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At least 487 records · Page 27

Language Independent Static Analysis (LISA)

Software is becoming increasingly important in nearly every aspect of global society and therefore in nearly every aspect of national security as well. While there have been major advancements in recent years in formally proving properties of program source code during development, such approaches are still in the minority among development teams, and the vast majority of code in this software explosion is produced without such properties. In these cases, the source code must be analyzed in order to establish whether the properties of interest hold. Because of the volume of software being produced, automated approaches to software analysis are necessary to meet the need. However, this software boom is not occurring in just one language. There are a wide range of languages of interest in national security spaces, including well-known languages such as C, C++, Python, Java, Javascript, and many more. But recent years have produced a wide range of new languages, including Nim, (2008), Go (2009), Rust (2010), Dart (2011), Kotlin (2011), Elixir (2011), Red (2011), Julia (2012), Typescript (2012), Swift (2014), Hack (2014), Crystal (2014), Ballerina (2017) and more. Historically, automated software analyses are implemented as tools that intermingle both the analysis question at hand with target language dependencies throughout their code, making re-use of components for different analysis questions or different target languages impractical. This project seeks to explore how mission-relevant, static software analyses can be designed and constructed in a language-independent fashion, dramatically increasing the reusability of software analysis investments.

97 MATHEMATICS AND COMPUTING↗

Development of a neural network model for peeling–ballooning stability analysis in the KSTAR tokamak pedestals

The neural network model, MISHKA-NN is developed to mitigate the computational burden associated with the linear ideal magnetohydrodynamic (MHD) stability analysis of the pedestal based on the peeling–ballooning (P–B) model. By utilizing both 1D plasma profiles (current density, pressure gradient, and safety factor) and 0D parameters (plasma geometry, total current, and toroidal mode number), the model predicts linear growth rate of edge-localized ideal MHD instability in a given equilibrium state. By enabling the prediction of each instability within a second, the model reduces the time required for plotting a pedestal P–B stability diagram (j - α diagram) from approximately 100 CPU hours to a few CPU minutes. Notably, even with the utilization of parametric pressure and current profiles and plasma boundary shapes for the training dataset, the model shows a satisfactory level of performance in benchmarking the j - α diagram for the reconstructed equilibrium from a KSTAR tokamak experiment. We anticipate the model to serve as a versatile alternative to 2D linear MHD stability codes, alleviating numerical costs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measurement of 139 La(p,x) cross sections from 35–60 MeV by stacked-target activation

A stacked-target of natural lanthanum foils (99.9119% 139 La) was irradiated using a 60 MeV proton beam at the LBNL 88-Inch Cyclotron. 139 La(p,x) cross sections are reported between 35–60 MeV for nine product radionuclides. The primary motivation for this measurement was the need to quantify the production of 134 Ce. As a positron-emitting analogue of the promising medical radionuclide 225 Ac, 134 Ce is desirable for in vivo applications of bio-distribution assays for this emerging radio-pharmaceutical. Finally, the results of this measurement were compared to the nuclear model codes TALYS, EMPIRE and ALICE (using default parameters), which showed significant deviation from the measured values.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cross sections and calculated yields of some radionuclides of yttrium, strontium and rubidium formed in proton-induced reactions on enriched strontium-86: possibility of production of 85g Sr, 83 Rb and 82m Rb in no-carrier-added form

Here, cross sections of the 86 Sr(p,3n) 84m Y, 86 Sr(p,αn) 82m Rb, and 86 Sr(p,x) 85g Sr reactions were measured from their respective thresholds up to 16.2 MeV and from 23.0 to 44.1 MeV at FZJ, and from 14.3 to 24.5 MeV at LBNL, using 96.4% enriched 86 SrCO 3 as target material. Thin targets prepared by sedimentation were irradiated with protons in a stacked-form, and the induced radioactivity was measured by high-resolution γ-ray spectrometry. Nuclear model calculations based on the code TALYS reproduced our experimental cross section data well. From the excitation functions, the integral yields of the above three radionuclides were calculated. The yield of 85g Sr via the natSr(n,γ) process was also measured using the TRIGA Mark-II reactor at AERE, Savar. A comparison of the reactor and cyclotron production of carrier-added 85g Sr is given. The production possibilities of the three investigated radionuclides in no-carrier-added forms at a 30 MeV cyclotron via new routes are discussed.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Code-to-code comparison between FLASH and HYDRA in gas-puff Z-pinch modeling

