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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Picking protein particles in cryo-electron microscopy (cryo-EM) micrographs is a crucial step in the cryo-EM-based structure determination. However, existing methods trained on a limited amount of cryo-EM data still cannot accurately pick protein particles from noisy cryo-EM images. The general foundational artificial intelligence–based image segmentation model such as Meta’s Segment Anything Model (SAM) cannot segment protein particles well because their training data do not include cryo-EM images. Here, we present a novel approach (CryoSegNet) of integrating an attention-gated U-shape network (U-Net) specially designed and trained for cryo-EM particle picking and the SAM. The U-Net is first trained on a large cryo-EM image dataset and then used to generate input from original cryo-EM images for SAM to make particle pickings. CryoSegNet shows both high precision and recall in segmenting protein particles from cryo-EM micrographs, irrespective of protein type, shape and size. On several independent datasets of various protein types, CryoSegNet outperforms two top machine learning particle pickers crYOLO and Topaz as well as SAM itself. The average resolution of density maps reconstructed from the particles picked by CryoSegNet is 3.33 Å, 7% better than 3.58 Å of Topaz and 14% better than 3.87 Å of crYOLO. It is publicly available at https://github.com/jianlin-cheng/CryoSegNet

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A self-supervised workflow for particle picking in cryo-EM

High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, a self-supervised workflow has been developed. This includes an iterative strategy, which uses a 2D class average to improve training particles, and a progressively improved convolutional neural network for particle picking. To automate the selection of particles, a threshold is defined (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. This workflow has been tested using six publicly available data sets with different particle sizes and shapes, and can automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. This workflow is a step towards automated single-particle cryo-EM data analysis at the stage of particle picking. It may be used in conjunction with commonly used single-particle analysis packages such as Relion , cryoSPARC , cisTEM , SPHIRE and EMAN2 .

2D class averages↗
DOE OSTI2023

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗
DOE OSTI2024

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

Abstract Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of high-resolution 3-Dimensional (3D) structures of large biological macromolecules. Protein particle picking, the process of identifying individual protein particles in cryo-EM micrographs for building protein structures, has progressed from manual and template-based methods to sophisticated artificial intelligence (AI)-driven approaches in recent years. This review critically examines the evolution and current state of cryo-EM particle picking methods, with an emphasis on the impact of AI. We conducted a comparative evaluation of popular AI-based particle picking methods, using both general machine learning metrics and specific cryo-EM structure determination metrics. This analysis involved constructing the 3D density map from the picked protein particles and assessing the obtained resolution and particle orientation diversity, underscoring the significant impact of AI on cryo-EM particle picking. Despite the advancements, we also identified key obstacles, such as handling complex micrographs with small proteins. The analysis provides insights into the future development of more sophisticated and fully automated AI methods in cryo-EM particle recognition.

Biochemistry & Molecular Biology↗
DOE OSTI2024

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Model-based Reconstruction for Single Particle Cryo-Electron Microscopy

Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying individual particle projections by orientation, and finally using the individual particle projections to reconstruct a 3D map of the electron density profile. The reconstruction is challenging because of the low signal-to-noise ratio of the data, the unknown orientation of the particles, and the sparsity of data especially when dealing with flexible proteins where there may not be sufficient data corresponding to each class to obtain an accurate reconstruction using standard algorithms. In this paper we present a model-based image reconstruction technique that uses a regularized cost function to reconstruct the 3D density map by assuming known orientations for the particles. Our method casts the reconstruction as minimizing a cost function involving a novel forward model term that accounts for the contrast transfer function of the microscope, the orientation of the particles and the center of rotation offsets. We combine the forward model term with a regularizer that enforces desirable properties in the volume to be reconstructed. Using simulated data, we demonstrate how our method can significantly improve upon the typically used approach.

