Search

1. 2-km resolution oversampled NH3 data

Author(s):
Wang, Rui; Guo, Xuehui; Pan, Da; Kelly, James; Bash, Jesse; Sun, Kang; Paulot, Fabien; Clarisse, Lieven; Van Damme, Martin; Whitburn, Simon; Coheur, Pierre-François; Clerbaux, Cathy; Zondlo, Mark
Abstract:
Monthly, high resolution (~2 km) ammonia (NH3) column maps from the Infrared Atmospheric Sounding Interferometer (IASI) were developed across the contiguous United States and adjacent areas. Ammonia hotspots (95th percentile of the column distribution) were highly localized with a characteristic length scale of 12 km and median area of 152 km2. Five seasonality classes were identified with k-means++ clustering. The Midwest and eastern United States had a broad, spring maximum of NH3 (67% of hotspots in this cluster). The western United States, in contrast, showed a narrower mid-summer peak (32% of hotspots). IASI spatiotemporal clustering was consistent with those from the Ammonia Monitoring Network. CMAQ and GFDL-AM3 modeled NH3 columns have some success replicating the seasonal patterns but did not capture the regional differences. The high spatial-resolution monthly NH3 maps serve as a constraint for model simulations and as a guide for the placement of future, ground-based network sites.
Type:
Dataset
Issue Date:
December 2020

3. 60 degree Inclined Pulsar

Abstract:
Current sheet and open field lines with footpoints near the edge of the polar cap. The magnetic axis is inclined relative to the rotation axis by 60 degrees. Red field lines originate on the north polar cap and green field lines in the right panel originate on the south polar cap. Purple and grey colors indicate positive and negative net local charge density in the current sheet, which is shown between 1.2-2 light cylinder radii.
Type:
moving image
Issue Date:
21 November 2013

4. 90 degree Inclined Pulsar

Abstract:
Current sheet and open field lines with footpoints near the edge of the polar cap. The magnetic axis is inclined relative to the rotation axis by 90 degrees. Red field lines originate on the north polar cap and green field lines in the right panel originate on the south polar cap. Purple and grey colors indicate positive and negative net local charge density in the current sheet, which is shown between 1.2-2 light cylinder radii.
Type:
moving image
Issue Date:
21 November 2013

5. 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

6. 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

7. 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

11. A reduced-turbulence regime in the Large Helical Device upon injection of low-Z materials powders

Author(s):
Nespoli, Federico; Tanaka, Kenji; Masuzaki, Suguru; Ashikawa, Naoko; Shoji, Mamoru; Gilson, Erik; Lunsford, Robert; Oishi, Tetsutarou; Ida, Katsumi; Yoshinuma, Mikirou; Takemura, Yuki; Kinoshita, Toshiki; Motojima, Gen; Osakabe, Masaki; Kenmochi, Naoki; Kawamura, Gakushi; Suzuki, Chihiro; Nagy, Alex; Bortolon, Alessandro; Pablant, Novimir; Mollén, Albert; Tamura, Naoki; Gates, David; Morisaki, Tomohiro
Type:
Dataset
Issue Date:
2023

12. 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

13. 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

14. 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

15. 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

16. Achromonodin-1 NMR spectra

Author(s):
Link, A. James; Carson, Drew V.; So, Larry; Cheung-Lee, Wai Ling
Abstract:
This entry encompasses the raw NMR spectra used to determine the structure of the lasso peptide achromonodin-1. Within one file are included the five following spectra: COSY, TOCSY, NOESY (150 ms mixing time), NOESY (700 ms mixing time), and C,H HSQC. The file requires Mestrenova software to read. These spectra were used to develop the 3D structure models of achromonodin-1 that are deposited at the protein data bank (PDB) as entry 8SVB.
Type:
Dataset
Issue Date:
June 2023

17. 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

18. Aligned Nonspinning Dipoles

Abstract:
Magnetic field lines and current sheets for an orbiting neutron star binary with the magnetic moments of both stars aligned with the rotation axis. The stars are not spinning, i.e., R_{LC,∗} = ∞. Fields are by and large confined to the half of the magnetosphere closer to their source star. This movie shows the corotating field pattern as the orbit progresses.
Type:
moving image
Issue Date:
21 November 2013

19. Aligned Rapidly Spinning Dipoles

Abstract:
Magnetic field lines and current sheets for an orbiting neutron star binary with the magnetic moments of both stars aligned with the rotation axis. The stars are spinning rapidly at ∼ ms periods, with R_{LC,∗}/R_∗ = 2.7. Stellar spin winds fields backwards toroidally, and they can propagate to the far side of the magnetosphere closer to the opposing star. This movie shows the corotating field pattern as the orbit progresses.
Type:
moving image
Issue Date:
21 November 2013

20. Alternative energy vehicle deployment coupled with decarbonizing electricity generation amplifies climate, air quality and health co-benefits in China

Author(s):
Peng, Liqun; Liu, Feiqi; Zhou, Mi; Li, Mingwei; Zhang, Qiang; Mauzerall, Denise L.
Abstract:
China is the world's largest carbon emitter and suffers from severe air pollution. About one million deaths in China were attributable to air pollution in 2017. Alternative energy vehicles (AEVs), e.g. electric, hydrogen fuel cell, and natural gas vehicles, can help achieve both carbon emission mitigation and air quality improvement. However, climate, air quality and health co-benefit of AEVs powered by deeply decarbonized electricity generation remain poorly quantified. Here, we conduct a quantitative integrated assessment of the air quality, health, carbon emission mitigation and economic benefits of AEV deployment as the electricity grid decarbonizes in China. We find population-weighted annual PM2.5 and summer O3 concentration can decrease as large as 5.7μgm−3 and 4.9ppb. Annual avoided premature mortalities and years of life lost resulting from improved ambient air pollution can be as large as ~329,000 persons and ~1,611,000 years. We thus show that maximizing climate, air quality and health benefits of AEV deployment in China requires rapid decarbonization of the power system.
Type:
Dataset
Issue Date:
17 June 2021

