with high efficiency using laser-driven 3D microstructures

Laser-driven ion acceleration in plasma is being proposed as a source of ion beams with a high peak current that can be useful in many fields of science and medicine. Using this method, high proton energies have been achieved by increasing the laser power and by using ultrathin (≤ 200 nm) foils. However, this approach is limited by survivability of the nanotargets to laser prepulses and by difficulty in controlling the plasma acceleration properties. Here, we introduce a new target platform using two-photon polymerization, 3D laser-printed “clone” microstructures with average densities lower than solid that are relatively insensitive to the laser prepulse. Two types of microstructured targets consisting of either a multilayered log-pile or a stochastic arrangement of one micron diameter wires are used. Both demonstrate a higher energy and higher yield proton acceleration compared to thin solid-density foil targets by the robust target normal sheath acceleration (TNSA) mechanism. We find that when such 10–20 μm thick structures are irradiated with a petawatt laser, protons with energies up to 110 MeV and a laser-to-proton conversion efficiency of ~ 10% are obtained. Our work suggests that such microstructures optimized for 60–200 MeV compact proton accelerators are promising for future radiotherapy and other applications.

Physics - Plasma physics↗
DOE OSTI2024

Pushing the limits of size selectivity in nanoscale solute separations

Transport of a spherical solute through a cylindrical pore has been modelled for decades using well-established hindered transport theory, predicting solutes with a size smaller than the pore to be rejected nonetheless because of convective and diffusive hindrance; this rejection mechanism prevents extremely sharp solute separations by a membrane. Whereas the model has been historically verified, solute transport through near-perfect isoporous membranes may finally overcome this limitation. Here, in this study, encouraging solute rejections are achieved using nanofabricated, defect-free silicon nitride isoporous membranes. The membrane is challenged by a recirculated feed to increase the opportunity for interactions between solutes and the pore array. Results show the membrane completely reject solutes with greater size than the pore size while effectively allowing smaller solutes to permeate through. With effectively increasing the number of interactions, we propose that a steeper size-selective rejection curve may be achieved. With this traditional hurdle overcome, there is new promise for unprecedented membrane separations through judicious process design and extremely tight pore-size distributions.

Gao, Feng↗
DOE OSTI2024

Uncovering fast solid-acid proton conductors based on dynamics of polyanion groups and proton bonding strength

Achieving high proton conductivity in inorganic solids is key for advancing many electrochemical technologies, including low-energy nano-electronics and energy-efficient fuel cells and electrolyzers. A quantitative understanding of the physical traits of a material that regulate proton diffusion is necessary for accelerating the discovery of fast proton conductors. In this work, we have mapped the structural, chemical and dynamic properties of solid acids to the elementary steps of the Grotthuss mechanism of proton diffusion. Our approach combines ab initio molecular dynamics simulations, analysis of phonon spectra and atomic structure calculations. We have identified the donor–hydrogen bond lengths and the acidity of polyanion groups as key descriptors of local proton transfer and the vibrational frequencies of the cation framework as the key descriptor of lattice flexibility. The latter facilitates rotations of polyanion groups and long-range proton migration in solid acid proton conductors. The calculated lattice flexibility also correlates with the experimentally reported superprotonic transition temperatures. Using these descriptors, we have screened the Materials Project database and identified potential solid acid proton conductors with monovalent, divalent and trivalent cations, including Ag + , Sr 2+ , Ba 2+ and Er 3+ cations, which go beyond the traditionally considered monovalent alkali cations (Cs + , Rb + , K + , and NH 4 + ) in solid acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

QuTree: A tree tensor network package

Here we present QuTree, a C++ library for tree tensor network approaches. QuTree provides class structures for tensors, tensor trees, and related linear algebra functions that facilitate the fast development of tree tensor network approaches such as the multilayer multiconfigurational time-dependent Hartree approach or the density matrix renormalization group approach and its various extensions. We investigate the efficiency of relevant tensor and tensor network operations and show that the overhead for managing the network structure is negligible, even in cases with a million leaves and small tensors. QuTree focuses on providing simple, high-level routines while retaining easy access to the backend to facilitate novel developments. We demonstrate the capabilities of the package by computing the eigenstates of coupled harmonic oscillator Hamiltonians and performing random circuit simulations on a virtual quantum computer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Toward machine-learning-assisted PW-class high-repetition-rate experiments with solid targets

