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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Natural switches in behaviour rapidly modulate hippocampal coding

Throughout their daily lives, animals and humans often switch between different behaviours. However, neuroscience research typically studies the brain while the animal is performing one behavioural task at a time, and little is known about how brain circuits represent switches between different behaviours. Here we tested this question using an ethological setting: two bats flew together in a long 135 m tunnel, and switched between navigation when flying alone (solo) and collision avoidance as they flew past each other (cross-over). Bats increased their echolocation click rate before each cross-over, indicating attention to the other bat. Hippocampal CA1 neurons represented the bat’s own position when flying alone (place coding). Notably, during cross-overs, neurons switched rapidly to jointly represent the interbat distance by self-position. This neuronal switch was very fast—as fast as 100 ms—which could be revealed owing to the very rapid natural behavioural switch. The neuronal switch correlated with the attention signal, as indexed by echolocation. Interestingly, the different place fields of the same neuron often exhibited very different tuning to interbat distance, creating a complex non-separable coding of position by distance. Theoretical analysis showed that this complex representation yields more efficient coding. Overall, our results suggest that during dynamic natural behaviour, hippocampal neurons can rapidly switch their core computation to represent the relevant behavioural variables, supporting behavioural flexibility.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evaluating Performance Portability with the CMS Heterogeneous Pixel Reconstruction code

In the past years the landscape of tools for expressing parallel algorithms in a portable way across various compute accelerators has continued to evolve significantly. There are many technologies on the market that provide portability between CPU, GPUs from several vendors, and in some cases even FPGAs. These technologies include C++ libraries such as Alpaka and Kokkos, compiler directives such as OpenMP, the SYCL open specification that can be implemented as a library or in a compiler, and standard C++ where the compiler is solely responsible for the offloading. Given this developing landscape, users have to choose the technology that best fits their applications and constraints. For example, in the CMS experiment the experience so far in heterogeneous reconstruction algorithms suggests that the full application contains a large number of relatively short computational kernels and memory transfer operations. In this work we use a stand-alone version of the CMS heterogeneous pixel reconstruction code as a realistic use case of HEP reconstruction software that is capable of leveraging GPUs effectively. We summarize the experience of porting this code base from CUDA to Alpaka, Kokkos, SYCL, std::par, and OpenMP offloading. We compare the event processing throughput achieved by each version on NVIDIA and AMD GPUs as well as on a CPU, and compare those to what a native version of the code achieves on each platform.

Andriotis, Nikolaos↗
DOE OSTI2020

Quantitative metrics for evaluating thermonuclear design codes and physics models applied to the National Ignition Campaign

In this study, physics models and design codes for hot dense plasmas undergoing thermonuclear burn are evaluated objectively using statistical metrics that compare the difference between calculations and data relative to the experimental uncertainties. The analysis is applied to the National Ignition Campaign (NIC) because it is relevant, comprehensive, and well documented. The statistics confirm that a key process afflicting NIC performance is mix driven by hydrodynamic instabilities as approximated here using the KL model [G. Dimonte and R. Tipton, Phys. Fluids 18, 085101 (2006)]. New physics models are also presented for instability-driven magnetic fields [B. Srinivasan et al., Phys. Rev. Lett. 108, 165002 (2012)] and the Coulomb logarithm for electron–ion thermal relaxation [G. Dimonte and J. Daligault, Phys. Rev. Lett. 101, 135001 (2008)]. The plasma-generated magnetic fields improve the agreement between code and data in a statistically significant manner by reducing the electron thermal conduction in the hot-spot via the Hall term. The Coulomb logarithm is presented in a numerically practical form that incorporates recent theoretical advances. However, it does not improve the agreement between the code and data because the thermal relaxation is so fast in non-ignited NIC plasmas that the typical 20% error does not change the tight coupling between electrons and ions. Even with these improved physics models, the one-dimensional simulations presented here are not able to describe the high-convergence NIC implosions in a statistically acceptable manner. Of the heroic multi-dimensional simulations of Clark et al. [Phys. Plasmas 23, 056302 (2016)], only those in three-dimensions satisfy the statistical acceptance criterion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Modeling of a chain of three plasma accelerator stages with the WarpX electromagnetic PIC code on GPUs

