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- Creator:
- Zetterberg, Daniel S., Huang, Xianglei, Hörner, Johannes, Voigt, Aiko, and Chen, Xiuhong
- Description:
- The data and code stored in this repository present the results of the paper "Instantaneous radiative effect of surface long wave spectral emissivity in a Snowball Earth simulation." In this paper, we calculate the instantaneous radiative effects of surface spectral emissivity for a Snowball Earth simulation, and find that including surface spectral emissivity has a moderate effect on the radiation budget. For clear-sky conditions, using ice or snow spectral emissivity can decrease outgoing long wave radiation by 2.9 or 1.0 W/m^2, respectively, globally averaged. This large effect could impact the simulated climate state of a Snowball Earth and potentially strengthen the Jormungand mechanism. Additionally, the large difference between ice and snow highlights the importance of precipitation processes in Snowball modeling. , This repository contains the results of the calculations and the data and code needed to recreate the manuscript figures. It contains atmospheric conditions from the simulations run by JH and AV that were processed by DSZ. It also contains emissivity datasets that were compiled by Huang et al. 2016 ("A global data set of surface spectral emissivity for GCM and NWP use"). MODTRAN calculations of the outgoing longwave radiation were processed by DSZ, XLH, and XC. The results of the study are contained in netcdf files. The README file offers a description, and the Jupyter notebook demonstrates how to access, use, and plot the calculations. , and ***Changes on 10 June, 2025*** New data files contain the outgoing longwave radiation from MODTRAN calculations, but with multiple scattering enabled in MODTRAN. The result is that downward atmospheric radiation can reflect off the surface back to the top of the atmosphere. The result is that the effect of surface emissivity is slightly decreased, though the conclusions and discussion remain unchanged. Additionally, Xiuhong Chen was added as an author, as her expertise in MODTRAN aided in resolving this issue. Data for a plot of a sample emission spectrum was also added, as this was used in the revised manuscript. Key points were updated to match those in the related article.
- Keyword:
- Spectral surface emissivity, Snowball Earth, paleoclimate modeling
- Citation to related publication:
- Zetterberg, D.S., Huang, X.L., Hörner, J., & Voigt, A. Instantaneous radiative effect of surface long wave spectral emissivity in a Snowball Earth simulation. Submitted to Journal of Geophysical Research: Atmospheres, February 2025
- Discipline:
- Science
-
- Creator:
- Colón-Rodríguez, Stephanie, Liemohn, Michael, Raines, Jim, and Lepri, Susan T.
- Description:
- During its trajectory, Wind spent a significant amount of time in the magnetotail, where its SupraThermal Ion Composition Spectrometer (STICS) measured the mass and mass per charge of protons, alpha particles, and heavy ions with an energy/charge ratio up to 226 keV/e. Although STICS originally aimed to measure the abundance of these ion species in the solar wind, its measurements within the magnetosphere from 1995 to 2002 help us identify preferential entry between the different solar wind ion species. This study statistically analyzes how the ratio between solar wind heavy ions and alpha particles (Heavies Solar Wind / He2+) varies for different upstream conditions and locations within the magnetosphere: northward vs. southward Interplanetary Magnetic Field (IMF), low vs. high solar wind density (Nsw), low vs. high solar wind dynamic pressure (PDyn), slow vs. fast solar wind (Vsw), and dawn vs. dusk. Our results indicate that the HeaviesSolar Wind enter the magnetosphere more efficiently than He2+ during northward IMF and that the Heavies Solar Wind / He2+ ratios decrease during high PDyn. In addition, the Heavies Solar Wind / He2+ ratios exhibit a dawn-dusk asymmetry, highly skewed towards the dawn side for all upstream cases likely due to charge-exchange processes.
- Keyword:
- Magnetosphere, Wind STICS, Solar wind heavy ions, Alpha particles, and dawn-dusk asymmetry
- Citation to related publication:
- Colón-Rodríguez, S., Liemohn, M. W., Raines, J. M, & Lepri, S.T. (2024). Solar wind heavy ions and alpha particles within Earth’s magnetosphere and their variability with upstream conditions. Journal of Geophysical Research Space Physics. In preparation.
