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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
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 OSTI2026

Direct cross section measurement of 102 Pd ⁢(𝛾,𝑝) and 102 Pd ⁢(𝛾,𝛼) for the astrophysical 𝑝 process

Background: A handful of neutron-deficient stable nuclei, known as the “p nuclei,” cannot be produced through astrophysical neutron capture processes. Instead, some of these nuclei are proposed to be produced by 𝛾-induced reactions on existing r- and s-process seeds. The specific astrophysical site or sites are not yet identified, however, with uncertainties in the cross sections of these 𝛾-induced reactions playing a role. Databases of reaction rates for astrophysical simulations often rely on theoretical statistical model calculations, such as Hauser-Feshbach, for rates where no experimental information is known. However, reasonable variations in the choice of parametrizations of various nuclear properties can create order-of-magnitude variations in the final predicted cross sections and reaction rates, which are then propagated through the models to the predicted final abundances. Purpose: To better constrain these statistical model calculations and ultimately reduce the uncertainties from the nuclear physics on our understanding of the p nuclei, a measurement of the cross sections of 𝛾-induced reactions on the p-nucleus 102 Pd was undertaken. This work represents the first measurement of its kind, using segmented silicon detectors to measure prompt charged particle emission from 𝛾-induced reactions. Methods: Quasimonoenergetic gamma beams from the High Intensity 𝛾 Source facility bombarded an enriched 102 Pd target. A segmented silicon array was arranged to detect the particles emitted from (𝛾,𝑝) and (𝛾,𝛼) reactions. Results: Reaction cross sections were deduced at multiple 𝛾-beam energies between 10 and 19 MeV, and compared to statistical model calculations using talys-1.96. The 102 Pd ⁢(𝛾,𝑝)⁢ 101 Rh reaction cross section was reasonably well reproduced by a subset of photon strength functions and level densities, though the strength to the ground state of 101 Rh was underestimated at higher incident gamma energies. The 102 Pd ⁢(𝛾,𝛼)⁢ 98 Ru was in general overpredicted by the various alpha-nucleus optical model potentials. Conclusions: While the theoretical cross sections used to model the (𝛾,𝑝) reactions for the p process may be reasonable, a more careful approach is needed in the case of (𝛾,𝛼). Further work to probe gamma-induced reaction cross sections at and near the p nuclei is warranted.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Advanced Physics Models for Particle-Particle Interactions (UCD final report)

The LDRD "Advanced Physics Models for Particle-Particle Interactions” collaborative research with Professor Jennifer Sinclair Curtis and PhD student Chanh Nguyen at the University of California, Davis involved meso-scale, discrete element method (DEM) modeling of micron-sized particles impacting a substrate. Using DEM, physical insight into the details of particle response upon impact can be obtained. Such details provide the type of information necessary to enhance existing continuum or macro-scale simulation tools so that modeling for material strength and particle breakage models is based on particle physics versus empirical relationships. While molecular dynamics simulations of atoms can also provide physical insight into the particle response to impact, the scale of particles that are treated is on the order of angstroms, not microns. This study gives evidence to the ability of the DEM simulation technique to provide such fundamental, detailed insight for micron-sized particles as a function of particle properties and impact velocity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1991

Time-reversibility and particle sedimentation

This paper studies an ODE model, called the Stokeslet model, and describes sedimentation of small clusters of particles in a highly viscous fluid. This model has a trivial solution in which the n particles arrange themselves at the vertices of a regular n-sided polygon. When n = 3, Hocking and Caflisch et al. (1988) proved the existence of periodic motion (in the frame moving with the center of gravity in the cluster) in which the particles form an isosceles triangle. Here, the study of periodic and quasi-periodic solutions of the Stokeslet model is continued, with emphasis on the spatial and time-reversal symmetry of the model. For three particles, the existence of a second family of periodic solutions and a family of quasi-periodic solutions is proved. It is also indicated how the methods generalize to the case of n particles.