The fully electromagnetic particle-in-cell code WarpX is being developed by a team of the U.S. DOE Exascale Computing Project (with additional non-U.S. collaborators on part of the code) to enable the modeling of chains of tens to hundreds of plasma accelerator stages on exascale supercomputers, for future collider designs. The code is combining the latest algorithmic advances (e.g., Lorentz boosted frame and pseudo-spectral Maxwell solvers) with mesh refinement and runs on the latest computer processing unit and graphical processing unit (GPU) architectures. In this paper, we summarize the strategy that was adopted to port WarpX to GPUs, report on the weak parallel scaling of the pseudo-spectral electromagnetic solver, and then present solutions for decreasing the time spent in data exchanges from guard regions between subdomains. In Sec. IV, we demonstrate the simulations of a chain of three consecutive multi-GeV laser-driven plasma accelerator stages.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Toward exascale whole-device modeling of fusion devices: Porting the GENE gyrokinetic microturbulence code to GPU

GENE solves the five-dimensional gyrokinetic equations to simulate the development and evolution of plasma microturbulence in magnetic fusion devices. The plasma model used is close to first principles and computationally very expensive to solve in the relevant physical regimes. In order to use the emerging computational capabilities to gain new physics insights, several new numerical and computational developments are required. Here, we focus on the fact that it is crucial to efficiently utilize GPUs (graphics processing units) that provide the vast majority of the computational power on such systems. In this paper, we describe the various porting approaches considered and given the constraints of the GENE code and its development model, justify the decisions made, and describe the path taken in porting GENE to GPUs. We introduce a novel library called gtensor that was developed along the way to support the process. Performance results are presented for the ported code, which in a single node of the Summit supercomputer achieves a speed-up of almost 15× compared to running on central processing unit (CPU) only. Typical GPU kernels are memory-bound, achieving about 90% of peak. Our analysis shows that there is still room for improvement if we can refactor/fuse kernels to achieve higher arithmetic intensity. We also performed a weak parallel scalability study, which shows that the code runs well on a massively parallel system, but communication costs start becoming a significant bottleneck.

Germaschewski, K. (ORCID:0000000284956354)↗
DOE OSTI2021

Emission spectroscopy with coded apertures for enhanced dimensionality

A coded aperture is used to demonstrate emission spectroscopy from multiple one-dimensional measurement locations simultaneously with a single camera. The coded aperture mask has several columns of periodic apertures, each with a unique spatial frequency. Light transmitted through all mask columns is detected through an imaging spectrometer. Dispersed light from the various mask columns overlaps on the spectrometer camera but is separated using Fourier-domain filtering using the known spatial frequencies of the mask. As the coded aperture is placed at an image plane, each Fourier-filtered spectrogram comes from a unique one-dimensional measurement location. This technique represents a significant increase in the amount of spatially and spectrally resolved emission data available using a single emission spectrometer and camera at the expense of some spatial resolution due to the Fourier filtering. This instrument is particularly useful for studying transient, non-repeating events. Megahertz-rate emission spectroscopy from five one-dimensional measurement locations is demonstrated with explosive fireballs using a single camera. Optical design parameters and instrument performance characteristics are discussed.

42 ENGINEERING↗
DOE OSTI2025

Reproducibility of fixed-node diffusion Monte Carlo across diverse community codes: The case of water–methane dimer

Fixed-node diffusion quantum Monte Carlo (FN-DMC) is a widely trusted many-body method for solving the Schrödinger equation, known for its reliable predictions of material and molecular properties. Furthermore, its excellent scalability with system complexity and near-perfect utilization of computational power make FN-DMC ideally positioned to leverage new advances in computing to address increasingly complex scientific problems. Even though the method is widely used as a computational gold standard, reproducibility across the numerous FN-DMC code implementations has yet to be demonstrated. This difficulty stems from the diverse array of DMC algorithms and trial wave functions, compounded by the method’s inherent stochastic nature. Here, this study represents a community-wide effort to assess the reproducibility of the method, affirming that yes, FN-DMC is reproducible (when handled with care). Using the water–methane dimer as the canonical test case, we compare results from eleven different FN-DMC codes and show that the approximations to treat the non-locality of pseudopotentials are the primary source of the discrepancies between them. In particular, we demonstrate that, for the same choice of determinantal component in the trial wave function, reliable and reproducible predictions can be achieved by employing the T-move, the determinant locality approximation, or the determinant T-move schemes, while the older locality approximation leads to considerable variability in results. These findings demonstrate that, with appropriate choices of algorithmic details, fixed-node DMC is reproducible across diverse community codes—highlighting the maturity and robustness of the method as a tool for open and reliable computational science.

