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DOE OSTI2020

Spray Mechanism of Contained-Electrospray Ionization

Analytical characteristics of contained electrospray ionization (ESI) are summarized in terms of its potential to modify the analyte solution during the stages of droplet formation to provide opportunities to generate native versus denatured biomolecular gas-phase ions, without the need for bulk-phase analyte modifications. The real-time modification of the charged microdroplets occurs in a cavity that is included in the outlet of the contained-ESI ion source. Close examination of the inside of the cavity using a high-speed camera revealed the formation of discrete droplets as well as thin liquid films in the droplets wake. When operated at 20 psi N2 pressure, the droplets were observed to move at an average speed of 8 mm/s providing ~1 s mixing time in a 10 mm cavity length. Evidence is provided for the presence of highly reactive charged droplets based on myoglobin charge state distribution, apo-myoglobin contents, and ion mobility drift time profiles under different spray conditions. Mechanistic insights for the capture of vapor-phase reagents and droplet dynamics as influenced by different operational modes are also described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Axisymmetric gyrokinetic simulation of ASDEX-Upgrade scrape-off layer using a conservative implicit BGK collision operator

Collisions play an important role in turbulence and transport of fusion plasmas. For kinetic simulations, as the collisionality increases in the domain of interest, the size of the time step to resolve the collisional physics can become overly restrictive in an explicit time integration scheme, leading to high computational cost. With the aim of overcoming such restriction, we have implemented an implicit Bhatnagar–Gross–Krook (BGK) collision operator for use in the discontinuous Galerkin full-f gyrokinetic solver within the Gkeyll framework, which, when combined with Gkeyll's traditional explicit time integrator for collisionless advection, can significantly increase the time step in gyrokinetic simulations of highly collisional regimes. To ensure conservation of density, momentum, and energy, we utilize an iterative scheme to correct the discretized approximation to the equilibrium Maxwellian distribution to which the BGK collision operator relaxes. We have further generalized the BGK infrastructure, both the implicit scheme and the correction routine, to handle cross-species collisions. This improved implicit and conservative BGK operator is benchmarked against the more accurate but more computationally expensive Lenard–Bernstein–Dougherty (LBD) operator, which has been utilized in prior studies with Gkeyll. The implicit BGK operator enables 2D axisymmetric simulations of the ASDEX-Upgrade scrape-off layer to run 56 times faster to completion than the simulations with the LBD operator, because the BGK operator is more robust and converges at a lower resolution than is required by the LBD operator. Additionally, in this more collisional limit, we demonstrate that the results of our simulations utilizing the implicit BGK operator agreed well with simulations utilizing the more computationally expensive LBD operator.

Gyrokinetic simulations↗

DOE OSTI2022

Exotic invertible phases with higher-group symmetries

We investigate a family of invertible phases of matter with higher-dimensional exotic excitations in even spacetime dimensions, which includes and generalizes the Kitaev’s chain in 1+1d. The excitation has \mathbb{Z}_2 ℤ 2 higher-form symmetry that mixes with the spacetime Lorentz symmetry to form a higher group spacetime symmetry. We focus on the invertible exotic loop topological phase in 3+1d. This invertible phase is protected by the \mathbb{Z}_2 ℤ 2 one-form symmetry and the time-reversal symmetry, and has surface thermal Hall conductance not realized in conventional time-reversal symmetric ordinary bosonic systems without local fermion particles and the exotic loops. We describe a UV realization of the invertible exotic loop topological order using the SO(3)_- S O ( 3 ) − gauge theory with unit discrete theta parameter, which enjoys the same spacetime two-group symmetry. We discuss several applications including the analogue of ``fermionization’’ for ordinary bosonic theories with \mathbb{Z}_2 ℤ 2 non-anomalous internal higher-form symmetry and time-reversal symmetry.

