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362. Thermodynamic and Dynamics Data for Coarse-grained Intrinsically Disordered Proteins Generated by Active Learning

Author(s):
Webb, Michael; Jacobs, William; An, Yaxin; Oliver, Wesley
Abstract:
This distribution compiles thermodynamic and (where available) dynamic properties of short protein sequences as obtained from coarse-grained molecular dynamics simulations. The dataset features 2114 protein sequences with sequence lengths ranging from N=20 up to N=50 amino acids. The simulation and analysis of these sequences is described in "Active learning of the thermodynamics--dynamics tradeoff in protein condensates'' by Yaxin An, Michael A. Webb*, and William M. Jacobs* (https://doi.org/10.48550/arXiv.2306.03696). Of the 2114 protein sequences, 80 are homomeric polypeptides (replicating a single amino acid for N = 20, 30, 40, and 50), 1266 are sourced from version 9.0 of the DisProt database, and the remaining 768 sequences are novel sequences generated during an active learning campaign described in the aforementioned manuscript. The simulations were performed using the LAMMPS molecular dynamics engine. The interactions used for simulation are obtained from R. M. Regy , J. Thompson , Y. C. Kim and J. Mittal , Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins, Protein Sci., 2021, 1371 —1379. Properties included in this distribution include second virial coefficients, pressure-density data, expectation for phase behavior at 300 K, estimated condensed-phase densities at 300 K (if exist), and condensed-phase self-diffusion coefficients at 300 K (if exist).
Type:
Dataset
Issue Date:
6 June 2023

363. Three New Extreme Ultraviolet Spectrometers on NSTX-U for Impurity Monitoring

Author(s):
Weller, M.E.; Beiersdorfer, P.; Soukhanovskii, V.; Magee, E.W.; Scotti, F.
Abstract:
Three extreme ultraviolet (EUV) spectrometers have been mounted on the National Spherical Torus Experiment-Upgrade (NSTX-U). All three are flat-field grazing-incidence spectrometers and are dubbed X-ray and Extreme Ultraviolet Spectrometer (8 ñ 70 ≈), Long-Wavelength Extreme Ultraviolet Spectrometer (190 ñ 440 ≈), and Metal Monitor and Lithium Spectrometer Assembly (MonaLisa, 50 ñ 220 ≈). XEUS and LoWEUS were previously implemented on NSTX to monitor impurities from low- to high-Z sources and to study impurity transport while MonaLisa is new and provides the system increased spectral coverage. The spectrometers will also be a critical diagnostic on the planned laser blow-off (LBO) system for NSTX-U, which will be used for impurity edge and core ion transport studies, edge-transport code development, and benchmarking atomic physics codes.
Type:
Dataset
Issue Date:
November 2016

364. Three dimensional archaeocyathide and coral imagery for morphologic analysis

Author(s):
Manzuk, Ryan; Maloof, Adam
Abstract:
In our study, we compare the three dimensional (3D) morphologic characteristics of Earth's first reef-building animals (archaeocyath sponges) with those of modern, photosynthetic corals. Within this repository are the 3D image data products for both groups of animals. The archaeocyath images were produced through serial grinding and imaging with the Grinding, Imaging, and Reconstruction Instrument at Princeton University. The images in this repository are the downsampled data products used in our study, and the full resolution (>2TB) image stacks are available upon request from the author. For the coral image data, the computed tomography (CT) images of all samples are included at full resolution. Also included in this repository are the manual and automated outline coordinates of the archaeocyath and coral branches, which can be directly used for morphological study.
Type:
Dataset, Image, MovingImage, and StillImage
Issue Date:
August 2022

365. Time dependent analysis of visible helium line-ratios for electron temperature and density diagnostic using synthetic simulations on NSTX-U