Venkatakrishnan, Singanallur↗
DOE OSTI2026

Closure models for the feedback of energetic particles on plasma turbulence

Energetic particles interact with the plasma surrounding them, resonating with certain types of plasma waves to stabilize them while destabilizing others, and changing the character of the background turbulence in ways that have not been fully quantified or understood. Interaction with the turbulent background plasma is key to the acceleration of many types of energetic particles including high-energy cosmic rays, solar energetic particles, and pick-up ions. The acceleration of particles is a process that would ideally be described by a kinetic model, a type of model that follows a probability distribution function (PDF) for all particles in 7-dimensional (x, y, z, v x , v y , v z , t) space. Because of the high dimensionality of a kinetic model, simulations that solve kinetic equations use the largest computational resources currently available, and are yet unable to simulate a realistic number of particles, reach the large scales necessary for astrophysical problems, and use high-precision numerical methods. Two available alternatives to kinetic plasma models have been explored for this problem, with limited success. One is a multi-fluid model produced by a cumulant discarding closure, which evolves coupled equations for the velocity, magnetic field, and internal energy for both the background plasma and the fluid of energetic particles. However, simulations that solve multi-fluid magnetohydrodynamic (MHD) equations are able to include the interaction with energetic particles only in crude ways, typically as an add-on pressure term. The second alternative is to use a hybrid method to couple a fluid description of the background plasma to a kinetic model or a Fokker–Planck model for the energetic particles. These methods are hampered by the physical modeling of the coupling. In this work, we develop a new model, which follows the PDF for all particles; this can be viewed as a step toward physical realism above a multi-fluid MHD model, while also being more computationally efficient than a kinetic model. The equations we develop model both the background plasma and the energetic particles self-consistently. Over the last decade, similar PDF methods have been developed to a high level of sophistication to model reactive flows and turbulent combustion for engineering applications. For treatment of the feedback of the energetic particles on a background plasma, a PDF closure approach should evaluate the mean characteristics, including the density, with better statistical quality than will particle-sampling procedures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Kinetic Simulations of Radiative Magnetic Reconnection in the Coronae of Accreting Black Holes

We perform 2D and 3D particle-in-cell simulations of reconnection in magnetically dominated e ± plasmas subject to strong Compton cooling. Magnetic reconnection under such conditions can operate in accretion disk coronae around black holes, which produce hard X-rays through Comptonization. Our simulations show that most of the plasma in the reconnection layer is kept cold by Compton losses and locked in magnetically dominated plasmoids with a small thermal pressure. Compton drag clears cavities inside plasmoids and also affects their bulk motions. These effects, however, weakly change the reconnection rate and the plasmoid size distribution from those in nonradiative reconnection. This demonstrates that the reconnection dynamics is governed by similar magnetic stresses in both cases and weakly affected by thermal pressure. We examine the energy distribution of particles energized by radiative reconnection and observe two distinct components: (1) A mildly relativistic peak, which results from bulk motions of cooled plasmoids. This component receives most of the dissipated reconnection power and dominates the output X-ray emission. The peak has a quasi-Maxwellian shape with an effective temperature of ~100 keV. Thus, it mimics thermal Comptonization used previously to fit hard-state spectra of accreting black holes. (2) A high-energy tail, which receives ~20% of the dissipated reconnection power. It is populated by particles accelerated impulsively at X-points or "picked up" by fast outflows from X-points. The high-energy particles immediately cool, and their inverse Compton emission explains the MeV spectral tail detected in the hard state of Cyg X-1. Our first-principle simulations support magnetic reconnection as a mechanism powering hard X-ray emission from magnetically dominated regions of accreting black holes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Probing criticality with deep learning in relativistic heavy-ion collisions

Systems with different interactions could develop the same critical behavior due to the underlying symmetry and universality. Using this principle of universality, we can embed critical correlations modeled on the 3D Ising model into the simulated data of heavy-ion collisions, hiding weak signals of a few inter-particle correlations within a large particle cloud. Employing a point cloud network with dynamical edge convolution, we are able to identify events with critical fluctuations through supervised learning, and pick out a large fraction of signal particles used for decision-making in each single event.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Robotic Assembly of SRF Cavity Pair

Superconducting Radio Frequency (SRF) cavities for particle accelerators require tight tolerances, ultrahigh vacuum, and strict cleanliness during assembly. As in the semiconductor industry, defects such as particles and residues are deleterious to performance, possibly rendering a cavity unfit for use. This problem is addressed primarily through cleanroom assembly during sensitive steps and rigorous chemical processing to prevent and remove such defects. Human workers are often the largest source of contamination, even with proper gowning and practices. The semiconductor industry has long integrated robots in cleanroom operation, but this has not occurred for SRF cavity production; SRF cavities, unlike wafers, are complex shapes, require more hands-on mechanical assembly, and are low-volume production items. At Jefferson Laboratory, a co-operative robot (cobot) has been setup to overcome these problems. Cobots are safe for use alongside human workers and can integrate new tools such as a 3D camera part detection and gripper for item manipulation. Therefore, cobots represent a promising avenue for reducing particulate generated during a variety of assembly tasks. A mockup of a cavity pair and coupler was setup and the cobot programmed to automatically pick up the coupler and place on the mating cavity flange. Particle counting methods were setup to measure human vs cobot assembly particulate generation inside a cavity mockup. Other potential uses will be discussed for further improving SRF cavity assembly steps, where a cobot can replace or assist a human operator, and what potential gains are expected.

