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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Gyrokinetic GENE simulations of DIII-D near-edge L-mode plasmas

We present gyrokinetic simulations with the GENE code addressing the near-edge region of an L-mode plasma in the DIII-D tokamak. At radial position ρ = 0.80, simulations with the ion temperature gradient (ITG) increased by 40% above the nominal value give electron and ion heat fluxes that are in simultaneous agreement with the experiment. This gradient increase is consistent with the combined statistical and systematic uncertainty σ of the charge exchange recombination spectroscopy measurements at the 1.6σ level. Multiscale simulations are carried out with a realistic mass ratio and geometry for the first time in the near-edge. These multiscale simulations suggest that the highly unstable ion temperature gradient (ITG) modes of the flux-matched ion-scale simulations suppress electron-scale transport, such that ion-scale simulations are sufficient at this location. At radial position ρ = 0.90, nonlinear simulations show a hybrid state of ITG and trapped electron modes, which was not expected from linear simulations. The nonlinear simulations reproduce the total experimental heat flux with the inclusion of E × B shear effects and an increase in the electron temperature gradient by ∼23%. This gradient increase is compatible with the combined statistical and systematic uncertainty of the Thomson scattering data at the 1.3σ level. These results are consistent with previous findings that gyrokinetic simulations are able to reproduce the experimental heat fluxes by varying input parameters close to their experimental uncertainties, pushing the validation frontier closer to the edge region.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Gene flow simulations demonstrate resistance of long-lived species to genetic erosion from habitat fragmentation

Habitat fragmentation restricts the movement of individuals across a landscape. In terrestrial and aquatic systems, barriers to movement can modify population and community dynamics at local or regional scales. This research contrasted life history traits related to lifespan with habitat fragmentation to determine impacts on species population genetic structure in the Neuse River Basin, USA. For this, we simulated gene flow among evenly-spaced populations in a river network and tracked individual and population genetics for 200 years. The modeled scenarios represent a full cross between five life history strategies and four riverscapes representing varying degrees of fragmentation. The five life history strategies include species (based on freshwater mussels) with average lifespans ranging from 10 to 50 years and age at maturity from 2 to 6 years. The movement landscapes included a (1) panmictic, (2) stepping-stone landscape allowing movement to only neighboring populations during each dispersal event, (3) partially-fragmented landscape divided by dams currently in the network, and (4) fully-fragmented landscape. Results suggest species with shorter lifespans have higher population genetic structure in fragmented landscapes than species with longer lifespans. Additionally, species with shorter lifespans in highly fragmented landscapes may be harboring genetic degradation or decline as allele fixation and loss. Although anthropogenic fragmentation of many river systems is only 100–200 years old, the simulation indicates that species can respond genetically in that period of time. Moreover, the time frame of the simulation suggests that genetic impacts of habitat fragmentation in some species present in the Neuse River Basin may not yet be manifesting and restoration activities could be successful.

13 HYDRO ENERGY↗
DOE OSTI2024

Assessing the impact of alpha particles on thermal confinement in JET D-T plasmas through global GENE-Tango simulations

The capability of the global, electromagnetic gyrokinetic GENE code interfaced with the transport Tango solver is exploited to address the impact of fusion alpha particles (in their dual role of fast particles and heating source) on plasma profiles and performance at JET in the discharges with the highest quasi-stationary peak fusion power during the DTE2 experimental campaigns. Employing radially global nonlinear electromagnetic GENE-Tango simulations, we compare results with/without alpha particles and alpha heating. Our findings reveal that alpha particles have a negligible impact on turbulent transport, with GENE-Tango converging to similar plasma profiles regardless of their inclusion as a kinetic species in GENE. On the other hand, alpha heating is found to contribute to the peaking of the electron temperature profiles, leading to a 1 keV drop on the on-axis electron temperature when alpha heating is neglected in Tango. The minimal impact of alpha particles on turbulent transport in this JET discharge–despite this being the shot with the highest fusion output–is attributed to the low content of fusion alpha in this discharge. To assess the potential impact of alpha particles on turbulent transport in regimes with higher alpha particle density, as expected in ITER and fusion reactors, we artificially increased the alpha particle concentration to levels expected for ITER. By performing global nonlinear GENE standalone simulations, we found that increasing the alpha particle density beyond five times the nominal value lead to significant overall turbulence destabilization. These results demonstrate that an increased alpha particle concentration can significantly impact transport properties under simulated JET experimental conditions. However, these findings cannot be directly extrapolated to ITER due to the substantial differences in parameters such as plasma size, magnetic field, plasma current, and thermal pressure.