The numerical modeling of gas-puff Z pinches involves the nonlinear coupling of a broad range of complex, multi-physics phenomena that makes such simulations challenging. The challenge is further compounded by nonlinear instabilities that can impact the dynamics of imploding gas-puff Z pinches, such as the magneto Rayleigh–Taylor instability (MRTI). If the growth rate and amplitude of the latter is comparable to the relevant timescales and properties of the imploding plasma, the MRTI can dramatically alter implosion dynamics, dictate pinch stability, and govern the plasma properties achievable in pulsed-power-driven laboratory experiments. National Laboratories and academic teams have developed numerical tools that can accurately model Z-pinch configurations and provide reliable design capabilities that can guide experimental choices and assist in interpreting experimental results. Most such tools, however, are not broadly available. Here, we present newly developed Z-pinch simulation capabilities of the publicly available FLASH code, applied in the study of MRTI growth and dynamical effects in gas-puff implosions. To verify the new implementations, we perform a comparison of FLASH gas-puff implosion simulations with previously published calculations with the HYDRA code from Lawrence Livermore National Laboratory, which have been validated with experimental data from the CESZAR pulsed-power driver at the University of California, San Diego. The experiments involved double- and triple-nozzle configurations, in an experimental attempt to stabilize the pinch to the MRTI. The code-to-code comparison shows similar results between the FLASH and HYDRA simulations, supporting the use of FLASH in the modeling of future gas-puff Z-pinch experiments at CESZAR.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

tih_vqe [SWR-23-32]

This software supports the paper, "Exploring the scaling limitations of the variational quantum eigensolver with the bond dissociation of hydride diatomic molecules," published in the International Journal of Quantum Chemistry, whose abstract is as follows: Materials simulations involving strongly correlated electrons pose fundamental challenges to state-of-the-art electronic structure methods but are hypothesized to be the ideal use case for quantum computing. To date, no quantum computer has simulated a molecule of a size and complexity relevant to real-world applications, despite the fact that the variational quantum eigensolver (VQE) algorithm can predict chemically accurate total energies. Nevertheless, because of the many applications of moderately-sized, strongly correlated systems, such as molecular catalysts, the successful use of the VQE stands as an important waypoint in the advancement toward useful chemical modeling on near-term quantum processors. In this paper, we take a significant step in this direction. We lay out the steps, write, and run parallel code for an (emulated) quantum computer to compute the bond dissociation curves of the TiH, LiH, NaH, and KH diatomic hydride molecules using VQE. TiH was chosen as a relatively simple chemical system that incorporates d orbitals and strong electron correlation. Because current VQE implementations on existing quantum hardware are limited by qubit error rates, the number of qubits available, and the allowable gate depth, recent studies have focused on chemical systems involving s and p block elements. Through VQE + UCCSD calculations of TiH, we evaluate the near-term feasibility of modeling a molecule with d-orbitals on real quantum hardware. We demonstrate that the inclusion of d-orbitals and the use of the UCCSD ansatz, which are both necessary to capture the correct TiH physics, dramatically increase the cost of this problem. We estimate the approximate error rates necessary to model TiH on current quantum computing hardware using VQE+UCCSD and show them to likely be prohibitive until significant improvements in hardware and error correction algorithms are available.

Graf, Peter↗

The EIC accelerator: design highlights and project status

The design of the electron-ion collider (EIC) at Brookhaven National Laboratory is well underway, aiming at a peak electron-proton luminosity of 10e+34 cm^-1·sec^-1. This high luminosity, the wide center-of-mass energy range from 29 to 141 GeV (e-p) and the high level of polarization require innovative solutions to maximize the performance of the machine, which makes the EIC one of the most challenging accelerator projects to date. The complexity of the EIC will be discussed, and the project status and plans will be presented.