Duzik, Adam [Thomas Jefferson National Accelerator↗
DOE OSTI2021

Investigation of δ zirconium hydride morphology in a single crystal using quantitative phase field simulations supported by experiments

In light water nuclear reactors, waterside corrosion of the cladding material leads to the production of hydrogen, a fraction of which is picked up by the zirconium cladding and precipitates into brittle hydride particles. These nanoscale hydride particles aggregate into mesoscale hydride clusters. The principal stacking direction of the nanoscale hydrides precipitated in the cladding tube changes from circumferential in the absence of applied stress to radial under circumferential applied stress. A quantitative phase field model has been developed to predict the hydride morphology observed experimentally and identify the mechanisms responsible for nanoscale hydride stacking. The model focuses on nanoscale hydride precipitation in a single zirconium grain with a detailed description of the anisotropic elastic contribution. The model predictions concerning the shape, orientation, and stacking behavior of nanoscale hydride are analyzed and compared with experimental observations. The model accurately accounts for the experimentally observed elongated nanoscale hydride shape and the stacking of hydrides along the basal plane of the hexagonal zirconium matrix. When investigating the role of applied stress in hydride morphology, the model challenges some of the mechanisms previously proposed to explain hydride reorientation. Finally, although hydride reorientation has been hypothesized to be caused by a change in nanoscale hydride shape, the current study shows that these mechanisms are unlikely to occur.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Gravothermal collapse and the diversity of galactic rotation curves

The rotation curves of spiral galaxies exhibit a great diversity that challenges our understanding of galaxy formation and the nature of dark matter. Previous studies showed that in self-interacting dark matter (SIDM) models with a cross section per unit mass of σ/m ≈ $\mathscr{O}$(1) cm 2 /g, the predicted dark matter central densities are a good match to the observed densities in galaxies. Here, in this work, we explore a regime with a larger cross section of σ/m ≈ 20−40 cm 2 /g in dwarf galactic halos. We will show that such strong dark matter self-interactions can further amplify the diversity of halo densities inherited from their assembly history. High concentration halos can enter the gravothermal collapse phase within 10 Gyr, resulting in a high density, while low concentration ones remain in the expansion phase and have a low density. We fit the rotation curves of 14 representative low surface brightness galaxies and demonstrate how the large range of observed central densities is naturally accommodated in the strong SIDM regime of σ/m ≈ 20 – 40 cm 2 /g. Galaxies that are outliers in the previous studies, due to their high halo central densities, are no longer outliers in this SIDM regime as their halos would be in the collapse phase. For galaxies with a low density, the SIDM fits are robust to the variation of the cross section. Our findings open up a new window for testing gravothermal collapse, the unique signature of strong dark matter self-interactions, and exploring a broader SIDM model space. As an example, we illustrate how the larger cross sections favored by our fits, together with upper limits from strong lensing observations in clusters, pick out the preferred SIDM model space for a dark matter particle coupled to a light gauge boson in the Born regime.

dark matter↗
DOE OSTI2024

The study of high-frequency pick-ups for electron beam position measurements in the AWAKE common beamline

The common beamline of the AWAKE experiment at CERN involves the co-propagation of two particle beams: protons with 48 nC bunch charge and 250 ps bunch length, and electrons with up to 600 pC bunch charge and approximately 4 ps bunch length. The existing operational beam position monitors at AWAKE cannot measure the electron bunches whilst the more-intense proton bunches are present, due to their low operating frequency. In order to try to address this challenge, two different types of high-frequency pick-ups were studied, a conical-shaped button pick-up and a Cherenkov diffraction radiation-based pick-up designed to operate at around 30 GHz. Both devices were installed at AWAKE and were connected to two identical read-out systems designed by TRIUMF. This contribution presents and discusses the results obtained from beam-based measurements during the current experimental year.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Quest for Cooper Pair Transfer in Heavy-Ion Reactions: The 206 Pb + 118 Sn Case

