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DOE OSTI2021

Automated theoretical chemical kinetics: Predicting the kinetics for the initial stages of pyrolysis

Large scale implementation of high level computational theoretical chemical kinetics offers the prospect for dramatically improving the fidelity of combustion chemical modeling. To facilitate such efforts, we have developed a suite of codes, collectively referred to as AutoMech, that allow for the automatic prediction of the kinetics for large sets of reactions via ab initio transition-state-theory based master-equation calculations. The primary input is simply the mechanism, a dictionary relating chemically identifiable species descriptors (e.g., SMILES or InChIs) to species labels in the mechanism, and a specification of the electronic structure and transition state theory models to be implemented. Here we illustrate the current utility of AutoMech through a study of the initial stages of pyrolysis for 3 sets of fuels: sequences of alkanes, alcohols, and aldehydes. For simplicity, the analysis focuses on abstractions from the fuel by H, CH 3 , and OH, and the decomposition of the resulting radicals. Altogether, there are a total of 166 input channels in these sets (more than 363 forward reactions when expanded to the full set of elementary reactions). The code successfully produces high quality rate estimates (with apparent uncertainties less than a factor of two in limited comparisons with experiment) for > 95% of these. For the radical decomposition reactions, the analysis includes predictions for the pressure dependence of the kinetics. This wide-ranging exploration illustrates (i) the effect of different levels of prediction on the expected accuracy, (ii) the branching between abstractions at different sites for different abstractors, (iii) the dependence of the rates on the chemical structure, and (iv) the variation in radical stabilities across chemical families. These results, as well as the demonstrated feasibility of the methodology, should find further utility in the development of accurate rate expressions for arbitrary fuels. (c) 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Elliott, Sarah N.↗

DOE OSTI2021

Implementation of Relativistic Coupled Cluster Theory for Massively Parallel GPU-Accelerated Computing Architectures

In this paper, we report reimplementation of the core algorithms of relativistic coupled cluster theory aimed at modern heterogeneous high-performance computational infrastructures. The code is designed for parallel execution on many compute nodes with optional GPU coprocessing, accomplished via the new ExaTENSOR back end. The resulting ExaCorr module is primarily intended for calculations of molecules with one or more heavy elements, as relativistic effects on the electronic structure are included from the outset. In the current work, we thereby focus on exact two-component methods and demonstrate the accuracy and performance of the software. The module can be used as a stand-alone program requiring a set of molecular orbital coefficients as the starting point, but it is also interfaced to the DIRAC program that can be used to generate these. We therefore also briefly discuss an improvement of the parallel computing aspects of the relativistic self-consistent field algorithm of the DIRAC program.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Prediction of the energetic particle redistribution by an improved critical gradient model and analysis of the transport threshold

Based on the theory of critical gradient model (CGM) and following the simulation method proposed by Waltz et al., a combination of TGLFEP and EPtran code is employed to predict the energetic particle (EP) transport induced by Alfvén eigenmodes (AEs). To be consistent with the experiment, recent improvements to the simulation method include consideration of threshold evolution and orbit loss due to finite orbit width. The revised CGM is applied to simulate two DIII-D experimental discharges (#142111 and #153071). It well reproduces the experimental profiles with multiple unstable AEs and large-scale EP transport. Discharge #142111 had previously been simulated using a nonlinear MHD-kinetic code MEGA with a transport mechanism based on stochasticity induced by overlapping AE. By comparing the simulated EP profiles, we find that the AE transport threshold is approximated by both the MEGA nonlinear stability threshold and the proposed CGM threshold (error <5% for single n and <17% for multiple n simulation). Both of them are larger than the linear stability threshold of the most unstable AE mode by a quantity of the order of the flux needed to sustain EP transport by the background turbulence. Additionally, we have also applied the improved CGM to simulate the α particle redistribution for a China Fusion Engineering Test Reactor steady state scenario. Because of the clear separation between the AE unstable region and the loss cone, only a moderate α particle loss of ~9.6% is predicted.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Enhanced sensitivity to target offset when using cross-beam energy transfer mitigation techniques in direct-drive inertial confinement fusion implosions