21. 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

22. An extended MHD study of the 16 October 2015 MMS diffusion region crossing

Abstract:
The Magnetospheric Multiscale (MMS) mission has given us unprecedented access to high cadence particle and field data of magnetic reconnection at Earth's magnetopause. MMS first passed very near an X-line on 16 October 2015, the Burch event, and has since observed multiple X-line crossings. Subsequent 3D particle-in-cell (PIC) modeling efforts of and comparison with the Burch event have revealed a host of novel physical insights concerning magnetic reconnection, turbulence induced particle mixing, and secondary instabilities. In this study, we employ the Gkeyll simulation framework to study the Burch event with different classes of extended, multi-fluid magnetohydrodynamics (MHD), including models that incorporate important kinetic effects, such as the electron pressure tensor, with physics-based closure relations designed to capture linear Landau damping. Such fluid modeling approaches are able to capture different levels of kinetic physics in global simulations and are generally less costly than fully kinetic PIC. We focus on the additional physics one can capture with increasing levels of fluid closure refinement via comparison with MMS data and existing PIC simulations. In particular, we find that the ten-moment model well captures the agyrotropic structure of the pressure tensor in the vicinity of the X-line and the magnitude of anisotropic electron heating observed in MMS and PIC simulations. However, the ten-moment model has difficulty resolving the lower hybrid drift instability, which has been observed to plays a fundamental role in heating and mixing electrons in the current layer.
Type:
Dataset

23. 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

24. 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

25. Antialigned Nonspinning Dipoles

Abstract:
Magnetic field lines and current sheets for an orbiting neutron star binary with the magnetic moment of one star aligned with the rotation axis, and the magnetic moment of the other star tilted and antialigned with the rotation axis. The stars are not spinning, i.e., R_{LC,∗} = ∞. Fields from each star encircle the other star and force fields coming off the second star backwards toroidally. This movie shows the corotating field pattern as the orbit progresses.
Type:
moving image
Issue Date:
21 November 2013

26. Antialigned Rapidly Spinning Dipoles

Abstract:
Magnetic field lines and current sheets for an orbiting neutron star binary with the magnetic moment of one star aligned with the rotation axis, and the magnetic moment of the other star tilted and antialigned with the rotation axis. The stars are spinning rapidly at ∼ ms periods, with R_{LC,∗} /R_∗ = 2.7. Stellar spin winds fields backwards toroidally. This movie shows the corotating field pattern as the orbit progresses.
Type:
moving image
Issue Date:
21 November 2013

27. 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

28. 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

29. 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

30. 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

31. 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

33. 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

35. Basin-Scale Leakage Risks from Geologic Carbon Sequestration: Impact on Carbon Capture and Storage Energy Market Competitiveness

Abstract:
This three-year project, performed by Princeton University in partnership with the University of Minnesota and Brookhaven National Laboratory, examined geologic carbon sequestration in regard to CO2 leakage and potential subsurface liabilities. The research resulted in basin-scale analyses of CO2 and brine leakage in light of uncertainties in the characteristics of leakage processes, and generated frameworks to monetize the risks of leakage interference with competing subsurface resources. The geographic focus was the Michigan sedimentary basin, for which a 3D topographical model was constructed to represent the hydrostratigraphy. Specifically for Ottawa County, a statistical analysis of the hydraulic properties of underlying sedimentary formations was conducted. For plausible scenarios of injection into the Mt. Simon sandstone, leakage rates were estimated and fluxes into shallow drinking-water aquifers were found to be less than natural analogs of CO2 fluxes. We developed the Leakage Impact Valuation (LIV) model in which we identified stakeholders and estimated costs associated with leakage events. It was found that costs could be incurred even in the absence of legal action or other subsurface interference because there are substantial costs of finding and fixing the leak and from injection interruption. We developed a model framework called RISCS, which can be used to predict monetized risk of interference with subsurface resources by combining basin-scale leakage predictions with the LIV method. The project has also developed a cost calculator called the Economic and Policy Drivers Module (EPDM), which comprehensively calculates the costs of carbon sequestration and leakage, and can be used to examine major drivers for subsurface leakage liabilities in relation to specific injection scenarios and leakage events. Finally, we examined the competitiveness of CCS in the energy market. This analysis, though qualitative, shows that financial incentives, such as a carbon tax, are needed for coal combustion with CCS to gain market share. In another part of the project we studied the role of geochemical reactions in affecting the probability of CO2 leakage. A basin-scale simulation tool was modified to account for changes in leakage rates due to permeability alterations, based on simplified mathematical rules for the important geochemical reactions between acidified brines and caprock minerals. In studies of reactive flows in fractured caprocks, we examined the potential for permeability increases, and the extent to which existing reactive transport models would or would not be able to predict it. Using caprock specimens from the Eau Claire and Amherstburg, we found that substantial increases in permeability are possible for caprocks that have significant carbonate content, but minimal alteration is expected otherwise. We also found that while the permeability increase may be substantial, it is much less than what would be predicted from hydrodynamic models based on mechanical aperture alone because the roughness that is generated tends to inhibit flow.
Type:
text
Issue Date:
5 June 2014

