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DOE OSTI2020

On Simulating the Formation of Structured, Crystalline Systems via Non-classical Pathways

Observations in crystal growth and assembly from recent in situ methods suggest alternative, non-classical crystallization pathways play an important role in the determination of the micro- and meso- structures in crystalline systems. These processes display parallels that cross-cut multiple disciplines investigating crystallization across four orders of magnitude in size scales and widely differing environments, hinting that alternative crystal growth pathways may be a fundamental scheme in natural crystal formation. Using a system of short-range attractive microbeads, we demonstrate that the addition of a small concentration of sub-species incommensurate with the lattice spacing of the dominant species results in a stark change in crystal size and morphology. These changes are attributed to the presence of fleeting, amorphous-like configurations of beads that ultimately change the melting and growth dynamics in preferred directions. From these real-time observations, we hypothesize the amorphous mineral precursors present in biological mineralized tissues undergo similar non-classical crystallization processes resulting in the complex structures found in biomineralization.

36 MATERIALS SCIENCE↗

DOE OSTI2017

On the Structure of the AGN Torus through the Fraction of Optically Selected Type 1 AGNs

The ratio in number between unobscured (type 1) and obscured (type 2) active galactic nuclei (AGNs) is often used to explore the structure of the torus in the unified scheme for AGNs. Oh et al. (2015) investigated the type 1 AGN fraction on two-dimensional space in terms of black hole mass (M{sub BH}) and bolometric luminosity (L{sub bol}) and found that the fraction changes depending on both M{sub BH} and L{sub bol}, forming a ridge-shaped distribution. In this study, based on the up-to-date type 1 AGN catalog of Oh et al. (2015), we examine how the trend of the type 1 AGN fraction in the M{sub BH}–L{sub bol} plane is affected by the different methods used to derive M{sub BH} and L{sub bol}, and suggest an analytic model to explain the observations. We use galaxies from the Sloan Digital Sky Survey Data Release 7 in the redshift range 0.01⩽z⩽0.2. In estimating L{sub bol}, we employ two different methods using [O III] and/or [O I] emission lines, and find that the L{sub bol} values obtained from the two methods agree well. We consider the M{sub BH}--σ{sub ∗} relation, the M{sub BH}–L {sub bulge} relation, and the single-epoch Hα-based M{sub BH} estimate in calculating M{sub BH}. We find that the trends of the type 1 AGN fraction with respect to M{sub BH} and L{sub bol} are similar for the different methods of deriving L{sub bol} but different when using different methods to derive M{sub BH}. We present a model based on the clumpy-torus scheme that reproduces the ridge-shaped distribution of the fraction parallel to the iso-Eddington ratio lines.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

A Many-Task Parallel Approach for Multiscale Simulations of Subsurface Flow and Reactive Transport

Continuum-scale models have long been used to study subsurface flow, transport, and reactions but lack the ability to resolve processes that are governed by pore-scale mixing. Recently, pore-scale models, which explicitly resolve individual pores and soil grains, have been developed to more accurately model pore-scale phenomena, particularly reaction processes that are controlled by local mixing. However, pore-scale models are prohibitively expensive for modeling application-scale domains. This motivates the use of a hybrid multiscale approach in which continuum- and pore-scale codes are coupled either hierarchically or concurrently within an overall simulation domain (time and space). This approach is naturally suited to an adaptive, loosely-coupled many-task methodology with three potential levels of concurrency. Each individual code (pore- and continuum-scale) can be implemented in parallel; multiple semi-independent instances of the pore-scale code are required at each time step providing a second level of concurrency; and Monte Carlo simulations of the overall system to represent uncertainty in material property distributions provide a third level of concurrency. We have developed a hybrid multiscale model of a mixing-controlled reaction in a porous medium wherein the reaction occurs only over a limited portion of the domain. Loose, minimally-invasive coupling of pre-existing parallel continuum- and pore-scale codes has been accomplished by an adaptive script-based workflow implemented in the Swift workflow system. We describe here the methods used to create the model system, adaptively control multiple coupled instances of pore- and continuum-scale simulations, and maximize the scalability of the overall system. We present results of numerical experiments conducted on NERSC supercomputing systems; our results demonstrate that loose many-task coupling provides a scalable solution for multiscale subsurface simulations with minimal overhead.

high performance computing↗

DOE OSTI2016

Method of fabricating high-density hermetic electrical feedthroughs using insulated wire bundles

