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At least 811 records · Page 45

Consistent structures and interactions by density functional theory with small atomic orbital basis sets

A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust “high-speed” computational tool in theoretical chemistry and physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Image quality assessment for CT used on small animals

Image acquisition on a CT scanner is nowadays necessary in almost any kind of medical study. Its purpose, to produce anatomical images with the best achievable quality, implies the highest diagnostic radiation exposure to patients. Image quality can be measured quantitatively based on parameters such as noise, uniformity and resolution. This measure allows the determination of optimal parameters of operation for the scanner in order to get the best diagnostic image. A human Phillips CT scanner is the first one minded for veterinary-use exclusively in Colombia. The aim of this study was to measure the CT image quality parameters using an acrylic phantom and then, using the computational tool MATLAB, determine these parameters as a function of current value and window of visualization, in order to reduce dose delivery by keeping the appropriate image quality.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Mode penetration induced by transient magnetic perturbations

Three dimensional magnetic fields in tokamaks can induce forced magnetic reconnection (FMR) and produce magnetic islands on resonant surfaces. Conventional analytic solutions to FMR focus on describing the time asymptotic state given a steady-state field error. The purpose of this report is to understand the nonlinear dynamics of mode penetration, an evolution from a high-slip, flow-screened metastable equilibrium into a low-slip, field-penetrated metastable equilibrium. Here, we extend previous work by incorporating a temporally varying external magnetic field as a simple model for a magnetohydrodynamic (MHD) event that produces resonant magnetic perturbations. Proof-of-principle, extended-MHD, NIMROD computations vary parameterizations of the transient external perturbation to probe the threshold for mode penetration. We test these computational results against analytical theory that captures the temporal evolution properties of the electromagnetic and viscous forces during and after a transient. We find qualitative agreement between computational and analytical results. However, computational tools are necessary to accurately capture the threshold conditions for mode penetration induced by an MHD transient.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Elucidating size effects on the yield strength of single-crystal Cu via the Richtmyer–Meshkov instability

Capturing the dynamic response of a material under high strain-rate deformation often demands challenging and time consuming experimental effort. While shock hydrodynamic simulation methods can aid in this area, a priori characterizations of the material strength under shock loading and spall failure are needed in order to parameterize constitutive models needed for these computational tools. Moreover, parameterizations of strain-rate-dependent strength models are needed to capture the full suite of Richtmyer–Meshkov instability (RMI) behavior of shock compressed metals, creating an unrealistic demand for these training data solely on experiments. Herein, we sweep a large range of geometric, crystallographic, and shock conditions within molecular dynamics (MD) simulations and demonstrate the breadth of RMI in Cu that can be captured from the atomic scale. In this work, yield strength measurements from jetted and arrested material from a sinusoidal surface perturbation were quantified as Y RMI = 0.787 ± 0.374 GPa, higher than strain-rate-independent models used in experimentally matched hydrodynamic simulations. Defect-free, single-crystal Cu samples used in MD will overestimate Y RMI , but the drastic scale difference between experiment and MD is highlighted by high confidence neighborhood clustering predictions of RMI characterizations, yielding incorrect classifications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Nonequilibrium statistical thermodynamics of multicomponent interfaces

Nonequilibrium interfacial thermodynamics has important implications for crucial biological, physical, and industrial-scale transport processes. Here, we discuss a theory of local equilibrium for multiphase multicomponent interfaces that builds upon the “sharp” interface concept first introduced by Gibbs, allowing for a description of nonequilibrium interfacial processes such as those arising in evaporation, condensation, adsorption, etc. By requiring that the thermodynamics be insensitive to the precise location of the dividing surface, one can identify conditions for local equilibrium and develop methods for measuring the values of intensive variables at the interface. We then use extensive, high-precision nonequilibrium molecular dynamics (NEMD) simulations to verify the theory and establish the validity of the local equilibrium hypothesis. In particular, we demonstrate that equilibrium equations of state are also valid out of equilibrium, and can be used to determine interfacial temperature and chemical potential(s) that are consistent with nonequilibrium generalizations of the Clapeyron and Gibbs adsorption equations. We also show, for example, that, far from equilibrium, temperature or chemical potential differences need not be uniform across an interface and may instead exhibit pronounced discontinuities. However, even in these circumstances, we demonstrate that the local equilibrium hypothesis and its implications remain valid. These results provide a thermodynamic foundation and computational tools for studying or revisiting a wide variety of interfacial transport phenomena.