37. 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

39. Bubble pinch-off in turbulence

Abstract:
Experimental data, simulation code, and Python scripts to reproduce the data presented in "Bubble pinch-off in turbulence"
Type:
Dataset and Software

41. 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

42. CPCB continuous monitoring air quality data for India, from 2015-2019

Author(s):
Sharma, Disha; Mauzerall, Denise
Abstract:
The dataset is a compilation of real time ground observations of criteria pollutants monitored at the Central Pollution Control Board (CPCB) continuous stations in India, from 2015-2019. Pollutants included are PM2.5, PM10, SO2, NO2 and O3 and are archived at every hour for all stations across India.
Type:
Dataset
Issue Date:
15 October 2021

44. Calibrated VIC Model Parameters over CONUS

Author(s):
Yang, Yuan; Pan, Ming; Beck, Hylke; Fisher, Colby; Beighley, R. Edward; Kao, Shih-Chieh; Hong, Yang; Wood, Eric
Abstract:
Conventional basin-by-basin approaches to calibrate hydrologic models are limited to gauged basins and typically result in spatially discontinuous parameter fields. Moreover, the consequent low calibration density in space falls seriously behind the need from present-day applications like high resolution river hydrodynamic modeling. In this study we calibrated three key parameters of the Variable Infiltration Capacity (VIC) model at every 1/8° grid-cell using machine learning-based maps of four streamflow characteristics for the conterminous United States (CONUS), with a total of 52,663 grid-cells. This new calibration approach, as an alternative to parameter regionalization, applied to ungauged regions too. A key difference made here is that we tried to regionalize physical variables (streamflow characteristics) instead of model parameters whose behavior may often be less well understood. The resulting parameter fields no longer presented any spatial discontinuities and the patterns corresponded well with climate characteristics, such as aridity and runoff ratio. The calibrated parameters were evaluated against observed streamflow from 704/648 (calibration/validation period) small-to-medium-sized catchments used to derive the streamflow characteristics, 3941/3809 (calibration/validation period) small-to-medium-sized catchments not used to derive the streamflow characteristics) as well as five large basins. Comparisons indicated marked improvements in bias and Nash-Sutcliffe efficiency. Model performance was still poor in arid and semiarid regions, which is mostly due to both model structural and forcing deficiencies. Although the performance gain was limited by the relative small number of parameters to calibrate, the study and results here served as a proof-of-concept for a new promising approach for fine-scale hydrologic model calibrations.
Type:
Dataset
Issue Date:
4 September 2019

45. 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

47. Chinese overseas development financing of electric power generation: A comparative analysis

Author(s):
Chen, Xu; Gallagher, Kevin P.; Mauzerall, Denise L.
Abstract:
Global power generation must rapidly decarbonize by mid-century to meet the goal of stabilizing global warming below 2 degree Celsius. To meet this objective, multilateral development banks (MDBs) have gradually reduced fossil fuel and increased renewable energy financing. Meanwhile, globally active national development finance institutions (DFIs) from Japan and South Korea have continued to finance overseas coal plants. Less is known about the increasingly active Chinese DFIs. Here we construct a new dataset of China’s policy banks’ overseas power generation financing and compare their technology choices and impact on generation capacity with MDBs and Japanese and South Korean DFIs. We find Chinese DFI power financing since 2000 has dramatically increased, surpassing other East Asian national DFIs and the major MDBs’ collective public sector power financing in 2013. As most Chinese DFI financing is currently in coal, decarbonization of their power investments will be critical in reducing future carbon emissions from recipient countries.
Type:
Dataset
Issue Date:
23 October 2020

48. Chiral Tetramer Molecular Model

Author(s):
Petsev, Nikolai D.; Stillinger, Frank H.; Debenedetti, Pablo G.
Abstract:
Source code for our energy-conserving reformulation of the 4-site molecular model for chiral phenomena originally introduced by Latinwo et al. [F. Latinwo, F. H. Stillinger, and P. G. Debenedetti, Molecular Model for Chirality Phenomena, J. Chem. Phys. 145, 154503 (2016)]. The reformulation includes an additional 8-body force that arises from an explicit configuration-dependent term in the potential energy function, resulting in a coarse-grained energy-conserving force field for molecular dynamics simulations of chirality phenomena. In this model, the coarse-grained interaction energy between two tetramers depends on their respective chiralities, and is controlled by a parameter λ, where favors local configurations involving tetramers of opposite chirality, and gives energetic preference to configurations involving tetramers of the same chirality. The source code is for use with the LAMMPS simulation package.
Type:
Software
Issue Date:
3 August 2021

49. 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

50. 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

51. Collapse of reacted fracture surface decreases permeability and frictional strength

Author(s):
Peters, Catherine A.; Spokas, Kasparas
Abstract:
Geochemical and geomechanical perturbations of the subsurface caused by the injection of fluids present the risk of leakage and seismicity. This study investigated how flow of acidic fluids affects hydraulic and frictional properties of fractures using experiments with 3.8 cm-long specimens of Eagle Ford shale, a laminated shale with carbonate-rich strata. In low-pressure flow cells, one set of samples was exposed to an acidic brine and another set was exposed to a neutral brine. X-ray computed tomography and x-ray fluorescence analysis revealed that samples exposed to the acidic brine were calcite-depleted and had developed a porous altered layer, while the other set showed little evidence of alteration. After reaction, samples were compacted and sheared in a triaxial cell that supplied normal stress and differential pore pressure at prescribed sliding velocities, independently measuring friction and permeability. During the initial compaction, the porous altered layer collapsed into fine particles that filled the fracture aperture. This effectively impeded flow and sealed the fracture, resulting in a decrease in fracture permeability by 1 to 2 orders of magnitude relative to the compressed unaltered fractures. During shear, the collapsed layer of fine-grained particles prevented the formation of interlocking micro-asperities resulting in lower frictional strength. With regard to subsurface risks, this study showcases how coupled geochemical and geomechanical processes could favorably seal fractures to inhibit leakage, but also could increase the likelihood of induced seismicity. These findings have important implications for geological carbon sequestration, pressurized fluid energy storage, geothermal energy, and other subsurface technologies.
Type:
Dataset
Issue Date:
2018

