This deposit contains data related to clay formwork 3D printing for fabricating reinforced concrete beams. Two sets of data are provided: (1) point cloud deviations representing the clay formwork deformations during concrete casting, and (2) the load-displacement behavior of the resulting concrete beams during the four-point flexural tests. For more details, please see the corresponding article.
This item contains two files. A multi-layer perceptron (MLP) neural network is built using the MATLAB Deep Network Designer (.m file). It imports a quantum cascade laser (QCL) dataset and splits it into 70% training, 15% validation, and 15% testing subsets. The network consists of an input layer, three hidden layers (each having a normalization and activation layer), and a regression output layer. All of the layers are fully connected, and the root-mean-square error (RMSE) is used to evaluate the accuracy of the network. An algorithm is trained on the [-5, +20] QCL dataset using 50 neurons, ReLU activation function, solver Adam, 0.001 learning rate, over 50 epochs, and is saved to be used in the prediction of figure of merit values for QCL designs (.mat file).
A dataset of 2400 quantum cascade structures at 15 electric field iterations, for a total of 36000 unique designs. The structures are generated by randomly altering a starting 10-layer design of alternating Al0.48In0.52As barrier material and In0.53Ga0.47As well material, with layer thickness sequence of 9/57/11/54/12/45/25/34/14/33 Angstroms (starting with well material). The random tolerance range is from -5 to +20 Angstroms in 5 Angstrom increments. The laser transition Figure of Merit, among other quantities of interest, is identified for each design using a method found in:
A. C. Hernandez, M. Lyu and C. F. Gmachl, "Generating Quantum Cascade Laser Datasets for Applications in Machine Learning," 2022 IEEE Photonics Society Summer Topicals Meeting Series (SUM), 2022, pp. 1-2, doi: 10.1109/SUM53465.2022.9858281
This dataset encompasses three distinct sets of data analyzed in the study, namely the survey data on favorability to the US, the survey data on trust in Americans, and the social media data.
The first part of the dataset comprises the analysis in Study 1 and Study 3, which is collected from three surveys, including the Social Attitude Questionnaire of Urban and Rural Residents (SAQURR) in 2019 and 2020, the COVID-19 Multi-Wave Study (CMWS) between 2020 and 2022, and the Survey on Living Conditions (SLC) in 2023.
The second part of the datasets provides information used in Study 4, involving the 2018 and 2020 waves of the CFPS, Baidu Index data, and the COVID-19 cases and deaths data.
The third dataset is provided to depict trends in attitudes toward the US in Study 2.
This item contains two files. A multi-layer perceptron (MLP) neural network is built using the MATLAB Deep Network Designer (.m file). It imports a quantum cascade laser (QCL) dataset and splits it into 70% training, 15% validation, and 15% testing subsets. The network consists of an input layer, three hidden layers (each having a normalization and activation layer), and a regression output layer. All of the layers are fully connected, and the root-mean-square error (RMSE) is used to evaluate the accuracy of the network. An algorithm is trained on the [-2, +3] QCL dataset using 50 neurons, ReLU activation function, solver Adam, 0.001 learning rate, over 150 epochs, and is saved to be used in the prediction of figure of merit values for QCL designs (.mat file).
A code to identify the laser transition for a quantum cascade laser design based on the figure of merit. Variables such as the number of layers, and layer thicknesses, as well the applied electric field, materials composition, number of period repetitions, and layer tolerance ranges to generate random designs are specified. A folder containing a .csv file with all electronic state-pair transitions collected, a .png file of the bandstructure and the laser transition chosen (in red), for all electric field iterations, and a summary .csv file of all these laser transitions for a structure at each electric field is generated by the code. To use, first install ErwinJr2 on your computer. Then locate the "ErwinJr2" folder and copy these 6 files into that directory, overwriting the previous five files (Material.py, QCLayers.py, QCPlotter.py, QuantumTab.py, rFittings.py). Lastly, run the "acej-qcl-layer_10-lwrandom-v23.py" script using Python.
The "summary-fomstar-3lu-eVmiddle-19.csv" file is generated after running the laser transition code, with all of the data collected for one structure at many electric fields. Running the script various times will generate random structures with the same electric field range. Joining these "summary" .csv files makes a QCL dataset.
The Volumetric Camera Calibration Dataset is used for a camera calibration system. Intersecting laser beams are traversed over a volume in the test domain. At each location, the intersecting beams are imaged by camera1 and camera2. A test object is imaged for evaluation.
These files contain code used to segment D. virilis acoustic duets, quantification of courtship behaviors during acoustic duets, and measurements of duet song features.
Data set for "Film drop production over a wide range of liquid conditions." One .csv file is provided that contains data about the number of film drops produced by bursting bubbles of multiple sizes in various liquid conditions.
Data from the 2007 Developmental Idealism survey conducted in Gansu province in China's northwestern borderlands reveal that Muslims of the Hui and Dongxiang ethnicities reported much higher rates of cohabitation experience than the secular majority Han. Based on follow-up qualitative interviews, we found the answer to lie in the interplay between the highly interventionist Chinese state and the robust cultural resilience of local Islamic communities. Using the 2000 census data and the 2010 China Family Panel Studies data, we further show that women in almost all ten Muslim ethnic groups have higher percentages of underage births and premarital births than Han women, both nationally and in the northwest where most Chinese Muslims live. As the once-outlawed behavior of cohabitation became more socially acceptable during the reform and opening-up era, young Muslim Chinese often found themselves in “arranged cohabitations” as de facto marriages formed at younger-than-legal ages.