Author(s):
Munoz Burgos, J.M.; Barbui, T.; Schmitz, O.; Stutman, D.; Tritz, K.
Abstract:
Helium line-ratios for electron temperature (Te) and density (ne) plasma diagnostic in the Scrape-Off-Layer (SOL) and Edge regions of tokamaks are widely used. Due to their intensities and proximity of wavelengths, the singlet 667.8 and 728.1 nm, and triplet 706.5 nm visible lines have been typically preferred. Time- dependency of the triplet line (706.5 nm) has been previously analyzed in detail by including transient effects on line-ratios during gas-puff diagnostic applications. In this work, several line-ratio combinations within each of the two spin systems are analyzed with the purpose of eliminating transient effects to extend the application of this powerful diagnostic to high temporal resolution characterization of plasmas. The analysis is done using synthetic emission modeling and diagnostic for low electron density NSTX SOL plasma conditions for several visible lines. This analysis employs both quasi-static equilibrium and time-dependent models in order to evaluate transient effects of the atomic population levels that may affect the derived electron temperatures and densities as a helium gas-puff penetrates the plasma. Ratios between the most intense lines are usually preferred due to their higher signal to noise ratio. The analysis of a wider range of spectral lines will help to extend this powerful diagnostic to experiments where the wavelength range of the measured spectra may be constrained either by limitations of the spectrometer, or by other conflicting lines from different ions.
Type:
Dataset
Issue Date:
November 2016

366. To dee or not to dee: costs and benefits of altering the triangularity of a steady-state DEMO-like reactor

Author(s):
Schwartz, Jacob A.; Nelson, A. O.; Kolemen, Egemen
Abstract:
Shaping a tokamak plasma to have a negative triangularity may allow operation in an ELM-free L-mode regime and with a larger strike-point radius, ameliorating divertor power-handling requirements. However, the shaping has a potential drawback in the form of a lower no-wall ideal beta limit, found using the MHD codes CHEASE and DCON. Using the new fusion systems code FAROES, we construct a steady-state DEMO2 reactor model. This model is essentially zero-dimensional and neglects variations in physical mechanisms like turbulence, confinement, and radiative power limits, which could have a substantial impact on the conclusions deduced herein. Keeping its shape otherwise constant, we alter the triangularity and compute the effects on the levelized cost of energy (LCOE). If the tokamak is limited to a fixed B field, then unless other means to increase performance (such as reduced turbulence, improved current drive efficiency or higher density operation) can be leveraged, a negative-triangularity reactor is strongly disfavored in the model due to lower \beta_N limits at negative triangularity, which leads to tripling of the LCOE. However, if the reactor is constrained by divertor heat fluxes and not by magnet engineering, then a negative-triangularity reactor with higher B0 could be favorable: we find a class of solutions at negative triangularity with lower peak heat flux and lower LCOE than those of the equivalent positive triangularity reactors.
Type:
Dataset
Issue Date:
April 2022

369. Toward fusion plasma scenario planning for NSTX-U using machine-learning-accelerated models

Author(s):
Mark D. Boyer
Abstract:
One of the most promising devices for realizing power production through nuclear fusion is the tokamak. To maximize performance, it is preferable that tokamak reactors achieve advanced operating scenarios characterized by good plasma confinement, improved magnetohydrodynamic (MHD) stability, and a largely non-inductively driven plasma current. Such scenarios could enable steady-state reactor operation with high \emph{fusion gain} --- the ratio of produced fusion power to the external power provided through the plasma boundary. Precise and robust control of the evolution of the plasma boundary shape as well as the spatial distribution of the plasma current, density, temperature, and rotation will be essential to achieving and maintaining such scenarios. The complexity of the evolution of tokamak plasmas, arising due to nonlinearities and coupling between various parameters, motivates the use of model-based control algorithms that can account for the system dynamics. In this work, a learning-based accelerated model trained on data from the National Spherical Torus Experiment Upgrade (NSTX-U) is employed to develop planning and control strategies for regulating the density and temperature profile evolution around desired trajectories. The proposed model combines empirical scaling laws developed across multiple devices with neural networks trained on empirical data from NSTX-U and a database of first-principles-based computationally intensive simulations. The reduced execution time of the accelerated model will enable practical application of optimization algorithms and reinforcement learning approaches for scenario planning and control development. An initial demonstration of applying optimization approaches to the learning-based model is presented, including a strategy for mitigating the effect of leaving the finite validity range of the accelerated model. The approach shows promise for actuator planning between experiments and in real-time.
Type:
Dataset
Issue Date:
May 2020