53. 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

54. 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

55. 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

56. 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

58. Complete Dataset for Williams Site Pore Water Chemistry, March 2011 - April 2012

Abstract:
Complete dataset of pore water chemical parameters measured at the Marsh Resource Meadowlands Mitigation Bank, a tidal marsh within the New Jersey Meadowlands, from March 2011 to April 2012. Analytes measured include dissolved methane, sulfate, dissolved organic carbon, temperature, salinity, and pH. Measurements were conducted using porewater dialysis samplers, and water was sampled from the surface to a depth of 60 cm.
Type:
Dataset
Issue Date:
7 March 2014

61. 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

62. 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

63. Data and code for 'Hydrological cycle amplification reshapes warming-driven oxygen loss in Atlantic Ocean'

Author(s):
Hogikyan, Allison
Abstract:
Physical and biogeochemical variables from the NOAA-GFDL Earth System Model 2M experiments (pre-processed), previously published observation-based datasets, and code to reproduce figures from these datasets, used for the study 'Hydrological cycle amplification reshapes warming-driven oxygen loss in Atlantic Ocean'.
Type:
Dataset and Software
Issue Date:
June 2023

64. 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

65. Data corresponding to our paper on "Chemotactic smoothing of collective migration"

Author(s):
Bhattacharjee, Tapomoy; Amchin, Daniel; Alert, Ricard; Ott, Jenna; Datta, Sujit
Abstract:
Collective migration -- the directed, coordinated motion of many self-propelled agents -- is a fascinating emergent behavior exhibited by active matter that has key functional implications for biological systems. Extensive studies have elucidated the different ways in which this phenomenon may arise. Nevertheless, how collective migration can persist when a population is confronted with perturbations, which inevitably arise in complex settings, is poorly understood. Here, by combining experiments and simulations, we describe a mechanism by which collectively migrating populations smooth out large-scale perturbations in their overall morphology, enabling their constituents to continue to migrate together. We focus on the canonical example of chemotactic migration of Escherichia coli, in which fronts of cells move via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We identify two distinct modes in which chemotaxis influences the morphology of the population: cells in different locations along a front migrate at different velocities due to spatial variations in (i) the local nutrient gradient and in (ii) the ability of cells to sense and respond to the local nutrient gradient. While the first mode is destabilizing, the second mode is stabilizing and dominates, ultimately driving smoothing of the overall population and enabling continued collective migration. This process is autonomous, arising without any external intervention; instead, it is a population-scale consequence of the manner in which individual cells transduce external signals. Our findings thus provide insights to predict, and potentially control, the collective migration and morphology of cell populations and diverse other forms of active matter.
Type:
Dataset
Issue Date:
24 June 2021

66. Data for "A New Open-path Eddy Covariance Method for N2O and Other Trace Gases that Minimizes Temperature Corrections"

Author(s):
Pan, Da; Gelfand, Ilya; Tao, Lei; Abraha, Michael; Sun, Kang; Guo, Xuehui; Chen, Jiquan; Robertson, G. Philip; Zondlo, Mark A.
Abstract:
This dataset contains spectroscopic simulations, experimental results for the 2202 cm-1 N2O absorption line, and N2O flux measurements shown in "A New Open-path Eddy Covariance Method for N2O and Other Trace Gases that Minimizes Temperature Corrections" by Da Pan, Ilya Gelfand, Lei Tao, Michael Abraha, Kang Sun, Xuehui Guo, Jiquan Chen, G. Philip Robertson, and Mark A. Zondlo. The HITRAN Application Programming Interface (HAPI) with HITRAN 2016 was used for spectroscopic simulations. Experiments were conducted to quantify H2O-broadened half-width at half maximum and validate spectroscopic simulations. N2O flux was measured with both eddy covariance and static chamber methods.
Type:
Dataset
Issue Date:
26 October 2021

67. Data for "Ammonia Dry Deposition in an Alpine Ecosystem Traced to Agricultural Emission Hotpots"

Author(s):
Pan, Da; Benedict, Katherine; Golston, Levi; Wang, Rui; Collett, Jeffrey Jr; Tao, Lei; Sun, Kang; Guo, Xuehui; Ham, Jay; Prenni, Anthony; Schichtel, Bret; Mikoviny, Tomas; Müller, Markus; Wisthaler, Armin; Zondlo, Mark
Abstract:
Elevated reactive nitrogen (Nr) deposition is a concern for alpine ecosystems, and dry NH3 deposition is a key contributor. Understanding how emission hotspots impact downwind ecosystems through dry NH3 deposition provides opportunities for effective mitigation. However, direct NH3 flux measurements with sufficient temporal resolution to quantify such events are rare. Here, we measured NH3 fluxes at Rocky Mountain National Park (RMNP) during two summers and analyzed transport events from upwind agricultural and urban sources in northeastern Colorado. We deployed open-path NH3 sensors on a mobile laboratory and an eddy covariance tower to measure NH3 concentrations and fluxes. Our spatial sampling illustrated an upslope event that transported NH3 emissions from the hotspot to RMNP. Observed NH3 deposition was significantly higher when backtrajectories passed through only the agricultural region (7.9 ng m-2 s-1) versus only the urban area (1.0 ng m-2 s-1) and both urban and agricultural areas (2.7 ng m-2 s-1). Cumulative NH3 fluxes were calculated using observed, bidirectional modeled, and gap-filled fluxes. More than 40% of the total dry NH3 deposition occurred when air masses were traced back to agricultural source regions. More generally, we identified that 10 (25) more national parks in the U.S. are within 100 (200) km of an NH3 hotspot, and more observations are needed to quantify the impacts of these hotspots on dry NH3 depositions in these regions.
Type:
Dataset
Issue Date:
2021

