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Start Over Domain Natural Sciences

1. A Reduced Resistive Wall Mode Kinetic Stability Model for Disruption Forecasting

Author(s):
Berkery, J.W.; Sabbagh, S.A.; Bell, R.E.; Gerhardt, S.P.; LeBlanc, B.P.
Abstract:
Kinetic modification of ideal stability theory from stabilizing resonances of mode-particle interaction has had success in explaining resistive wall mode (RWM) stability limits in tokamaks. With the goal of real-time stability forecasting, a reduced kinetic stability model has been implemented in the new Disruption Event Characterization and Forecasting (DECAF) code, which has been written to analyze disruptions in tokamaks. The reduced model incorporates parameterized models for ideal limits on beta, a ratio of plasma pressure to magnetic pressure, which are shown to be in good agreement with DCON code calculations. Increased beta between these ideal limits causes a shift in the unstable region of delta W_K space, where delta W_K is the change in potential energy due to kinetic effects that is solved for by the reduced model, such that it is possible for plasmas to be unstable at intermediate beta but stable at higher beta. Gaussian functions for delta W_K are defined as functions of E cross B frequency and collisionality, with parameters reflecting the experience of the National Spherical Torus Experiment (NSTX). The reduced model was tested on a database of discharges from NSTX and experimentally stable and unstable discharges were separated noticeably on a stability map in E cross B frequency, collisionality space. The reduced model only failed to predict an unstable RWM in 15.6% of cases with an experimentally unstable RWM and performed well on predicting stability for experimentally stable discharges as well.
Type:
Dataset
Issue Date:
May 2017

2. A Riccati Solution for the Ideal MHD Plasma Response with Applications to Real-time Stability Control

Author(s):
Glasser, A.; Kolemen, E.; Glasser, A.H.
Abstract:
To effectuate near real-time feedback control of ideal MHD instabilities in a tokamak geometry, a rapid solution for stability analysis is a prerequisite. Toward this end, we reformulate the δW stability method with a Hamilton-Jacobi theory, elucidating analytical and numerical features of the generic tokamak ideal MHD stability problem. The plasma response matrix is demonstrated to be the solution of an ideal MHD matrix Riccati differential equation (MRDE). Since Riccati equations are prevalent in the control theory literature, such a shift in perspective brings to bear a range of numerical methods that are well-suited to the robust, fast solution of control problems. We discuss the usefulness of Riccati techniques in solving the stiff ODEs often encountered in ideal MHD stability analyses-—for example, in tokamak edge and stellarator physics. We then demonstrate the applicability of such methods to an existing 2D ideal MHD stability code—DCON—enabling its parallel operation in near real-time. Output is shown to match with high accuracy, and with wall-clock time ≪ 1s. Such speed may help enable active feedback ideal MHD stability control, especially in tokamak plasmas whose ideal MHD equilibria evolve with inductive timescale τ > 1s-—as in ITER.
Type:
Dataset
Issue Date:
March 2018

3. A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

Author(s):
Martin, James K; Sheehan, Joseph P; Bratton, Benjamin P; Moore, Gabriel M; Mateus, André; Li, Sophia Hsin-Jung; Kim, Hahn; Rabinowitz, Joshua D; Typas, Athanasios; Savitski, Mikhail M; Wilson, Maxwell Z; Gitai, Zemer
Abstract:
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates that SCH-79797 has two independent cellular targets, folate metabolism and bacterial membrane integrity, and outperforms combination treatments in killing MRSA persisters. Building on the molecular core of SCH-79797, we developed a derivative, Irresistin-16, with increased potency and showed its efficacy against Neisseria gonorrheae in a mouse vaginal infection model. This promising antibiotic lead suggests that combining multiple MoAs onto a single chemical scaffold may be an underappreciated approach to targeting challenging bacterial pathogens.
Type:
Dataset
Issue Date:
20 May 2020

4. A dynamic magnetic tension force as the cause of failed solar eruptions

Abstract:
Coronal mass ejections are solar eruptions driven by a sudden release of magnetic energy stored in the Sun’s corona. In many cases, this magnetic energy is stored in long-lived, arched structures called magnetic flux ropes. When a flux rope destabilizes, it can either erupt and produce a coronal mass ejection or fail and collapse back towards the Sun. The prevailing belief is that the outcome of a given event is determined by a magnetohydrodynamic force imbalance called the torus instability. This belief is challenged, however, by observations indicating that torus-unstable flux ropes sometimes fail to erupt. This contradiction has not yet been resolved because of a lack of coronal magnetic field measurements and the limitations of idealized numerical modelling. Here we report the results of a laboratory experiment that reveal a previously unknown eruption criterion below which torus-unstable flux ropes fail to erupt. We find that such ‘failed torus’ events occur when the guide magnetic field (that is, the ambient field that runs toroidally along the flux rope) is strong enough to prevent the flux rope from kinking. Under these conditions, the guide field interacts with electric currents in the flux rope to produce a dynamic toroidal field tension force that halts the eruption. This magnetic tension force is missing from existing eruption models, which is why such models cannot explain or predict failed torus events.
Type:
Dataset
Issue Date:
11 December 2015

5. A multi-machine scaling of halo current rotation

Author(s):
Myers, C.E.; Eidietis, N.W.; Gerasimov, S.N.; Gerhardt, S.Pl.; Granetz, R.S.; Hender, T.C.; Pautasso, G.
Abstract:
Halo currents generated during unmitigated tokamak disruptions are known to develop rotating asymmetric features that are of great concern to ITER because they can dynamically amplify the mechanical stresses on the machine. This paper presents a multi-machine analysis of these phenomena. More specifically, data from C-Mod, NSTX, ASDEX Upgrade, DIII-D, and JET are used to develop empirical scalings of three key quantities: (1) the machine-specific minimum current quench time, tauCQ; (2) the halo current rotation duration, trot; and (3) the average halo current rotation frequency, <fh>. These data reveal that the normalized rotation duration, trot/tauCQ, and the average rotation velocity, <vh>, are surprisingly consistent from machine to machine. Furthermore, comparisons between carbon and metal wall machines show that metal walls have minimal impact on the behavior of rotating halo currents. Finally, upon projecting to ITER, the empirical scalings indicate that substantial halo current rotation above <fh> = 20 Hz is to be expected. More importantly, depending on the projected value of tauCQ in ITER, substantial rotation could also occur in the resonant frequency range of 6-20 Hz. As such, the possibility of damaging halo current rotation during unmitigated disruptions in ITER cannot be ruled out.
Type:
Dataset
Issue Date:
October 2017