In direct-drive inertial confinement fusion, target offset from the target chamber center (or center of beam convergence) may lead to significant implosion asymmetry and fusion yield degradation. In addition, cross-beam energy transfer (CBET) has been shown to be a significant source of laser energy scattering and leads to a reduction in implosion velocity and yield. To improve energy coupling and implosion performance, several techniques for CBET mitigation have been proposed. Recent simulations, however, have shown that CBET also substantially mitigates the effect of target offset on implosion asymmetry and yield [Anderson et al., Phys. Plasmas 27, 112713 (2020)]. Furthermore, the inclusion of CBET models in radiation-hydrodynamics codes was shown to greatly improve agreement between simulations and experiments involving substantial target offset distances. This paper explores the intensity dependence of this CBET–offset effect. In addition, it is shown that enhanced sensitivity to target offset can be expected when CBET-mitigation techniques are used in direct-drive implosions. This is shown through simulations of two such CBET-mitigation techniques on the OMEGA laser: (1) decreased beam-to-target radius, and (2) beam-to-beam frequency detuning. For the typical target offset distances (<15 μm) observed in experiments on OMEGA, however, overall yield is still anticipated to be substantially higher when CBET-mitigation techniques are employed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Numerical simulation of the hot-tail runaway electron production mechanism using CQL3D and comparison with Smith–Verwichte analytical model

Abstract The hot-tail mechanism of runaway electron (RE) production (Harvey et al 2000 Phys. Plasmas 7 4590) is the primary source of RE in the case of rapidly cooling tokamak plasma. Quantifying this mechanism is very important as it can provide most of the post-thermal-quench (TQ) current, or a seed current for the secondary source of RE through the avalanche mechanism. An analytic model which omits pitch-angle scattering is often used in literature for estimating the hot-tail RE density (Smith and Verwichte 2008 Phys. Plasmas 15 072502). In the present study, we use the CQL3D bounce-averaged Fokker–Planck code (Harvey and McCoy 1992 Proc. IAEA Technical Committee Meeting on Advances in Simulation and Modeling of Thermonuclear Plasmas p 527) to test the limits of validity of the model. In particular, we examine the cases of Z = 1 and Z = 18 ions, for sets of different initial temperature, density, electric field and the characteristic time of temperature decay. We show that for Z = 1 plasma, the ratio of RE density computed by CQL3D to that estimated from the model is within 0.6–6.0 in studied cases. For the Z = 18 case, this factor is systematically a much smaller number, typically 0.02–0.6. We suggest a simple correction to the model that narrows down the range of this ratio to 0.3–3.8 in all of the cases, including Z = 1 and Z = 18 plasmas.

Physics↗

DOE OSTI2022

Measuring the mass of the black widow PSR J1555-2908

ABSTRACT Accurate measurements of the masses of neutron stars are necessary to test binary evolution models, and to constrain the neutron star equation of state. In pulsar binaries with no measurable post-Keplerian parameters, this requires an accurate estimate of the binary system’s inclination and the radial velocity of the companion star by other means than pulsar timing. In this paper, we present the results of a new method for measuring this radial velocity using the binary synthesis code Icarus. This method relies on constructing a model spectrum of a tidally distorted, irradiated star as viewed for a given binary configuration. This method is applied to optical spectra of the newly discovered black widow PSR J1555–2908. By modeling the optical spectroscopy alongside optical photometry, we find that the radial velocity of the companion star is 397 ± 4 km s−1 (errors quoted at 95 per cent confidence interval), as well as a binary inclination of >75°. Combined with γ-ray pulsation timing information, this gives a neutron star mass of 1.67$^{+0.15}_{-0.09}$ M⊙ and a companion mass of 0.060$^{+0.005}_{-0.003}$ M⊙, placing PSR J1555–2908 at the observed upper limit of what is considered a black widow system.

Kennedy, M. R.↗

DOE OSTI2025

Impact of increased smoothing by spectral dispersion bandwidth on stimulated Brillouin scattering in laser driven Hohlraums

Experiments were conducted at the National Ignition Facility (NIF) to investigate the impact of increased smoothing by spectral dispersion (SSD) bandwidth on the production of stimulated Brillouin scattering (SBS) within an indirect-drive inertial confinement fusion (ICF) Hohlraum. This was done in a subscale gold Hohlraum driven by 192 laser beams depositing 1.1 MJ of energy. The laser bandwidth was increased from 45 to 118 GHz (before frequency tripling) on the 30° and 50° cones, where backscatter could be measured using the Full Aperture Backscatter Station (FABS). It was expected that this 2.6-fold increase in bandwidth would suppress SBS generated within the Hohlraum plasma and lower the backscattered SBS energy on the 50° cones by over a factor of four. Experimental results, however, show that this SSD change only reduced the 50° cone SBS during the main capsule drive by -18±31% and -4.5±7.8% over the entire pulse. This is small compared to expected shot-to-shot SBS reproducibility (∼30%), such that the result can be considered within normal performance fluctuations. New 3D parallel paraxial code (pF3D) simulations, accounting for beam refractive intensification reproduce this result, suggesting that closer to 300 GHz of bandwidth would have been required to mitigate SBS to the expected level. Delivering such a high bandwidth is not feasible at NIF when operating at high peak power and would potentially prevent NIF’s ability to use cross-beam energy transfer (CBET) for implosion symmetry tuning.