Hsin, Po-Shen↗

DOE OSTI2021

PyGDH: Python Grid Discretization Helper

Mathematical models expressed in the form of discretized equations play an important role inmany scientific disciplines. In our experience, few domain scientists have sufficient backgroundin numerical computing (or the time required to acquire such a background) to use manyflexible and powerful but complex open source packages, such as FEniCS (Alnæs et al., 2015)and OpenFOAM (The OpenFOAM Foundation Ltd, n.d.). Many user-friendly open sourcepackages, such as FiPy (J. E. Guyer & Warren, 2009), and many commercial packages, suchas COMSOL Multiphysics (COMSOL AB, n.d.) and Simcenter STAR-CCM+ (Siemens DigitalIndustries Software, n.d.), provide limited flexibility in the equations that users can express.Additionally, the use of commercial packages, which by nature do not perform calculationstransparently, can hinder reproducibility, which is vital to the scientific process. PyGDH(“pigged”) is a Python 2 / Python 3 (Python Software Foundation, 1991–2020) package thatis meant to be accessible to scientists who might not be specialists in scientific computing,while approaching the level of flexibility associated with writing dedicated programs tailoredto solving specific problems. The PyGDH User’s Guide provides detailed instructions forcreating numerical models, including a brief introduction to necessary command line andPython (Python Software Foundation, 1991–2020) skills, and discussions of discretization andvalidation. Note that PyGDH emphasizes flexibility and simplicity over performance, and wasnot designed for high-performance applications or models describing complex spatial domains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Primitive quantum gates for an S U ( 3 ) discrete subgroup: Σ ( 36 × 3 )

We construct the primitive gate set for the digital quantum simulation of the 108-element Σ ( 36 × 3 ) group. This is the first time a non-Abelian crystal-like subgroup of S U ( 3 ) has been constructed for quantum simulation. The gauge link registers and necessary primitives—the inversion gate, the group multiplication gate, the trace gate, and the Σ ( 36 × 3 ) Fourier transform—are presented for both an eight-qubit encoding and a heterogeneous three-qutrit plus two-qubit register. For the latter, a specialized compiler was developed for decomposing arbitrary unitaries onto this architecture. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Devising novel methods for the controlled synthesis with morphology and size control of scintillator materials

Nanoscale scintillators represent an important class of materials underlying the functioning of high resolution, high ‘light yield’ radiation detection equipment, applicable for medicine in addition to security and environmental monitoring. This current study has focused on the controlled synthesis of Cs 2 ZnX 4 (X = Cl, Br) not only due to its very fast and promising radioluminescence decay time but also because no reliable synthesis protocols have been reported for producing nanoscale motifs of this material, to date. Solution-based methods can be used to synthesize products, possessing different, discrete morphologies with the ability to dictate particle size and shape. Specifically, we have demonstrated that a hot injection technique can be used to fabricate nanoscale rods and plates. Using this method, we systematically studied the effect of varying reaction variables, such as (i) reaction temperature, (ii) surfactants, and (iii) reaction time. As synthesized nanorods of Cs 2 ZnCl 4 possessed lengths of 101.3 ± 24.4 nm with widths of 17.3 ± 4.5 nm, whereas Cs 2 ZnBr 4 , created under identical conditions, were characterized by lengths of 206 ± 50 nm and widths of 26.7 ± 12.6 nm. Ligand-assisted re-precipitation (LARP) was used to produce the corresponding micron-sized particles. Under these conditions, we successfully synthesized spindles and spherical particles of Cs 2 ZnCl 4 with sizes of 1.58 ± 0.16 μm and 1.03 ± 0.34 μm, respectively, whereas plates of Cs 2 ZnBr 4 were prepared with average sizes of 0.76 ± 0.21 μm. High resolution synchrotron mapping, using the hard X-ray nanoprobe at NSLS II, was used to confirm the expected spatial distribution of Cs, Zn, and Cl within the as-produced crystals. Nanorods of Cs 2 ZnCl 4 and Cs 2 ZnBr 4 were subsequently tested for scintillation light yield and decay times. Preliminary results showed that Cs 2 ZnCl 4 maintained a light yield of 100–300 photons per MeV with a fast decay component of 2.6 ns. Finally, the Cs 2 ZnBr 4 analogue did not give rise to any perceptible scintillation emission.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Adaptive immersed isogeometric level-set topology optimization

Here, this paper presents for the first time an adaptive immersed approach for level-set topology optimization using higher-order truncated hierarchical B-spline discretizations for design and state variable fields. Boundaries and interfaces are represented implicitly by the iso-contour of one or multiple level-set functions. An immersed finite element method, the eXtended IsoGeometric Analysis, is used to predict the physical response. The proposed optimization framework affords different adaptively refined higher-order B-spline discretizations for individual design and state variable fields. The increased continuity of higher-order B-spline discretizations together with local refinement enables direct control over the accuracy of the representation of each field while simultaneously reducing computational cost compared to uniformly refined discretizations. A flexible mesh adaptation strategy enables local refinement based on geometric measures or physics-based error indicators. These adaptive discretization and analysis approaches are integrated into gradient-based optimization schemes, evaluating the design sensitivities using the adjoint method. Numerical studies illustrate the features of the proposed framework with static, linear elastic, multi-material, two- and three-dimensional problems. The examples provide insight into the effect of refining the design variable field on the optimization result and the convergence rate of the optimization process. Using coarse higher-order B-spline discretizations for level-set fields promotes the development of smooth designs and suppresses the emergence of small features. Moreover, adaptive mesh refinement for state variable fields results in a reduction of overall computational cost. Higher-order B-spline discretizations are especially interesting when evaluating gradients of state variable fields due to their higher inter-element continuity.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Challenges of measuring spin Seebeck noise