6. A novel scheme for error field correction in permanent magnet stellarators

Author(s):
Rutkowski, Adam; Hammond, Kenneth; Zhu, Caoxiang; Gates, David; Chambliss, Amelia
Abstract:
Stellarators offer a promising path towards fusion reactors, but their design and construction are complicated by stringent tolerance requirements on highly complex 3D coils. A potential way to simplify the engineering requirements for stellarators is to use simple planar toroidal field coils along with permanent magnet arrays to generate shaping fields. In order to ensure sufficient field accuracy while minimizing engineering complexity and system cost, new techniques are required to correct the field produced by the permanent magnet arrays to within requirements set by plasma physics. This work describes a novel correction method developed for this purpose. This analysis is applied to the design of a quasi-axisymmetric stellarator that employs a combination of permanent magnets and planar toroidal field coils to generate its magnetic field. Analysis techniques and initial results using the method for error correction on a proposed permanent magnet stellarator are shown, and it is demonstrated that the method successfully meets the design requirements of the project.
Type:
Dataset
Issue Date:
7 December 2022

7. A scalable real-time framework for Thomson scattering analysis: Application to NSTX-U

Author(s):
F. M. Laggner, A. Diallo, B. P. LeBlanc, R. Rozenblat, G. Tchilinguirian, E.Kolemen, the NSTX-U team
Abstract:
A detailed description of a prototype setup for real-time (rt) Thomson scattering (TS) analysis is presented and implemented in the multi-point Thomson scattering (MPTS) diagnostic system at the National Spherical Torus Experiment Upgrade(NSTX-U). The data acquisition hardware was upgraded with rt capable electronics (rt-analog digital converters (ADCs) and a rt server) that allow for fast digitization of the laser pulse signal of eight radial MPTS channels. In addition, a new TS spectrum analysis software for a rapid calculation of electron temperature (Te) and electron density (ne) was developed. Testing of the rt hardware and data analysis soft-ware was successfully completed and benchmarked against the standard, post-shot evaluation. Timing tests were performed showing that the end-to-end processing time was reproducibly below 17 ms for the duration of at least 5 s, meeting a 60 Hz deadline by the laser pulse repetition rate over the length of a NSTX-U discharge. The presented rt framework is designed to be scalable in system size, i.e. incorporation of additional radial channels by solely adding additional rt capable hardware. Furthermore, it is scalable in its operation duration and was continuously run for up to 30 min, making it an attractive solution for machines with long discharge duration such as advanced, non-inductive tokamaks or stellarators.
Type:
Dataset
Issue Date:
March 2019

8. A software package for plasma facing component analysis and design: the Heat flux Engineering Analysis Toolkit (HEAT)

Author(s):
Looby, Tom; Reinke, Matthew; Wingen, Andreas; Menard, Jonathan; Gerhardt, Stefan; Gray, Travis; Donovan, David; Unterberg, Ezekial; Klabacha, Jonathan; Messineo, Mike
Abstract:
The engineering limits of plasma facing components (PFCs) constrain the allowable operational space of tokamaks. Poorly managed heat fluxes that push the PFCs beyond their limits not only degrade core plasma performance via elevated impurities, but can also result in PFC failure due to thermal stresses or melting. Simple axisymmetric assumptions fail to capture the complex interaction between 3D PFC geometry and 2D or 3D plasmas. This results in fusion systems that must either operate with increased risk or reduce PFC loads, potentially through lower core plasma performance, to maintain a nominal safety factor. High precision 3D heat flux predictions are necessary to accurately ascertain the state of a PFC given the evolution of the magnetic equilibrium. A new code, the Heat flux Engineering Analysis Toolkit (HEAT), has been developed to provide high precision 3D predictions and analysis for PFCs. HEAT couples many otherwise disparate computational tools together into a single open source python package. Magnetic equilibrium, engineering CAD, finite volume solvers, scrape off layer plasma physics, visualization, high performace computing, and more, are connected in a single web-based user interface. Linux users may use HEAT without any software prerequisites via an appImage. This manuscript introduces HEAT, discusses the software architecture, presents first HEAT results, and outlines physics modules in development.
Type:
Dataset
Issue Date:
March 2021

9. A thermodynamic phase transition in magnetic reconnection

Author(s):
Jara-Almonte, Jonathan; Hantao, Ji
Abstract:
Data supporting the manuscript "A thermodynamic phase transition in magnetic reconnection" published in Physical Review Letters.
Type:
Dataset
Issue Date:
7 July 2021

10. Accessing Real-Life Episodic Information from Minutes versus Hours Earlier Modulates Hippocampal and High-Order Cortical Dynamics

Author(s):
Chen, Janice; Honey, Christopher; Simony, Erez; Arcaro, Michael; Norman, Kenneth; Hasson, Uri
Abstract:
It is well known that formation of new episodic memories depends on hippocampus, but in real-life settings (e.g., conversation), hippocampal amnesics can utilize information from several minutes earlier. What neural systems outside hippocampus might support this minutes-long retention? In this study, subjects viewed an audiovisual movie continuously for 25 min; another group viewed the movie in 2 parts separated by a 1-day delay. Understanding Part 2 depended on retrieving information from Part 1, and thus hippocampus was required in the day-delay condition. But is hippocampus equally recruited to access the same information from minutes earlier? We show that accessing memories from a few minutes prior elicited less interaction between hippocampus and default mode network (DMN) cortical regions than accessing day-old memories of identical events, suggesting that recent information was available with less reliance on hippocampal retrieval. Moreover, the 2 groups evinced reliable but distinct DMN activity timecourses, reflecting differences in information carried in these regions when Part 1 was recent versus distant. The timecourses converged after 4 min, suggesting a time frame over which the continuous-viewing group may have relied less on hippocampal retrieval. We propose that cortical default mode regions can intrinsically retain real-life episodic information for several minutes.
Type:
Dataset
Issue Date:
3 August 2015

11. Advances in boronization on NSTX-Upgrade

Author(s):
Skinner, C.H.; Bedoya, F.; Scotti, F.; Allain, J.P.; Blanchard, W.; Cai, D.; Jaworski, M.; Koel, B.E.
Abstract:
Boronization has been effective in reducing plasma impurities and enabling access to higher density, higher confinement plasmas in many magnetic fusion devices. The National Spherical Torus eXperiment, NSTX, has recently undergone a major upgrade to NSTX-U in order to develop the physics basis for a ST-based Fusion Nuclear Science Facility (FNSF) with capability for double the toroidal field, plasma current, and NBI heating power and increased pulse duration from 1–1.5 s to 5–8 s. A new deuterated tri-methyl boron conditioning system was implemented together with a novel surface analysis diagnostic. We report on the spatial distribution of the boron deposition versus discharge pressure, gas injection and electrode location. The oxygen concentration of the plasma facing surface was measured by in-vacuo XPS and increased both with plasma exposure and with exposure to trace residual gases. This increase correlated with the rise of oxygen emission from the plasma.
Type:
Dataset
Issue Date:
January 2017