Physics↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.23

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Modeling Snowflake Divertors in MAST-U Tokamak

We report that in a snowflake (SF) divertor, two magnetic field nulls are placed close to each other, creating four strike points (SPs) compared to two in a standard X-point divertor. In preparation for MAST-U experiments, magnetic configurations with the standard and SF divertors with various locations and separation distances of the nulls were modeled using the two-dimensional multi-fluid code UEDGE with a full plasma transport model featuring charge-state-resolved sputtered carbon impurities. The complex interplay of the plasma transport and magnetic configurations was comprehensively studied using a simple model for the theoretically predicted fast plasma mixing driven by the 'churning' mode instability in the two-null SF region. The modeling results show that (1) all SF-plus configurations and SF-minus configuration with closely located nulls produce the same plasma parameters and heat fluxes at the same SPs; (2) SF divertors approach the outer and inner SP detachment conditions at lower upstream density w.r.t. the standard divertor; (3) heat flux profiles at primary SPs are substantially broadened and peak values are reduced in SF configurations w.r.t. SN divertors; this broadening becomes more pronounced with the fast plasma mixing increase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H 2 O 2 -producing enzymes with H 2 O 2 -consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Nonlinear excitation of energetic particle driven geodesic acoustic mode by resonance overlap with Alfvén instability in ASDEX Upgrade

The Alfvén instability nonlinearly excited the energetic-particle-driven geodesic acoustic mode on the ASDEX-Upgrade tokamak, as demonstrated experimentally. The mechanism of the energetic-particle-driven geodesic acoustic mode excitation and the mode nonlinear evolution is not yet fully understood. In the present work, a first-principles simulation using the MEGA code investigated the mode properties in both the linear growth and nonlinear saturated phases. Here we show that the simulation successfully reproduced the excitation and coexistence of these two modes, and agreed with the experimental results well. Conclusive evidence showed that the resonance overlap is the excitation mechanism of the energetic-particle-driven geodesic acoustic mode. In the linear growth phase, energetic particles that satisfied different resonance conditions excited the Alfvén instability, which then caused energetic particle redistribution in phase space. These redistributed energetic particles caused resonance overlap, exciting the energetic-particle-driven geodesic acoustic mode in the nonlinear phase.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

First observation of increased DT yield over prediction due to addition of hydrogen

Here, in a number of reported instances, implosions utilizing fuel mixtures have resulted in anomalously low fusion yields below those predicted by radiation-hydrodynamics simulations. Inter-species ion diffusion has been suggested as a possible cause of the observed yield degradation in fuel mixture implosions. An experimental platform utilizing hydro-equivalent deuterium–tritium (DT), deuterium–tritium–hydrogen (DTH), and deuterium-tritium-helium3 (DT 3 He) capsule implosions was developed to determine whether the inter-species ion diffusion theory may describe the resulting fuel mixture implosion behavior. The implosion experiments were performed at the Omega laser facility. X-ray images and shell areal density diagnostics results show that the hydro-equivalent three capsules (DT, DTH, and DT 3 He) have similar compression behavior. However, nuclear yield deviation was observed from the scaling determined using a fusion yield formula. In the DT 3 He mixture, a reduced yield of a factor of 0.65 ± 0.13 was observed, which is similar to a yield reduction observed in D 3 He mixture by Rygg et al. (i.e., Rygg effect). In contrast, in the DTH mixture, a factor of 1.17 ±0.15 yield increase was observed, which we named the inverse Rygg effect. The yield increase observed in the DTH mixture is consistent with the inter-species ion diffusion theory where lighter H diffuses away from the core and concentrated DT in the core produces higher yield. An inter-species ion diffusion model, the Zimmerman–Paquette–Kagan–Zhdanov model, implemented in a Lagrangian radiation-hydrodynamics fluid code, was also used to analyze the present data, without the need to assume hydrodynamic equivalence of the capsules, but it does not completely explain the DTH or DT 3 He capsules although its effects are in the correct direction. Simulation-based Bayesian inference was used in the latter analysis to quantify the uncertainty in the numerical simulations. The simulation-based analysis resulted in an inferred Rygg-effect yield decrease factor of 0.91 ± 0.02 for the DT 3 He mixture, and an inferred inverse-Rygg yield increase factor of 1.21 ± 0.04 for the DTH mixture, based on simulations ignoring ion diffusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Measurement of L-shell emission from mid-Z targets under non-LTE conditions using Transmission Grating Spectrometer and DANTE power diagnostics