Just as electronic shot noise in driven conductors results from the granularity of charge and the statistical variation in the arrival times of charge carriers, there are predictions for fundamental noise in magnon currents due to angular momentum being carried by discrete excitations. The inverse spin Hall effect as a transduction mechanism to convert spin current into charge current raises the prospect of experimental investigations of such magnon shot noise. Spin Seebeck effect measurements have demonstrated the electrical detection of thermally driven magnon currents and have been suggested as an avenue for accessing spin current fluctuations. Using spin Seebeck structures made from yttrium iron garnet on gadolinium gallium garnet, we demonstrate the technical challenges inherent in such noise measurements. While there is a small increase in voltage noise in the inverse spin Hall detector at low temperatures associated with adding a magnetic field, the dependence on field orientation implies that this is not due to magnon shot noise. We describe theoretical predictions for the expected magnitude of magnon shot noise, highlighting ambiguities that exist. Further, we show that magnon shot noise detection through the standard inverse spin Hall approach is likely impossible due to geometric factors. Implications for future attempts to measure magnon shot noise are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Particle scale impacts on deconstruction energy of pine residues

The goal of this Case Study was to quantify the impacts of variable moisture and ash on hammer mill throughput and energy consumption and on generation of fines that are not able to be fed to conversion, as compared to a status quo Base Case system. Also considered was convertible carbon content (minimum carbon specification) and maximum ash content and the delivered feedstock cost impacts of not being able to feed residue not meeting both specifications to the conversion reactor. Laboratory data on the impacts of input particle size and moisture content on the exit particle size were received from FCIC Subtask 5.2 from their single particle impact population balance modeling study. Additional throughput and energy consumption data were obtained from FCIC Subtask 5.2 for the same grinder with a 6 mm screen in place. These data were utilized to develop the necessary response surface equations to perform throughput analysis using discrete event simulation. Because the ash contents in the separated fines had not been analyzed in the laboratory at the time of the model runs, we chose to assume that the ash distributed proportionally with total mass into the overs and unders in the disk screen following grinding. Key takeaways from this Case Study are that it is significantly more cost effective to hammer mill the residue prior to drying, even though the grinder throughput is lower and energy consumption is higher versus drying first before grinding. An effect of dry grinding versus high moisture grinding is the production of higher amounts of fines during dry grinding, leading to significantly more of the ground feedstock being rejected by conversion for being below a minimum particle size. With wet grinding the system is still able to produce more preprocessed feedstock meeting the minimum particle size specification even though the instantaneous throughput is lower than for the case of grinding dry feedstock. Additionally, even without the higher fines production from dry grinding, the status quo would still be more costly than wet grinding because the material is rejected after the drying energy has already been input for the dry grinding case. Finally, significant reductions in drying energy are obtained by drying after grinding, and those reductions are of far greater magnitude than the grinding energy increase.

09 BIOMASS FUELS↗

DOE OSTI2021

Benchmarking numerical methods for impact and cratering applications

Large scale computational models are important for studying impact cratering events that are prevalent both on Earth and, more broadly, in this solar system. To address these problems, models must reliably account for both large length scales (e.g., kilometers) and relatively long time scales (hundreds of seconds). This work benchmarks two such approaches, a more traditional hydrodynamics approach and a finite-discrete element method (FDEM), for impact cratering applications. Both 2D and 3D results are discussed for two different impact velocities, 5 km/s and 20 km/s, striking normal to the target and, for 3D simulations, 45° from vertical. In addition, comparisons to previously published data are presented. Finally, differences in how these methods model damage are discussed. Ultimately, both approaches show successful modeling of several different impact scenarios.

58 GEOSCIENCES↗

DOE OSTI2022

Fractional Buffer Layers: Absorbing Boundary Conditions for Wave Propagation

Not provided.