12. Amplification of local changes along the timescale processing hierarchy

Author(s):
Yeshurun, Yaara; Nguyen, Mai; Hasson, Uri
Abstract:
Small changes in word choice can lead to dramatically different interpretations of narratives. How does the brain accumulate and integrate such local changes to construct unique neural representations for different stories? In this study we created two distinct narratives by changing only a few words in each sentence (e.g. “he” to “she” or “sobbing” to “laughing”) while preserving the grammatical structure across stories. We then measured changes in neural responses between the two stories. We found that the differences in neural responses between the two stories gradually increased along the hierarchy of processing timescales. For areas with short integration windows, such as early auditory cortex, the differences in neural responses between the two stories were relatively small. In contrast, in areas with the longest integration windows at the top of the hierarchy, such as the precuneus, temporal parietal junction, and medial frontal cortices, there were large differences in neural responses between stories. Furthermore, this gradual increase in neural difference between the stories was highly correlated with an area’s ability to integrate information over time. Amplification of neural differences did not occur when changes in words did not alter the interpretation of the story (e.g. “sobbing” to “crying”). Our results demonstrate how subtle differences in words are gradually accumulated and amplified along the cortical hierarchy as the brain constructs a narrative over time.
Type:
Dataset
Issue Date:
August 2017

13. Analytic stability boundaries for compressional and global Alfven eigenmodes driven by fast ions. I. Interaction via ordinary and anomalous cyclotron resonances.

Author(s):
Lestz J.B., Gorelenkov N.N., Belova E.V., Tang S.X., Crocker N.A.
Abstract:
Conditions for net fast ion drive are derived for beam-driven, sub-cyclotron compressional (CAE) and global (GAE) Alfven eigenmodes, such as those routinely observed in spherical tokamaks such as NSTX(-U) and MAST. Both co- and counter-propagating CAEs and GAEs are investigated, driven by the ordinary and anomalous Doppler-shifted cyclotron resonance with fast ions. Whereas prior results were restricted to vanishingly narrow distributions in velocity space, broad parameter regimes are identified in this work which enable an analytic treatment for realistic fast ion distributions generated by neutral beam injection. The simple, approximate conditions derived in these regimes for beam distributions of realistic width compare well to the numerical evaluation of the full analytic expressions for fast ion drive. Moreover, previous results in the very narrow beam case are corrected and generalized to retain all terms in omega/omega_{ci} and k_{||}/kperp, which are often assumed to be small parameters but can significantly modify the conditions of drive and damping when they are non-negligible. Favorable agreement is demonstrated between the approximate stability criterion, simulation results, and a large database of NSTX observations of cntr-GAEs.
Type:
Dataset
Issue Date:
September 2019

14. Analytic stability boundaries for compressional and global Alfven eigenmodes driven by fast ions. II. Interaction via Landau resonance.

Author(s):
Lestz, J.B.; Gorelenkov, N.N.; Belova, E.V.; Tang, S.X.; Crocker, N.A.
Abstract:
Conditions for net fast ion drive are derived for beam-driven, co-propagating, sub-cyclotron compressional (CAE) and global (GAE) Alfven eigenmodes driven by the Landau resonance with super-Alfvenic fast ions. Approximations applicable to realistic neutral beam distributions and mode characteristics observed in spherical tokamaks enable the derivation of marginal stability conditions for these modes. Such conditions successfully reproduce the stability boundaries found from numerical integration of the exact expression for local fast ion drive/damping. Coupling between the CAE and GAE branches of the dispersion due to finite \omega/\omega_{ci} and k_\parallel/k_\perp is retained and found to be responsible for the existence of the GAE instability via this resonance. Encouraging agreement is demonstrated between the approximate stability criterion, simulation results, and a database of NSTX observations of co-CAEs.
Type:
Dataset
Issue Date:
January 2020

15. Application of Benchmarked Kinetic Resistive Wall Mode Stability Codes to ITER, Including Additional Physics

Author(s):
Berkery, J.W.; Wang, Z.R.; Sabbagh, S.A.; Liu, Y.Q.; Betti, R.; Guazotto, L.
Abstract:
Leading resistive wall mode (RWM) stability codes MARS-K [Y. Liu, et al., Phys. Plasmas 15, 112503 (2008)] and MISK [B. Hu, et al., Phys. Plasmas 12, 057301 (2005)] have been previously benchmarked. The benchmarking has now been extended to include additional physics, and used to project the stability of ITER in a realistic operating space. Due to ITER's relatively low plasma rotation and collisionality, collisions and non-resonance rotational effects were both found to have little impact on stability, and these non-resonance rotational effects also will not self-consistently affect the ITER RWM eigenfunction. Resonances between thermal ions and electrons and the expected level of ITER toroidal rotation were found to be important to stability, as were alpha particles, which are not in rotational resonance. MISK calculations show that without alpha particles, ITER is projected to be unstable to the RWM, but the expected level of alphas is calculated to provide a sufficient level of stability.
Type:
Dataset
Issue Date:
October 2017

16. Application of IR imaging for free-surface velocity measurement in liquid-metal systems

Author(s):
Hvasta, M.H.; Kolemen, E.; Fisher, A.
Abstract:
Measuring free-surface, liquid-metal flow velocity is challenging to do in a reliable and accurate manner. This paper presents a non-invasive, easily-calibrated method of measuring the surface velocities of open-channel liquid-metal flows using an IR camera. Unlike other spatially-limited methods, this IR camera particle tracking technique provides full field-of-view data that can be used to better understand open-channel flows and determine surface boundary conditions. This method could be implemented and automated for a wide range of liquid-metal experiments, even if they operate at high-temperatures or within strong magnetic fields.
Type:
Dataset
Issue Date:
January 2017

17. Application of IR imaging for free-surface velocity measurement in liquid-metal systems

Author(s):
Hvasta, M. G.; Kolemen, E.; Fisher, A.
Abstract:
Measuring free-surface, liquid-metal flow velocity is challenging to do in a reliable and accurate manner. This paper presents a non-invasive, easily-calibrated method of measuring the surface velocities of open-channel liquid-metal flows using an IR camera. Unlike other spatially-limited methods, this IR camera particle tracking technique provides full field-of-view data that can be used to better understand open-channel flows and determine surface boundary conditions. This method could be implemented and automated for a wide range of liquid-metal experiments, even if they operate at high-temperatures or within strong magnetic fields.
Type:
Dataset
Issue Date:
January 2017