68. Data for "Caught in the Crossfire: Fears of Chinese-American Scientists"

Author(s):
Xie, Yu; Lin, Xihong; Li, Ju; He, Qian; Huang, Junming
Abstract:
This dataset encompasses two distinct sets of data analyzed in the study, namely Asian American Scholar Forum survey data and Microsoft Academic Graph bibleometrics data: Yu Xie, Xihong Lin, Ju Li, Qian He, Junming Huang, Caught in the Crossfire: Fears of Chinese-American Scientists, Proceedings of the National Academy of Sciences, in press (2023).
Type:
Dataset
Issue Date:
May 2023

70. Data for "First-principles-based Machine Learning Models for Phase Behavior and Transport Properties of CO2"

Author(s):
Nicola Barbosa Muniz, Maria Carolina
Abstract:
This dataset contains example input files, training data sets and potential files related to the publication "First-principles-based Machine Learning Models for Phase Behavior and Transport Properties of CO2." by Mathur et al (2023). In this work, we developed machine learning models for CO2 based on different exchange-correlation DFT functionals. We assessed their performance on liquid densities, vapor-liquid equilibrium and transport properties.
Type:
Dataset
Issue Date:
10 April 2023

71. Data for "Spatial heterogeneity of ammonia fluxes in a deciduous forest and adjacent grassland"

Author(s):
Guo, Xuehui; Pan, Da; Daly, Ryan; Chen, Xi; Walker, John; Tao, Lei; McSpiritt, James; Zondlo, Mark
Abstract:
Gas-phase ammonia (NH3), emitted primarily from agriculture, contributes significantly to reactive nitrogen (Nr) deposition. Excess deposition of Nr to the environment causes acidification, eutrophication, and loss of biodiversity. The exchange of NH3 between land and atmosphere is bidirectional and can be highly heterogenous when underlying vegetation and soil characteristics differ. Direct measurements that assess the spatial heterogeneity of NH3 fluxes are lacking. To this end, we developed and deployed two fast-response, quantum cascade laser-based open-path NH3 sensors to quantify NH3 fluxes at a deciduous forest and an adjacent grassland separated by 700 m in North Carolina, United States from August to November, 2017. The sensors achieved 10 Hz precisions of 0.17 ppbv and 0.23 ppbv in the field, respectively. Eddy covariance calculations showed net deposition of NH3 (-7.3 ng NH3-N m−2 s−1) to the forest canopy and emission (3.2 ng NH3-N m−2 s−1) from the grassland. NH3 fluxes at both locations displayed diurnal patterns with absolute magnitudes largest midday and with smaller peaks in the afternoons. Concurrent biogeochemistry data showed over an order of magnitude higher NH3 emission potentials from green vegetation at the grassland compared to the forest, suggesting a possible explanation for the observed flux differences. Back trajectories originating from the site identified the upwind urban area as the main source region of NH3. Our work highlights the fact that adjacent natural ecosystems sharing the same airshed but different vegetation and biogeochemical conditions may differ remarkably in NH3 exchange. Such heterogeneities should be considered when upscaling point measurements, downscaling modeled fluxes, and evaluating Nr deposition for different natural land use types in the same landscape. Additional in-situ flux measurements accompanied by comprehensive biogeochemical and micrometeorological records over longer periods are needed to fully characterize the temporal variabilities and trends of NH3 fluxes and identify the underlying driving factors.
Type:
Dataset
Issue Date:
September 2022

72. Data for "Stability and Kinetics of Iron-Terephthalate MOFs with Diverse Structures in Aqueous Pollutant Degradation"

Author(s):
Sarazen, Michele; Moore, Samuel
Abstract:
Numerical data is tabulated for all plots (Figures 2, 3a-b, 4-89, S1, S4a-b,d, S5a-b,d, S6-S156) and included as separate spreadsheets categorized by figure in a .zip file in the Supplementary Material. Error bars in Figure 4 show the spread of data observed for 4 and 5 trials on independent samples for MIL-101 and MOF-235, respectively. Figure 6a shows the average of triplicate filtrate test conversions with error propagated based on this spread. Figures 6b and S165 error bars on rate constants are determined based on propagated conversion uncertainty for independent trials and extracted standard deviations of pseudo-first order rate constants from linearized plots. Error bars on other plots represent propagation of experimental uncertainty on single trials.
Type:
Dataset
Issue Date:
19 June 2023

