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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

AlignOT: An Optimal Transport Based Algorithm for Fast 3D Alignment With Applications to Cryogenic Electron Microscopy Density Maps

Aligning electron density maps from Cryogenic electron microscopy (cryo-EM) is a first key step for studying multiple conformations of a biomolecule. As this step remains costly and challenging, with standard alignment tools being potentially stuck in local minima, we propose here a new procedure, called AlignOT, which relies on the use of computational optimal transport (OT) to align EM maps in 3D space. By embedding a fast estimation of OT maps within a stochastic gradient descent algorithm, our method searches for a rotation that minimizes the Wasserstein distance between two maps, represented as point clouds. Here, we quantify the impact of various parameters on the precision and accuracy of the alignment, and show that AlignOT can outperform the standard local alignment methods, with an increased range of rotation angles leading to proper alignment. We further benchmark AlignOT on various pairs of experimental maps, which account for different types of conformational heterogeneities and geometric properties. As our experiments show good performance, we anticipate that our method can be broadly applied to align 3D EM maps.

3D alignment↗
DOE OSTI2025

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Abstract Motivation Cryogenic electron microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational heterogeneity. Although various global and local map-sharpening techniques are widely employed to improve cryo-EM density maps, it is still challenging to efficiently improve their quality for building better protein structures from them. Results In this study, we introduce CryoTEN—a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their corresponding simulated maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, automatic de novo protein structure modeling shows that protein structures built from the density maps processed by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing state-of-the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality of density maps, while running >10 times faster and requiring much less GPU memory than them. Availability and implementation The source code and data are freely available at https://github.com/jianlin-cheng/cryoten.

Biochemistry & Molecular Biology↗
DOE OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

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

Hydrogen density mapping in biomolecular crystals through dynamic nuclear polarization

Many fundamental biological processes, including those in photosynthetic reaction centers and enzyme active sites, involve charge and energy transfer, bond cleavage, protonation and hydrogen bonding. Because H atoms play such central roles in these reactions, accurately determining their positions is essential. Yet, conventional X-ray crystallography primarily resolves the heavy atoms in biological structures and provides limited insight into hydrogen, even at atomic resolution. Neutron macromolecular crystallography (NMC) overcomes this limitation by offering exceptional sensitivity to hydrogen and deuterium. Here, we present a theoretical framework for the development of dynamic nuclear polarization NMC (DNP-NMC) techniques, which exploit the alignment of neutron and proton nuclear spins to enhance and tune the hydrogen signal contribution. The DNP-NMC approach advances the resolution of H atoms within biomolecular crystals, whether bound to protein residues or present in solvent. The method establishes key relationships for the coherent structure factor of polarized neutron scattering from hydrogenous matter. It theoretically achieves full accuracy in phase reconstruction and offers a path to improve neutron structure determination, achieving accuracies exceeding ≳80% by incorporating titration states. Using a variant of the hybrid input/output phase-retrieval algorithm, it allows recovery of the hydrogen density with ≳90% phase accuracy. In conclusion, we further discuss sources of experimental uncertainty for the upcoming DNP-enabled, quasi-Laue IMAGINE-X experiment at Oak Ridge National Laboratory's High Flux Isotope Reactor.

dynamic nuclear polarization↗
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Kinetic Plasma Simulation in the MOOSE Framework: Verification of Electrostatic Particle In Cell Capabilities

In magnetic confinement nuclear fusion reactors, the interaction between the plasma edge and plasma facing components is extremely important. At the plasma edge, a kinetic representation such as particle-in-cell (rather than a fluid representation) is required to accurately capture the plasma behavior. General purpose particle-in-cell plasma simulation capabilities have been developed in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. This new capability is a part of the development of a new MOOSE-based framework for modeling plasma facing components, the Fusion ENergy Integrated multiphys-X (FENIX) framework. In this work, the verification of foundational particle-in-cell capabilities in FENIX is presented. This new plasma simulation capability has three main components: moving particles in discrete steps on the finite element mesh, mapping charge density from the particle's location to the finite element mesh, and solving for the electrostatic potential based on the charge density mapped from particles to the mesh. In this paper, simple verification problems demonstrating each of these new capabilities are presented, and future work includes electromagnetic capabilities and Monte Carlo collisions with neutral gas particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting

Many existing object counting methods rely on density map estimation (DME) of the discrete grid representation by decoding extracted image semantic features from designed convolutional neural networks (CNNs). Relying on discrete density maps not only leads to information loss dependent on the original image resolution, but also has a scalability issue when analyzing high-resolution images with cubically increasing memory complexity. Furthermore, none of the existing methods can offer reliable uncertainty quantification (UQ) for the derived count estimates. To overcome these limitations, we design UNcertainty-aware, hypernetwork-based Implicit neural representations for Counting (UNIC) to assign probabilities and the corresponding counting confidence over continuous spatial coordinates. We derive a sampling-based Bayesian counting loss function and develop the corresponding model training algorithm. UNIC outperforms existing methods on the Remote Sensing Object Counting (RSOC) dataset with reliable UQ and improved interpretability of the derived count estimates. Our code is available at https://github.com/SiyuanXu-tamu/UNIC.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Laser-driven flash x-ray radiography of a shocked metallic foil

Characterizing hydrodynamic instability evolution in millimeter-scale, high-Z foils is crucial for understanding complex phenomena in high-energy-density physics. Here, we demonstrate a proof-of-concept, laser-driven flash x-ray radiography platform tailored for two-dimensional linear density mapping in shocked high-Z foils. Using chromium (Cr) foils with internal shockwaves (∼100 μm width), our platform achieves a spatial resolution of 59.8 ± 1.4 μm by employing a broadband x-ray source extending into the hundreds of keV range. The setup combines a compound parabolic concentrator cone with a tantalum wire target, a magnetic field to deflect residual transmitted electrons, and a copper casing to shield the sides and rear of the image plate pack. By varying the delay of the short-pulse beam driving the flash x-ray source, we resolve shockwave dynamics, specifically the velocity, position, width, and density profile, within the Cr foil. Reported experimental results are consistent with the corresponding hydrodynamics and radiation transport simulations, which accurately reproduce the measured electron and x-ray source terms. These developments enable the conversion of shockwave radiographs into two-dimensional density maps, enhancing interpretability for hydrodynamic instability evolution applications and validating the simulation approach.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Quantitative radiography for determining density fluctuations in HED experiments

We have developed a method to extract density fluctuation measurements from x-ray radiographs of high-energy density (HED) instability growth and turbulence experiments. We use this information to calculate density fluctuation statistics for constraining the performance of turbulent mix models in HED systems. The density calculation combines image filtering, removal of systemic effects such as backlighter variation, calculation of transmission across multiple materials, and use of tracer materials to generate an approximate single-material density field. From the density map, we calculate both average density and a variance-like moment b (density-specific-volume covariance), which we compare to our models. We infer both quantities from a single image, which is significantly more information than the historic single scalar mix width measurements. We also develop a method of analyzing simulation outputs that incorporate both the density fluctuation metric from a turbulence model and the bulk material maps from the hydrodynamic code. This analysis helps address the question of how to initialize the simulations for best comparison to data from systems with large separations of scale in the mixing perturbation initial condition. We find that our data analysis method yields 1D average density and b curves with similar morphology and amplitudes as those from preliminary simulation comparisons.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Determining the nanostructure of polymer foams using 3D ptycho-tomography for inertial fusion energy applications

Polymer foams play a critical role in contemporary inertial fusion energy (IFE) target designs by enhancing energy yield and optimizing implosion dynamics. However, the lack of high-resolution characterization of the nanostructure of these foams restricts progress in fusion science. In this work, we demonstrate the first high-resolution three-dimensional (3D) reconstruction of a low-density, Si-doped polymer foam fabricated via two-photon polymerization, using ptychographic x-ray computed tomography (PXCT) at an x-ray free electron laser (XFEL). This imaging method reconstructs two-dimensional (2D) attenuation and phase information at multiple sample angles that are combined into a 3D density map used to extract local mass density and determine structural dimensions. We achieve a 2D spatial resolution of 19 ± 3 nm on a high-contrast Ronchi pattern target and 78.7 ± 3 nm for low-contrast polymer foams, marking a significant advancement for XFEL-based ptychography of low-density materials. Furthermore, our experimental results reveal an average foam strut thickness of 1.17 ± 0.4 μm, consistent with fabrication expectations, and a reconstructed average mass density of 0.35 g/cc, aligning closely with the predicted density of 0.29 g/cc. These findings provide important insights for improving foam design and refining radiation hydrodynamics modeling in future IFE experiments. Our study establishes PXCT at an XFEL as a powerful tool for high-resolution characterization of fusion-relevant materials, paving the way for enhanced target performance in IFE research.