Della Pia, Flaviano [Univ. of Cambridge (United Ki↗
DOE OSTI2020

Modeling of gap conductance for LWR fuel rods applied in the BISON code

A new gap conductance model is proposed in this study as a combination of Toptan’s model and the Ross-Stoute model. A variance-based sensitivity analysis is performed to understand how simulation results depend on all input parameters of the proposed model. Additionally, new modeling options (e.g. fill gas thermal conductivity, temperature jump distance, thermal accommodation coefficient, etc.) are added into the nuclear fuel performance code, BISON. The need for further investigation of the gap heat transfer between fuel and cladding in BISON motivated this study to evaluate its impact on the code’s predictions. New gap conductance modeling is proposed. A series of integral-effects validation tests is performed: (1) to demonstrate the impact of the proposed model on the code’s fuel temperature predictions at the beginning of life and through the reactor’s life; (2) to ensure that the proposed model is capable of accurately modeling gap heat transfer characteristics in real-world problems; and (3) to investigate the impact of the estimation of fission gas release on the fuel temperature predictions with the proposed model. Overall, the results indicate that the proposed gap conductance model improves BISON’s predictions.

42 ENGINEERING↗
DOE OSTI2025

Assessment of RELAP5-3D Code with Molten Salt Heat Transfer Experiments

The accurate thermal-hydraulic assessment of thermal storage systems is crucial for addressing the integrity and performance of the storage system design. This is particularly important for thermal storage systems using molten salts as a heat transport and storage medium, as the chemical corrosion and erosion by the high-temperature molten salts can cause serious damage to the structural components of the storage system. To understand these effects for TerraPower’s Natrium® Demonstration Reactor design, the system thermal-hydraulic analysis code, RELAP5-3D, is utilized to analyze the thermal storage system. This study evaluates two heat transfer correlations implemented in the RELAP5-3D code—the Dittus-Boelter and Gnielinski correlations—using selected benchmark cases from two molten salt heat transfer experiments conducted at Xi’an Jiao Tong University and the German Aerospace Center. The Nusselt numbers calculated using the Gnielinski correlation agree with the experimental data within ±5% of the relative deviations at 300°C and 400°C. With the increasing Reynolds numbers, the Dittus-Boelter correlation underestimates the Nusselt numbers by up to 22% compared to the Gnielinski correlation. Comparison of the RELAP5-3D calculation results with experimental data at a high temperature of 550°C revealed that the thermo-chemical characteristics of solar salt at high temperatures surpassing the decomposition temperatures of nitrate salts reduce the accuracy of heat transfer model of the RELAP5-3D code. Specifically, it has been observed that the temperatures of the wall surface and liquid near the wall can surpass the decomposition temperatures, even though the bulk temperature of molten salts remains significantly lower than these decomposition temperatures. In summary, this study recommends the use of the Gnielinski correlation for the heat transfer analysis of molten salt, rather than the Dittus-Boelter correlation.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗
DOE OSTI2025

Implementation of the D1S Methodology for Shutdown Dose Rate Calculations in the OpenMC Monte Carlo Particle Transport Code

We present an implementation of the direct one-step (D1S) methodology for shutdown dose rate (SDR) calculations in the OpenMC Monte Carlo particle transport code. In addition to being the first fully open-source D1S implementation, it is also the first to require no ad hoc source code or nuclear data library modifications. The code can seamlessly switch between production of prompt and decay photons based on a user input parameter, and the decay data needed for decay photon generation are made available through a depletion chain file, which is already used for OpenMC’s built-in depletion/activation solver. A set of Python functions significantly eases the burden of computing and applying time correction factors needed to properly account for the time dependence of radionuclide activity. To assess the accuracy of the D1S implementation, SDR calculations have been carried out for three problems: a prism of iron irradiated by 14-MeV neutrons, the ITER port plug computational benchmark, and the Frascati Neutron Generator (FNG) ITER dose rate benchmark problem from the Shielding INtegral Benchmark Archive and Database (SINBAD). For each of these problems, comparisons were made to calculations using the rigorous two-step (R2S) method. The results on the iron prism problem illustrate how the D1S method achieves superior spatial resolution compared to the R2S method without the need for spatial discretization of the activation regions. The D1S and R2S results for the ITER port plug benchmark agree well with previously reported results in the literature. While the D1S results are 10% to 15% lower than the R2S results, this may be due to stochastic uncertainty and/or spatial discretization in the R2S calculations. On the FNG dose rate benchmark problem, the D1S method produces dose rate estimates that are within 4% of the dose rates predicted using a cell-based R2S workflow. The D1S estimates of the SDR are also in reasonable agreement with the experimental measurements and show the same basic trends that have been observed in previous works. A qualitative analysis of the execution time and uncertainty for the R2S and D1S workflows suggests that the D1S method would attain a higher figure of merit.