74. Data for 'Environmental Benefits and Household Costs of Clean Heating Options in Northern China'

Author(s):
Zhou, Mi; Peng, Liqun; Zhang, Lin; Mauzerall, Denise L.
Abstract:
This dataset is created for the paper titled 'Environmental Benefits and Household Costs of Clean Heating Options in Northern China' and published on Nature Sustainability. Based on a 2015 regional anthropogenic emission inventory (base case), we propose seven counterfactual scenarios in which all 2015 residential solid fuel heating in northern China switches to one of the following non-district heating options: clean coal with improved stoves (CCIS), natural gas heaters (NGH), resistance heaters (RH), or air-to-air heat pumps (AAHP). This dataset provides the following gridded information for the base case and each clean heating scenario: (1) annual residential heating emissions for PM2.5/NOx/SO2; (2) monthly mean surface PM2.5 concentrations from the WRF-Chem model; (3) annual PM2.5-related premature deaths calculated by the GEMM model; (4) 2015 population in China; (5) mask for provinces in China; (6) longitude and latitude of each grid center.
Type:
Dataset
Issue Date:
22 December 2021

75. Data for Coarse-grained Intrinsically Disordered Proteins

Author(s):
Webb, Michael; Patel, Roshan; Borca, Carlos
Abstract:
This distribution compiles numerous physical properties for 2,585 intrinsically disordered proteins (IDPs) obtained by coarse-grained molecular dynamics simulation. This combination comprises "Dataset A" as reported in "Featurization strategies for polymer sequence or composition design by machine learning" by Roshan A. Patel, Carlos H. Borca, and Michael A. Webb (DOI: 10.1039/D1ME00160D). The specific IDP sequences are sourced from version 9.0 of the DisProt database. 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.
Type:
Dataset
Issue Date:
6 May 2022

76. Data for Configurations and Characteristics of Simulated Single-Chain Nanoparticles

Author(s):
Webb, Michael; Patel, Roshan; Colmenares, Sophia
Abstract:
This item provides access to all configurations of single-chain nanoparticles analyzed in the manuscript "Sequence Patterning, Morphology, and Dispersity in Single-Chain Nanoparticles: Insights from Simulation and Machine Learning" by Roshan A. Patel, Sophia Colmenares, and Michael A. Webb (DOI: 10.1021/acspolymersau.3c00007). The single-chain nanoparticles derive from 320 unique precursor chains that are distinguished by the fraction of linker beads that decorate a fixed-length polymer backbone and the distribution or blockiness of those linker beads. The data is provided in the form of serialized object using the `pickle' python module. The data was compiled using Python version 3.8.8 and Clang 10.0.0. The Python object loaded from the .pkl file is a nested list, with the first dimension having 7,680 entries for the 7,680 unique single-chain nanoparticles produced in the aforementioned paper. Each of those 7,680 entries is itself a list with 20 entries, representing the 20 different simulation snapshots of the given single-chain nanoparticle. Each of the 20 entries is another list with two entries, with the first being a numpy.ndarray containing the x,y,z coordinates of all the beads comprising the single-chain nanoparticle and the second being a numpy.ndarray with a numerical encoding to indicate whether the beads are backbone (indicated as '0') or linker beads (indicated as '1'). Altogether, this provides 153,600 configurations of single-chain nanoparticles.
Type:
Dataset
Issue Date:
2 June 2023

77. 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

78. Data for food consumption strategies in China

Author(s):
Guo, Yixin; Mauzerall, Denise; He, Pan
Abstract:
This dataset provides the data generated during the project analyzing ‘Food Consumption Strategies for Addressing Air Pollution, Climate Change, Water Use, and Public Health in China’. It includes the code for generating the alternative dietary scenarios, for analyzing the health impacts of alternative diets, and for visualization of results.
Type:
Dataset
Issue Date:
31 October 2020

79. 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

80. Data for: "Financing Carbon Lock-in in Developing Countries: Bilateral Financing for Power Generation Technologies from China, Japan, and the United States"

Author(s):
Chen, Xu; Li, Zhongshu; Gallagher, Kevin P.; Mauzerall, Denise L.
Abstract:
Power sector decarbonization requires a fundamental redirection of global finance from fossil fuel infrastructure towards low carbon technologies. Bilateral finance plays an important role in the global energy transition to non-fossil energy, but an understanding of its impact is limited. Here, for the first time, we compare the influence of overseas finance from the three largest economies – United States, China, and Japan – on power generation development beyond their borders and evaluate the associated long-term CO2 emissions. We construct a new dataset of Japanese and U.S. overseas power generation finance between 2000-2018 by analyzing their national development finance institutions’ press releases and annual reports and tracking their foreign direct investment at the power plant level. Synthesizing this new data with previously developed datasets for China, we find that the three countries’ overseas financing concentrated in fossil fuel power technologies over the studied period. Financing commitments from China, Japan, and the United States facilitated 101 GW, 95 GW, and 47 GW overseas power capacity additions, respectively. The majority of facilitated capacity additions are fossil fuel plants (64% for China, 87% for Japan, and 66% for the United States). Each of the countries’ contributions to non-hydro renewable generation was less than 15% of their facilitated capacity additions. Together, we estimate that overseas fossil fuel power financing through 2018 from these three countries will lock in 24 Gt CO2 emissions by 2060. If climate targets are to be met, replacing bilateral fossil fuel financing with financing of renewable technologies is crucial.
Type:
Dataset
Issue Date:
8 July 2021

81. 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

82. 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

83. 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

84. 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

85. Data for: Persistent hepatitis B virus and HIV coinfections in dually humanized mice engrafted with human liver and immune system

