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41. 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

43. 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

44. 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

45. Large-Eddy Simulation Results for Half Ice / Half Water Surfaces

Author(s):
Fogarty, Joseph
Abstract:
Large-eddy simulations were employed over half-ice and half-water surfaces, with varying surface temperatures, wind speeds, directions, as to test if the atmospheric interaction with the heterogeneous surface can be predicted via a heterogeneity Richardson number. This dataset was used to determine that surface heat fluxes over ice, water, and the aggregate surface seem to be captured reasonably well by the wind direction and the heterogeneity Richardson number, but the mean wind and turbulent kinetic energy (TKE) profiles were not, suggesting that not only the difference in stability between the two surface, but also the individual stabilities over each surface influence the dynamics.
Type:
Dataset
Issue Date:
24 May 2023

46. 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

47. Supporting GFDL data for Southern Ocean Freshwater release model experiments Initiative (SOFIA)

Author(s):
Griffies, Stephen M; Beadling, Rebecca L; Krasting, John P; Hurlin, William J
Abstract:
This output was produced in coordination with the Southern Ocean Freshwater release model experiments Initiative (SOFIA) and is the Tier 1 experiment where freshwater is delivered in a spatially and temporally uniform pattern at the surface of the ocean at sea surface temperature in a 1-degree latitude band extending from Antarctica’s coastline. The total additional freshwater flux imposed as a monthly freshwater flux entering the ocean is 0.1 Sv. Users are referred to the methods section of Beadling et al. (2022) for additional details on the meltwater implementation in CM4 and ESM4. The datasets in this collection contain model output from the coupled global climate model, CM4, and Earth System Model, ESM4, both developed at the Geophysical Fluid Dynamics Laboratory (GFDL) of the National Oceanic and Atmospheric Administration (NOAA). The ocean_monthly_z and ocean_annual_z output are provided as z depth levels in meters as opposed to the models native hybrid vertical ocean coordinate which consists of z* (quasi-geopotential) coordinates in the upper ocean through the mixed layer, transitioning to isopycnal (referenced to 2000 dbar) in the ocean interior. Please see README for further details.
Type:
Dataset
Issue Date:
18 April 2023

48. 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

49. 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

50. 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

53. Telomere Length in Preterm Infants

Author(s):
Notterman, Daniel A; Schneper, Lisa M; Drake, Amanda; Piyasena, Chinthika
Abstract:
This entry contains the data used in the PLOS ONE publication entitled, "Characteristics of salivary telomere length shortening in preterm infants" by Schneper et al. The objective of the study was to examine the association between gestational age, telomere length (TL) and rate of shortening in newborns. Genomic DNA was isolated from buccal samples of 39 term infants at birth and one year and 32 preterm infants at birth, term-adjusted age (40 weeks post-conception) and age one-year corrected for gestational duration. Telomere length was measured by quantitative real-time PCR. Demographic and clinical data were collected during clinic or research visits and from hospital records. Socioeconomic status was estimated using the deprivation category (DEPCAT) scores derived from the Carstairs score of the subject's postal code.
Type:
Dataset
Issue Date:
5 January 2023

54. 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