18. Application of Townsend avalanche theory to tokamak startup by coaxial helicity injection

Author(s):
Hammond, K.C.; Raman, R.; Volpe, F.A.
Abstract:
Townsend avalanche theory is employed to model and interpret plasma initiation in NSTX by Ohmic heating and coaxial helicity injection (CHI). The model is informed by spatially resolved vacuum calculations of electric field and magnetic field line connection length in the poloidal cross-section. The model is shown to explain observations of Ohmic startup including the duration and location of breakdown. Adapting the model to discharges initiated by CHI offers insight into the causes of upper divertor (absorber) arcs in cases where the discharge fails to initiate in the lower divertor gap. Finally, upper and lower limits are established for vessel gas fill based on requirements for breakdown and radiation. It is predicted that CHI experiments on NSTX-U should be able to use as much as four times the amount of prefill gas employed in CHI experiments in NSTX. This should provide greater flexibility for plasma start-up, as the injector flux is projected to be increased in NSTX-U.
Type:
Dataset
Issue Date:
September 2017

19. Application of transient CHI plasma startup to future ST and AT devices

Author(s):
Hammond, K.C.; Raman, R.; Jardin, S.C.
Abstract:
Employment of non-inductive plasma start-up techniques would considerably simplify the design of a spherical tokamak fusion reactor. Transient coaxial helicity injection (CHI) is a promising method, expected to scale favorably to next-step reactors. However, the implications of reactor-relevant parameters on the initial breakdown phase for CHI have not yet been considered. Here, we evaluate CHI breakdown in reactor-like configurations using an extension of the Townsend avalanche theory. We find that a CHI electrode concept in which the outer vessel wall is biased to achieve breakdown, while previously successful on NSTX and HIT-II, may exhibit a severe weakness when scaled up to a reactor. On the other hand, concepts which employ localized biasing electrodes such as those used in QUEST would avoid this issue. Assuming that breakdown can be successfully attained, we then apply scaling relationships to predict plasma parameters attainable in the transient CHI discharge. Assuming the use of 1 Wb of injector flux, we find that plasma currents of 1 MA should be achievable. Furthermore, these plasmas are expected to Ohmically self-heat with more than 1 MW of power as they decay, facilitating efficient hand-off to steady-state heating sources. These optimistic scalings are supported by TSC simulations.
Type:
Dataset
Issue Date:
February 2019

20. Attention and awareness in the dorsal attention network

Author(s):
Wilterson, Andrew; Nastase, Samuel; Bio, Branden; Guterstam, Arvid; Graziano, Michael
Abstract:
The attention schema theory (AST) posits a specific relationship between subjective awareness and attention, in which awareness is the control model that the brain uses to aid in the endogenous control of attention. We proposed that the right temporoparietal junction (TPJ) is involved in that interaction between awareness and attention. In previous experiments, we developed a behavioral paradigm in human subjects to manipulate awareness and attention. The paradigm involved a visual cue that could be used to guide a shift of attention to a target stimulus. In task 1, subjects were aware of the visual cue, and their endogenous control mechanism was able to use the cue to help control attention. In task 2, subjects were unaware of the visual cue, and their endogenous control mechanism was no longer able to use it to control attention, even though the cue still had a measurable effect on other aspects of behavior. Here we tested the two tasks while scanning brain activity in human volunteers. We predicted that the right TPJ would be active in relation to the cue in task 1, but not in task 2. This prediction was confirmed. The right TPJ was active in relation to the cue in task 1; it was not measurably active in task 2; the difference was significant. In our interpretation, the right TPJ is involved in a complex interaction in which awareness aids in the control of attention.
Type:
Dataset
Issue Date:
2020

21. Attentional Modulation of Brain Responses to Primary Appetitive and Aversive Stimuli

Author(s):
Cara L. Buck; Jonathan D. Cohen; Field, Brent; Daniel Kahneman; Samuel M. McClure; Leigh E. Nystrom
Abstract:
Studies of subjective well-being have conventionally relied upon self-report, which directs subjects’ attention to their emotional experiences. This method presumes that attention itself does not influence emotional processes, which could bias sampling. We tested whether attention influences experienced utility (the moment-by-moment experience of pleasure) by using functional magnetic resonance imaging (fMRI) to measure the activity of brain systems thought to represent hedonic value while manipulating attentional load. Subjects received appetitive or aversive solutions orally while alternatively executing a low or high attentional load task. Brain regions associated with hedonic processing, including the ventral striatum, showed a response to both juice and quinine. This response decreased during the high-load task relative to the low-load task. Thus, attentional allocation may influence experienced utility by modulating (either directly or indirectly) the activity of brain mechanisms thought to represent hedonic value.
Type:
Dataset, Software, and text
Issue Date:
11 February 2015

22. Blob Structure and Motion in the Edge and SOL of NSTX

Author(s):
Zweben, S.J.; J.R. Myra; W.M. Davis; D.A. D'Ippolito; T.K. Gray; S.M. Kaye; B.P. LeBlanc; R.J. Maqueda; D.A. Russell; D.P. Stotler
Abstract:
Blob analysis dataset
Type:
Dataset
Issue Date:
January 2016

23. Blob wakes in NSTX

Author(s):
Zweben SJ, Myra JR, Diallo A, Russell DA, Scotti F, Stotler DP
Abstract:
Transient small-scale structures were identified in the wake of blobs movingpoloidally through the SOL of high-powered H-mode plasmas in NSTX, using the gaspuff imaging (GPI) diagnostic. These blob wakes had a poloidal wavelength in therange 3.5 cm, which is significantly smaller than the average blob scale of~12 cm, and the wakes had a poloidal velocity of 1.5 km/sec in theelectron diamagnetic direction, which is opposite to the blob poloidal velocity inthese shots. These wakes were radially localized 0-4 cm outside the separatrix andoccurred within ~50 microsec after the passage of a blob through the GPI field of view.The clearest wakes were seen when the GPI viewing angle was well aligned with thelocal B field line, as expected for such small-scale structures given the diagnosticgeometry. A plausible theoretical interpretation of the wakes is discussed: theobserved wakes share some features of drift waves and/or drift-Alfven waves whichcould be excited
Type:
Dataset
Issue Date:
July 2019