- Discipline:
- Science
-
Publicly available repository for "Polariton Chern Bands in 2D Photonic Crystals beyond Dirac Cones"
- Creator:
- Xie, Xin, Sun, Kai, and Deng, Hui
- Description:
- This study explores new platforms for realizing polariton Chern bands in 2D photonic crystals (PhCs) by moving beyond the traditional Dirac cone framework. It focuses on band structures with symmetry-protected bound states in the continuum and Γ-point degeneracies, enabling larger topological gaps, higher Chern numbers, and more uniform Berry curvature—features crucial for experiments and device applications. Eigenvalue and Berry curvature calculations were performed using MATLAB and Mathematica, while Lumerical FDTD was used to simulate photonic and polaritonic band structures in realistic TMD-PhC systems, as well as edge-state dispersion. Reproducing the data requires access to these software tools.
- Keyword:
- Topological photonics, Topological polariton, Topological insulator, and Chern insulator
- Citation to related publication:
- Xie, Xin, Sun, Kai, Deng, Hui. Polariton Chern Bands in 2D Photonic Crystals beyond Dirac Cones. Phys. Rev. X, 15(2), 021061 (2025). https://doi.org/10.1103/PhysRevX.15.021061
- Discipline:
- Science
-
- Creator:
- Gergely Koban, Judit Szente, Bart van der Holst, Gabor Toth, and Enrico Landi
- Description:
- This study aims to assess the performance of coronal models across multiple solar cycles and to analyze long-term variations in solar coronal structures observed in multiple EUV channels. To achieve this, we developed a comprehensive database of solar corona (data cubes) and inner heliosphere simulation outputs using the Alfvén Wave Solar atmosphere Model (AWSoM) within the Space Weather Modeling Framework (SWMF) for Solar Cycles 24 and 25 (SC24 and SC25). This database enables us to investigate the temporal evolution of solar wind source regions—Coronal Holes (CH) and Active Regions (AR). Model accuracy was assessed by comparing synthetic images with concurrent AIA observations in six EUV channels (94, 131, 171, 193, 211, and 335 Å). Additionally, we evaluated the reliability of AWSoM’s solar wind plasma outputs at 1 AU by comparing them with OMNI data for each Carrington Rotation (CR).
- Keyword:
- Solar Corona, SWMF, Solar Physics, Solar Cycle, and MHD Modelling
- Citation to related publication:
- Koban et al. (2025). Validation of Long-Term Solar Coronal Modeling Using FORWARD (Under review).
- Discipline:
- Science
-
- Creator:
- Gerber, Elisabeth R., Morenoff, Jeffrey D., Ostfeld, Mara C. , Sand, Sharon L., and Fan, Yucheng
- Description:
- Survey topics included: Household Composition, Residence and Housing Status; Health, Social Determinants of Health, Long COVID, Mental Health; Disability; Perceptions of Neighborhood; Transportation mode; Financial Precarity; Perception of Control; Voting; Employment; Demographics. This data file contains 1,379 Grand Rapids residents' close-ended responses. The full dataset will be published on ICPSR.
- Keyword:
- Grand Rapids, MI, Household composition , Housing status , Health , Long COVID symptom, Mental health , Disability , Perceptions of neighborhood , Transportation mode , Perceptions of control , Voting , Financial precarity , Employment , and Demographics
- Discipline:
- News and Current Events and Social Sciences
-
- Creator:
- Haynes, Laura M, Holding, Matthew L, Woodard, Jaie, Siemieniak, David, and Ginsburg, David
- Description:
- A phage displayed amino acid site-saturated variant library of plasminogen activator inhibitor (PAI-1) was screened for thermodynamic functional stability. The data are interpreted in the context of protein evolution and computational variant effect/protein stability predictors. This data set contains FASTQ files of the PAI-1 sequence variants that affect its thermodynamic stability, as well as scripts needed to analyze these files.