D1S method↗
DOE OSTI2023

HPC-driven computational reproducibility in numerical relativity codes: a use case study with IllinoisGRMHD

Abstract Reproducibility of results is a cornerstone of the scientific method. Scientific computing encounters two challenges when aiming for this goal. Firstly, reproducibility should not depend on details of the runtime environment, such as the compiler version or computing environment, so results are verifiable by third-parties. Secondly, different versions of software code executed in the same runtime environment should produceconsistent numerical results for physical quantities. In this manuscript, we test the feasibility of reproducing scientific results obtained using theIllinoisGRMHDcode that is part of an open-source community software for simulation in relativistic astrophysics, theEinstein Toolkit. We verify that numerical results of simulating a single isolated neutron star withIllinoisGRMHDcan be reproduced, and compare them to results reported by the code authors in 2015. We use two different supercomputers: Expanse at SDSC, and Stampede2 at TACC. By compiling the source code archived along with the paper on both Expanse and Stampede2, we find thatIllinoisGRMHDreproduces results published in its announcement paper up to errors comparable to round-off level changes in initial data parameters. We also verify that a current version ofIllinoisGRMHDreproduces these results once we account for bug fixes which have occurred since the original publication.

Astronomy & Astrophysics↗
DOE OSTI2024

The fastVFP code for solution of the Vlasov–Fokker–Planck equation

Abstract We describe the fast VFP code for solution of the Vlasov–Fokker–Planck equation for non-local electron transport and the generation of magnetic field, especially for application to laser-produced plasmas. We describe the essential features of the code that make it fast and robust and suitable for inclusion as a transport package in a fluid simulation. We present a few sample results that demonstrate the abilities of the code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

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↗
DOE OSTI2022

AR reactor neutronics multi-code validation*

The affordable, robust, compact (ARC) reactor is a tokamak fusion reactor concept currently under development by Commonwealth Fusion Systems and Massachusetts Institute of Technology. There are three important neutronics considerations for the operation of the ARC reactor: (1) breeding of enough tritium in the blanket to sustain the D–T reaction in the plasma; (2) ensuring low fluence on the superconducting toroidal field coils; and (3) assessing neutron volumetric heating in structural components. Here, this work aims to perform a validation of the neutronics analysis approach by code-to-code comparison. State-of-the-art software stacks are employed for the neutronics analysis of the ARC reactor, and a computer-aided design (CAD) model is used directly for Monte Carlo (MC) neutron transport calculations. Three software stacks, Attila-MCNP, OpenMC-DAGMC, and Shift-DAGMC, are used to perform neutronic analyses of a 90° sector CAD model of the ARC reactor. In conclusion, results show that the flux tallies calculated by the three software stacks are very close. Also, the volumetric heating and tritium breeding values have less than 0.6% relative difference between codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

MAS: A versatile Landau-fluid eigenvalue code for plasma stability analysis in general geometry

We have developed a new global eigenvalue code, Multiscale Analysis for plasma Stabilities (MAS), for studying plasma problems with wave toroidal mode number (n) and frequency (ω) in a broad range of interest in general tokamak geometry, based on a five-field Landau-fluid description of thermal plasmas. Beyond keeping the necessary plasma fluid response, we further retain the important kinetic effects including diamagnetic drift, ion finite Larmor radius, finite parallel electric field (E||), ion and electron Landau resonances in a self-consistent and non-perturbative manner without sacrificing the attractive efficiency in computation. The physical capabilities of the code are evaluated and examined in the aspects of both theory and simulation. In theory, the comprehensive Landau-fluid model implemented in MAS can be reduced to the well-known ideal MHD model, electrostatic ion-fluid model, and drift-kinetic model in various limits, which clearly delineates the physics validity regime. In simulation, MAS has been well benchmarked with theory and other gyrokinetic and kinetic-MHD hybrid codes in a manner of adopting the unified physical and numerical framework, which covers the kinetic Alfv\'en wave (KAW), ion sound wave (ISW), low-n kink, high-n ion temperature gradient mode (ITG) and kinetic ballooning mode (KBM). Moreover, MAS is successfully applied to model the Alfv\'en eigenmode (AE) activities in DIII-D discharge #159243, which faithfully captures the frequency sweeping of reversed shear Alfv\'en eigenmode (RSAE), the tunneling damping of toroidal Alfv\'en eigenmode (TAE), as well as the polarization characteristics of kinetic beta-induced Alfv\'en eigenmode (KBAE) and beta-induced Alfv\'en-acoustic eigenmode (BAAE) being consistent with former gyrokinetic theory and simulation. With respect to the key progress contributed to the community, MAS has the advantage of combining rich physics ingredients, realistic global geometry and high computation efficiency together for plasma stability analysis in linear regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Analysis and design of fast flow liquid Li divertor for fusion nuclear science facility (FNSF) using coupled plasma boundary and LM MHD/heat transfer codes *

