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At least 415 records · Page 23
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 OSTI2026

MCNPy

SAND2026-20425O MCNPy runs and analyzes simulations from MCNP, a software that models radiation transport of neutrons and gamma rays. MCNPy uses Python to start MCNP, retrieve event data files, and convert them into graph structures for detailed analysis. It offers visualization tools, including 2D views of particle histories, making complex simulation data easier to interpret for researchers and engineers. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Nowack, Aaron [Sandia National Lab. (SNL-CA), Live↗
DOE OSTI2022

An Efficient, Scalable IO Framework for Sparse Data: larcv3

Neutrino physics is one of the fundamental areas of research into the origins and properties of the Universe. Many experimental neutrino projects use sophisticated detectors to observe properties of these particles, and have turned to deep learning and artificial intelligence techniques to analyze their data. From this, we have developed \texttt{larcv}, a \texttt{C++} and \texttt{Python} based framework for efficient IO of sparse data with particle physics applications in mind. We describe in this paper the \texttt{larcv} framework and some benchmark IO performance tests. \texttt{larcv} is designed to enable fast and efficient IO of ragged and irregular data, at scale on modern HPC systems, and is compatible with the most popular open source data analysis tools in the Python ecosystem.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Cosmological implications of photon-flux upper limits at ultrahigh energies in scenarios of Planckian-interacting massive particles for dark matter

Here using the data of the Pierre Auger Observatory, we report on a search for signatures that would be suggestive of super-heavy particles decaying in the Galactic halo. From the lack of signal, we present upper limits for different energy thresholds above ≳10 8 GeV on the secondary by-product fluxes expected from the decay of the particles. Assuming that the energy density of these super-heavy particles matches that of dark matter observed today, we translate the upper bounds on the particle fluxes into tight constraints on the couplings governing the decay process as a function of the particle mass. Instantons, which are nonperturbative solutions to Yang-Mills equations, can give rise to decay channels otherwise forbidden and transform stable particles into metastable ones. Assuming such instanton-induced decay processes, we derive a bound on the reduced coupling constant of gauge interactions in the dark sector: α X ≲ 0.09, for 10 9 ≲ M X /GeV < 10 19 . Conversely, we obtain that, for instance, a reduced coupling constant α X = 0.09 excludes masses M X ≳ 3 x 10 13 GeV . In the context of dark matter production from gravitational interactions alone during the reheating epoch, we derive constraints on the parameter space that involves, in addition to M X and α X , the Hubble rate at the end of inflation, the reheating efficiency, and the nonminimal coupling of the Higgs with curvature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Improving High-Energy Particle Detectors with Machine Learning

Microseconds after the Big Bang, the universe existed in a state called the quark-gluon plasma (QGP). To experimentally study its properties, the QGP is recreated in high-energy nuclear collisions at the LHC, and the particles produced from the QGP are reconstructed from their energy deposition in the ATLAS calorimeter. This requires both classifying the particles and calibrating their deposited energy. The objective of this project is to improve the reconstruction by using machine learning techniques, where the energy depositions of clusters of cells, formed by ATLAS topo-clustering methods, are treated as three-dimensional images when inputted to neural networks. This approach significantly improves the calibration of deposited energies when cross-validating while training, and models trained on idealized data predict the calibrated energies of particles in more complex data sets well. Additionally, implementation of a data generator using uproot allows the program to load input data into memory as needed while training or predicting, significantly reducing the amount of memory used. The data generator also allows for use of multiprocessing to speed up training and evaluating. This work illustrates that using machine learning methods for both classification and calibration has the potential to significantly improve particle reconstruction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Theory, observations, and simulations of kinetic entropy in a magnetotail electron diffusion region

In this work, we examine velocity-space kinetic entropy, a spatially local measure of entropy for systems out of thermal equilibrium, during an encounter of an electron diffusion region at a magnetic reconnection site in Earth’s magnetotail by the Magnetospheric Multiscale (MMS) mission. We start by generalizing the theory of kinetic entropy to the case of non-uniform velocity space grids and transforming the equations into spheri- cal energy coordinates useful to experimental plasma detectors. The theory is then applied to MMS data and compared to particle-in-cell simulations of reconnection. We demonstrate that the entropy-based non-Maxwellianity measure from the MMS data is of sufficiently high precision to reliably identify non-Maxwellian distributions and therefore the measurements when kinetic effects are most significant. By comparing two different non-Maxwellian measures, we show that total entropy density suffers from “information loss” because it lacks a dependence on the velocity space grid, and so has lost information about how well a distribution function is resolved. Local velocity-space kinetic entropy density recovers this information. We quantify information loss and argue that the considerations needed to minimize it are crucial for instruments designed to measure distribution functions in situ.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