- Keyword:
- serpins, deep mutational scanning, thermodynamics, metastable proteins, and purifying selection
- Citation to related publication:
- Haynes LM, Holding ML,Woodard J, Siemieniak D, Ginsburg D. Thermodynamics and selection of the plasminogen activator inhibitor-1 latency transition. bioRxiv [Preprint]. 2025.06.03.655624; doi: https://doi.org/10.1101/2025.06.03.655624
- Discipline:
- Science
-
- Creator:
- Delacroix, Emerson, Austin, Sarah, Bacon, Elizabeth, Rice, John, Hanson, Erika N., Stoffel, Elena Martinez, Roberts, Scott, Ulhmann, Wendy, Griggs, Jennifer J., Koeppe, Erika, and Resnicow, Ken
- Description:
- Participant-reported results from the MiGHT study Baseline Survey, including knowledge, motivators, and barriers for hereditary cancer genetic testing uptake. This is raw dataset is saved in comma separated value (.csv) format.
- Keyword:
- Hereditary Genetic Testing, Genetic Testing, NCCN Guidelines, and Genetic Counseling
- Discipline:
- Social Sciences and Health Sciences
-
- Creator:
- Wittkopp, Patricia J and Massey, Jonathan H
- Description:
- Data provided in this record were collected in the course of studying the genetic basis of differences in wing pigmentation and wing display between Drosophila elegans and Drosophila gunungcola.
- Citation to related publication:
- Massey, J. H., Rice, G. R., Firdaus, A. S., Chen, C.-Y., Yeh, S.-D., Stern, D. L., & Wittkopp, P. J. (2020). Co-evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution, 74(6), 1098–1111. https://doi.org/10.1111/evo.13990
- Discipline:
- Science
-
- Creator:
- Moore, Talia Y., Danforth, Shannon M., Larson, Joanna G., and Davis Rabosky, Alison R.
- Description:
- Warning signals in chemically defended organisms are critical components of predator-prey interactions, often requiring multiple coordinated display components for a signal to be effective. When threatened by a predator, venomous coral snakes (genus Micrurus) display a vigorous, non-locomotory thrashing behaviour that has been only qualitatively described. Given the high-contrast and often colourful banding patterns of these snakes, this thrashing display is hypothesized to be a key component of a complex aposematic signal under strong stabilizing selection across species in a mimicry system. By experimentally testing snake response across simulated predator cues, we analysed variation in the presence and expression of a thrashing display across five species of South American coral snakes. Although the major features of the thrash display were conserved across species, we found significant variation in the propensity to perform a display at all, the duration of thrashing, and the curvature of snake bodies that was mediated by predator cue type, snake body size, and species identity. We also found an interaction between curve magnitude and body location that clearly shows which parts of the display vary most across individuals and species. Our results suggest that contrary to the assumption in the literature that all species and individuals perform the same display, a high degree of variation persists in thrashing behaviour exhibited by Micrurus coral snakes despite presumably strong selection to converge on a common signal. This quantitative behavioural characterization presents a new framework for analysing the non-locomotory motions displayed by snakes in a broader ecological context, especially for signalling systems with complex interaction across multiple modalities.
- Keyword:
- aposematism, biomechanics, coral snake mimicry, curvature, Elapidae, non-locomotory motion, Peruvian Amazon, and snake behaviour
- Citation to related publication:
- Moore, T. Y., Danforth, S. M., Larson, J. G., & Davis Rabosky, A. R. (2020). A Quantitative Analysis of Micrurus Coral Snakes Reveals Unexpected Variation in Stereotyped Anti-Predator Displays Within a Mimicry System. Integrative Organismal Biology, 2(1). https://doi.org/10.1093/iob/obaa006
- Discipline:
- Science
-
- Creator:
- Ridley, Aaron and Cnossen, Ingrid
- Description:
- These are modeling results of the thermospheric and ionospheric response to the solar eclipse of August 21, 2017. The results are discussed in a research paper published in the Journal of Geophysical Research (doi: 10.1029/2018JA026402) .