energetic particles↗
DOE OSTI2022

Global gyrokinetic simulations of ASDEX Upgrade up to the transport timescale with GENE–Tango

An accurate description of turbulence up to the transport timescale is essential for predicting core plasma profiles and enabling reliable calculations for designing advanced scenarios and future devices. Here, we exploit the gap separation between turbulence and transport timescales and couple the global gyrokinetic code GENE to the transport-solver Tango, including kinetic electrons, collisions, realistic geometries, toroidal rotation and electromagnetic effects for the first time. This approach overcomes gyrokinetic codes' limitations and enables high-fidelity profile calculations in experimentally relevant plasma conditions, significantly reducing the computational cost. We present numerical results of GENE–Tango for two ASDEX Upgrade discharges, one of which exhibits a pronounced peaking of the ion temperature profile not reproduced by TGLF–ASTRA. We show that GENE–Tango can correctly capture the ion temperature peaking observed in the experiment. By retaining different physical effects in the GENE simulations, e.g., collisions, toroidal rotation and electromagnetic effects, we show that the ion temperature profile's peaking can be linked to electromagnetic effects of submarginal (stable) KBM modes. Furthermore, based on these results, the expected GENE–Tango speedup for the ITER standard scenario is larger than two orders of magnitude compared to a single gyrokinetic simulation up to the transport timescale, possibly making first-principles ITER simulations feasible on current computing resources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Quasilinear modelling of collisional trapped electron modes

The simplification of collision operators is necessary for quasilinear turbulence modelling used with integrated modelling frameworks, such as the gyrokinetic code QuaLiKiz. The treatment of collisions greatly impacts the accuracy of trapped electron mode (TEM) modelling, which is necessary to predict the electron heat flux and the balance between inward and outward particle fluxes. In particular, accurate particle flux predictions are necessary to successfully model density peaking in the tokamak core. We explored two ways of improving collisional TEM model reduction for tokamak core plasmas. First, we carried out linear GENE simulations to study the complex interplay between collisions and trapped electrons. We then used these simulations to define an effective trapped fraction to characterize the collisional TEM based on two key parameters, the local inverse-aspect ratio $\epsilon$ and the collisionality $\nu ^\ast$. One aspect missing from analytical TEM research is that the collisional frequency and the bounce-transit frequency are both velocity dependent; this effective trapped fraction takes both into account. In doing so, we determined that two parameters are not enough to model the collisional TEM, as an additional third free parameter was necessary. We determined that this model, as currently formulated, is not suitable for integrated modelling purposes. Second, we directly improved QuaLiKiz's Krook operator, which relies on two free parameters. We determined that these parameters required adjustments against higher-fidelity collisional models. In order to improve density profile predictions when paired with integrated models, we refined the Krook operator by using GENE simulations as a higher-fidelity point of comparison. We then demonstrate strong improvement of density peaking predictions of QuaLiKiz within the integrated modelling framework JETTO.

fusion plasma↗
DOE OSTI2023

Isotope mass scaling and transport comparison between JET Deuterium and Tritium L-mode plasmas

The dimensionless isotope mass scaling experiment between pure Deuterium and pure Tritium plasmas with matched $\rho^*$, $\nu^*$ , β n , q and $T_e/T_i$ has been achieved in JET L-mode with dominant electron heating (NBI+ohmic) conditions. 28% higher scaled energy confinement time $B_t\tau_{E,\mathrm{th}}/A$ is found in favour of the Tritium plasma. This can be cast in the form of the dimensionless energy confinement scaling law as $\Omega_i \tau_{E,\mathrm{th}} \sim A^{0.48 \pm 0.16}$. This significant isotope mass scaling is consequently seen in the scaled one-fluid heat diffusion coefficient $A \chi_{\mathrm{eff}}/B_t$ which is around 50% lower in the Tritium plasma throughout the whole plasma radius. The isotope mass dependence in the particle transport channel is negligible, supported also by the perturbative particle transport analysis with gas puff modulation. The comparison of the edge particle fuelling or ionisation profiles from the EDGE2D-EIRENE simulations show that the absolute density differences that are necessary for the dimensionless match in the confined plasma dominate over any isotope mass dependencies of particle fuelling and ionization profiles at the plasma edge. Local GENE simulation results indicate a mild anti-gyroBohm effect at $\rho_\mathrm{tor}$ = 0.6 and thereby a small isotope mass dependence in favour of Tritium on heat transport and a negligible effect on particle transport. A significant fraction of the isotope scaling and reduced heat transport observed in the Tritium plasma is not captured in the GENE and ASTRA-TGLF-SAT2 simulations by simply changing the isotope mass for the same input profiles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Identifying the microtearing modes in the pedestal of DIII-D H-modes using gyrokinetic simulations