24. Blob-hole correlation model for edge turbulence and comparisons with NSTX GPI data

Author(s):
Myra, J.R.; Zweben, S.J.; Russell, D.A.
Abstract:
Gas puff imaging (GPI) observations made in NSTX [Zweben S J, et al., 2017 Phys. Plasmas 24 102509] have revealed two-point spatial correlations of edge and scrape-off layer turbulence in the plane perpendicular to the magnetic field. A common feature is the occurrence of dipole-like patterns with significant regions of negative correlation. In this paper, we explore the possibility that these dipole patterns may be due to blob-hole pairs. Statistical methods are applied to determine the two-point spatial correlation that results from a model of blob-hole pair formation. It is shown that the model produces dipole correlation patterns that are qualitatively similar to the GPI data in several respects. Effects of the reference location (confined surfaces or scrape-off layer), a superimposed random background, hole velocity and lifetime, and background sheared flows are explored and discussed with respect to experimental observations. Additional analysis of the experimental GPI dataset is performed to further test this blob-hole correlation model. A time delay two-point spatial correlation study did not reveal inward propagation of the negative correlation structures that were postulated to correspond to holes in the data nor did it suggest that the negative correlation structures are due to neutral shadowing. However, tracing of the highest and lowest values (extrema) of the normalized GPI fluctuations shows strong evidence for mean inward propagation of minima and outward propagation of maxima, in qualitative agreement with theoretical expectations. Other properties of the experimentally observed extrema are discussed.
Type:
Dataset
Issue Date:
July 2018

25. CKavity Library: Next-Generation Sequencing

Abstract:
Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate this question, the Hecht lab has created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. These libraries were subjected to screens and selections, leading to the identification of sequences with roles in catalysis, modulating gene regulation, and metal homeostasis. However, the resulting functional proteins formed dynamic rather than well-ordered structures. This impeded structural characterization and made it difficult to ascertain a mechanism of action. To address this, Christina Karas's thesis work focuses on developing a new model of libraries based on the de novo protein S-824, a four-helix bundle with a very stable three-dimensional structure. The first part of this research focused on mutagenesis of S-824 and characterization of the resulting proteins, revealing that this scaffold tolerates amino acid substitutions, including buried polar residues and the removal of hydrophobic side chains to create a putative cavity. Distinct from previous libraries, Karas targeted variability to a specific region of the protein, seeking to create a cavity and potential active site. The second part of this work details the design and creation of a library encoding 1.7 x 10^6 unique proteins, assembled from degenerate oligonucleotides. The third and fourth parts of this work cover the screening effort for a range of activities, both in vitro and in vivo. I found that this collection binds heme readily, leading to abundant peroxidase activity. Hits for lipase and phosphatase activity were also detected. This work details the development of a new strategy for creating de novo sequences geared toward function rather than structure.
Type:
Dataset

26. CLEVR-Matrices

Author(s):
Mondal, Shanka Subhra; Webb, Taylor; Cohen, Jonathan
Abstract:
A dataset of Raven’s Progressive Matrices (RPM)-like problems using realistically rendered 3D shapes, based on source code from CLEVR (a popular visual-question-answering dataset) (Johnson, J., Hariharan, B., Van Der Maaten, L., Fei-Fei, L., Lawrence Zitnick, C., & Girshick, R. (2017). Clevr: A diagnostic dataset for compositional language and elementary visual reasoning. In Proceedings of the IEEE conference on computer vision and pattern recognition (pp. 2901-2910)).
Type:
Dataset
Issue Date:
1 March 2023

28. Calibrationless rotating Lorentz-force flowmeters for low flow rate applications

Author(s):
Hvasta, M. G.; Dudt, D.; Fisher, A. E.; Kolemen, E.
Abstract:
A 'weighted magnetic bearing' has been developed to improve the performance of rotating Lorentz-force flowmeters (RLFFs). Experiments have shown that the new bearing reduces frictional losses within a double-sided, disc-style RLFF to negligible levels. Operating such an RLFF under 'frictionless' conditions provides two major benefits. First, the steady-state velocity of the RLFF magnets matches the average velocity of the flowing liquid at low flow rates. This enables an RLFF to make accurate volumetric flow measurements without any calibration or prior knowledge of the fluid properties. Second, due to minimized frictional losses, an RLFF is able to measure low flow rates that cannot be detected when conventional, high-friction bearings are used. This paper provides a brief background on RLFFs, gives a detailed description of weighted magnetic bearings, and compares experimental RLFF data to measurements taken with a commercially available flowmeter.
Type:
Dataset
Issue Date:
29 May 2018

29. Climate Impacts from Large Volcanic Eruptions in a High-resolution Climate Model: the Importance of Forcing Structure

Author(s):
Yang, Wenchang; Vecchi, Gabriel; Fueglistaler, Stephan; Horowitz, Larry; Luet, David; Muñoz, Ángel; Paynter, David; Underwood, Seth
Abstract:
Explosive volcanic eruptions have large climate impacts, and can serve as observable tests of the climatic response to radiative forcing. Using a high resolution climate model, we contrast the climate responses to Pinatubo, with symmetric forcing, and those to Santa Maria and Agung, which had meridionally asymmetric forcing. Although Pinatubo had larger global-mean forcing, asymmetric forcing strongly shifts the latitude of tropical rainfall features, leading to larger local precipitation/TC changes. For example, North Atlantic TC activity over is enhanced/reduced by SH-forcing (Agung)/NH-forcing (Santa Maria), but changes little in response to the Pinatubo forcing. Moreover, the transient climate sensitivity estimated from the response to Santa Maria is 20% larger than that from Pinatubo or Agung. This spread in climatic impacts of volcanoes needs to be considered when evaluating the role of volcanoes in global and regional climate, and serves to contextualize the well-observed response to Pinatubo.
Type:
Dataset
Issue Date:
2019

30. Code and data from "Comparative genomic analysis reveals varying levels of mammalian adaptation to coronavirus infections"

Author(s):
King, Sean
Abstract:
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively. Included in this repository are the instructions and corresponding code required to build the dataset and run the analysis in the manuscript.
Type:
Dataset
Issue Date:
28 September 2021

31. Collisional dependence of Alfven mode saturation in tokamaks

Author(s):
Zhou, M.; White, R.
Abstract:
Saturation of \alfven modes driven unstable by a distribution of high energy particles as a function of collisionality is investigated with a guiding center code, using numerical eigenfunctions produced by linear theory and numerical high energy particle distributions. The most important resonance is found and it is shown that when the resonance domain is bounded, not allowing particles to collisionlessly escape, the saturation amplitude is given by the balance of the resonance mixing time with the time for nearby particles to collisionally diffuse across the resonance width. Saturation amplitudes are in agreement with theoretical predictions as long as the mode amplitude is not so large that it produces stochastic loss from the resonance domain.
Type:
Dataset
Issue Date:
December 2016

