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

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

42. Shock Compression of Fluorapatite to 120 GPa: Wave Profile Data

Author(s):
Rucks, Melinda
Abstract:
The item included here is a collection of wave profiles collected and presented in the accompanying paper: Rucks, M. J., Winey, J. M., Toyoda, T., Gupta, Y. M., & Duffy, T. S. (in review). "Shock compression of fluorapatite to 120 GPa" Submitted to Journal of Geophysical Research: Planets.
Type:
Dataset
Issue Date:
19 October 2022

43. TIGRESS simulation data

Author(s):
Kim, Chang-Goo; Ostriker, Eve; Gong, Munan; Kim, Jeong-Gyu
Abstract:
We present the public data release of the TIGRESS (Three-phase Interstellar Medium in Galaxies Resolving Evolution with Star Formation and Supernova Feedback) simulations. This release includes simulations representing the solar neighborhood environment at spatial resolutions of 2 and 4 pc. The original magneto-hydrodynamic simulation data is published along with data products from post-processing, including chemistry, CO emission line, and photoionization (HII regions). Data reading and analysis examples are provided in Python.
Type:
Dataset
Issue Date:
6 September 2022

44. 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

45. Genetic Algorithm Crystal Optimization in a Chiral Tetramer Model System

Author(s):
Petsev, Nikolai D.; Nikoubashman, Arash; Latinwo, Folarin
Abstract:
Source code for our genetic algorithm optimization investigation of conglomerate and racemic chiral crystals. In this work, we address challenges in determining the stable structures formed by chiral molecules by applying the framework of genetic algorithms to predict the ground state crystal lattices formed by a chiral tetramer model. Using this code, we explore the relative stability and structures of the model’s conglomerate and racemic crystals, and extract a structural phase diagram for the stable Bravais crystal types in the zero-temperature limit.
Type:
Software
Issue Date:
8 August 2022

46. Three dimensional archaeocyathide and coral imagery for morphologic analysis

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

47. 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

48. Princeton Dynamic Stall Database: Upward ramp-type pitching motions

Author(s):
Kiefer, Janik; Brunner, Claudia E.; Hansen, Martin O. L.; Hultmark, Marcus
Abstract:
This data set contains data of a NACA 0021 airfoil as it undergoes upward ramp-type pitching motions at high Reynolds numbers and low Mach numbers. The parametric study covers a wide range of chord Reynolds numbers, reduced frequencies and pitching geometries characterized by varying mean angle and angle amplitude. The data were acquired in the High Reynolds number Test Facility at Princeton University, which is a closed-loop wind tunnel that can be pressurized up to 23 MPa and allowed for variation of the chord Reynolds number over a range of 5.0 × 10^5 ≤ Re_c ≤ 5.5 × 10^6. Data were acquired using 32 pressure taps along the surface of the airfoil. The data are the phase-averaged results of 150 individual half-cycles for any given test case.
Type:
Dataset
Issue Date:
6 July 2022

50. 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

51. High Reynolds Number Wind Turbine Wake Data

Author(s):
Pique, Alexander
Abstract:
This dataset is affiliated with the publication https://doi.org/10.1007/s00348-022-03455-0. All of the data provided is necessary to reproduce the results with the aforementioned publication. The data in this repository is for the wake of a wind turbine at high Reynolds numbers. The data is mainly used for reproducing the statistics (deficit and variance profiles) and the phase averaged results.
Type:
Dataset
Issue Date:
16 June 2022

52. Supplement to PhD Dissertation: "Subsurface Computational Modeling and Policy Analysis of Large-Scale Carbon Capture, Utilization, and Storage (2022)"

Author(s):
Tao, Yiheng
Abstract:
This dataset contains supplementary materials for Chapter 4 and Chapter 5 of Yiheng Tao's PhD dissertation (2022). The dissertation’s abstract is provided here: Carbon capture, utilization, and storage (CCUS) mitigates climate change by capturing carbon dioxide (CO2) emissions from large point sources, or CO2 from the ambient air, and subsequently reusing the captured CO2 or injecting it into deep geological formations for long-term and secure storage. Almost all current decarbonization pathways include large-scale CCUS, on the order of a billion tonnes (Gt) of CO2 captured and stored each year globally starting in 2030, yet the actual deployment has lagged far behind (around 0.04 Gt CO2 was captured in 2021). In this dissertation, I contribute to several aspects of largescale deployment of CCUS by (1) developing and applying efficient numerical models to simulate geological CO2 storage and (2) identifying key policies to address the bottlenecks of overall CCUS deployment. This dissertation concerns the United States, China, and the Belt and Road Initiative (BRI) region through research projects that are consistent with each location’s current development stage of CCUS. Chapters 2 and 3 contain computational modeling studies. In Chapter 2, I develop a new series of vertical-equilibrium (VE) models in the dual-continuum modeling framework to simulate CO2 injection and migration in fractured geological formations. Those models are shown to be effective and efficient when properties of the formation allow for the VE assumption. In Chapter 3, I apply a VE model to simulate basin-scale CO2 injection in the Junggar Basin of Northwestern China. The results show that current regional emissions of more than 100 million tonnes of CO2 per year can be stored effectively, thereby confirming the great potential of the Junggar Basin for early CCUS deployment. Chapters 4 and 5 contain policy analyses. In Chapter 4, I propose a dynamic system consisting of new CO2 pipelines and novel Allam-cycle power plants in the Central United States, and examine how government policies, including an extended Section 45Q tax credit, may improve the economic feasibility of this system. Lastly, in Chapter 5, I investigate and quantify CO2 emissions implications of power plant projects associated with the BRI. I also propose a “greenness ratio” to measure the level of environmental sustainability of BRI in the power sector.
Type:
Dataset
Issue Date:
18 May 2022

53. 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

54. Molecular Dynamics Trajectories and Analysis Code Demonstrating Liquid-Liquid Criticality in the WAIL Water Model

Author(s):
Weis, Jack
Abstract:
These GROMACS trajectories show the existence of a critical point in deeply supercooled WAIL water. Also included is the code necessary to reproduce the figures in the corresponding paper from these trajectories. From this data the critical temperature, pressure, and density of the model can be found, and critical fluctuations in the deeply supercooled liquid can be directly observed (in a computer-simulation sense).
Type:
Dataset
Issue Date:
13 May 2022

55. 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

56. 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

58. Single-crystal X-ray diffraction of fluorapatite to 61 GPa: Structural Data

Author(s):
Rucks, Melinda J.
Abstract:
This dataset includes individual CIF files with the refined structure of fluorapatite under compression to 61 GPa. The structures have been discussed in detail in the accompanying manuscript "Single-crystal X-ray diffraction of fluorapatite to 61 GPa"
Type:
Dataset
Issue Date:
8 April 2022

59. 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

60. 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