Recent evidence points toward the microtearing mode (MTM) as an important fluctuation in the H-mode pedestal for anomalous electron heat transport. A study of the instabilities in the pedestal region carried out using gyrokinetic simulations to model an ELMy H-mode DIII-D discharge (USN configuration, 1.4 MA plasma current, and 3 MW heating power) is presented. The simulations produce MTMs, identified by predominantly electromagnetic heat flux, small particle flux, and a substantial degree of tearing parity. The magnetic spectrogram from Mirnov coils exhibits three distinct frequency bands—two narrow bands at lower frequency (~35–55 kHz and ~70–105 kHz) and a broader band at higher frequency (~300–500 kHz). Global linear GENE simulations produce MTMs that are centered at the peak of the ω* profile and correspond closely with the bands in the spectrogram. The three distinctive frequency bands can be understood from the basic physical mechanisms underlying the instabilities. For example (i) instability of certain toroidal mode numbers (n) is controlled by the alignment of their rational surfaces with the peak in the ω* profile, and (ii) MTM instabilities in the lower n bands are the conventional collisional slab MTM, whereas the higher n band depends on curvature drive. While many features of the modes can be captured with the local approximation, a global treatment is necessary to quantitatively reproduce the detailed band gaps of the low-n fluctuations. Notably, the transport signatures of the MTM are consistent with careful edge modeling by SOLPS.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Extracting the turbulent flow-field from beam emission spectroscopy images using velocimetry

The 2D turbulent E × B flow-field is inferred from density fluctuation images obtained with the beam emission spectroscopy diagnostic on DIII-D using the orthogonal dynamic programming velocimetry algorithm. A synthetic turbulence model is used to test the algorithm and optimize it for measuring zonal flows. Zonal flow measurements are found to require a signal-to-noise ratio above ~10 and a zonal flow wavelength longer than ~2 cm. Comparison between the velocimetry-estimated flow-field and the E × B flow-field using a nonlinear gyrokinetic GENE simulation finds that the flow-fields have identical spatial structure and differ only by the mean turbulence phase velocity, which is spatially uniform in this flux tube simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Collisionality driven turbulent particle transport changes in DIII-D H-mode plasmas

The results of the experimental dimensionless scan in this paper confirm that there is an increase in density peaking towards lower collisionality and that this can be partly linked to a shift in the turbulence regime from ITG towards TEM. However at the lowest collisionality, the changes in turbulence and transport are much more pronounced than expected from direct collisionality effect on the turbulence. In this paper, the collisionality, ν * is varied by a factor 5, while keeping ρ * , q , β , M , fixed. Additionally, a 3 Hz gas puff modulation is applied to modulate the electron density profile and extract the perturbed transport coefficients using two diagnostics. The transport analysis shows that the increase in density peaking at low ν * is linked to an increase in the inward particle pinch and not an increase in core fueling. These observations are not only in agreement with prior modeling scans of how turbulence changes as a function of collisionality and its impact upon the particle fluxes, but also with the multi-machine database (Fable E. et al 2010 Plasma Phys. Control. Fusion 52 015007) (Angioni C. et al 2003 Phys. Rev. Lett. 90 205003). The changes in turbulence across the collisionality scan were captured at large scale by the BES and at smaller scale by the DBS. A comparison with gradient-driven GENE simulations showed similar trends at both scales. Moreover, the changes observed in overall transport are in agreement with gradient-driven TGLF particle flux simulations. This indicates that TGLF/GENE when given the gradients as input, are able to reproduce the experimentally observed turbulence changes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Modeling Temperature Profiles in the Pedestal of NSTX with Reduced Models

This paper describes new modeling capabilities for predicting H-mode pedestal profiles in spherical tokamaks. Temperature profiles for NSTX discharges 132543 and 132588 are modeled by coupling the \textsc{astra} transport solver with neoclassical transport and gyrokinetic-based reduced models for electron temperature gradient (ETG) and kinetic ballooning mode (KBM) instabilities. A quasi-linear surrogate model for ion-scale transport is developed using linear \textsc{gene} simulations, requiring only a single free parameter calibrated to one discharge. Time-evolving the temperatures with fixed density yields good agreement with experiments for both discharges. Systematic analysis of the transport mechanisms reveals that neoclassical transport is huge across the entire pedestal region for the ion channel. ETG turbulence is large in the plasma edge and low density gradient region, contributing substantially to the electron channel. However, KBM/MHD-like modes also drive significant transport in both the ion and electron thermal channels, making them essential for accurate pedestal modeling. Further refinements, including explicit E×B shear suppression and scaled ETG transport, produce quantitative but not qualitative improvements. This work lays the foundation for predictive modeling of future devices. This paper is on arxiv and has been submitted to Nuclear Fusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