Golubitsky, Martin↗
DOE OSTI2022

On the S-matrix of Ising field theory in two dimensions

We explore the analytic structure of the non-perturbative S-matrix in arguably the simplest family of massive non-integrable quantum field theories: the Ising field theory (IFT) in two dimensions, which may be viewed as the Ising CFT deformed by its two relevant operators, or equivalently, the scaling limit of the Ising model in a magnetic field. Our strategy is that of collider physics: we employ Hamiltonian truncation method (TFFSA) to extract the scattering phase of the lightest particles in the elastic regime, and combine it with S-matrix bootstrap methods based on unitarity and analyticity assumptions to determine the analytic continuation of the 2 → 2 S-matrix element to the complex s-plane. Focusing primarily on the “high temperature” regime in which the IFT interpolates between that of a weakly coupled massive fermion and the E 8 affine Toda theory, we will numerically determine 3-particle amplitudes, follow the evolution of poles and certain resonances of the S-matrix, and exclude the possibility of unknown wide resonances up to reasonably high energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1983

Evaluation of a stochastic model of particle dispersion in a turbulent round jet

A stochastic model of particle dispersion by turbulence, proposed by Gosman and Ioannides (1981), is evaluated. The method employs a k-epsilon model to estimate turbulence properties. Dispersion is determined by computing particle motion, with random sampling to obtain instantaneous flow properties for a statistically significant number of particle trajectories. The stochastic model yields good results particularly when eddy lifetimes are evaluated. The method allows the effects of large relative velocities between the particles and the flow, drag properties at Reynolds numbers greater than the Stokes flow regime, and the variations of local turbulence properties to be readily handled, at least for boundary layer flows.

Shuen, J.-S.↗
DOE OSTI2020

Measurements of $\pi^-$ production in $^7$Be+$^9$Be collisions at beam momenta from 19$A$ to 150$A$GeV/$c$ in the NA61/SHINE experiment at the CERN SPS

The NA61/SHINE collaboration studies at the CERN Super Proton Synchrotron (SPS) the onset of deconfinement in hadronic matter by the measurement of particle production in collisions of nuclei with various sizes at a set of energies covering the SPS energy range. This paper presents results on inclusive double-differential spectra and mean multiplicities of $\pi^{-}$ mesons produced in the 5% most central $^7$Be + $^9$Be collisions at beam momenta of 19$A$, 30$A$, 40$A$, 75$A$ and 150$A$ GeV/$c$ obtained by the so-called $h^-$ method which does not require any particle identification. The shape of the transverse mass spectra differs from the shapes measured in central Pb + Pb collisions and inelastic p + p interactions. The normalized width of the rapidity distribution decreases with increasing collision energy and is in between the results for inelastic nucleon-nucleon and central Pb + Pb collisions. The mean multiplicity of pions per wounded nucleon in central $^7$Be + $^9$Be collisions is close to that in central Pb + Pb collisions up to 75$A$GeV/$c$. However, at the top SPS energy the result is close to the one for inelastic nucleon-nucleon interactions. The results are discussed in the context of predictions for the onset of deconfinement at the CERN SPS collision energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Atmospheric processing and aerosol aging responsible for observed increase in absorptivity of long-range-transported smoke over the southeast Atlantic

Biomass burning aerosol (BBA) from agricultural fires in southern Africa contributes about one-third of the global carbonaceous aerosol load. These particles have strong radiative effects in the southeast Atlantic (SEA), which depend in part on the radiative contrast between the aerosol layer in the free troposphere (FT) and the underlying cloud layer. However, there is large disagreement in model estimates of aerosol-driven climate forcing due to uncertainties in the vertical distribution, optical properties, and life cycle of these particles. This study applies a novel method combining remote sensing observations with regional model outputs to investigate the aging of the BBA and its impact on the optical properties during transatlantic transport from emission sources in Africa to the SEA. Results show distinct variations in extinction Ångström exponent (EAE) and single-scattering albedo (SSA) as aerosols age. Near the source, fresh aerosols are characterized by low mean SSA (0.84) and high EAE (1.85), indicating smaller, highly absorbing particles. By isolating marine contributions from the total column during BBA transport across the SEA, our analysis reveals an initial decrease in BBA absorptivity, with mean FT SSA of 0.87 after 6–7 d, followed by increased absorptivity with mean FT SSA of 0.84 after 10 d, suggesting enhanced absorption due to chemical aging. These findings indicate that BBA becomes more absorbing during extended transport across the SEA, with implications for reducing model uncertainties. Our remote-sensing-based results agree well with previous in situ studies and offer new insights into aerosol–radiation interactions and the energy balance over the SEA.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1972