A method of fabricating electrical feedthroughs coats of a plurality of electrically conductive wires with an electrically insulating material and bundles the coated wires together in a substantially parallel arrangement. The bundled coated wires are secured to each other by joining the electrically insulating material of adjacent wires together to form a monolithic block which is then cut transverse to the wires to produce a block section having opposing first and second sides with a plurality of electrically conductive feedthroughs extending between them.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Application of the TITAN Hybrid Deterministic Transport Code to Medical Physics - Paper 118

The TITAN code is a 3-dimensional parallel deterministic transport code that solves the linear Boltzmann equation. The TITAN code has hybrid algorithms that are ideal for medical physics applications: i) SN and characteristics method and ii) SN with a fictitious quadrature set and ray-tracing. These hybrid algorithms have been used in the simulation of computed tomography (CT) and single photon emission computed tomography (SPECT) In this paper, the hybrid algorithms developed for medical physics applications in the TITAN code are discussed. First, the TITAN code's block-oriented approach for utilizing SN and characteristic solvers for CT is presented and results for a simple test case are given. Second, the paper describes a hybrid formulation for SPECT with an SN solver in the phantom, a fictitious quadrature set for directions from the phantom surface passing through the collimator, and a simplified ray-tracing algorithm for particle transport to the detector. Finally, ongoing work is described and concluding remarks are given. The TITAN code's hybrid algorithms allow it to efficiently solve problems with low-scatter regions, which are frequently found in medical physics applications. The TITAN code has been used to solve a simplified CT problem and generate projection images for SPECT simulations. The WCOS technique was developed to improve the TITAN code's collimator representation. For these applications, the TITAN code was shown to require significantly less computation time than MCNP5. Work is currently underway to implement an iterative image reconstruction algorithm in the TITAN code. A script that calls the TITAN code to complete the forward projection step in SPECT has already been used to reconstruction a 2-dimensional phantom. The ability of TITAN to fully model particle transport in the patient in short computation times is expected to be a great advantage to iterative reconstruction. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2024

Accelerating Thermochemical Equilibrium Calculations for Nuclear Reactor Applications

Thermochemical properties play a key role in modeling and simulation of several key phenomena in nuclear reactors. There has been an increasing interest in incorporating CALPHAD-based formulations in multiphysics simulations including for Molten Salt Reactors where knowledge of phase evolution of the salt and the chemical potentials of various elements are of utmost importance in source term analyses and redox control. However, the size of such simulations is often limited by the high computational cost of full thermodynamic equilibrium calculations. This work discusses the current efforts aimed at accelerating thermochemical equilibrium calculations for multiphysics simulations performed using the open-source finite element / finite volume code Multiphysics Object Oriented Simulation Environment (MOOSE) [1]. While several methods have been proposed for accelerating phase equilibrium calculations [2], most focus on relatively small systems and often rely on a- priori knowledge of the state-space of the system. Nuclear materials, however, are often multi-component systems owing to the evolution of composition under irradiation and an approach based on a-priori mapping of phase diagram is often not enough. This work is aimed at demonstrating an on-the-fly surrogate modeling framework that uses active learning to reduce the number of full equilibrium calculations that must be performed. By combining with efficient coupling approaches, the surrogate framework helps in reducing the computational cost of thermodynamic equilibrium informed multiphysics simulations of nuclear materials. The performance is benchmarked against full coupling with the thermochemistry library Thermochimica [3]. This work uses a machine learning based approach for constructing surrogate models to predict the stable phases in a multicomponent system. The surrogates were constructed using neural networks and Gaussian process classification. In this work, we compare the relative performance of the two methods. We also demonstrate the use of caching previous calculations by interpolating the values from nearest neighbors. References [1] Lindsay, A.D., et al. "2.0 – MOOSE: Enabling massively parallel multiphysics simulation", SoftwareX, 20 (2022): 101202. [2] Roos, W.A. and Zietsman J.H. "Accelerating complex chemical equilibrium calculations – A Review", Calphad, 77 (2022): 102380. [3] Piro, M.H.A., et al. "The thermochemistry library Thermochimica", Computational Materials Science, 67 (2013): 266-272.

