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).
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.
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.
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.
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.
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.
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.