Physics↗

DOE OSTI2023

Particle Scale Impacts on Deconstruction Energy of Pine Residues

energy consumption↗

DOE OSTI2023

Exascale Multiphysics Nuclear Reactor Simulations for Advanced Designs

ENRICO is a coupled application developed under the U.S. Department of Energy's Exascale Computing Project (ECP) targeting the modeling of advanced nuclear reactors. It couples radiation transport with heat and fluid simulation, including the high-fidelity, highresolution Monte-Carlo code Shift and the Computational fluid dynamics code NekRS. NekRS is a highly-performant open-source code for simulation of incompressible and low-Mach fluid flow, heat transfer, and combustion with a particular focus on turbulent flows in complex domains. It is based on rapidly convergent high-order spectral element discretizations that feature minimal numerical dissipation and dispersion. State-of-the-art multilevel preconditioners, efficient high-order time-splitting methods, and runtime-adaptive communication strategies are built on a fast OCCA-based kernel library, libParanumal, to provide scalability and portability across the spectrum of current and future high-performance computing platforms. On Frontier, Nek5000/RS has recently achieved an unprecedented milestone in breaching over 1 billion spectral elements and 350 billion degrees of freedom. Shift has demonstrated the capability to transport upwards of 1 billion particles per second in full core nuclear reactor simulations featuring complete temperature-dependent, continuous-energy physics on Frontier. Shift achieved a weak-scaling efficiency of 97.8% on 8192 nodes of Frontier and calculated 6 reactions in 214,896 fuel pin regions below 1% statistical error yielding first-of-a-kind resolution for a Monte Carlo transport application.

Hamilton, Steven P.↗

DOE OSTI2020

A Comparison of Groundwater Sampling Technologies, Including Passive Diffusion Sampling, for Radionuclide Contamination - 20205

Using traditional high-flow purge methods for long-term water quality monitoring of deep groundwater wells can be expensive, affect contaminant migration, and produce excessive volumes of discharge water that can be difficult to manage. The use of low-flow pumping methods and depth discrete bailers (DDBs) can reduce the cost of sampling deep groundwater wells. In general, using different pumping methods to obtain reproducible and representative groundwater can be challenging. Passive diffusion samplers (PDSs) have successfully been used in long-term monitoring for volatile organic compounds, major ions, and trace-elements, but application has been limited for stable and radioactive isotopes. Beginning in 2018, the United States Geological Survey (USGS) conducted three sampling events to test the ability of PDSs and DDBs to obtain reproducible and representative groundwater samples. The sampled well is completed in a regional, permeable carbonate aquifer and is one in a set of wells that have historically been used for tritium tracer testing. All samples were obtained at 180 m (590 ft) below land surface (bls) in a 13.97 cm (5.5 inch) uncased well that has a total depth of 202 m (662 ft) bls. The first sampling event deployed a regenerated cellulose dialysis membrane (RCDM) PDS for 14 days with deionized water as the blank. The second sampling event deployed a RCDM for 27 days also with deionized water as the blank. The third sampling event deployed a Dual Membrane (DM) PDS for 65 days using a blank of tritium-dead carbonate water. The DM PDS was used to assess the effect of longer term deployment on tritium concentrations and address whether or not the PDSs reached equilibrium with ambient groundwater. The day after each of the three passive samplers were retrieved a DDB was used to obtain discrete non-integrated groundwater samples. For each DDB sampling day, the bailer was lowered into the well 10 consecutive times to determine if the water chemistry changed from the first to the last bailed sample. Quality assurance samples including blanks and duplicates were obtained during all three sampling events. All blank waters had tritium concentrations less than 21±33 pCi/L. Major ion (e.g. calcium, chloride, sodium, and sulfate) results were compared between all samples obtained with RCDM and DDB. Major ion concentrations showed a coefficient of variation of less than 6% between all RCDM and DDB samples; however, the coefficient of variation between the different deployment times and the two different methods for trace-element concentrations was much larger, particularly for manganese (82%), lead (41%), and zinc (33%). Stable isotope values were compared between the RCDM and DDB samples. The DDB sample results all fell within analytical uncertainty and were considered representative of the formation groundwater. The stable isotope values from the RCDM samples indicated that a longer deployment time was necessary to gain equilibrium and to obtain representative groundwater samples. Tritium results from groundwater samples obtained from the RCDM, DM, and DDB indicate that groundwaters obtained with PDSs produced tritium concentrations 2 to 3 times higher (between 1,426 and 3,060±87 pCi/L) than groundwaters obtained with a DDB (479 to 1,219±51 pCi/L). The longer the passive diffusion samplers were deployed, the higher the tritium concentration, suggesting that equilibrium with tritium was not reached within a 27-day deployment. DDB samples showed tritium results declining from the first to the last bailed sample for all three sampling events. This research suggests that tritium results from groundwater samples obtained from PDSs are more reproducible than samples obtained from DDBs. Also, PDSs likely do not accumulate isotopes of water but rather equilibrate with the ambient groundwater. On the other hand, both PDSs and DDBs were able to provide representative groundwater samples for major ions and have the potential to produce representative groundwater samples for stable isotopes of water (δD and δ{sup 18}O). Utilizing the most effective method for sampling groundwater is important for long-term groundwater monitoring. Quantifying the ability of passive diffusion groundwater samplers to obtain representative radioactive chemistry samples will help determine if these methods can be a useful alternative to pumping and purging wells for long-term monitoring. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Additive Polynomial Time Integrators, Part I: Framework and Fully Implicit-Explicit Collocation Methods