32. Comment on ‘Numerical modeling of tokamak breakdown phase driven by pure Ohmic heating under ideal conditions’

Author(s):
Yoo, Min-Gu; Na, Yong-Su
Abstract:
In this comment, we point out possible critical numerical flaws of recent particle simulation studies (Jiang et al 2016 Nucl. Fusion 56 126017, Peng et al 2018 Nucl. Fusion 58 026007) on the electrical gas breakdown in a simple one-dimensional periodic slab geometry. We show that their observations on the effects of the ambipolar electric fields during the breakdown, such as the sudden reversal of the ion flow direction, could not be real physical phenomena but resulting from numerical artifacts violating the momentum conservation law. We show that an incomplete implementation of the direct-implicit scheme can cause the artificial electric fields and plasma transports resulting in fallacies in simulation results. We also discuss that their simple plasma model without considering poloidal magnetic fields seriously mislead the physical mechanism of the electrical gas breakdown because it cannot reflect important dominant plasma dynamics in the poloidal plane (Yoo et al 2018 Nat. Commun. 9 3523).
Type:
Dataset
Issue Date:
June 2019

33. Compact and multi-view solid state neutral particle analyzer arrays on National Spherical Torus Experiment-Upgrade

Author(s):
Liu, D.; Heidbrink, W.W.; Tritz, K.; Fredrickson, E.D.; Hao, G.Z.; Zhu, Y.B.
Abstract:
A compact and multi-view Solid State Neutral Particle Analyzer (SSNPA) diagnostic based on silicon photodiode arrays has been successfully tested on the National Spherical Torus Experiment-Upgrade (NSTX-U). The SSNPA diagnostic provides spatially, temporally, and pitch-angle resolved measurements of fast-ion distribution by detecting fast neutral flux resulting from charge exchange (CX) reactions. The system consists of three 16-channel subsystems: t-SSNPA viewing the plasma mid-radius and neutral beam (NB) line #2 tangentially, r-SSNPA viewing the plasma core and NB line #1 radially and p-SSNPA with no intersection with any NB lines. Due to the setup geometry, the active CX signals of t-SSNPA and r-SSNPA are mainly sensitive to passing and trapped particles respectively. In addition, both t-SSNPA and r-SSNPA utilize three vertically stacked arrays with different filter thickness to obtain coarse energy information. The experimental data show that all channels are operational. The signal to noise ratio is typically larger than 10 and the main noise is x-ray induced signal. The active and passive CX signals are clearly observed on t-SSNPA and r-SSNPA during NB modulation. The SSNPA data also indicate significant losses of passing particles during sawteeth, while trapped particles are weakly affected. Fluctuations up to 120 kHz, have been observed on SSNPA, and they are strongly correlated with magnetohydrodynamics (MHD) instabilities.
Type:
Dataset
Issue Date:
November 2016

34. Compact steady-state tokamak performance dependence on magnet and core physics limits

Author(s):
Menard, J.E.
Abstract:
Compact tokamak fusion reactors utilizing advanced high-temperature superconducting magnets for the toroidal field coils have received considerable recent attention due to the promise of more compact devices and more economical fusion energy development. Facilities with combined Fusion Nuclear Science (FNS) and Pilot Plant missions to provide both the nuclear environment needed to develop fusion materials and components while also potentially achieving sufficient fusion performance to generate modest net electrical power are considered. The performance of the tokamak fusion system is assessed using a range of core physics and toroidal field magnet performance constraints to better understand which parameters most strongly influence the achievable fusion performance.
Type:
Dataset
Issue Date:
December 2018

35. Competitive learning modulates memory consolidation during sleep

Author(s):
Antony, James W.; Cheng, Larry Y.; Brooks, Paula P.; Paller, Ken A.; Norman, Kenneth A.
Abstract:
Competition between memories can cause weakening of those memories. Here we investigated memory competition during sleep in human participants by presenting auditory cues that had been linked to two distinct picture-location pairs during wake. We manipulated competition during learning by requiring participants to rehearse picture-location pairs associated with the same sound either competitively (choosing to rehearse one over the other, leading to greater competition) or separately; we hypothesized that greater competition during learning would lead to greater competition when memories were cued during sleep. With separate-pair learning, we found that cueing benefited spatial retention. With competitive-pair learning, no benefit of cueing was observed on retention, but cueing impaired retention of well-learned pairs (where we expected strong competition). During sleep, post-cue beta power (16–30 Hz) indexed competition and predicted forgetting, whereas sigma power (11–16 Hz) predicted subsequent retention. Taken together, these findings show that competition between memories during learning can modulate how they are consolidated during sleep.
Type:
Dataset
Issue Date:
November 2018

37. Computation of Alfvèn eigenmode stability and saturation through a reduced fast ion transport model in the TRANSP tokamak transport code

Author(s):
Podesta, M.; Gorelenkova, M.; Gorelenkov, N.N.; White, R.B.
Abstract:
Alfvénic instabilities (AEs) are well known as a potential cause of enhanced fast ion transport in fusion devices. Given a specific plasma scenario, quantitative predictions of (i) expected unstable AE spectrum and (ii) resulting fast ion transport are required to prevent or mitigate the AE- induced degradation in fusion performance. Reduced models are becoming an attractive tool to analyze existing scenarios as well as for scenario prediction in time-dependent simulations. In this work, a neutral beam heated NSTX discharge is used as reference to illustrate the potential of a reduced fast ion transport model, known as kick model, that has been recently implemented for interpretive and predictive analysis within the framework of the time-dependent tokamak transport code TRANSP. Predictive capabilities for AE stability and saturation amplitude are first assessed, based on given thermal plasma profiles only. Predictions are then compared to experimental results, and the interpretive capabilities of the model further discussed. Overall, the reduced model captures the main properties of the instabilities and associated effects on the fast ion population. Additional information from the actual experiment enables further tuning of the model’s parameters to achieve a close match with measurements.
Type:
Dataset
Issue Date:
September 2017