43 PARTICLE ACCELERATORS↗

MicroRNAs in laser-induced choroidal neovascularization in mice and rats: their expression and potential therapeutic targets

Choroidal neovascularization characterizes wet age-related macular degeneration. Choroidal neovascularization formation involves a primarily angiogenic process that is combined with both inflammation and proteolysis. A primary cause of choroidal neovascularization pathogenesis is alterations in pro- and anti-angiogenic factors derived from the retinal pigment epithelium, with vascular endothelium growth factor being mainly responsible for both clinical and experimental choroidal neovascularization. MicroRNAs (miRNAs) which are short, non-coding, endogenous RNA molecules have a major role in regulating various pathological processes, including inflammation and angiogenesis. A review of recent studies with the mouse laser-induced choroidal neovascularization model has shown alterations in miRNA expression in choroidal neovascularization tissues and could be potential therapeutic targets for wet age-related macular degeneration. Upregulation of miR-505 (days 1 and 3 post-laser), miR-155 (day 14) occurred in retina; miR-342-5p (days 3 and 7), miR-126-3p (day 14) in choroid; miR-23a, miR-24, miR-27a (day 7) in retina/choroid; miR-505 (days 1 and 3) in retinal pigment epithelium/choroid; downregulation of miR-155 (days 1 and 3), miR-29a, miR-29b, miR-29c (day 5), miR-93 (day 14), miR-126 (day 14) occurred in retinal pigment epithelium/choroid. Therapies using miRNA mimics or inhibitors were found to decrease choroidal neovascularization lesions. Choroidal neovascularization development was reduced by overexpression of miR-155, miR-188-5p, miR-(5,B,7), miR-126-3p, miR-342-5p, miR-93, miR-126, miR-195a-3p, miR24, miR-21, miR-31, miR-150, and miR-184, or suppression of miR-505, miR-126-3p, miR155, and miR-23/27. Further studies are warranted to determine miRNA expression in mouse laser-induced choroidal neovascularization models in order to validate and extend the reported findings. Important experimental variables need to be standardized; these include the strain and age of animals, gender, number and position of laser burns to the eye, laser parameters to induce choroidal neovascularization lesions including wavelength, power, spot size, and duration.

therapeutic targets↗

High speed two-dimensional imaging with an analog interface

A quantitative pulse count (event detection) algorithm with linearity to high count rates is accomplished by combining a high-speed, high frame rate camera with simple logic code run on a massively parallel processor such as a GPU. The parallel processor elements examine frames from the camera pixel by pixel to find and tag events or count pulses. The tagged events are combined to form a combined quantitative event image.

Waugh, Justin↗

Global gyro-kinetic ion temperature gradient and trapped electron mode turbulence modelling in X -point geometry in negative and positive triangularity

Comparative modelling of ion temperature gradient (ITG)/trapped electron mode (TEM) turbulence in negative (NT) and positive (PT) triangularity plasma shapes was done using the nonlinear global full-f gyrokinetic particle code JOREK-GK in the realistic X-point tokamak geometry including the Scrape Off Layer (SOL) for TCV and DIII-D parameters. A comparison of JOREK-GK code with the gyrokinetic codes GS2 and GENE was done using NT/PT triangularity TCV L-modes parameters showing good agreement between codes in linear growth rates and clear beneficial effect of NT as compared to PT. Global non-linear modelling of the ITG/TEM saturated turbulence for realistic DIII-D NT pulses was done and compared with numerically constructed PT equilibrium with the same plasma profiles. Existence of longer correlation length of density fluctuations in PT compared to NT was demonstrated. Stronger and more sheared zonal flows are generated via Reynolds stress in NT compared to PT. These factors are stabilizing for TEM/ITG turbulence in NT and lead to smaller heat fluxes and heat conductivities in NT compared to PT configuration. Weak dependence of plasma confinement on collisionality and plasma rotation was found in modelling of DIII-D NT shots similar to the experiment. The confinement scaling with normalized ion gyro-radius ρ* was estimated both for NT and PT. Bohm-like scaling was obtained in both configurations, however with better confinement for NT compared to PT which could be favourable factor for reactor size machines.