First coupled GENE–XGC microturbulence simulations

Covering the core and the edge region of a tokamak, respectively, the two gyrokinetic turbulence codes Gyrokinetic Electromagnetic Numerical Experiment (GENE) and X-point Gyrokinetic Code (XGC) have been successfully coupled by exchanging three-dimensional charge density data needed to solve the gyrokinetic Poisson equation over the entire spatial domain. Certain challenges for the coupling procedure arise from the fact that the two codes employ completely different numerical methods. This includes, in particular, the necessity to introduce mapping procedures for the transfer of data between the unstructured triangular mesh of XGC and the logically rectangular grid (in a combination of real and Fourier space) used by GENE. Constraints on the coupling scheme are also imposed by the use of different time integrators. First, coupled simulations are presented. We have considered collisionless ion temperature gradient turbulence, in both circular and fully shaped plasmas. Coupled simulations successfully reproduce both GENE and XGC reference results, confirming the validity of the code coupling approach toward a whole device model. Here, many lessons learned in the present context, in particular, the need for a coupling procedure as flexible as possible, should be valuable to our and other efforts to couple different kinds of codes in pursuit of a more comprehensive description of complex real-world systems and will drive our further developments of a whole device model for fusion plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2007

Simulated Microgravity Regulates Gene Transcript Profiles of 2T3 Preosteoblasts: Comparison of the Random Positioning Machine and the Rotating Wall Vessel Bioreactor

Microgravity of spaceflight induces bone loss due in part to decreased bone formation by osteoblasts. We have previously examined the microgravity-induced changes in gene expression profiles in 2T3 preosteoblasts using the Random Positioning Machine (RPM) to simulate microgravity conditions. Here, we hypothesized that exposure of preosteoblasts to an independent microgravity simulator, the Rotating Wall Vessel (RWV), induces similar changes in differentiation and gene transcript profiles, resulting in a more confined list of gravi-sensitive genes that may play a role in bone formation. In comparison to static 1g controls, exposure of 2T3 cells to RWV for 3 days inhibited alkaline phosphatase activity, a marker of differentiation, and downregulated 61 genes and upregulated 45 genes by more than two-fold as shown by microarray analysis. The microarray results were confirmed with real time PCR for downregulated genes osteomodulin, bone morphogenic protein 4 (BMP4), runx2, and parathyroid hormone receptor 1. Western blot analysis validated the expression of three downregulated genes, BMP4, peroxiredoxin IV, and osteoglycin, and one upregulated gene peroxiredoxin I. Comparison of the microarrays from the RPM and the RWV studies identified 14 gravi-sensitive genes that changed in the same direction in both systems. Further comparison of our results to a published database showing gene transcript profiles of mechanically loaded mouse tibiae revealed 16 genes upregulated by the loading that were shown to be downregulated by RWV and RPM. These mechanosensitive genes identified by the comparative studies may provide novel insights into understanding the mechanisms regulating bone formation and potential targets of countermeasure against decreased bone formation both in astronauts and in general patients with musculoskeletal disorders.

Patel, Mamta J.↗
NASA NTRS2003

Using SPEEDES to simulate the blue gene interconnect network

JPL and the Center for Advanced Computer Architecture (CACR) is conducting application and simulation analyses of BG/L in order to establish a range of effectiveness for the Blue Gene/L MPP architecture in performing important classes of computations and to determine the design sensitivity of the global interconnect network in support of real world ASCI application execution.