39. Coupling between Alfven wave and Kelvin-Helmholtz waves in the low latitude boundary layer

Author(s):
Kim, Eun-Hwa; Johnson, Jay; Nykyri, Katariina
Abstract:
The Kelvin-Helmholtz (KH) instability of magnetohydrodynamic surface waves at the low latitude boundary layer is examined using both an eigenfrequency analysis and a time-dependent wave simulation. The analysis includes the effects of sheared flow and Alfven velocity gradient. When the magnetosheath flows are perpendicular to the ambient magnetic field direction, unstable KH waves that propagate obliquely to the sheared flow direction occur at the sheared flow surface when the Alfv\'en Mach number is higher than an instability threshold. Including a shear transition layer between the magnetosphere and magnetosheath leads to secondary KH waves (driven by the sheared flow) that are coupled to the resonant surface Alfven wave. There are remarkable differences between the primary and the secondary KH waves including wave frequency, the growth rate, and the ratio between transverse and the compressional component. The secondary KH wave energy is concentrated near the shear Alfven wave frequency at the magnetosheath with a lower frequency than the primary KH waves. Although the growth rate of the secondary KH waves is lower than the primary KH waves, the threshold condition is lower, so it is expected that these types of waves will dominate at lower Mach number. Because the transverse component of the secondary KH waves is stronger than the primary KH waves, more efficient wave energy transfer from the boundary layer to the inner magnetosphere is also predicted.
Type:
Dataset
Issue Date:
December 2021

40. CrvA and CrvB form a curvature-inducing module sufficient to induce cell shape complexity in Gram-negative bacteria

Author(s):
Martin, Nicholas R; Blackman, Edith; Bratton, Benjamin P; Chase, Katelyn J; Bartlett, Thomas M; Gitai, Zemer
Abstract:
Bacterial species have diverse cell shapes that enable motility, colonization, and virulence. The cell wall defines bacterial shape and is primarily built by two cytoskeleton-guided synthesis machines, the elongasome and the divisome. However, the mechanisms producing complex shapes, like the curved-rod shape of Vibrio cholerae, are incompletely defined. Previous studies have reported that species-specific regulation of cytoskeleton-guided machines enables formation of complex bacterial shapes such as cell curvature and cellular appendages. In contrast, we report that CrvA and CrvB are sufficient to induce complex cell shape autonomously of the cytoskeleton in V. cholerae. The autonomy of the CrvAB module also enables it to induce curvature in the Gram-negative species Escherichia coli, Pseudomonas aeruginosa, Caulobacter crescentus, and Agrobacterium tumefaciens. Using inducible gene expression, quantitative microscopy, and biochemistry we show that CrvA and CrvB circumvent the need for patterning via cytoskeletal elements by regulating each other to form an asymmetrically-localized, periplasmic structure that directly binds to the cell wall. The assembly and disassembly of this periplasmic structure enables dynamic changes in cell shape. Bioinformatics indicate that CrvA and CrvB may have diverged from a single ancestral hybrid protein. Using fusion experiments in V. cholerae, we find that a synthetic CrvA/B hybrid protein is sufficient to induce curvature on its own, but that expression of two distinct proteins, CrvA and CrvB, promotes more rapid curvature induction. We conclude that morphological complexity can arise independently of cell shape specification by the core cytoskeleton-guided synthesis machines.
Type:
Dataset
Issue Date:
2021

41. Data and code for “Structured foraging of soil predators unveils functional responses to bacterial defenses”

Author(s):
Gregor, Thomas; Rossine, Fernando
Abstract:
Microscopy images are part of a paper entitled "Structured foraging of soil predators unveils functional responses to bacterial defenses" by Fernando Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. For detailed acquisition methods see the paper. Experiments were performed between 2019 and 2020 at Princeton University. Two types of images are provided, macroscopic and microscopic widefiled Images. Macroscopic images all show Petri dishes covered in fluorescent bacteria being consumed by amoebae. Images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum. Images used for the creation of a profile were all taken within 30 minutes of each other. Within each directory numbered images are independent replicates. The raw video directory contains time series for dishes under drug treatments. Each numbered folder is a sequence of photos (taken 30 minutes apart of each other) of a single dish. Microscopic images all show amoebae consuming bacteria on a petri dish. The 45 minute videos show either edge cells (located at the edge of amoebae colonies), or inner cells (located 2.5 millimeters towards the center of the colony, from the edge). Videos are confocal stacks, with bacteria showing in green and amoebae appearing as black holes within the bacterial lawn. As was for the macroscopic images, images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum.
Type:
Dataset and Software
Issue Date:
11 November 2022

43. Data for "The value of fusion energy to a decarbonized United States electric grid"

Author(s):
Schwartz, Jacob A.; Ricks, Wilson; Kolemen, Egemen; Jenkins, Jesse D.
Abstract:
Fusion could be a part of future decarbonized electricity systems, but it will need to compete with other technologies. In particular, pulsed tokamaks plants have a unique operational mode, and evaluating which characteristics make them economically competitive can help select between design pathways. Using a capacity expansion and operations model, we determined cost thresholds for pulsed tokamaks to reach a range of penetration levels in a future decarbonized US Eastern Interconnection. The required capital cost to reach a fusion capacity of 100 GW varied from $3000 to $7200/kW, and the equilibrium penetration increases rapidly with decreasing cost. The value per unit power capacity depends on the variable operational cost and on cost of its competition, particularly fission, much more than on the pulse cycle parameters. These findings can therefore provide initial cost targets for fusion more generally in the United States.
Type:
Dataset
Issue Date:
2022

44. Data for Nature Climate Change article 'Regional dry-season climate changes due to three decades of Amazonian deforestation'

Author(s):
Khanna, Jaya; Medvigy, David; Fueglistaler, Stephan; Walko, Robert
Abstract:
More than 20% Amazon rainforest has been cleared in the past three decades triggering important hydroclimatic changes. Small-scale (~few kilometers) deforestation in the 1980s has caused thermally-triggered atmospheric circulations that increase regional cloudiness and precipitation frequency. However, these circulations are predicted to diminish as deforestation increases. Here we use multi-decadal satellite records and numerical model simulations to show a regime shift in the regional hydroclimate accompanying increasing deforestation in Rondônia, Brazil. Compared to the 1980s, present-day deforested areas in downwind western Rondônia are found to be wetter than upwind eastern deforested areas during the local dry season. The resultant precipitation change in the two regions is approximately ±25% of the deforested area mean. Meso-resolution simulations robustly reproduce this transition when forced with increasing deforestation alone, showing a negligible role of large-scale climate variability. Furthermore, deforestation-induced surface roughness reduction is found to play an essential role in the present-day dry season hydroclimate. Our study illustrates the strong scale-sensitivity of the climatic response to Amazonian deforestation and suggests that deforestation is sufficiently advanced to have caused a shift from a thermally- to a dynamically-driven hydroclimatic regime.
Type:
Dataset and Software
Issue Date:
2017