Hancock, Levi [Colorado State Univ., Fort Collins,↗
DOE OSTI2024

The Simons Observatory: Combining cross-spectral foreground cleaning with multitracer B -mode delensing for improved constraints on inflation

The Simons Observatory (SO), due to start full science operations in early 2025, aims to set tight constraints on inflationary physics by inferring the tensor-to-scalar ratio r from measurements of cosmic microwave background (CMB) polarization B-modes. Its nominal design including three small-aperture telescopes (SATs) targets a precision σ⁡(r = 0) ≤ 0.003 without delensing. Achieving this goal and further reducing uncertainties requires a thorough understanding and mitigation of other large-scale B-mode sources such as Galactic foregrounds and weak gravitational lensing. We present an analysis pipeline aiming to estimate r by including delensing within a cross-spectral likelihood, and demonstrate it for the first time on SO-like simulations accounting for various levels of foreground complexity, inhomogeneous noise and partial sky coverage. As introduced in an earlier SO delensing paper, lensing B-modes are synthesized using internal CMB lensing reconstructions as well as Planck-like cosmic infrared background maps and LSST-like galaxy density maps. We then extend SO’s power-spectrum-based foreground-cleaning algorithm to include all auto- and cross-spectra between the lensing template and the SAT B-modes in the likelihood function. This allows us to constrain r and the parameters of our foreground model simultaneously. Within this framework, we demonstrate the equivalence of map-based and cross-spectral delensing and use it to motivate an optimized pixel-weighting scheme for power spectrum estimation. We start by validating our pipeline in the simplistic case of uniform foreground spectral energy distributions. In the absence of primordial B-modes, we find that the 1⁢σ statistical uncertainty on r, σ⁡(r), decreases by 37% as a result of delensing. Tensor modes at the level of r = 0.01 are successfully detected by our pipeline. Even when using more realistic foreground models including spatial variations in the dust and synchrotron spectral properties, we obtain unbiased estimates of r both with and without delensing by employing the moment-expansion method. In this case, uncertainties are increased due to the higher number of model parameters, and delensing-related improvements range between 27% and 31%. These results constitute the first realistic assessment of the delensing performance at SO’s nominal sensitivity level.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Effect of local environment on Ly$α$ line profile in DESI/ODIN LAEs

Lyman-Alpha Emitters (LAEs) are star-forming galaxies with significant Ly$α$ emission and are often used as tracers of large-scale structure at high redshift. We explore the relationship between the Ly$α$ line profile and environmental density with spectroscopy from the Dark Energy Spectroscopic Instrument (DESI) of LAEs selected with narrow-band photometry through the One-hundred-deg$^2$ DECam Imaging in Narrowbands (ODIN) survey. We use LAE surface density maps in the N419 (z $\sim$ 2.45) and N501 (z $\sim$ 3.12) narrow bands to probe the relationship between local environmental density and the Ly$α$ line profile. In both narrow bands, we stack the LAE spectra in bins of environmental density and inside and outside of protocluster regions. The N501 data shows $\sim$15% higher Ly$α$ line luminosity for galaxies in protoclusters, suggesting increased star formation in these regions. However, the line luminosity is not appreciably greater in protocluster galaxies in the N419 band, suggesting a potential redshift evolution of this effect. The shape of the line profile itself does not vary with environmental density, suggesting that line shape changes are caused by local effects independent of a galaxy's environment. These data indicate a potential relationship between LAE local environmental density, ionized gas distribution, and Ly$α$ line luminosity.

Uzsoy, Ana M. [Harvard-Smithsonian Ctr. Astrophys.↗