An ensemble data assimilation modeling system for operational outdoor microalgae growth forecasting

Microalgae have received increasing attention as a potential feedstock for biofuel or biobased products. Forecasting the microalgae growth is beneficial for managers in planning pond operations and harvesting decisions. This study proposed a biomass forecasting system comprised of the Huesemann Algae Biomass Growth Model (BGM), the Modular Aquatic Simulation System in Two Dimensions (MASS2), ensemble data assimilation (DA), and numerical weather prediction Global Ensemble Forecast System (GEFS) ensemble meteorological forecasts. The novelty of this study is to seek the use of ensemble DA to improve both BGM and MASS2 model initial conditions with the assimilation of biomass and water temperature measurements and consequently improve short-term biomass forecasting skills. This study introduces the theory behind the proposed integrated biomass forecasting system, with an application undertaken in pseudo-real-time in three outdoor ponds cultured with Chlorella sorokiniana in Delhi, California, United States. Results from all three case studies demonstrate that the biomass forecasting system improved the short-term (i.e., 7-day) biomass forecasting skills by about 60% on average, comparing to forecasts without using the ensemble DA method. Given the satisfactory performances achieved in this study, it is probable that the integrated BGM-MASS2-DA forecasting system can be used operationally to inform managers in making pond operation and harvesting planning decisions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

No ν s is Good News

The baryon acoustic oscillation (BAO) analysis from the first year of data from the Dark Energy Spectroscopic Instrument (DESI), when combined with data from the cosmic microwave background (CMB), has placed an upper-limit on the sum of neutrino masses, ∑m ν < 70 meV (95%). In addition to excluding the minimum sum associated with the inverted hierarchy, the posterior is peaked at ∑m ν = 0 and is close to excluding even the minumum sum, 58 meV at 2σ. In this paper, we explore the implications of this data for cosmology and particle physics. The sum of neutrino mass is determined in cosmology from the suppression of clustering in the late universe. Allowing the clustering to be enhanced, we extended the DESI analysis to ∑m ν < 0 and find ∑m ν =160 ± 90 meV (68%), and that the suppression of power from the minimum sum of neutrino masses is excluded at 99% confidence. We show this preference for negative masses makes it challenging to explain the result by a shift of cosmic parameters, such as the optical depth or matter density. We then show how a result of ∑m ν = 0 could arise from new physics in the neutrino sector, including decay, cooling, and/or time-dependent masses. These models are consistent with current observations but imply new physics that is accessible in a wide range of experiments. In addition, we discuss how an apparent signal with ∑m ν < 0 can arise from new long range forces in the dark sector or from a primordial trispectrum that resembles the signal of CMB lensing.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Beyond Taylor’s hypothesis: a novel volumetric reconstruction of velocity and density fields for variable‑density and shear flows

Abstract This work presents a novel numerical procedure for reconstructing volumetric density and velocity fields from planar laser-induced fluorescence (PLIF) and stereoscopic particle image velocimetry (SPIV) data. This new method is theoretically and practically demonstrated to provide more accurate 3D vortical structures and density fields in high shear flows than reconstruction methods based on the mean convective velocity. While Taylor’s hypothesis of frozen turbulence is commonly applied by using the local mean streamwise velocity, the proposed algorithm uses the measured local instantaneous velocity for data convection. It consists of a step-by-step reconstruction based on a mixed Lagrangian–Eulerian solver that includes the 3D interpolation of scattered flow data and that relaxes the Taylor’s hypothesis by iterative enforcement of the incompressibility constraint on the velocity field. This methodology provides 3D fields with temporal resolution, spatial resolution, and accuracy comparable to that of real 3D snapshots, thus providing a practical alternative to tomographic measurements. The procedure is validated using numerical data of the constant-density channel flow available on the Johns Hopkins University Turbulence Database (JHTDB), showing the accurate reconstruction of the 3D velocity field. The algorithm is applied to an experimental dataset of PLIF and SPIV measurements of a variable-density jet flow, demonstrating its capability to provide 3D velocity and density fields that are more consistent with the Navier–Stokes equations compared to the mean flow convective method. Graphic abstract