45. Data for “Global adjoint tomography—model GLAD-M25”

Author(s):
Lei, Wenjie
Abstract:
The dataset contains the model file for the Global Adjoint Tomography Model 25 (GLAD-M25). The model file contains parameters defined on the spectral-element mesh and is recommend to be used in SPECFEM3D GLOBE for seismic wave simulation at the global scale.
Type:
Dataset
Issue Date:
5 April 2022

46. Data for: "Structure and Density of Silicon Carbide to 1.5 TPa and Implications for Extrasolar Planets"

Author(s):
Kim, Donghoon
Abstract:
There has been considerable recent interest in the high-pressure behavior of silicon carbide, a potential major constituent of carbon-rich exoplanets. In this work, the atomic-level structure of SiC was determined through in situ X-ray diffraction under laser-driven ramp compression up to 1.5 TPa; stresses more than seven times greater than previous static and shock data. Here we show that the B1-type structure persists over this stress range and we have constrained its equation of state (EOS). Using this data we have determined the first experimentally based mass-radius curves for a hypothetical pure SiC planet. Interior structure models are constructed for planets consisting of a SiC-rich mantle and iron-rich core. Carbide planets are found to be ~10% less dense than corresponding terrestrial planets.
Type:
Dataset
Issue Date:
28 April 2022

47. Data for: "The origin of non-skeletal carbonate mud and implications for global climate"

Author(s):
Geyman, Emily C.; Wu, Ziman; Nadeau, Matthew D.; Edmonsond, Stacey; Turner, Andrew; Purkis, Sam J.; Howes, Bolton; Dyer, Blake; Ahm, Anne-Sofie C.; Yao, Nan; Deutsch, Curtis A.; Higgins, John A.; Stolper, Daniel A.; Maloof, Adam C.
Abstract:
Carbonate mud represents one of the most important geochemical archives for reconstructing ancient climatic, environmental, and evolutionary change from the rock record. Mud also represents a major sink in the global carbon cycle. Yet, there remains no consensus about how and where carbonate mud is formed. In this contribution, we present new geochemical data that bear on this problem, including stable isotope and minor and trace element data from carbonate sources in the modern Bahamas such as ooids, corals, foraminifera, and green algae.
Type:
Dataset
Issue Date:
16 June 2022

48. Data for: 'Facies control on carbonate δ13C on the Great Bahama Bank'

Author(s):
Geyman, Emily C.; Maloof, Adam C.
Abstract:
The carbon isotopic (δ13C) composition of shallow-water carbonates often is interpreted to reflect the δ13C of the global ocean and is used as a proxy for changes in the global carbon cycle. However, local platform processes, in addition to meteoric and marine diagenesis, may decouple carbonate δ13C from that of the global ocean. To shed light on the extent to which changing sediment grain composition may produce δ13C shifts in the stratigraphic record, we present new δ13C measurements of benthic foraminifera, solitary corals, calcifying green algae, ooids, coated grains, and lime mud from the modern Great Bahama Bank (GBB). This survey of a modern carbonate environment reveals δ13C variability comparable to the largest δ13C excursions in the last two billion years of Earth history.
Type:
Dataset
Issue Date:
6 May 2021

49. Data for: 'How is sea level change encoded in carbonate stratigraphy?'

Author(s):
Geyman, Emily C.; Maloof, Adam C.; Dyer, Blake
Abstract:
The history of organismal evolution, seawater chemistry, and paleoclimate is recorded in layers of carbonate sedimentary rock. Meter-scale cyclic stacking patterns in these carbonates often are interpreted as representing sea level change. A reliable sedimentary proxy for eustasy would be profoundly useful for reconstructing paleoclimate, since sea level responds to changes in temperature and ice volume. However, the translation from water depth to carbonate layering has proven difficult, with recent surveys of modern shallow water platforms revealing little correlation between carbonate facies (i.e., grain size, sedimentary bed forms, ecology) and water depth. We train a convolutional neural network with satellite imagery and new field observations from a 3,000 km2 region northwest of Andros Island (Bahamas) to generate a facies map with 5 m resolution. Leveraging a newly-published bathymetry for the same region, we test the hypothesis that one can extract a signal of water depth change, not simply from individual facies, but from sequences of facies transitions analogous to vertically stacked carbonate strata. Our Hidden Markov Model (HMM) can distinguish relative sea level fall from random variability with ∼90% accuracy. Finally, since shallowing-upward patterns can result from local (autogenic) processes in addition to forced mechanisms such as eustasy, we search for statistical tools to diagnose the presence or absence of external forcings on relative sea level. With a new data-driven forward model that simulates how modern facies mosaics evolve to stack strata, we show how different sea level forcings generate characteristic patterns of cycle thicknesses in shallow carbonates, providing a new tool for quantitative reconstruction of ancient sea level conditions from the geologic record.
Type:
Dataset
Issue Date:
1 February 2021

50. Data for: Three-Dimensional Morphometry of Ooids in Oolites: a new tool for more accurate and precise paleoenvironmental interpretation

Author(s):
Howes, Bolton; Mehra, Akshay; Maloof, Adam
Abstract:
The prevalence of ooids in the stratigraphic record, and their association with shallow-water carbonate environments, make ooids an important paleoenvironmental indicator. Recent advances in the theoretical understanding of ooid morphology, along with empirical studies from Turks and Caicos, Great Salt Lake, and The Bahamas, have demonstrated that the morphology of ooids is indicative of depositional environment and hydraulic conditions. To apply this knowledge from modern environments to the stratigraphic record of Earth history, researchers measure the size and shape of lithified ooids on two-dimensional surfaces (i.e., thin sections or polished slabs), often assuming that random 2D slices intersect the nuclei and that the orientation of the ooids is known. Here we demonstrate that these assumptions rarely are true, resulting in errors of up to 35% on metrics like major axis length. We present a method for making 3D reconstructions by serial grinding and imaging, which enables accurate measurement of the morphology of individual ooids within an oolite, as well as the sorting and porosity of a sample. We also provide three case studies that use the morphology of ooids in oolites to extract environmental information. Each case study demonstrates that 2D measurements can be useful if the environmental signal is large relative to the error from 2D measurements. However, 3D measurements substantially improve the accuracy and precision of environmental interpretations. This study focuses on oolites, but errors from 2D measurements are not unique to oolites; this method can be used to extract accurate grain and porosity measurements from any lithified granular sample.
Type:
Dataset
Issue Date:
22 February 2021