370. Two-dimensional full-wave simulations of waves in space and tokamak plasmas

Author(s):
Kim, E.-W.; Bertelli, N.; Johnson, J.R.; Valeo, E.; Hosea, J.; Perkins, R.
Abstract:
We illustrate the capabilities of a recently developed two-dimensional full wave code (FW2D) in space and tokamak plasmas by adopting various values of density, magnetic field configuration and strength as well as boundary shape. As example, we first showed fast compressional wave propagation in the inner magnetosphere is dramatically modified by a plasmaspheric plume at Earth's magnetosphere. The results show that wave energy is trapped in the plume showing a leaky eigenmode-like structure with plume, which is similar to the detected magnetosonic waves. We also performed simulations of high harmonic fast waves in the scrape-off layer (SOL) plasmas of the National Spherical Torus eXperiment (NSTX)/NSTX-Upgrade. Comparison the results with previous full-wave simulations show that although the FW2D code uses a cold plasma approximation, the electric field and the fraction of the power losses in the SOL plasmas show excellent consistency and agreement with the previous full wave simulations performed by the AORSA code.
Type:
Dataset
Issue Date:
October 2018

371. Two-dimensional turbulence cross-correlation functions in the edge of NSTX

Author(s):
Zweben, S.J.; Stotler, D.P.; Scotti, F.; Myra, J.R.
Abstract:
The 2-D radial vs. poloidal cross-correlation functions of edge plasma turbulence were measured near the outer midplane using the gas puff imaging (GPI) diagnostic on NSTX. These correlation functions were evaluated at radii r= 0 cm, ±3 cm, and ±6 cm from the separatrix and poloidal locations p=0 cm and ±7.5 cm from the GPI poloidal center line for 20 different shots. The ellipticity ε and tilt angle φ of the positive cross- correlation regions, and the minimum negative cross-correlation “cmin” and total negative over positive values “neg/pos” were evaluated for each of these cases. The average results over this data set were ε=2.2±0.9, φ=87±34o (i.e. poloidally oriented), cmin= -0.30±0.15, and neg/pos=0.25±0.24. Thus there was significant variation in these correlation results within this database, with dependences on the location within the image, the magnetic geometry, and the plasma parameters. Possible causes for this variation are discussed, including the misalignment of the GPI view with the local B field line, the magnetic shear of field lines in the edge, the poloidal flow shear of the turbulence, blob-hole correlations, and the neutral density ‘shadowing’ effect in GPI.
Type:
Dataset
Issue Date:
September 2017

372. Type-I ELM mitigation by continuous lithium granule gravitational injection into the upper tungsten divertor in EAST

Author(s):
Sun, Zhen; Yuzhong, Qian; Maingi, Rajesh; Wang, Yifeng; Wang, Yumin; Nagy, Alexander; Tritz, Kevin; Lunsford, Robert; Gilson, Erik; Zuo, Guizhong; Xu, Wei; Huang, Ming; Meng, Xiancai; Mansfield, Dennis K.; Zang, Qing; Zhu, Xiang; Lin, Xin; Liu, Haiqing; Duan, Yanmin; Zhang, Ling; Lyu, Bo; Liu, Yong; Wang, Liang; Bortolon, Alessandro; Xu, Guosheng; Gong, Xianzu; Hu, Jiansheng
Type:
Dataset
Issue Date:
2021