42 ENGINEERING↗
DOE OSTI2020

Simulation of energy loss of fractionally charged particles using Geant4

Over the years several rare-event search experiments have shown increasing interest to search for Fractionally Charged Particles (FCPs) within the data acquired in those experiments. This, in turn, has required the need for a framework to calculate accurately the energy loss expected from FCPs as they pass through the detector material. We have developed Monte Carlo methods within Geant4 to simulate for the first time energy loss of FCPs through different physics processes. The program can be used to calculate energy deposition distributions, a major component of any FCP search analysis, as they interact with detector material. We discuss the implementation and validation of the energy loss of FCPs using a typical detector material.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

(Un)Explained EMIC Waves: Understanding Quiet Time EMIC Wave Drivers

Electromagnetic ion cyclotron (EMIC) waves are known to be generated through cyclotron resonance with the local ion particle population and grow when there is a large enough temperature anisotropy. In general, these temperature anisotropies necessary for wave growth are found to be associated with either solar wind pressure pulses or particle injections during geomagnetic storms or substorms. However, some EMIC events do not show any clear association with these known drivers and appear unexplained. In our analysis of high-amplitude (>1 nT) non-storm time EMIC waves, we find that 24 out of the 223 (~11%) EMIC events with peak amplitude greater than 1 nT were not found to be associated with any clear EMIC wave driver. This raises a compelling question: What magnetospheric or solar wind driver provides the free energy to grow these quiet-time EMIC waves? Here, we examine two EMIC events on 13 April 2017 and 13 February 2014, which were excited during extremely quiet solar wind and geomagnetic conditions. Furthermore, an in-depth analysis of field and particle measurements from multiple data sets, including ground and in situ data for these two events, indicates that extremely weak and otherwise insignificant pressure values and/or very weak substorm injections occurring multiple hours before the event play a significant role in quiet time wave generation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Numerical investigation of inertial sphere impaction on a cylinder in subcritical flow

We investigated the accuracy of a Lagrangian scheme for simulating both the motion and wall impaction of neutrally buoyant inertial spheres (8.85 ≤ St ≤ 18.04) moving in the subcritical regime (Re = 10,972 and 22,366) of flows past a circular cylinder. The accuracy of the eddy-resolving simulations of the flow field was verified based on available data at nearly comparable flow conditions. The accuracy of the eddy-resolving simulations of the flow field was verified based on available data at nearly comparable flow conditions. The accuracy of the particle tracking scheme was verified with respect to corresponding experimental data in a laboratory flume. Particle dispersion en route to the circular cylinder is mostly driven by the flow disturbance from the particle injector tube. The trends in collision rates are largely explained by the rate of particle entertainment into the boundary layer around the cylinder and the inertial condition of the spheres in this proximity region—both of which can be better assessed by post-processing of the numerical outcomes. Here, the primary incentive to undertake this work was the need for validating a particle-based method for quantifying the hydraulic stressors leading to bodily damage of fish passing flows influenced by hydraulic infrastructure.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Improved scaling law for the prediction of deuterium retention in beryllium co-deposits

Hydrogen isotope co-deposition with Be eroded from the first wall is expected to be the main fusion fuel retention mechanism in ITER. Since good fuel accounting is crucial for economic and safety reasons, reliable predictions of hydrogen isotope retention are needed. Furthermore, this study builds upon the well-established empirical De Temmerman scaling law that predicts D/Be ratios in co-deposited layers based on deposition temperature, deposition rate, and deuterium particle energy. Expanding the data used in the original development of the scaling law with an additional dataset obtained with more recent measurements using a different technique to the original De Temmerman approach, allows us to obtain new values for free parameters and improve the prediction capabilities of the new scaling law. In an effort to improve the model even further, scaling with D 2 background pressure was included and a new two-term model derived, describing D retention in low- and high-energy traps separately.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

FlameNEST: explicit profile likelihoods with the Noble Element Simulation Technique

We present FlameNEST, a framework providing explicit likelihood evaluations in noble element particle detectors using data-driven models from the Noble Element Simulation Technique. FlameNEST provides a way to perform statistical analyses on real data with no dependence on large, computationally expensive Monte Carlo simulations by evaluating the likelihood on an event-by-event basis using analytic probability elements convolved together in a single TensorFlow multiplication. Furthermore, this robust framework creates opportunities for simple inter-collaboration analyses which will be fundamental for the future of experimental dark matter physics.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Fast convolutional neural networks on FPGAs with hls4ml