36 MATERIALS SCIENCE↗

Protein Identification Using Top-Down

In the last two years, due to advances in protein separation and mass spectrometry, top-down mass spectrometry moved from analyzing single proteins to analyzing complex samples and identifying hundreds and even thousands of proteins. However, computational tools for database search of top-down spectra against protein databases are still in infancy. We describe MS-Align+, a fast algorithm for top-down protein identification based on spectral alignment that enables searches for unexpected post-translational modifications (PTMs). We also propose a method for evaluating statistical significance of top-down protein identifications and further benchmark MS-Align+ along with PIITA, ProSightPTM and SEQUEST, which were previously used for top-down MS/MS database searches. We demonstrate that MS-Align+ and PIITA significantly increase the number of identified proteins as compared to ProSightPTM and SEQUEST.

Environmental Molecular Sciences Laboratory↗

SCALE 6.2.4 Validation for Light Water Reactor Decay Heat Analysis

Energy release from the decay of radionuclides in nuclear fuel after its discharge from reactor is a critical parameter for design, safety, and licensing analyses of used nuclear fuel storage, transportation, and repository systems. Well-validated computational tools and nuclear data are essential for decay heat prediction. This paper summarizes the validation of the SCALE nuclear analysis code system version 6.2.4, used with ENDF/B-VII.1 libraries, for decay heat analysis of light water reactor used fuel. The experimental data used for validation include full-assembly decay heat measurements that cover assembly burnups of 5 to 51 GWd/tonne U, cooling times after discharge in the 2- to 27-year range, and initial fuel enrichments up to 4 wt% 235U. The comparison between calculated (C) and experimental (E) decay heat showed very good agreement, with an average C/E over all considered measurements of 1.006 (σ = 0.016) for pressurized water reactor and 0.984 (σ = 0.077) for boiling water reactor assembly measurements. The effect of using assembly-average versus axially varying modeling data on the calculated decay heat, important to thermal analyses for used fuel transportation and storage systems, is discussed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

An Evaluation and Qualification of U.S.-Based Research Reactors for Irradiation Capabilities Supporting Advanced Nuclear Systems

Irradiation experiments are a prerequisite for evaluating nuclear reactor system designs, analyzing the performance of these systems, and obtaining licenses. Likewise, irradiation facilities are necessary for producing the radioisotopes used in industrial and medical applications. Recent developments in modeling and simulation capabilities and advancements in computational resources have further enabled the design of irradiation experiments for evaluating radiation-induced phenomena and determining nuclear fuel, material, and system design and safety criteria pertaining to both normal and accident scenarios. These computational tools and models require comprehensive experimental datasets acquired under prototypic radiation conditions—for exploring material and system performance under the uniquely harsh environments found in nuclear reactors—to enable verification and validation for qualification and licensing purposes. However, qualification of irradiation experimental facilities, primarily research and test reactors (RTRs), necessitates that their performance be evaluated based on the irradiation environment (e.g. flux, power, testing capabilities) using an appropriate scoring matrix. Although many university campus RTRs are available for research and development (R&D) activities and initiatives, this study focuses on evaluating and qualifying the irradiation facilities (mostly RTRs) within the United States that are suitable for advanced nuclear fuel, material, and system irradiation experiments aimed at establishing operational-performance limits and informing component and fuel designs so as to improve operational efficiencies and mitigate proliferation vulnerabilities, as well as for radioisotope production aimed at multipurpose applications. As a result, the findings of the present study support the acceleration of nuclear fuel and material qualifications, thus hastening new and advanced nuclear energy system demonstrations and radioisotope production efforts by using extended R&D.

irradiation experiment↗

Spatial Proteomics towards cellular Resolution

Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level. Areas covered: This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution. Expert opinion: The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. In conclusion, achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.