373. Understanding the dynamics and energetics of magnetic reconnection in a laboratory plasma: Review of recent progress on selected fronts

Author(s):
Yamada, M.; Yoo, J.; Myers, C. E.
Abstract:
Magnetic reconnection is a fundamental process at work in laboratory, space and astrophysical plasmas, in which magnetic field lines change their topology and convert magnetic energy to plasma particles by acceleration and heating. One of the most important problems in reconnection research has been to understand why reconnection occurs so much faster than predicted by MHD theory. Following the recent pedagogical review of this subject [M. Yamada, R. Kulsrud, and H. Ji, Rev. Mod. Phys. {\bf 82}, 603 (2010)], this paper presents a review of more recent discoveries and findings in the research of fast magnetic reconnection in laboratory, space, and astrophysical plasmas. In spite of the huge difference in physical scales, we find remarkable commonality between the characteristics of the magnetic reconnection in laboratory and space plasmas. In this paper, we will focus especially on the energy flow, a key feature of the reconnection process. In particular the experimental results on the energy conversion and partitioning in a laboratory reconnection layer [M. Yamada {\it et al.}, Nat. Commu. {\bf 5}, 4474 (2014)] are discussed and compared with quantitative estimates based on two-fluid analysis. In the Magnetic Reconnection Experiment (MRX), we find that energy deposition to electrons is localized near the X-point and is mostly from the electric field component perpendicular to the magnetic field. The mechanisms of ion acceleration and heating are also identified and a systematic and quantitative study on the inventory of converted energy within a reconnection layer with a well-defined but variable boundary. The measured energy partition in a reconnection region of similar effective size ($L \approx$ 3 ion skin depths) of the Earth's magneto-tail [J. Eastwood {\it et al.}, Phys. Rev. Lett. {\bf 110}, 225001 (2013)] is notably consistent with our laboratory results. Finally, to study the global aspects of magnetic reconnection, we have carried out a laboratory experiment on the stability criteria for solar flare eruptions, including {\textquotedblleft}storage and release{\textquotedblright} mechanisms of magnetic energy. We show that toroidal magnetic flux generated by magnetic relaxation (reconnection) processes generates a new stabilizing force which prevents plasma eruption. This result has lead us to discovery of a new stabilizing force for solar flares [C. E. Myers {\it et al.}, Nature {\bf 528}, 526 (2015)]
Type:
Dataset
Issue Date:
May 2016

376. Verification of the global gyrokinetic stellarator code XGC-S for linear ion temperature gradient driven modes

Author(s):
Cole M; Hager R; Moritaka T; Dominski J; Kleiber R; Ku S; Lazerson S; Riemann J; Chang C
Abstract:
XGC (X-point Gyrokinetic Code) is a whole-volume, total-f gyrokinetic particle-in-cell code developed for modelling tokamaks.In recent work, XGC has been extended to model more general 3D toroidal magnetic configurations, such as stellarators.These improvements have resulted in the XGC-S version.In this paper, XGC-S is benchmarked in the reduced delta-f limit for linear electrostatic ion temperature gradient-driven microinstabilities, which can underlie turbulent transport in stellarators.An initial benchmark of XGC-S in tokamak geometry shows good agreement with the XGC1, ORB5, and global GENE codes.A benchmark between XGC-S and the EUTERPE global gyrokinetic code for stellarators has also been performed, this time in geometry of the optimised stellarator Wendelstein 7-X.Good agreement has been found for the mode number spectrum, mode structure, and growth rate.
Type:
Dataset
Issue Date:
August 2019