Hepatitis B virus (HBV) infection remains a major public health problem and, in associated co-infection with hepatitis delta virus (HDV), causes the most severe viral hepatitis and accelerated liver disease progression. As a defective satellite RNA virus, HDV can only propagate in the presence of HBV infection, which makes HBV DNA and HDV RNA the standard biomarkers for monitoring the virological response upon antiviral therapy, in co-infected patients. Although assays have been described to quantify these viral nucleic acids in circulation independently, a method for monitoring both viruses simultaneously is not available, thus hampering characterization of their complex dynamic interactions. Here, we describe the development of a dual fluorescence channel detection system for pan-genotypic, simultaneous quantification of HBV DNA and HDV RNA through a one-step quantitative PCR. The sensitivity for both HBV and HDV is about 10 copies per microliter without significant interference between these two detection targets. This assay provides reliable detection for HBV and HDV basic research in vitro and in human liver chimeric mice. Preclinical validation of this system on serum samples from patient on or off antiviral therapy also illustrates a promising application that is rapid and cost-effective in monitoring HBV and HDV viral loads simultaneously.
This dataset is created for the paper titled 'Co-benefits of Transport Demand Reductions from Compact Urban Development in Chinese Cities' and published on Nature Sustainability. We construct 6 scenarios of compact urban development, alternative energy vehicle deployment, and power decarbonization to explore the co-benefits of transport demand reductions via compact urban development for carbon emissions, energy use, air quality, and human health in China in 2050. This dataset provides the following gridded information for the scenarios: (1) monthly mean surface PM2.5 concentrations from the WRF-Chem model; (2) annual PM2.5-related premature deaths calculated by the GEMM model; (3) 2015 population in China; (4) mask for provinces in China; (5) longitude and latitude of each grid center.
This dataset encompasses three distinct sets of data analyzed in the study, namely the survey data on favorability to the US, the survey data on trust in Americans, and the social media data.
This dataset contains 1800 quantum cascade (QC) structures generated by randomly modifying an initial 10-layer design in the tolerance range of -2 to +3 Angstroms at an applied electric field range of 0 to 150 kV/cm (in 10 kV/cm increments). One structure at one electric field is one design, thus there are 27000 unique designs, represented as a row in the dataset. The layer thicknesses (in angstroms) and the electric field are inputs which get evaluated using a Schrödinger solver, ErwinJr2, to identify the laser transition Figure of Merit (fom*), among other reported outputs.
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.
This repository contains the raw photon-by-photon single-molecule FRET (smFRET) trajectories, SAXS data, and MD simulation trajectories, multi-sequence alignment, and gel images for the paper titled "Sub-Domain Dynamics Enables Chemical Chain Reactions in Nonribosomal Peptide Synthetases."
Large-eddy simulations were employed over five different sea ice patterns, with a constant ice fraction, to test if the overlying atmospheric boundary layer (ABL) dynamics and thermodynamics differs. The results of these simulations were used to determine that there were differences in vertical heat flux, momentum flux, and horizontal wind speed, and that more surface information is needed to predict the ABL over the sea ice surface. To see what other surface information is needed, twenty-two landscape metrics were calculated over forty-four different maps at differing resolutions, using the FRAGSTATs program. The results of that analysis are available in a .csv file in this dataset.
O'Neill, Eric; Lark, Tyler; Xie, Yanhua; Basso, Bruno
Abstract:
Collection of the underlying spatially explicit data for Available Land for Cellulosic Biofuel Production: A Supply Chain Centered Comparison. Includes raw biomass yield data and soil carbon sequestration potential data for three types of marginal land for the USA midwest at the field level including field areas. Collection also includes raw land rasters for the three types of marginal land, model parameters for the MILP model used in the study, and results used to generate the figures in the paper.
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.
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.
Webb, Michael; Jacobs, William; An, Yaxin; Oliver, Wesley
Abstract:
This distribution compiles thermodynamic and (where available) dynamic properties of short protein sequences as obtained from coarse-grained molecular dynamics simulations. The dataset features 2114 protein sequences with sequence lengths ranging from N=20 up to N=50 amino acids. The simulation and analysis of these sequences is described in "Active learning of the thermodynamics--dynamics tradeoff in protein condensates'' by Yaxin An, Michael A. Webb*, and William M. Jacobs* (https://doi.org/10.48550/arXiv.2306.03696). Of the 2114 protein sequences, 80 are homomeric polypeptides (replicating a single amino acid for N = 20, 30, 40, and 50), 1266 are sourced from version 9.0 of the DisProt database, and the remaining 768 sequences are novel sequences generated during an active learning campaign described in the aforementioned manuscript. The simulations were performed using the LAMMPS molecular dynamics engine. The interactions used for simulation are obtained from R. M. Regy , J. Thompson , Y. C. Kim and J. Mittal , Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins, Protein Sci., 2021, 1371 —1379. Properties included in this distribution include second virial coefficients, pressure-density data, expectation for phase behavior at 300 K, estimated condensed-phase densities at 300 K (if exist), and condensed-phase self-diffusion coefficients at 300 K (if exist).
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.
Physical and biogeochemical variables from the NOAA-GFDL Earth System Model 2M experiments, and previously published observation-based datasets, used for the study 'Hydrological cycle amplification reshapes warming-driven oxygen loss in Atlantic Ocean'.
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.
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'.
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.
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).
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.
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.
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)).
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.
The materials include codes and example input / output files for Monte Carlo simulations of lattice chains in the grand canonical ensemble, for determining phase behavior, critical points, and formation of aggregates.
In this publication we provide the LAMMPS example files to reproduce simulations for the manuscript "A Deep Potential model for liquid-vapor equilibrium and cavitation rates of water"
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