Charged-particle transport in turbulent astrophysical plasmas

The effect of electromagnetic fluctuations, or plasma turbulence, on the motion of the individual particles in a plasma is investigated. Two alternative methods are used to find a general equation governing the time-evolution of a distribution of charged particles subject to both an external force field and the random fields of the fluctuations. It is found that, for the high-temperature, low-density plasmas frequently encountered in the study of astrophysics, the presence of even a small amount of turbulence can have a very important effect on the behavior of the plasma. Two problems in which turbulence plays an important role are treated.

Newman, C. E., Jr.↗
DOE OSTI2020

Starting-point-independent quantum Monte Carlo calculations of iron oxide

Quantum Monte Carlo (QMC) methods are useful for studies of strongly correlated materials because they are many body in nature and use the physical Hamiltonian. Typical calculations assume as a starting point a wave function constructed from single-particle orbitals obtained from one-body methods, e.g., density functional theory. However, mean-field-derived wave functions can sometimes lead to systematic QMC biases if the mean-field result poorly describes the true ground state. In this study, we examine the accuracy and flexibility of QMC trial wave functions using variational and fixed-node diffusion QMC estimates of the total spin density and lattice distortion of antiferromagnetic iron oxide (FeO) in the ground state B1 crystal structure. We found that for relatively simple wave functions the predicted lattice distortion was controlled by the choice of single-particle orbitals used to construct the wave function, rather than by subsequent wave function optimization techniques within QMC. By optimizing the orbitals with QMC, we then demonstrate starting-point independence of the trial wave function with respect to the method by which the orbitals were constructed by demonstrating convergence of the energy, spin density, and predicted lattice distortion for two qualitatively different sets of orbitals. The results suggest that orbital optimization is a promising method for accurate many-body calculations of strongly correlated condensed phases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Excipient screening by lyophilization provides insights into spray drying formulations for nanoparticle vaccines

Nanoparticles have shown great promise as delivery platforms in the development of tunable and safe vaccines. Nanolipoprotein particles (NLPs), also known as nanodiscs, are discoidal nanoparticles composed of a lipid bilayer stabilized at their periphery by apolipoproteins. Under the right conditions, the NLP self-assembly process is highly customizable in terms of lipids and apolipoprotein constituents, allowing for tunable physical and chemical characteristics. This flexibility allows a wide range of vaccine antigens and adjuvants to be incorporated onto the NLP platform for tailored vaccine design. The stability of NLPs during long term storage is a very important factor in developing a vaccine delivery platform suitable for widespread global use. When stored in a solution for extended periods of time, NLPs dissociate into their corresponding lipids and protein constituents, leading to particle degradation. Proper stabilization of NLPs can often be achieved by lyophilization (i.e. freeze-drying), a method widely used for various applications including pharmaceuticals. This process, however, can be damaging to particles without the presence of lyoprotectants or excipients that help maintain particle stability during lyophilization. Another method used to stabilize vaccines and pharmaceuticals is spray drying, a process that converts liquid formulations into dry powders through controlled heating and airflow. While spray drying is rapid, scalable, and cost-effective, lyophilization is typically a gentler process that better retains biomolecule structure and function. Both processes use excipients for particle stabilization, so lyophilization can be used as a surrogate to test stability of NLPs, to down-select formulations that may withstand the harsher conditions of spray drying. To screen different formulations, NLPs were synthesized and purified to homogeneity by size exclusion chromatography (SEC) and samples were prepared with a wide range of lyoprotectants and/or excipients. To assess the protective effects of excipients on NLPs upon spray drying, both pre- and post-lyophilized samples were analyzed by SEC. To assess the protective effects upon heating (encountered during the spray drying process), NLP samples were incubated at elevated temperatures prior to SEC analysis. The lyoprotectants and excipients evaluated in this study had different efficiencies in protecting NLPs during lyophilization and heating tests. Trehalose, for example, exhibits stabilization on NLPs both upon lyophilization and heating whereas leucine accelerated NLP dissociation. Although some lyoprotectants are effective by themselves, different combinations can decrease the stabilization of NLPs. Shelf-stable vaccines that do not require cold-chain storage are essential for global accessibility and our findings provide fundamental insight into how to advance NLP-based vaccines for these applications.