Author(s):
Ploss, Alexander; Hogan, Glenn; Winer, Benjamin; Ahodantin, James; Sellau, Julie; Huang, Tiffany; Douam, Florian; Funaki, Masaya; Chiriboga, Luis; Su, Lishan
Abstract:
Chronic hepatitis B (CHB), caused by hepatitis B virus (HBV), remains a major medical problem. HBV has a high propensity for progressing to chronicity and can result in severe liver disease, including fibrosis, cirrhosis and hepatocellular carcinoma. CHB patients frequently present with viral coinfection, including HIV and hepatitis delta virus. About 10% of chronic HIV carriers are also persistently infected with HBV which can result in more exacerbated liver disease. Mechanistic studies of HBV-induced immune responses and pathogenesis, which could be significantly influenced by HIV infection, have been hampered by the scarcity of immunocompetent animal models. Here, we demonstrate that humanized mice dually engrafted with components of a human immune system and a human liver supported HBV infection, which was partially controlled by human immune cells, as evidenced by lower levels of serum viremia and HBV replication intermediates in the liver. HBV infection resulted in priming and expansion of human HLA-restricted CD8+ T cells, which acquired an activated phenotype. Notably, our dually humanized mice support persistent coinfections with HBV and HIV which opens opportunities for analyzing immune dysregulation during HBV and HIV coinfection and preclinical testing of novel immunotherapeutics.
Type:
Dataset
Issue Date:
12 June 2023

86. 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

87. Data from "A Neural Network Water Model Based on the MB-pol Many-Body Potential"

Author(s):
Muniz, Maria Carolina
Abstract:
This dataset contains input files, training data and other files related to the machine learning models developed during the work by Muniz et al. In this work, we construct machine learning models based on the MB-pol many-body model. We find that the training set should include cluster configurations as well as liquid phase configurations in order to accurately represent both liquid and VLE properties. The results attest for the ability of machine learning models to accurately represent many-body potentials and provide an efficient avenue for water simulations.
Type:
Dataset
Issue Date:
27 September 2023

88. Data from "Critical behavior in a chiral molecular model"

Author(s):
Piaggi, Pablo
Abstract:
Understanding the condensed-phase behavior of chiral molecules is important in biology, as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid, into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature T ~ 0.985 Tc and our findings indicate that the free energy barrier for this transformation increases with system size as N^2/3 where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically-enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.
Type:
Dataset
Issue Date:
9 June 2023

89. Data from "Homogeneous ice nucleation in an ab initio machine learning model"

Author(s):
Piaggi, Pablo
Abstract:
This dataset contains input and output files to reproduce the results of the manuscript "Homogeneous ice nucleation in an ab initio machine learning model" by Pablo M. Piaggi, Jack Weis, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, and Roberto Car (arXiv preprint https://arxiv.org/abs/2203.01376). In this work, we studied the homogeneous nucleation of ice from supercooled liquid water using a machine learning model trained on ab initio energies and forces. Since nucleation takes place over times much longer than the simulation times that can be afforded using molecular dynamics simulations, we make use of the seeding technique that is based on simulating an ice cluster embedded in liquid water. The key quantity provided by the seeding technique is the size of the critical cluster (i.e., a size such that the cluster has equal probabilities of growing or shrinking at the given supersaturation). Using data from the seeding simulations and the equations of classical nucleation theory we compute nucleation rates that can be compared with experiments.
Type:
Dataset
Issue Date:
4 April 2022

90. Data from "Liquid-liquid transition in water from first principles"

Author(s):
Gartner, Thomas
Abstract:
This dataset contains all data relevant to a forthcoming publication in which we used molecular simulation methods to study the phase behavior of supercooled water. The dataset contains simulation input and output files, processed data files, and image files used to create all plots in the manuscript. Python analysis scripts are also included, including instructions for how to re-generate all plots in the manuscript.
Type:
Dataset
Issue Date:
26 July 2022

91. Data from "Manifestations of metastable criticality in glassy water-like models detected by large-scale structural properties"

Author(s):
Gartner III, Thomas E.; Torquato, Salvatore; Car, Roberto; Debenedetti, Pablo G.
Abstract:
This dataset contains all data related to the publication "Manifestations of metastable criticality in glassy water-like models detected by large-scale structural properties" by Gartner et al., in preparation 2020. In this work, we used molecular dynamics simulations to explore the relationship between water's polyamorphism (multiple amorphous solid states) and its hypothesized liquid-liquid transition. Using the TIP4P/2005 molecular model of water, we found a surprising signature of water's liquid-liquid critical point in the long-range structure of water's amorphous solid states formed by isobaric cooling at different pressures. This structural signature was absent in two other systems that lack a critical point. This dataset contains molecular dynamics simulation trajectories, as well as processed data, analysis codes, and image files used in the publication.
Type:
Dataset
Issue Date:
3 December 2020

92. Data from "Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point"

Author(s):
Piaggi, Pablo M; Gartner, Thomas E; Car, Roberto; Debenedetti, Pablo G
Abstract:
The possible existence of a liquid-liquid critical point in deeply supercooled water has been a subject of debate in part due to the challenges associated with providing definitive experimental evidence. Pioneering work by Mishima and Stanley [Nature 392, 164 (1998) and Phys.~Rev.~Lett. 85, 334 (2000)] sought to shed light on this problem by studying the melting curves of different ice polymorphs and their metastable continuation in the vicinity of the expected location of the liquid-liquid transition and its associated critical point. Based on the continuous or discontinuous changes in slope of the melting curves, Mishima suggested that the liquid-liquid critical point lies between the melting curves of ice III and ice V. Here, we explore this conjecture using molecular dynamics simulations with a purely-predictive machine learning model based on ab initio quantum-mechanical calculations. We study the melting curves of ices III, IV, V, VI, and XIII using this model and find that the melting lines of all the studied ice polymorphs are supercritical and do not intersect the liquid-liquid transition locus. We also find a pronounced, yet continuous, change in slope of the melting lines upon crossing of the locus of maximum compressibility of the liquid. Finally, we analyze critically the literature in light of our findings, and conclude that the scenario in which melting curves are supercritical is favored by the most recent computational and experimental evidence. Thus, although the preponderance of experimental and computational evidence is consistent with the existence of a second critical point in water, the behavior of the melting lines of ice polymorphs does not provide strong evidence in support of this viewpoint, according to our calculations.
Type:
Dataset
Issue Date:
February 2023