In this paper we generalize the polynomial time integration framework to additively partitioned initial value problems. The framework we present is general and enables the construction of many new families of additive integrators with arbitrary order-of-accuracy and varying degree of implicitness. In this first work, we focus on a new class of implicit-explicit polynomial block methods that are based on fully implicit Runge–Kutta methods with Radau nodes and that possess high stage order. Here, we show that the new fully implicit-explicit (FIMEX) integrators have improved stability compared to existing IMEX Runge–Kutta methods, while also being more computationally efficient due to recent developments in preconditioning techniques for solving the associated systems of nonlinear equations. For PDEs on periodic domains where the implicit component is trivial to invert, we will show how parallelization of the right-hand side evaluations can be exploited to obtain significant speedup compared to existing serial IMEX Runge–Kutta methods. For parallel (in space) finite element discretizations, the new methods can achieve orders of magnitude better accuracy than existing IMEX Runge–Kutta methods and/or achieve a given accuracy several times times faster in terms of computational runtime.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Scalability of OpenFOAM Density-Based Solver with Runge–Kutta Temporal Discretization Scheme

Compressible density-based solvers are widely used in OpenFOAM, and the parallel scalability of these solvers is crucial for large-scale simulations. In this paper, we report our experiences with the scalability of OpenFOAM’s native rhoCentralFoam solver, and by making a small number of modifications to it, we show the degree to which the scalability of the solver can be improved. The main modification made is to replace the first-order accurate Euler scheme in rhoCentralFoam with a third-order accurate, four-stage Runge-Kutta or RK4 scheme for the time integration. The scaling test we used is the transonic flow over the ONERA M6 wing. This is a common validation test for compressible flows solvers in aerospace and other engineering applications. Numerical experiments show that our modified solver, referred to as rhoCentralRK4Foam, for the same spatial discretization, achieves as much as a 123.2% improvement in scalability over the rhoCentralFoam solver. As expected, the better time resolution of the Runge–Kutta scheme makes it more suitable for unsteady problems such as the Taylor–Green vortex decay where the new solver showed a 50% decrease in the overall time-to-solution compared to rhoCentralFoam to get to the final solution with the same numerical accuracy. Finally, the improved scalability can be traced to the improvement of the computation to communication ratio obtained by substituting the RK4 scheme in place of the Euler scheme. All numerical tests were conducted on a Cray XC40 parallel system, Theta, at Argonne National Laboratory.

Li, Sibo↗

DOE OSTI2024

A new method for solving the linearized 1D Vlasov–Poisson system yielding a new class of solutions

We describe a new method for solving the linearized 1D Vlasov–Poisson system by using properties of Cauchy-type integrals. Our method remedies critical flaws of the two standard methods, reveals a previously unrecognized Gaussian-in-time-like decay, and can also account for an externally applied electric field. The Landau approximation involves deforming the Bromwich contour around the poles closest to the real axis due to the analytically continued dielectric function, finding the long-time behavior for a stable system: Landau damping. Jackson's generalization encircles all poles while sending the contour to infinity, assuming its contribution vanishes, which is not true in general. This gives incorrect solutions for physically reasonable configurations and can exhibit pathological behavior, of which we show examples. The van Kampen method expresses the solution for a stable equilibrium as a continuous superposition of waves, resulting in an opaque integral. Case's generalization includes unstable systems and predicts a decaying discrete mode for each growing discrete mode, an apparent contradiction to both the Jackson solution and ours. We show, without imposing additional constraints, that the decaying modes are never present in the time evolution due to an exact cancellation with part of the continuum. Our solution is free of integral expressions, is obtained using algebra and Laurent series expansions, does not rely on analytic continuations, and results in a correct asymptotically convergent form in the case of infinite sums. The analysis used can be readily applied in higher-dimensional, electromagnetic systems and also provides a new technique for evaluating certain inverse Laplace transforms.

Physics↗