Serrano, Litzay J [Lawrence Livermore National Lab↗
NASA NTRS2019

Serendipitous Geodesy from Bennu's Short-Lived Moonlets

The Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx; or OREx) spacecraft arrived at its target, near-Earth asteroid (101955) Bennu, on December 3, 2018. The OSIRIS-REx spacecraft has since collected a wealth of scientific information in order to select a suitable site for sampling. Shortly after insertion into orbit on December 31, 2018, particles were identified in starfield images taken by the navigation camera (NavCam 1). Several groups within the OSlRlS-REx team analyzed the particle data in an effort to better understand this newfound activity of Bennu and to investigate the potential sensitivity of the particles to Bennu's geophysical parameters. A number of particles were identified through automatic and manual methods in multiple images, which could be turned into short sequences of optical tracking observations. Here, we discuss the precision orbit determination (OD) effort focused on these particles at NASA GSFC, which involved members of the Independent Navigation Team (INT) in particular. The particle data are combined with other OSIRIS-REx tracking data (radiometric from OSN and optical landmark data) using the NASA GSFC GEODYN orbit determination and geodetic parameter estimation software. We present the results of our study, particularly those pertaining to the gravity field of Bennu. We describe the force modeling improvements made to GEODYN specifically for this work, e.g., with a raytracing-based modeling of solar radiation pressure. The short-lived, low-flying moonlets enable us to determine a gravity field model up to a relatively high degree and order: at least degree 6 without constraints, and up to degree 10 when applying Kaula-like regularization. We can backward- and forward-integrate the trajectory of these particles to the ejection and landing sites on Bennu. We assess the recovered field by its impact on the OSIRIS-REx trajectory reconstruction and prediction quality in the various mission phases (e.g., Orbital A, Detailed Survey, and Orbital B).

Mazarico, Erwan↗
NASA NTRS1975

Perturbation theory for charged-particle transport in one dimension

Perturbation theory, when applied to charged-particle transport, generates a series solution that requires a double quadrature per term. The continuity of higher-order terms leads to numerical evaluation of the series. The high rate of convergence of the series makes the method a practical tool for charged-particle transport problems. The coupling of the neutron component in the case of proton transport in tissue does not greatly alter the rate of convergence. The method holds promise for a practical high-energy proton transport theory.

Wilson, J. W.↗
DOE OSTI2021

High-Resolution Momentum Imaging—From Stern’s Molecular Beam Method to the COLTRIMS Reaction Microscope [Book Chapter]

Multi-particle momentum imaging experiments are now capable of providing detailed information on the properties and the dynamics of quantum systems in Atomic, Molecular and Photon (AMO) physics. Historically, Otto Stern can be considered the pioneer of high-resolution momentum measurements of particles moving in a vacuum and he was the first to obtain sub-atomic unit (a.u.) momentum resolution (Schmidt-Böcking et al. in The precision limits in a single-event quantum measurement of electron momentum and position, these proceedings). A major contribution to modern experimental atomic and molecular physics was his so-called molecular beam method, which Stern developed and employed in his experiments. With this method he discovered several fundamental properties of atoms, molecules and nuclei. As corresponding particle detection techniques were lacking during his time, he was only able to observe the averaged footprints of large particle ensembles. Today it is routinely possible to measure the momenta of single particles, because of the tremendous progress in single particle detection and data acquisition electronics. A “state-of-the-art” COLTRIMS reaction microscope can measure, for example, the momenta of several particles ejected in the same quantum process in coincidence with sub-a.u. momentum resolution. Such setups can be used to visualize the dynamics of quantum reactions and image the entangled motion of electrons inside atoms and molecules. This review will briefly summarize Stern’s work and then present in longer detail the historic steps of the development of the COLTRIMS reaction microscope. Furthermore, some benchmark results are shown which initially paved the way for a broad acceptance of the COLTRIMS approach. Finally, a small selection of milestone work is presented which has been performed during the last two decades.