377. Vertical forces during VDEs in an ITER plasma and the role of halo currents

Author(s):
Clasuer, C; Jardin, S; Ferraro, N
Abstract:
Vertical displacement events (VDEs) can occur in elongated tokamaks causing large currents to flow in the vessel and other adjacent metallic structures. To better understand the potential magnitude of the associated forces and the role of the so called ``halo currents'' on them, we have used the M3D-C1 code to simulate potential VDEs in ITER. We used actual values for the vessel resistivity and pre-quench temperatures and, unlike most of the previous studies, the halo region is naturally formed by triggering the thermal quench with an increase in the plasma thermal conductivity. We used the 2D non-linear version of the code and vary the post-thermal quench thermal conductivity profile as well as the boundary temperature in order to generate a wide range of possible cases that could occur in the experiment. We also show that, for a similar condition, increasing the halo current does not increase the total force on the wall since it is offset by a decrease in the toroidal contribution.
Type:
Dataset
Issue Date:
February 2020

378. Visual Analogy Extrapolation Challenge (VAEC)

Author(s):
Webb, Taylor; Dulberg, Zachary; Frankland, Steven; Petrov, Alexander; O'Reilly, Randall; Cohen, Jonathan
Abstract:
Extrapolation -- the ability to make inferences that go beyond the scope of one's experiences -- is a hallmark of human intelligence. By contrast, the generalization exhibited by contemporary neural network algorithms is largely limited to interpolation between data points in their training corpora. In this paper, we consider the challenge of learning representations that support extrapolation. We introduce a novel visual analogy benchmark that allows the graded evaluation of extrapolation as a function of distance from the convex domain defined by the training data. We also introduce a simple technique, context normalization, that encourages representations that emphasize the relations between objects. We find that this technique enables a significant improvement in the ability to extrapolate, considerably outperforming a number of competitive techniques.
Type:
Dataset and Image
Issue Date:
2020

379. Wall conditioning and ELM mitigation with boron nitride powder injection in KSTAR

Author(s):
Gilson, Erik; Lee, H; Bortolon, A; Choe, W; Diallo, A; Hong, SH; Lee, HM; Maingi, R; Mansfield, DK; Nagy, A; Park, SH; Song, IW; Song, JI; Yun, SW; Nazikian, R
Abstract:
Results from KSTAR powder injection experiments, in which tens of milligrams of boron nitride (BN) were dropped into low-power H-mode plasmas, show an improvement in wall conditions in subsequent discharges and, in some cases, a reduction or elimination of edge-localized modes (ELMs). Injected powder is distributed by the plasma flow and is deposited on the wall and, over the course of several discharges, was observed to gradually reduce recycling by 33%, and decrease both the ELM amplitude and frequency. This is the first demonstration of the use of BN for ELM mitigation. In all of these experiments, an Impurity Powder Dropper (IPD) was used to introduce precise, controllable amounts of the materials into ELMy H-mode KSTAR discharges. The plasma duration was between 10 s and 15 s, 𝐼𝑝 = 500 kA, 𝐵𝑇 = 1.8 T, 𝑃NBI = 1.6 MW, and 𝑃ECH = 0.6 MW. Plasma densities were between 2 and 3 × 1019 m−3. In all cases, the pre-fill and startup gas-fueling was kept constant, suggesting that the decrease in baseline D𝛼 emission is in fact due to a reduction in recycling. The results presented herein highlight the viability of powder injection for intra-shot and between-shot wall conditioning.
Type:
Dataset
Issue Date:
September 2021

380. Wave-kinetic approach to zonal-flow dynamics: recent advances

Author(s):
Zhu, Hongxuan; Dodin, I. Y.
Abstract:
Basic physics of drift-wave turbulence and zonal flows has long been studied within the framework of wave-kinetic theory. Recently, this framework has been re-examined from first principles, which has led to more accurate yet still tractable "improved" wave-kinetic equations. In particular, these equations reveal an important effect of the zonal-flow "curvature" (the second radial derivative of the flow velocity) on dynamics and stability of drift waves and zonal flows. We overview these recent findings and present a consolidated high-level picture of (mostly quasilinear) zonal-flow physics within reduced models of drift-wave turbulence.
Type:
Dataset
Issue Date:
March 2021