ITG↗

A pseudo-kinetic model to simulate phase changes in gas hydrate bearing sediments

Herein, modeling of the phase transitions anticipated in gas hydrate bearing sediments (GHBS) is critical for a proper understanding of time-dependent changes in states and volumes (e.g. the production of methane from this type of soils). We propose a new pseudo-kinetic approach to simulate the typical phase changes anticipated in GHBS, using published experimental results involving gas hydrate dissociation that are the basis of a widely used kinetic model. The proposed pseudo-kinetic model is formulated in the pressure-temperature (P-T) plane and assumes a rate of gas hydrate dissociation (or formation) proportional to the distance between the current state and the phase boundary. The model consists of only one parameter and is simple to implement in numerical simulators. A similar concept is used to model ice formation/thawing phenomena, but based on the ice/liquid-water phase boundary. We implemented the pseudo-kinetic model in a fully coupled thermo-hydro-chemo-mechanical (THCM) finite element code and validated it against experimental results performed on the dissociation of synthetic gas hydrate. We also evaluated the pseudo-kinetic model using synthetic cases covering several scenarios associated with gas hydrate formation/dissociation and ice formation/thawing. The model successfully reproduced the gas production test from a natural GHBS core from Korea (scaled gas venting experiment over 14 h), and also the formation of gas hydrate and ice in permafrost in Alaska (over 2 × 10 6 years). -The analyses show the versatility of the proposed pseudo-kinetic approach by applying it to model the different types of phase transitions typically encounter in GHBS. The simple formulation, easy implementation in numerical simulator, and reduced number of parameters (only one per phase change) make this model an attractive option for simulating phase transformations in problems involving GHBS.

58 GEOSCIENCES↗

Multimodal representation learning for predicting molecule–disease relations

Motivation: Predicting molecule–disease indications and side effects is important for drug development and pharmacovigilance. Comprehensively mining molecule–molecule, molecule–disease and disease–disease semantic dependencies can potentially improve prediction performance. Methods: We introduce a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP) by incorporating clinical semantics learned from electronic health records (EHR) of 12.6 million patients. Specifically, M2REMAP first learns a multimodal molecule representation that synthesizes chemical property and clinical semantic information by mapping molecule chemicals via a deep neural network onto the clinical semantic embedding space shared by drugs, diseases and other common clinical concepts. To infer molecule–disease relations, M2REMAP combines multimodal molecule representation and disease semantic embedding to jointly infer indications and side effects. Results: We extensively evaluate M2REMAP on molecule indications, side effects and interactions. Results show that incorporating EHR embeddings improves performance significantly, for example, attaining an improvement over the baseline models by 23.6% in PRC-AUC on indications and 23.9% on side effects. Further, M2REMAP overcomes the limitation of existing methods and effectively predicts drugs for novel diseases and emerging pathogens. Availability and implementation: The code is available at https://github.com/celehs/M2REMAP, and prediction results are provided at https://shiny.parse-health.org/drugs-diseases-dev/.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring the scaling limitations of the variational quantum eigensolver with the bond dissociation of hydride diatomic molecules

Abstract Materials simulations involving strongly correlated electrons pose fundamental challenges to state‐of‐the‐art electronic structure methods but are hypothesized to be the ideal use case for quantum computing algorithms. To date, no quantum computer has simulated a molecule of a size and complexity relevant to real‐world applications, despite the fact that the variational quantum eigensolver (VQE) algorithm can predict chemically accurate total energies. Nevertheless, because of the many applications of moderately sized, strongly correlated systems, such as molecular catalysts, the successful use of the VQE stands as an important waypoint in the advancement toward useful chemical modeling on near‐term quantum processors. In this paper, we take a significant step in this direction. We lay out the steps, write, and run parallel code for an (emulated) quantum computer to compute the bond dissociation curves of the TiH, LiH, NaH, and KH diatomic hydride molecules using the VQE. TiH was chosen as a relatively simple chemical system that incorporates d orbitals and strong electron correlation. Because current VQE implementations on existing quantum hardware are limited by qubit error rates, the number of qubits available, and the allowable gate depth, recent studies using it have focused on chemical systems involving s and p block elements. Through VQE + UCCSD calculations of TiH, we evaluate the near‐term feasibility of modeling a molecule with d‐orbitals on real quantum hardware. We demonstrate that the inclusion of d‐orbitals and the use of the UCCSD ansatz, which are both necessary to capture the correct TiH physics, dramatically increase the cost of this problem. We estimate the approximate error rates necessary to model TiH on current quantum computing hardware using VQE + UCCSD and show them to likely be prohibitive until significant improvements in hardware and error correction algorithms are available.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Core-edge modeling of gyrokinetic turbulence by coupling the delta-f and total-f models in the XGC code