59 BASIC BIOLOGICAL SCIENCES↗

Integration of the Full Tokamak Reference Model with the Complex Model for ITER Neutronic Analysis

The ITER International Organization has developed a number of reference Monte Carlo N-Particle (MCNP) models including the tokamak machine C-model, the Tokamak Complex model, and the neutral beam injection (NBI) systems model. The Tokamak Complex model primarily describes building structures beyond the bioshield. Representation of the tokamak and its systems are not included in this model. The Oak Ridge National Laboratory Radiation Transport Group has conducted two ITER neutronic analysis model integrations: (1) integration of the tokamak C-model with the Tokamak Complex model for shutdown dose rate characterization in Port Cell 16 at level B1, and (2) integration of the NBI model with the Tokamak Complex model for estimating the spatial distribution of biological dose rate at levels L1, L2, and L3 of the Tokamak Complex. The integrated models were further extended to include models of system components that are essential to the neutronic analyses. Furthermore, this paper presents the approach and computer tools used to integrate existing reference models, describes the additional design details implemented in the integrated models, and provides representative neutronic calculations based on the extended models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Development, Verification, and Validation of an OpenFOAM-Based Solver for Modeling Inertial Fusion Energy Chambers

Our work seeks to introduce a computational tool tailored to the physics of inertial fusion energy chambers, in particular, those concepts based on thick liquid walls. In this approach, the structural materials are protected by several neutron mean-free-paths of renewable liquid and thus will be able to survive much longer than un-shielded walls, with virtually all structures lasting for the life of the plant and enabling the use of commercially available and qualified materials. The OpenFOAM-based solver named rhoCentralFoam has been used as a starting point. rhoCentralFoam belongs to the standard OpenFOAM solver toolset. It is a high-speed, explicit compressible flow solver with shock-capturing capability. While the main features have been retained, the solver had to be restructured to make use of tabular data for equations of states, a necessary addition to model the complex thermo-physical properties of ionized gasses. This entailed the need to change the independent state variables used by the solver, resulting in a new thermodynamic library and slightly different solution algorithm. Moreover, a radiation heat transfer model based on the P-1 approximation was added to the solver. The solver is verified against an analytical solution from the Sedov-Taylor-Neumann test problem to showcase the ability of the hydrodynamic solvers to handle strong shocks, whereas the P-1 model was verified using a simple one-dimensional problem with an analytical solution. Additionally, a validation case involving shock-wave propagation through jet array is presented, and the results are compared with experimental data from the open literature. Lastly, in order to showcase the utility of the solver for practical cases, we applied the refined solver to two representative scenarios: gas venting within the HYLIFE-II chamber and the compression of the gas following the partial ablation of the liquid wall.

Chamber dynamics↗

BUBBLES AND KNOTS IN THE KINEMATICAL STRUCTURE OF THE BIPOLAR PLANETARY NEBULA NGC 2818

High-resolution Hubble Space Telescope archive imaging and high-dispersion spectroscopy are used to study the complex morphological and kinematical structure of the planetary nebula, NGC 2818. We analyze narrowband H{alpha}, [O III], [N II], [S II], and He II images, addressing important morphological features. Ground-based long-slit echelle spectra were obtained crossing NGC 2818 at five different positions to precisely determine kinematical features in the structure of the nebula. A distance of 2.5 kpc was used to determine physical scales. Constructing models to fit the data with modern computational tools, we find NGC 2818 is composed of (1) a non-uniform bipolar structure with a semimajor axis of 0.92 pc (75''), possibly deformed by the stellar wind, (2) a 0.17 pc (14'') diameter central region, which is potentially the remnant of an equatorial enhancement, and (3) a great number of cometary knots. These knots are preferentially located inside a radius of 0.24 pc (20'') around the central star. The major axis of the main structure is oriented at i {approx_equal} 60 Degree-Sign with respect to the line of sight and at P.A. = +89 Degree-Sign on the plane of the sky. Expansion velocities of this nebula are V{sub pol} = 105 km s{sup -1} and V{sub eq} = 20 km s{sup -1}, which lead to our estimate of the kinematical age of {tau}{sub k} {approx_equal} 8400 {+-} 3400 yr (assuming homologous expansion). Our observations do not support the idea that high-velocity collimated ejections are responsible for the formation of microstructures inside the nebula. We determine the systemic velocity of NGC 2818 to be V{sub HEL} = +26 {+-} 2 km s{sup -1}.