36 MATERIALS SCIENCE↗

DOE OSTI2013

DOMINO: A fast 3D cartesian discrete ordinates solver for reference PWR simulations and SPN validation

As part of its activity, EDF R and D is developing a new nuclear core simulation code named COCAGNE. This code relies on DIABOLO, a Simplified PN (SPN) method to compute the neutron flux inside the core for eigenvalue calculations. In order to assess the accuracy of SPN calculations, we have developed DOMINO, a new 3D Cartesian SN solver. The parallel implementation of DOMINO is very efficient and allows to complete an eigenvalue calculation involving around 300 x 10{sup 9} degrees of freedom within a few hours on a single shared-memory supercomputing node. This computation corresponds to a 26-group S{sub 8} 3D PWR core model used to assess the SPN accuracy. At the pin level, the maximal error for the SP{sub 5} DIABOLO fission production rate is lower than 0.2% compared to the S{sub 8} DOMINO reference for this 3D PWR core model. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2016

Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory

We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we develop a generalized framework for performing OF-DFT simulations with different variants of the electronic kinetic energy. In particular, we propose a self-consistent field (SCF) type fixed-point method for calculations involving linear-response kinetic energy functionals. In this framework, evaluation of both the electronic ground-state and forces on the nuclei are amenable to computations that scale linearly with the number of atoms. We develop a parallel implementation of this formulation using the finite-difference discretization. We demonstrate that higher-order finite-differences can achieve relatively large convergence rates with respect to mesh-size in both the energies and forces. Additionally, we establish that the fixed-point iteration converges rapidly, and that it can be further accelerated using extrapolation techniques like Anderson's mixing. We validate the accuracy of the results by comparing the energies and forces with plane-wave methods for selected examples, including the vacancy formation energy in Aluminum. Overall, the suitability of the proposed formulation for scalable high performance computing makes it an attractive choice for large-scale OF-DFT calculations consisting of thousands of atoms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗

DOE OSTI2016

Accelerating the Mining of Influential Nodes in Complex Networks through Community Detection

Computing the set of influential nodes with a given size to ensure maximal spread of influence on a complex network is a challenging problem impacting multiple applications. A rigorous approach to influence maximization involves utilization of optimization routines that comes with a high computational cost. In this work, we propose to exploit the existence of communities in complex networks to accelerate the mining of influential seeds. We provide intuitive reasoning to explain why our approach should be able to provide speedups without significantly degrading the extent of the spread of influence when compared to the case of influence maximization without using the community information. Additionally, we have parallelized the complete workflow by leveraging an existing parallel implementation of the Louvain community detection algorithm. We then conduct a series of experiments on a dataset with three representative graphs to first verify our implementation and then demonstrate the speedups. Our method achieves speedups ranging from 3x - 28x for graphs with small number of communities while nearly matching or even exceeding the activation performance on the entire graph. Complexity analysis reveals that dramatic speedups are possible for larger graphs that contain a correspondingly larger number of communities. In addition to the speedups obtained from the utilization of the community structure, scalability results show up to 6.3x speedup on 20 cores relative to the baseline run on 2 cores. Finally, current limitations of the approach are outlined along with the planned next steps.

community detection↗

DOE OSTI2016

Poster - 19: Investigation of Electron Reference Dosimetry Based on Optimal Chamber Shift

An addendum/revision to AAPM TG-51 electron reference dosimetry is highly expected to meet the clinical requirement with the increasing usage of new ion chambers not covered in TG-51. A recent study, Med. Phys. 41, 111701, proposed a new fitting equation for the beam quality conversion factor k’{sub Q} to a wide spectrum of chambers. In the study, an optimal Effective Point of Measurement (EPOM) from Monte Carlo calculations was recommended and the fitting parameters to k’{sub Q} was based on it. We investigated the absolute dose obtained based on the optimal EPOM method and the original TG-51 method with k’{sub R50} determined differently. The results showed that using the Markus curve is a better choice than the well-guarded chamber fitting for an IBA PPC-05 parallel plate chamber if we need to strictly follow the AAPM TG-51 protocol. We also examined the usage of the new fitting equation with measurement performed at the physical EPOM, instead of the optimal EPOM. The former is more readily determined and more practical in clinics. Our study indicated that the k’{sub Q} fitting based on the optimal EPOM can be used to measurement at the physical EPOM with no significant clinical impact. The inclusion of Farmer chamber gradient correction P{sub gr} in k’{sub Q}, as in the mentioned study, asks for the precise positioning of chamber center at dref. It is not recommended in clinics to avoid over-correction for low electron energies, especially for an institute having matching Linacs implemented.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Solar panel truss mounting systems and methods

An exemplary embodiment of the present invention provides a solar panel truss mounting system comprising a base and a truss assembly coupled to the base. The truss assembly comprises a first panel rail mount, second panel rail mount parallel to the first panel rail mount, base rail mount parallel to the first and second panel rail mounts, and a plurality of support members. A first portion of the plurality of support members extends between the first and second panel rail mounts. A second portion of the plurality of support members extends between the first panel rail mount and the base rail mount. A third portion of the plurality of support members extends between the second panel rail mount and the base rail mount. The system can further comprise a plurality of connectors for coupling a plurality of photovoltaic solar panels to the truss assembly.