Whole device gyrokinetic turbulence is modeled using a delta-f model in the core coupled to a total-f model in the edge. This new model is implemented in the gyrokinetic code X-Point Included Gyrokinetic Code (XGC) and works within a single simulation. It employs a canonical Maxwellian background in the core and the usual local Maxwellian in the edge. These different core and edge backgrounds are coupled over an overlap region. A thermal-bath operator is used to keep δf small in the core.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Interplay between beam-driven chirping modes and plasma confinement transitions in spherical tokamak ST40

Experiments on the high field spherical tokamak ST40 have led to the recent observation of interplay between beam-driven modes of sweeping frequency (chirping modes) and transitions to the enhanced global confinement regime (H-mode) and back to the low confinement regime (L-mode). The H-modes of plasma confinement are identified from decreased intensity of D α signal and from clear distinctions in the edge gradients of the visible plasma boundary (observed as a sharp plasma edge in camera images). The beam-driven chirping modes, identified as ideal magnetohydrodynamics beta-induced Alfvén acoustic eigenmodes modes, are observed in Mirnov coil signals, interferometry, and soft x-ray diagnostics. A moderate amplitude ‘primer’ chirping mode usually precedes an H–L transition. This is followed by a ‘dominant’ chirping mode with higher amplitude during the L-mode. The L–H transition back to the improved confinement occurs on a longer time scale of tens of ms, consistent with the slowing down time scale of fast beam ions. A dramatic decrease in toroidal plasma rotation is systematically observed associated with chirping modes sweeping down to zero frequency. Resonance maps built for the beam-driven chirping modes with the ASCOT (accelerated simulation of charged particle orbits in torodoial devices) code show that the resonant beam ions have orbits near the trapped-passing boundary. The ASCOT modelling assesses how losses of the resonant fast ions caused by the chirping modes with high enough amplitude modify the torque, potentially affecting the plasma rotation.

magnetic confinement fusion↗

Dielectronic satellite emission from a solid-density Mg plasma: Relationship to models of ionization potential depression

Here, we report on experiments where solid-density Mg plasmas are created by heating with the focused output of the Linac Coherent Light Source x-ray free-electron laser. We study the K-shell emission from the helium- and lithium-like ions using Bragg crystal spectroscopy. Observation of the dielectronic satellites in lithium-like ions confirms that the M-shell electrons appear bound for these high charge states. An analysis of the intensity of these satellites indicates that when modeled with an atomic-kinetics code, the ionization potential depression model employed needs to produce depressions for these ions which lie between those predicted by the well known Stewart-Pyatt and Ecker-Kroll models. These results are largely consistent with recent density functional theory calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Vadose Zone Model for U Plant Area for Composite Analysis