79 ASTRONOMY AND ASTROPHYSICS↗

Review of Neutron Yield from (α, n) Reactions: Data, Methods, and Prospects

Understanding the radiogenic neutron production rate through the (α, n) reaction is crucial in many areas of physics, including dark matter searches, neutrino studies, and nuclear astrophysics. In addition to its relevance for fundamental research, the (α, n) reaction also plays a significant role in nuclear energy technologies, for example by contributing to neutron production in subcritical systems using UO2, as well as in applications such as medical physics. This review examines the current state of (α, n) yield calculations and neutron spectra, describes the computational tools used for their estimation, and discusses the available cross-section data. We discuss the uncertainties affecting (α, n) yield estimations and propose a strategy to enhance their accuracy. Furthermore, this paper discusses and emphasizes the need for new measurements of (α, n) cross-sections for a variety of relevant materials. Such measurements are essential for improving neutron flux predictions, which are crucial for reducing uncertainties in sensitivity estimates for next-generation physics experiments operating in the keV—MeV range.

(α, n)reactions↗

Kinetic simulations of collision-less plasmas in open magnetic geometries

Laboratory plasmas in open magnetic geometries can be found in many different applications such as (a) scrape-of-layer (SOL) and divertor regions in toroidal confinement fusion devices, (b) linear divertor simulators, (c) plasma-based thrusters and (d) magnetic mirrors etc. A common feature of these plasma systems is the need to resolve, in addition to velocity space, at least one physical dimension (e.g. along flux lines) to capture the relevant physics. In general, this requires a kinetic treatment. Fully kinetic particle-in-cell (PIC) simulations can be applied but at the expense of large computational effort. A common way to resolve this is to use a hybrid approach: kinetic ions and fluid electrons. In the present work, the development of a hybrid PIC computational tool suitable for open magnetic geometries is described which includes (a) the effect of non-uniform magnetic fields, (b) finite fully-absorbing boundaries for the particles and (c) volumetric particle sources. Analytical expressions for the momentum transport in the paraxial limit are presented with their underlying assumptions and are used to validate the results from the PIC simulations. A general method is described to construct discrete particle distribution functions in a state of mirror-equilibrium. This method is used to obtain the initial state for the PIC simulation. Collisionless simulations in a mirror geometry are performed. The results show that the effect of magnetic compression is correctly described and momentum is conserved. The self-consistent electric field is calculated and is shown to modify the ion velocity distribution function in a manner consistent with analytic theory. Based on this analysis, the ion distribution function is understood in terms of a loss-cone distribution and an isotropic Maxwell-Boltzmann distribution driven by a volumetric plasma source. Finally, the inclusion of a Monte Carlo based Fokker-Planck collision operator is discussed in the context of future work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Validating the simulation of beam-ion charge exchange in MAST Upgrade

Abstract Simulation of the impact of charge-exchange (CX) reactions on beam ions in the Mega Amp Spherical Tokamak (MAST) Upgrade was compared to measurements carried out with a fission chamber (neutron fluxes) and a fast ion deuterium-alpha (FIDA) diagnostic. A simple model was developed to reconstruct the outer-midplane neutral density based on measurements of deuterium-alpha emission from edge neutrals, and on Thomson scattering measurements of electron density and temperature. The main computational tools used were the ASCOT orbit-following code and the FIDASIM code for producing synthetic FIDA signals. The neutral density reconstruction agrees qualitatively with SOLPS-ITER modelling and yields a synthetic passive FIDA signal that is consistent with measurement. When CX losses of beam ions are accounted for, predicted neutron emission rates are quantitatively more consistent with measurement. It was necessary to account for CX losses of beam ions in simulations to reproduce the measured passive FIDA signal quantitatively and qualitatively. The results suggest that the neutral density reconstruction is a good approximation, that CX with edge neutrals causes significant beam-ion losses in MAST Upgrade, typically 20% of beam power, and that the ASCOT fast-ion CX model can be used to accurately predict the redistribution and loss of beam ions due to CX.