93. Data from "Signatures of a liquid-liquid transition in an ab initio deep neural network model for water"

Author(s):
Gartner, Thomas III; Zhang, Linfeng; Piaggi, Pablo; Car, Roberto; Panagiotopoulos, Athanassios; Debenedetti, Pablo
Abstract:
This dataset contains all data related to the publication "Signatures of a liquid-liquid transition in an ab initio deep neural network model for water", by Gartner et al., 2020. In this work, we used neural networks to generate a computational model for water using high-accuracy quantum chemistry calculations. Then, we used advanced molecular simulations to demonstrate evidence that suggests this model exhibits a liquid-liquid transition, a phenomenon that can explain many of water's anomalous properties. This dataset contains links to all software used, all data generated as part of this work, as well as scripts to generate and analyze all data and generate the plots reported in the publication.
Type:
Dataset
Issue Date:
July 2020

94. Data from "Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases"

Author(s):
Yue, Shuwen; Riera, Marc
Abstract:
This dataset comprises of data associated with the publication "Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases", which can be found at https://doi.org/10.1063/5.0080061. The data includes calculations for a Many-Body decomposition, virial coefficient calculations, orientational molecular scan energies, potential energy fields, correlation plots of training and testing data, vapor-liquid equilibrium simulations, liquid density simulations, and solid cell simulations.
Type:
Dataset
Issue Date:
30 March 2022

95. Data from "Vapor-liquid equilibrium of water with the MB-pol many-body potential"

Author(s):
Muniz, Maria Carolina; Gartner III, Thomas E.; Riera, Marc; Knight, Christopher; Yue, Shuwen; Paesani, Francesco; Panagiotopoulos, Athanassios Z.
Abstract:
This dataset contains all data (including input files, simulation trajectories as well as other data files and analysis scripts) related to the publication "Vapor-liquid equilibrium of water with the MB-pol many-body potential" by Muniz et al. in preparation (2021). In this work, we assessed the performance of the MB-pol many-body potential with respect to water's vapor-liquid equilibrium properties. Through the use of direct coexistence molecular dynamics, we calculated properties such as coexistence densities, surface tension, vapor pressures and enthalpy of vaporization. We found that MB-pol is able to predict these properties in good agreement with experimental data. The results attest to the chemical accuracy of MB-pol and its large range of application across water's phase diagram.
Type:
Dataset
Issue Date:
2021

96. Data from a flume experiment of passive scalar diffusion within vegetation canopies using laser-induced fluorescence

Author(s):
Ghannam, Khaled; Poggi, Davide; Katul, Gabriel; Bou-Zeid, Elie
Abstract:
This dataset is a sequence of laser-induced fluorescence images of a dye injected in a channel flow with canopy-like stainless steel rods simulating a vegetation canopy stand. The data is acquired close to the channel bottom at z/h=0.2, where z is the height referenced to the channel bed and h is the canopy height. The dataset provides spatial distribution of scalar concentration in a plane parallel to the channel bed. The data has been used (but the data itself has not been published or available to the public) in previous work. The references are: Ghannam, K., Poggi, D., Porporato, A., & Katul, G. (2015). The spatio-temporal statistical structure and ergodic behaviour of scalar turbulence within a rod canopy. Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information entropy of passive scalars in submerged canopy flows. Geophysical Research Letters (accepted).
Type:
Dataset
Issue Date:
22 April 2020

97. Data on Enzyme Activity Retention in glucose oxidase, lipase, and horseradish peroxidase

Author(s):
Webb, Michael; Patel, Roshan; Gormley, Adam; Tamasi, Matt; Borca, Carlos; Kosuri, Shashank
Abstract:
This distribution contains experimentally measured data for the extent of retained enzyme activity post thermal stressing for three distinct enzymes: glucose oxidase, lipase, and horseradish peroxidase. The data is used to form conclusions and develop machine learning models as reported in the publication "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids" by Matthew Tamasi, Roshan Patel, Carlos Borca, Shashank Kosuri, Heloise Mugnier, Rahul Upadhya, N. Sanjeeva Murthy, Michael Webb*, and Adam Gormley. Details regarding the experimental protocols are reported in the aforementioned paper but are briefly discussed in the README.
Type:
Dataset
Issue Date:
17 May 2022

98. Data set for "NAPS: Integrating pose estimation and tag-based tracking"

Author(s):
Wolf, Scott W.
Abstract:
Data set corresponding to "NAPS: Integrating pose estimation and tag-based tracking." This dataset contains the corresponding videos, tracking scripts, and SLEAP models along with SLEAP, NAPS, and ArUco tracking results.
Type:
Dataset
Issue Date:
7 December 2022

99. Data set for "Ocean emission of microplastic by bursting bubble jet drops"

Author(s):
Shaw, Daniel B.; Deike, Luc
Abstract:
Data set for "Ocean emission of microplastic by bursting bubble jet drops." Two .csv files are provided: one for the size of a jet drop carrying microplastic, and another for the amount of microplastic captured by a jet drop.
Type:
Dataset
Issue Date:
21 December 2022