Jahnke, T.↗
DOE OSTI2023

A subdivision-stabilized B-spline mixed material point method

Subjected to external loadings, polymeric materials, e.g., biological tissues, hydrogels, and elastomers, may undergo extreme, nearly incompressible, (self-)contact deformations. For numerical modeling employing mesh-based techniques such as the finite element method (FEM), these deformations pose significant challenges due to large distortions in the deformed geometry, accuracy issues stemming from volumetric locking effects, and increased computational cost from complex contact searches. As an alternative to mesh-based methods, the material point method (MPM), a continuum-based particle technique, is gaining attention for its ability to handle extreme distortions and capture no-slip contact without added cost. For nearly incompressible material behaviors, while mixed formulations can address locking effects by treating displacements and pressure as independent fields, they can suffer from numerical instabilities close to the incompressibility limit due to the violation of the inf-sup condition, leading to inaccurate nodal pressure solutions. Here we propose an efficient and stable mixed B-spline material point method with highest achievable regularity for quasi-compressible polymeric materials. Using the two-scale relation of B-splines, we introduce a subdivision-stabilization for the two-field mixed MPM and obtain numerically stable, oscillation-free nodal solutions with equal-order interpolations with optimal regularity. Building on the Eulerian-Lagrangian nature of MPM, a previously-converged solution framework is adopted to mitigate issues related to cell-crossing and numerical fracture artifact present in standard MPM. We assess the stability and accuracy of the developed mixed MPM at large deformations for soft materials through the benchmark Cook’s membrane problem. Additionally, we test the robustness of the proposed MPM by modeling several examples, including the compression and indentation of a circular block into a quasi-compressible substrate and the twisting deformation of a rectangular block. The findings demonstrate the MPM’s capabilities for modeling practical soft material applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Deconstructing the High Voltage Degradation Mechanisms in Na 2/3 Ni 1/3 Mn 2/3 O 2 with Single Crystals and Advanced Electrolyte

Abstract Sodium layered oxide cathodes can uniquely benefit from the existing lithium‐ion battery industry as sodium‐ion batteries gain traction as a potential low‐cost, drop‐in replacement. However, achieving relevant energy density with a suitable cycle life remains a challenge for sodium layered oxides. At high operating potentials, several competing degradation mechanisms prevent P2‐type Na 2/3 Ni 1/3 Mn 2/3 O 2 (≈550 Wh kg −1 ) from achieving meaningful cycle life—with bulk structural instability and surface reactivity being the primary retractors. Herein, the issue of particle cracking is addressed through detailed synthesis methods of “single‐crystal” materials. By comparison to a polycrystalline baseline, the single‐crystal materials quantify the capacity loss due to isolation of active material caused by intergranular particle cracking. The single crystal materials are then employed in cells with an advanced, “localized saturated electrolyte” (LSE) to demonstrate the magnitude of capacity loss due to electrolyte decomposition at the cathode surface. Mitigation of the surface reactivity through the LSE electrolyte effectively demonstrates the elevated importance of surface reactivity at high voltages despite the onset of egregious particle cracking. This work aims to guide future research into understanding molten‐salt assisted syntheses and advance the debate on surface versus bulk degradation.

Darga, Joe↗
NASA NTRS1996

Multi-Particle Interferometry Based on Double Entangled States

A method for producing a 4-photon entangled state based on the use of two independent pair sources is discussed. Of particular interest is that each of the pair sources produces a two-photon state which is simultaneously entangled in both polarization and space-time variables. Performing certain measurements which exploit this double entanglement provides an opportunity for verifying the recent demonstration of nonlocality by Greenberger, Horne, and Zeilinger.

Pittman, Todd B.↗