Physics↗

Effect of net direct current on the properties of radio frequency sheaths: simulation and cross-code comparison

In order to understand, predict and control ion cyclotron range of frequency (ICRF) interactions with tokamak scrape-off layer plasmas, computational tools which can model radio frequency (RF) sheaths are needed. In particular, models for the effective surface impedance and DC rectified sheath potentials may be coupled with full wave RF simulation codes to predict self-consistent wave fields near surfaces and the resulting power dissipation and plasma-material interactions from ion sputtering. In this study, previous work assuming zero net DC current flow through the sheath is generalized to allow the surface to collect net positive or negative current, as is often observed in experiments. The waveforms, DC potential and RF admittance are investigated by means of analytical theory, nonlinear fluid and particle-in-cell (PIC) codes. Cross-code comparisons provide detailed model verification and elucidate the roles of ion and electron kinetics. When the sheath draws negative (positive) DC current, the voltage rectification is reduced (increased) compared with the zero-current case, and the magnitude of both the real and imaginary parts of the admittance are increased (reduced). In conclusion, a previous four-input parametrization of the sheath rectification and admittance properties is generalized to include a fifth parameter describing the DC sheath current.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Towards fully predictive gyrokinetic full- f simulations: validation and triangularity studies in TCV

Designing economical magnetic confinement fusion power plants motivates computational tools that can estimate plasma behavior from engineering parameters without direct reliance on experimental measurement of the plasma profiles. In this work, we present full-f global long-wavelength gyrokinetic simulations of edge and scrape-off layer turbulence in tokamaks that use only magnetic geometry, heating power, and particle inventory as inputs. Unlike many modeling approaches that employ free parameters fitted to experimental data, raising uncertainties when extrapolating to reactor scales. This approach directly simulates turbulence and resulting profiles through gyrokinetics without such empirical adjustments. This is achieved via an adaptive sourcing algorithm in Gkeyll that strictly controls energy injection and emulates particle sourcing due to neutral recycling. We show that the simulated kinetic profiles compare reasonably well with Thomson scattering and Langmuir probe data for Tokamak á Configuration Variable (TCV) discharge #65125, and that the simulations reproduce characteristic features such as blob transport and self-organized electric fields. Applying the same framework to study triangularity effects suggests mechanisms contributing to the improved confinement reported for negative triangularity (NT). Simulations of TCV discharges #65125 and #65130 indicate that NT increases the E x B flow shear (by about 20% in these cases), which correlates with reduced turbulent losses and a modest change in the distribution of power exhaust to the vessel wall. While the physical models contain approximations that can be refined in future work, the predictive capability demonstrated here, evolving multiple profile relaxation times with kinetic electron and ion models in hundreds of GPU hours, indicates the feasibility of using Gkeyll to support design studies of fusion devices.

Hoffmann, Antoine Cyril David [Princeton Plasma Ph↗

CMS Analysis and Data Reduction with Apache Spark

Experimental Particle Physics has been at the forefront of analyzing the world's largest datasets for decades. The HEP community was among the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems for distributed data processing, collectively called "Big Data" technologies have emerged from industry and open source projects to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and tools, promising a fresh look at analysis of very large datasets that could potentially reduce the time-to-physics with increased interactivity. Moreover these new tools are typically actively developed by large communities, often profiting of industry resources, and under open source licensing. These factors result in a boost for adoption and maturity of the tools and for the communities supporting them, at the same time helping in reducing the cost of ownership for the end-users. In this talk, we are presenting studies of using Apache Spark for end user data analysis. We are studying the HEP analysis workflow separated into two thrusts: the reduction of centrally produced experiment datasets and the end-analysis up to the publication plot. Studying the first thrust, CMS is working together with CERN openlab and Intel on the CMS Big Data Reduction Facility. The goal is to reduce 1 PB of official CMS data to 1 TB of ntuple output for analysis. We are presenting the progress of this 2-year project with first results of scaling up Spark-based HEP analysis. Studying the second thrust, we are presenting studies on using Apache Spark for a CMS Dark Matter physics search, comparing Spark's feasibility, usability and performance to the ROOT-based analysis.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