We introduce an automated tool for deploying ultra low-latency, low-power deep neural networks with convolutional layers on field-programmable gate arrays (FPGAs). By extending the hls4ml library, we demonstrate an inference latency of 5 µs using convolutional architectures, targeting microsecond latency applications like those at the CERN Large Hadron Collider. Considering benchmark models trained on the Street View House Numbers Dataset, we demonstrate various methods for model compression in order to fit the computational constraints of a typical FPGA device used in trigger and data acquisition systems of particle detectors. In particular, we discuss pruning and quantization-aware training, and demonstrate how resource utilization can be significantly reduced with little to no loss in model accuracy. We show that the FPGA critical resource consumption can be reduced by 97% with zero loss in model accuracy, and by 99% when tolerating a 6% accuracy degradation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Direct evaluation of the phase diagrams of dense multicomponent plasmas by integration of the Clapeyron equations

Accurate phase diagrams of multicomponent plasmas are required for the modeling of dense stellar plasmas, such as those found in the cores of white dwarf stars and the crusts of neutron stars. Those phase diagrams have been computed using a variety of standard techniques, which suffer from physical and computational limitations. Here we present an efficient and accurate method that overcomes the drawbacks of previously used approaches. In particular, finite-size effects are avoided as each phase is calculated separately; the plasma electrons and volume changes are explicitly taken into account; and arbitrary analytic fits to simulation data as well as particle insertions are avoided. Furthermore, no simulations at “uninteresting” state conditions, i.e., away from the phase coexistence curves, are required, which improves the efficiency of the technique. The method consists of an adaptation of the so-called Gibbs-Duhem integration approach to electron-ion plasmas, where the coexistence curve is determined by direct numerical integration of its underlying Clapeyron equation. The thermodynamics properties of the coexisting phases are evaluated separately using Monte Carlo simulations in the isobaric semigrand canonical ensemble (NPT Δ μ ). We describe this Monte Carlo-based Clapeyron integration method, including its basic physical and numerical principles, our extension to electron-ion plasmas, and our numerical implementation. We illustrate its applicability and benefits with the calculation of the melting curve of dense carbon-oxygen plasmas under conditions relevant for the cores of white dwarf stars and provide analytic fits to implement this new melting curve in white dwarf models. While this work focuses on the liquid-solid phase boundary of dense two-component plasmas, a wider range of physical systems and phase boundaries are within the scope of the Clapeyron integration method, which had until now only been applied to simple model systems of neutral particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

A copula-based rank histogram ensemble filter

Serial ensemble filters implement triangular probability transport maps to reduce high-dimensional inference problems to sequences of state-by-state univariate inference problems. The univariate inference problems are solved by sampling posterior probability densities obtained by combining constructed prior densities with observational likelihoods according to Bayes' rule. Many serial filters in the literature focus on representing the marginal posterior densities of each state. However, rigorously capturing the conditional dependencies between the different univariate inferences is crucial to correctly sampling multidimensional posteriors. This work proposes a new serial ensemble filter, called the copula rank histogram filter (CoRHF), that seeks to capture the conditional dependency structure between variables via empirical copula estimates; these estimates are used to rigorously implement the triangular (state-by-state univariate) Bayesian inference. The success of the CoRHF is demonstrated on two-dimensional examples and the Lorenz'63 problem. A practical extension to the high-dimensional setting is developed by localizing the empirical copula estimation, and is demonstrated on the Lorenz'96 problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The Ultra-High-Energy Source MGRO J1908+06

The TeV gamma-ray source MGRO J1908+06 is one of the highest-energy sources known, with observed emission by the High Altitude Water Cherenkov (HAWC) Observatory extending well past 100 TeV. The source exhibits both energy-dependent morphology and a spatially-dependent spectral index. The emission is likely to be dominantly leptonic, and associated with the radio-quiet PSR J1907+0602. However, one-population models do not describe the data well; a second particle population is needed to explain the shape of the spectral energy distribution at the highest energies. This component can be well-described by either leptonic or hadronic hypotheses. We discuss this feature and implications for detection by multi-wavelength and multi-messenger experiments.

79 ASTRONOMY AND ASTROPHYSICS↗