We present progress in utilizing a machine learning (ML) assisted optimization framework to study the trends in a parameter space defined by spectrally shaped, high-intensity, petawatt-class (8 J, 45 fs) laser pulses interacting with solid targets and give the first simulation-based overview of predicted trends. A neural network (NN) incorporating uncertainty quantification is trained to predict the number of hot electrons generated by the laser–target interaction as a function of pulse shaping parameters. The predictions of this NN serve as the basis function for a Bayesian optimization framework to navigate this space. For post-experimental evaluation, we compare two separate neural network (NN) models. One is based solely on data from experiments, and the other is trained only on ensemble particle-in-cell simulations. Reviewing the predicted and observed trends across the experiment-capable laser parameter search space, we find that both ML models predict a maximal increase in hot electron generation at a level of approximately 12%–18%; however, no statistically significant enhancement was observed in experiments. On direct comparison of the NN models, the average discrepancy is 8.5%, with a maximum of 30%. Since shot-to-shot fluctuations in experiments affect the observations, we evaluate the behavior of our optimization framework by performing virtual experiments that vary the number of repeated observations and the noise levels. Here, we discuss the implications of such a framework for future autonomous exploration platforms in high-repetition-rate experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Toward an integrated multi-gigahertz ionizing particle diagnostic

Needs arising at both current and future accelerator facilities call for the development of radiation-hardened position-sensing diagnostics that can operate with multi-GHz repetition rates. Such instruments are likely to also have applications in the diagnosis of rapid plasma behavior. Here, building on the recent work of our Advanced Accelerator Diagnostics Collaboration, we are exploring the development of integrated multi-GHz ionizing particle detection systems based on chemical-vapor deposition diamond sensors, with the initial goal of producing a quadrant detector that can determine the intensity and centroid position of a particle beam at a repetition rate between 5 and 10 GHz. Results from our initial high-speed characterization work are presented, including those from a single-channel sensor with a GHz response. Approaches to achieving multi-GHz (5–10 GHz) rate capability, including the design of a dedicated Application Specific Integrated Circuit and the use of 3D RF-solver computer aided design software, are presented and discussed in more detail. 3D RF simulations suggest clean pulses of duration less than 250 ps (FWHM less than 125 ps) can be achieved with the approaches developed by this work.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Extending GPU-accelerated Gaussian integrals in the TeraChem software package to f type orbitals: Implementation and applications

Here, the increasing availability of graphics processing units (GPUs) for scientific computing has prompted interest in accelerating quantum chemical calculations through their use. However, the complexity of integral kernels for high angular momentum basis functions often limits the utility of GPU implementations with large basis sets or for metal containing systems. In this work, we report the implementation of f function support in the GPU-accelerated TeraChem software package through the development of efficient kernels for the evaluation of Hamiltonian integrals. The high efficiency of the resulting code is demonstrated through density functional theory (DFT) calculations on increasingly large organic molecules and transition metal complexes, as well as coupled cluster singles and doubles calculations on water clusters. Preliminary investigations into Ni(I) catalysis with DFT and the photochemistry of MnH(CH 3 ) with complete active space self-consistent field are also carried out. Overall, our GPU-accelerated software appears to be well-suited for fast simulation of large transition metal containing systems, as well as organic molecules.

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

Characterization of laser-accelerated proton beams from a 0.5 kJ sub-picosecond laser for radiography applications

Laser-accelerated ion beams show promise for many applications, including high-resolution flash imaging of static or dynamic objects in next-generation radiography to probe materials and plasmas in extreme environments and inertial confinement fusion. To scale up ion beam production for radiography applications, we conducted experiments using sub-picosecond lasers up to 0.5 kJ at the OMEGA-EP facility to characterize proton beams from solid targets, primarily CH/CD sub-micron thin films from which ion beams were also used for static and dynamic radiography for the first time. For standalone sub-micron thin CH films, the highest detected proton energy is in the range of 72–97 MeV. Proton beams with highest energy near or above 60 MeV at full laser energy and similar beam profiles are also measured from low-density CD foams and flat CH foil target of micrometer-scale thickness. The ~ 700–800 nm CH/CD foils achieve the highest ion yield among the targets tested. For sub-micron thin films, the laser prepulse can expand the target and lead to complex interactions, which is simulated using coupled hydrodynamic and two-step kinetic models. Simulations suggest the presence of a micrometer-scale preplasma plateau with near-critical density and further indicate that target normal sheath acceleration, electron heating from Relativistic transparency in the preplasma plateau, and background proton reflection from carbon ion front at the rear side contribute to the resulting proton spectrum from these sub-micron thin targets at various stages. These proton beams show strong potential for radiography and for production of secondary sources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