In this Letter we report on effects of nucleon-nucleon correlations probed in nucleon transfer reactions with heavy ions. We measured with high efficiency and resolution a complete set of observables for neutron transfer channels in the ²⁰⁶Pb + ¹¹⁸Sn system employing a large solid angle magnetic spectrometer, which allowed us to study a wide range of internuclear distances via a detailed excitation function. The coupled channel theory, based on an independent particle transfer mechanism, follows the experimental transfer probabilities for one- and two-neutron pick-up and stripping channels. The experimental two-neutron transfer cross sections indicate that in reactions between pair-vibrational (closed shell) and pair-rotational (open shell) nuclei, correlations manifest via pair-addition and pair-removal modes, which constitute one of the elementary modes of excitations in nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Assembly and Testing of Scintillator Tile Modules for the CMS High-Granularity Calorimeter Upgrade

The High-Granularity Calorimeter (HGCAL), part of the upgrade to the Compact Muon Solenoid (CMS) experiment, employs silicon and scintillator tile modules in the endcaps to maintain detector performance during the High-Luminosity Large Hadron Collider (HL-LHC) era, scheduled to operate from 2030 to 2040. The upgraded calorimeter will provide highly segmented three-dimensional imaging, energy measurements, and precise timing for particle shower reconstruction. Approximately half of the HGCal plastic scintillator tile modules (1,834 total) will be assembled at Fermilab using an automated pick-and-place (PnP) machine. Following assembly, each tile module undergoes quality control (QC) procedures such as electrical validation, thermal testing, and physics validation using cosmic rays. This poster/talk presents the QC procedures and results from the tile module production in 2026, demonstrating the performance and quality of the assembled tile modules.

Bazimya, Jean Luc [Grambling State U.]↗
DOE OSTI2022

Positron Sources for Future High Energy Physics Colliders

An unprecedented positron average current is required to fit the luminosity demands of future $e^+e^-$ high energy physics colliders. In addition, in order to access precision-frontier physics, these machines require positron polarization to enable exploring the polarization dependence in many HEP processes cross sections, reducing backgrounds and extending the reach of chiral physics studies beyond the standard model. The ILC has a mature plan for the polarized positron source based on conversion in a thin target of circularly polarized gammas generated by passing the main high energy e-beam in a long superconducting helical undulator. Compact colliders (CLIC, C3 and advanced accelerator-based concepts) adopt a simplified approach and currently do not plan to use polarized positrons in their baseline design, but could greatly benefit from the development of compact alternative solutions to polarized positron production. Increasing the positron current, the polarization purity and simplifying the engineering design are all opportunities where advances in accelerator technology have the potential to make a significant impact. This white-paper describes the current status of the field and provides R&D short-term and long-term pathways for polarized positron sources.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Brill-Noether-general limit root bundles: absence of vector-like exotics in F-theory Standard Models

Root bundles appear prominently in studies of vector-like spectra of 4d F-theory compactifications. Of particular importance to phenomenology are the Quadrillion F-theory Standard Models (F-theory QSMs). In this work, we analyze a superset of the physical root bundles whose cohomologies encode the vector-like spectra for the matter representations ($3$, $2$) 1/6 , ($\overline{3}$, $1$) -2/3 and ($1$, $1$) 1 . For the family B 3 (Δ$^{°}_{4}$) consisting of $\mathcal{O}$(10 11 ) F-theory QSM geometries, we argue that more than 99.995% of the roots in this superset have no vector-like exotics. This indicates that absence of vector-like exotics in those representations is a very likely scenario in the O(10 11 ) QSM geometries B 3 (Δ$^{°}_{4}$). The QSM geometries come in families of toric 3-folds B 3 (Δ°) obtained from triangulations of certain 3-dimensional polytopes Δ°. The matter curves in X Σ $\large{ϵ}$ B 3 (Δ°) can be deformed to nodal curves which are the same for all spaces in B 3 (Δ°). Therefore, one can probe the vector-like spectra on the entire family B 3 (Δ°) from studies of a few nodal curves. We compute the cohomologies of all limit roots on these nodal curves. In our applications, for the majority of limit roots the cohomologies are determined by line bundle cohomology on rational tree-like curves. For this, we present a computer algorithm. The remaining limit roots, corresponding to circuit-like graphs, are handled by hand. The cohomologies are independent of the relative position of the nodes, except for a few circuits. On these jumping circuits, line bundle cohomologies can jump if nodes are specially aligned. This mirrors classical Brill-Noether jumps. B 3 (Δ°) admits a jumping circuit, but the root bundle constraints pick the canonical bundle and no jump happens.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