SPEEDES BlueGene/L BG/L system-on-a-chip↗
DOE OSTI2024

Simulated Microgravity Alters Gene Regulation Linked to Immunity and Cardiovascular Disease

Microgravity exposure induces a cephalad fluid shift and an overall reduction in physical activity levels which can lead to cardiovascular deconditioning in the absence of countermeasures. Future spaceflight missions will expose crew to extended periods of microgravity among other stressors, the effects of which on cardiovascular health are not fully known. In this study, we determined cardiac responses to extended microgravity exposure using the rat hindlimb unloading (HU) model. We hypothesized that exposure to prolonged simulated microgravity and subsequent recovery would lead to increased oxidative damage and altered expression of genes involved in the oxidative response. To test this hypothesis, we examined hearts of male (three and nine months of age) and female (3 months of age) Long–Evans rats that underwent HU for various durations up to 90 days and reambulated up to 90 days post-HU. Results indicate sex-dependent changes in oxidative damage marker 8-hydroxydeoxyguanosine (8-OHdG) and antioxidant gene expression in left ventricular tissue. Three-month-old females displayed elevated 8-OHdG levels after 14 days of HU while age-matched males did not. In nine-month-old males, there were no differences in 8-OHdG levels between HU and normally loaded control males at any of the timepoints tested following HU. RNAseq analysis of left ventricular tissue from nine-month-old males after 14 days of HU revealed upregulation of pathways involved in pro-inflammatory signaling, immune cell activation and differential expression of genes associated with cardiovascular disease progression. Taken together, these findings provide a rationale for targeting antioxidant and immune pathways and that sex differences should be taken into account in the development of countermeasures to maintain cardiovascular health in space.

Genetics & Heredity↗
DOE OSTI2018

Electron critical gradient scale length measurements of ICRF heated L-mode plasmas at Alcator C-Mod tokamak

A profile for the critical gradient scale length ( L c ) has been measured in L-mode discharges at the Alcator C-Mod tokamak, where electrons were heated by an ion cyclotron range of frequency through minority heating with the intention of simultaneously varying the heat flux and changing the local gradient. The electron temperature gradient scale length ( L Te -1 = |∇ T e |/ T e ) profile was measured via the B T -jog technique and it was compared with electron heat flux from power balance (TRANSP) analysis. The T e profiles were found to be very stiff and already above the critical values, however, the stiffness was found to be reduced near the q = 3/2 surface. The measured L c profile is in agreement with electron temperature gradient (ETG) models which predict the dependence of L c -1 on local , Z eff , T e /T i , and the ratio of the magnetic shear to the safety factor. The results from linear Gene gyrokinetic simulations suggest ETG to be the dominant mode of turbulence in the electron scale ( k ⊥ ρ s > 1), and ion temperature gradient/trapped electron mode modes in the ion scale ( k ⊥ ρ s > 1). Finally, the measured L c profile is in agreement with the profile of ETG critical gradients deduced from GENE simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2007

High-LET Patterns of DSBs in DNA Loops, the HPRT Gene and Phosphorylation Foci

We present new results obtained with our model based on the track structure and chromatin geometry that predicts the DSB spatial and genomic distributions in a cell nucleus with the full genome represented. The model generates stochastic patterns of DSBs in the physical space of the nucleus filled with the realistic configuration of human chromosomes. The model was re-used to find the distribution of DSBs in a physical volume corresponding to a visible phosphorylation focus believed to be associated with a DSB. The data shows whether there must more than one DSB per foci due to finite size of the visible focus, even if a single DSB is radiochemically responsible for the phosphorylation of DNA in its vicinity. The same model can predict patterns of closely located DSBs in a given gene, or in a DNA loop, one of the large-scale chromatin structures. We demonstrated for the example of the HPRT gene, how different sorts of radiation lead to proximity effect in DSB locations, which is important for modeling gene deletions. The spectrum of intron deletions and total gene deletions was simulated for the HPRT gene. The same proximity effect of DSBs in a loop can hinder DSB restitutions, as parts of the loop between DSBs is deleted with a higher likelihood. The distributions of DSBs and deletions of DNA in a loop are presented.

Ponomarev, Artem L.↗
DOE OSTI2024

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

Genome-wide association studies (GWAS) identify genetic variants underlying complex traits but are limited by stringent genome-wide significance thresholds. We present GRIN (Gene set Refinement through Interacting Networks), which increases confidence in the expanded gene set by retaining genes strongly connected by biological networks when GWAS thresholds are relaxed. GRIN was validated on both simulated interrelated gene sets as well as multiple GWAS traits. From multiple GWAS summary statistics of suicide attempt, a complex phenotype, GRIN identified additional genes that replicated across independent cohorts and retained biologically interrelated genes despite a relaxed significance threshold. We present a conceptual model of how these retained genes interact through neurobiological pathways that may influence suicidal behavior, and identify existing drugs associated with these pathways that would not have been identified under traditional GWAS thresholds. We demonstrate GRIN’s utility in boosting GWAS results by increasing the number of true positive genes identified from GWAS results.

60 APPLIED LIFE SCIENCES↗