14 SOLAR ENERGY↗

DOE OSTI2016

Solar panel truss mounting systems and methods

14 SOLAR ENERGY↗

DOE OSTI2018

Solar panel truss mounting systems and methods

14 SOLAR ENERGY↗

DOE OSTI2019

Solar panel truss mounting systems and methods

Goodman, Joseph Neal↗

DOE OSTI2019

Quantum interferences among Dexter energy transfer pathways

Dexter energy transfer in chemical systems moves an exciton (i.e., an electron–hole pair) from a donor chromophore to an acceptor chromophore through a bridge by a combination of bonded and non-bonded interactions. The transition is enabled by both one-electron/one-particle and two-electron/two-particle interaction mechanisms. Assuming that there is no real intermediate state population of an electron, hole, or exciton in the bridge, the transport involves two states that are coupled non-adiabatically. As such, coherent quantum interferences arise among the Dexter energy coupling pathways. These interferences, while related to well understood interferences in single-electron transfer, are much richer because of their two particle nature: the transfer of a triplet exciton involves the net transfer of both an electron and a hole. Despite this additional complexity, simple rules can govern Dexter coupling pathway interferences in special cases. As in the case of single-electron transfer, identical parallel coupling pathways can be constructively interfering and may enhance the Dexter transfer rate. Because of the virtual particle combinatorics associated with two-particle superexchange, two parallel Dexter coupling routes may be expected to enhance Dexter couplings by more than a factor of two. Here we explore Dexter coupling pathway interferences in non-covalent assemblies, employing a method that enables the assessment of Dexter coupling pathway strengths and interferences, in the context of one-particle and two-particle coupling interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

A scalable nonlinear fluid–structure interaction solver based on a Schwarz preconditioner with isogeometric unstructured coarse spaces in 3D

Nonlinear fluid-structure interaction (FSI) problems on unstructured meshes in 3D appear many applications in science and engineering, such as vibration analysis of aircrafts and patient-specific diagnosis of cardiovascular diseases. In this work, we develop a highly scalable, parallel algorithmic and software framework for FSI problems consisting of a nonlinear fluid system and a nonlinear solid system, that are coupled monolithically. The FSI system is discretized by a stabilized finite element method in space and a fully implicit backward difference scheme in time. To solve the large, sparse system of nonlinear algebraic equations at each time step, we propose an inexact Newton-Krylov method together with a multilevel, smoothed Schwarz preconditioner with isogeometric coarse meshes generated by a geometry preserving coarsening algorithm. Here ''geometry'' includes the boundary of the computational domain and the wet interface between the fluid and the solid. We show numerically that the proposed algorithm and implementation are highly scalable in terms of the number of linear and nonlinear iterations and the total compute time on a supercomputer with more than 10,000 processor cores for several problems with hundreds of millions of unknowns.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

A domain decomposition method of stochastic PDEs: An iterative solution techniques using a two-level scalable preconditioner

Recent advances in high performance computing systems and sensing technologies motivate computational simulations with extremely high resolution models with capabilities to quantify uncertainties for credible numerical predictions. A two-level domain decomposition method is reported in this investigation to devise a linear solver for the large-scale system in the Galerkin spectral stochastic finite element method (SSFEM). In particular, a two-level scalable preconditioner is introduced in order to iteratively solve the large-scale linear system in the intrusive SSFEM using an iterative substructuring based domain decomposition solver. The implementation of the algorithm involves solving a local problem on each subdomain that constructs the local part of the preconditioner and a coarse problem that propagates information globally among the subdomains. The numerical and parallel scalabilities of the two-level preconditioner are contrasted with the previously developed one-level preconditioner for two-dimensional flow through porous media and elasticity problems with spatially varying non-Gaussian material properties. A distributed implementation of the parallel algorithm is carried out using MPI and PETSc parallel libraries. The scalabilities of the algorithm are investigated in a Linux cluster.

42 ENGINEERING↗