In this work, we present the measurement of L-band emission from buried Sc/V targets in experiments performed at the OMEGA laser facility. The goal of these experiments was to study non-local thermodynamic equilibrium plasmas and benchmark atomic physics codes. The L-band emission was measured simultaneously by the time resolved DANTE power diagnostic and the recently fielded time integrated Soreq-Transmission Grating Spectrometer (TGS) diagnostic. The TGS measurement was used to support the spectral reconstruction process needed for the unfolding of the DANTE data. The Soreq-TGS diagnostic allows for broadband spectral measurement in the 120 eV–2000 eV spectral band, covering L- and M-shell emission of mid- and high-Z elements, with spectral resolution λ/Δλ = 8–30 and accuracy better than 25%. The Soreq-TGS diagnostic is compatible with ten-inch-manipulator platforms and can be used for a wide variety of high energy density physics, laboratory astrophysics, and inertial confinement fusion experiments.

Fraenkel, M. (ORCID:0000000291939544)↗

DOE OSTI2020

TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics

TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Simulation of electron Bernstein waves using FullWave with a 2D non-local hot plasma model

Hot plasma wave simulation capability is expanded in the FullWave code by updating the hybrid iterative solver in the code with a semi-implicit time stepping method. The new approach is used to simulate Electron Bernstein Wave (EBW) heating in over-dense spherical tokamak plasmas. The code’s hybrid iterative solver circumvents the prohibitive memory cost of direct methods by combining a time evolution of Maxwell’s equations with frequency-domain relaxation, while the conductivity kernel, calculated via 3D particle tracking, captures the essential non-local wave–particle interactions. One-dimensional EBW simulations verify the algorithm’s accuracy by demonstrating mode conversion from X-mode wave to EBW at the upper hybrid resonance and a strong cyclotron damping near the plasma core. Two-dimensional simulation reproduces the predicted short EBW wavelength and quantitatively matches the hot-plasma dispersion relation. This study demonstrates the fidelity of the hybrid solver for the electron cyclotron frequency range.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Vimercati, Lara↗

DOE OSTI2022

Multi-modal Energy-optimal Trip Scheduling in Real-time (METS-R) for Transportation Hubs (Final Report)

This report summarizes the work performed under the award number EE0008524. The project develops the Multi-modal Energy-optimal Trip Scheduling in Real-time (METS-R) platform as the next-generation transportation solution based on autonomous electric vehicles (AEV) serving passenger trips from and to urban transportation hubs, to substantially reduce transportation energy consumption. Extensive data collection and analyses were first conducted to understand the demand patterns and energy consumption of hub-based on-road trips. Then, a data-driven framework that consists of an analytical module and a simulation module was proposed. For the analytical module, five planning + operation tools were developed to support the planning and energy-efficient operations of urban AEV services: the charging station planning that robotically allocates charging supplies based on the stationary charging demand distribution; the transit planning and demand adaptive scheduling model that efficiently generates\ candidate transit routes from hubs to other places and dynamically adjusts the transit time table to fit the current demand; the online energy-efficient routing that learns the energy-optimal paths from observations of link-level energy consumption in real-time; the hub-based ridesharing that matches trip requests together with account for the uncertainty of future trip demand and vehicle supply; and finally, the integrated demand prediction and anomaly detection pipeline that leverages the flight/train time table and support other planning/operation tools. To demonstrate the performance of these tools, a scalable high-performance agent-based simulator was built. We divided the urban space into multiple service zones where each zone was considered as an agent for passenger generation and vehicle charging. Two types of AEV agents were coded to model two types of mobility services: AEV taxi and AEV transit. For the AEV taxi, the team implemented the functions of pickup/drop-off passengers, energy-efficient routing, ridesharing, fleet rebalancing, and recharging. For the AEV bus, the team implemented the functions of demand-adaptive route scheduling, passenger boarding, and recharging. A high-performance computing framework was introduced to receive various profiling information (such as link energy updates, vehicle speed) from the simulator instances and communicate the operational commands back to the instances. The numerical experiments show that each of the proposed operational algorithms can reduce energy consumption and improve system efficiency. Furthermore, there exists the need to collectively consider multiple planning + operational strategies as multiple strategies can influence each other in terms of performance impacts. Recommendations for future work related to AEV planning and simulation are discussed.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