The objectives of the vadose modeling for the updated Hanford Site composite analysis (CA) are to simulate the flow and transport of water and radionuclide releases from the surface to the water table and to provide radionuclide transfer rates for the plateau to river (P2R) model, version 8.3 (CP-57037, Model Package Report: Plateau to River Groundwater Model, Version 8.3). Water additions include natural recharge and water discharged to the ground as a result of industrial processes associated with Hanford Site operations. Contaminant sources include radionuclides in water discharged to the ground during operations and radionuclides disposed “dry” in solid waste burial grounds or other means. The following 16 radionuclides were selected for this modeling effort: carbon-14 (C-14), chlorine-36 (Cl-36), tritium (H-3), iodine-129 (I-129), neptunium-237 (Np-237), rhenium-187 (Re-187), strontium-90 (Sr-90), technetium-99 (Tc-99), uranium-232 (U-232), uranium-233 (U-233), uranium-234 (U-234), uranium-235 (U-235), uranium-236 (U-236), uranium-238 (U-238), radium-226 (Ra-226), and thorium-230 (Th-230). The simulation time starts in 1943 and ends at 12070, which is 10,000 years after assumed Hanford Site closure in 2070. The parallel version of the Subsurface Transport Over Multiple Phases (STOMP1) simulator, officially named the exascale Subsurface Transport Over Multiple Phases (eSTOMP), is used to simulate flow and transport for the vadose models. The documentation for the STOMP code is comprehensive. The theoretical and numerical approaches applied in the STOMP code are documented in a published theory guide (PNNL-12030, STOMP Subsurface Transport Over Multiple Phases Version 2.0 Theory Guide). The code has undergone a rigorous verification procedure against analytical solutions, laboratory-scale experiments, and field-scale demonstrations. The application guide (PNNL-11216, STOMP Subsurface Transport Over Multiple Phases Application Guide) provides instructive examples in the application of the code to classical groundwater problems. The user’s guide (PNNL-15782, STOMP: Subsurface Transport Over Multiple Phases Version 4.0: User’s Guide) describes the general use, input file formatting, compilation, and execution of the code. The primary output of the vadose zone modeling is radionuclide transfer rates to the groundwater for input into the P2R model. The rates will be summed over the 100 by 100 m P2R grid cells that fall within the vadose zone model source domain.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Vadose Zone Model for M Pond Area for Composite Analysis

The objectives of the vadose modeling for the updated Hanford Site composite analysis (CA) are to simulate the flow and transport of water and radionuclide releases from the surface to the water table and to provide radionuclide transfer rates for the plateau to river (P2R) model, version 8.3 (CP-57037, Model Package Report: Plateau to River Groundwater Model, Version 8.3). Water additions include natural recharge and water discharged to the ground as a result of industrial processes associated with Hanford Site operations. Contaminant sources include radionuclides in water discharged to the ground during operations and radionuclides disposed “dry” in solid waste burial grounds or other means. The following 16 radionuclides were selected for this modeling effort; carbon-14 (C-14), chlorine-36 (Cl-36), tritium (H-3), iodine-129 (I-129), neptunium-237 (Np-237), rhenium-187 (Re-187), strontium-90 (Sr-90), technetium-99 (Tc-99), uranium-232 (U-232), uranium-233 (U-233), uranium-234 (U-234), uranium-235 (U-235), uranium-236 (U-236), uranium-238 (U-238), radium-226 (Ra-226), and thorium-230 (Th-230). The simulation time starts in 1943 and ends at 12070, which is 10,000 years after assumed Hanford Site closure in 2070. The parallel version of the Subsurface Transport Over Multiple Phases (STOMP1) simulator, officially named the exascale Subsurface Transport Over Multiple Phases (eSTOMP), is used to simulate flow and transport for the vadose models. The documentation for the STOMP code is comprehensive. The theoretical and numerical approaches applied in the STOMP code are documented in a published theory guide (PNNL-12030, STOMP Subsurface Transport Over Multiple Phases Version 2.0 Theory Guide). The code has undergone a rigorous verification procedure against analytical solutions, laboratory-scale experiments, and field-scale demonstrations. The application guide (PNNL-11216, STOMP Subsurface Transport Over Multiple Phases Application Guide) provides instructive examples in the application of the code to classical groundwater problems. The user’s guide (PNNL-15782, STOMP: Subsurface Transport Over Multiple Phases Version 4.0: User’s Guide) describes the general use, input file formatting, compilation, and execution of the code. The primary output of the vadose zone modeling is radionuclide transfer rates to the groundwater for input into the P2R model. The rates will be summed over the 100 by 100 m P2R grid cells that fall within the vadose zone model source domain.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