The SOLPS-ITER code is utilized to analyze the boundary plasma associated with a fast-flow lithium (Li) divertor configuration in the fusion nuclear science facility (FNSF) tokamak and identify operational regimes with acceptable divertor and core conditions. Plasma transport from the SOLPS-ITER code has been coupled with a liquid metal (LM) MHD/heat transfer code to model a Li open-surface divertor design and assess its impact on the scrape-off-layer (SOL) and core plasma performance. Simulations with only Neon (Ne) impurity seeding have been conducted to evaluate its impact on meeting FNSF design demands for the divertor and upstream plasma parameters. Simulation results indicate that Ne seeding significantly mitigates divertor heat flux but potentially reduces both upstream electron and main ion density due to fuel dilution. The combined application of Ne seeding and deuterium (D 2 ) puffing is required to satisfy the FNSF design requirements on upstream density ($n^{OMP}_{e,sep}$~1× 10 20 m -3 ) and divertor energy flux ($q^{Odiv}_{\bot,max}$<10 MW m -2 ). D 2 puffing plays a role in counteracting upstream density drops and augmenting energy and momentum losses through atomic and molecular processes. The inlet Li flow velocity is systematically varied across a wide range to identify acceptable flows and corresponding LM surface temperatures. This comprehensive analysis identifies the acceptable Li flow parameters, LM surface temperature, and emitted Li fluxes necessary to meet the major design constraints. The emitted Li fluxes exhibit minimal impact on the main plasma at surface temperatures up to approximately ~525 °C, corresponding emitted Li fluxes of up to φ Li ~2X10 23 atoms s -1 . Uncertainties in the Li emission processes from the surface are also investigated, primarily influencing Li loss in the lower surface temperature range (<525 °C), with simulation results indicating a minor impact on the divertor and upstream plasma. Conversely, evaporation predominantly drives the Li loss processes at higher surface temperature ranges (>525 °C), contaminating both the divertor and upstream plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Divertor heat load estimates on NSTX and DIII-D using new and open-source 2D inversion analysis code

A thermography inversion algorithm has been developed in the open-source Python-based computer code, HYPERION, to calculate the heat flux incident on plasma-facing components (PFCs) in axisymmetric tokamaks. The chosen mesh size at the surface significantly affects the calculated transient heat flux results. The calculated transient heat flux will exceed the real value when the mesh size tends to zero but will underestimate the real value when the mesh size is large. A criterion for determining the appropriate mesh size for the transient heat flux calculation will be discussed. The numerical scheme for HYPERION uses a 2D fully implicit finite-difference approach, allowing temperature-dependent thermal properties of PFC materials. The inversion algorithm is benchmarked against established heat flux calculation codes, TACO and THEODOR, based on thermography data from NSTX and DIII-D respectively. The primary benefits of HYPERION compared to TACO and THEODOR are that it is open-source and it allows for the optimization of mesh thickness along the substrate. The algorithm also accounts for the thermal properties of thin surface layers that characteristically form on PFCs due to plasma-material interactions. The agreement between HYPERION and THEODOR is excellent, as the percent difference between the codes is ~5% on average in the case of the DIII-D data for moderate to high heat flux. Verification tests with TACO show slightly higher average percent differences of 8% and 12%. In using HYPERION to study filaments in heat flux, the initial results indicate that small ELMs filaments significantly broaden the divertor heat flux, and decrease divertor peak flux. Compared to the inter-ELM, the small ELM filaments decrease the divertor peak surface temperature. With intermittent divertor filaments, the divertor heat flux width is comparable with that found in L-mode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