- Citation to related publication:
- Cnossen, I., Ridley, A. J., Goncharenko, L. P., and Harding, B. J.. ( 2019), The response of the ionosphere‐thermosphere system to the August 21, 2017 solar eclipse. J. Geophys. Res. Space Physics, 124. https://doi.org/10.1029/2018JA026402
- Discipline:
- Science
-
- Creator:
- Burgin, Tucker and Mayes, Heather B.
- Description:
- This project aimed to discover and analyze the molecular mechanism of synthesis of two particular fucosylated oligosaccharide products in a mutant enzyme, Thermatoga maratima Alpha-L-Fucosidase D224G, whose wild type performs the opposite reaction (cleavage of fucosyl glycosidic bonds). Discovery of the mechanism was performed using an unbiased simulations method known as aimless shooting, whereas analysis of the mechanism in terms of the energy profile was performed using a separate method known as equilibrium path sampling. The data here concerns the latter method. and The contents of the atesa_master.zip are the ATESA GitHub project. A Python program for automating transition path sampling with aimless shooting using Amber. https://github.com/team-mayes/atesa
- Keyword:
- Equilibrium Path Sampling, Transition Path Sampling, Enzymatic Mechanism, and GH29
- Citation to related publication:
- Burgin, T., & Mayes, H. B. (2019). Mechanism of oligosaccharide synthesis via a mutant GH29 fucosidase. Reaction Chemistry & Engineering, 4(2), 402–409. https://doi.org/10.1039/C8RE00240A
- Discipline:
- Engineering
-
- Creator:
- dos Santos, Thiago, Steiner, Allison, Keppel-Aleks, Gretchen, and De Roo, Roger
- Description:
- Model simulations were conducted to investigate the role of soil moisture on the terrestrial carbon and water cycles. The data are composed of NetCDF files generated by the simulations that contain the data variables analyzed in the paper. and CLM5 Documentation - http://www.cesm.ucar.edu/models/cesm2/land/.
- Keyword:
- Soil moisture, Community Land Model 5, Latent heat, GPP, Gross primary productivity, and Fluxnet
- Citation to related publication:
- Santos, T. dos, Keppel-Aleks, G., Roo, R. D., & Steiner, A. L. (2021). Can Land Surface Models Capture the Observed Soil Moisture Control of Water and Carbon Fluxes in Temperate-To-Boreal Forests? Journal of Geophysical Research: Biogeosciences, 126(4), e2020JG005999. https://doi.org/10.1029/2020JG005999
- Discipline:
- Science
-
- Creator:
- Ruas, Terry, Ferreira, Charles H. P., Grosky, William, França, Fabrício O., and Medeiros, Débora M. R,
- Description:
- The relationship between words in a sentence often tell us more about the underlying semantic content of a document than its actual words, individually. Recent publications in the natural language processing arena, more specifically using word embeddings, try to incorporate semantic aspects into their word vector representation by considering the context of words and how they are distributed in a document collection. In this work, we propose two novel algorithms, called Flexible Lexical Chain II and Fixed Lexical Chain II that combine the semantic relations derived from lexical chains, prior knowledge from lexical databases, and the robustness of the distributional hypothesis in word embeddings into a single decoupled system. In short, our approach has three main contributions: (i) unsupervised techniques that fully integrate word embeddings and lexical chains; (ii) a more solid semantic representation that considers the latent relation between words in a document; and (iii) lightweight word embeddings models that can be extended to any natural language task. Knowledge-based systems that use natural language text can benefit from our approach to mitigate ambiguous semantic representations provided by traditional statistical approaches. The proposed techniques are tested against seven word embeddings algorithms using five different machine learning classifiers over six scenarios in the document classification task. Our results show that the integration between lexical chains and word embeddings representations sustain state-of-the-art results, even against more complex systems. Github: https://github.com/truas/LexicalChain_Builder
- Keyword:
- document classification, lexical chains, word embeddings, synset embeddings, chain2vec, and natural language processing
- Citation to related publication:
- Terry Ruas, Charles Henrique Porto Ferreira, William Grosky, Fabrício Olivetti de França, Débora Maria Rossi de Medeiros, "Enhanced word embeddings using multi-semantic representation through lexical chains", Information Sciences, 2020, https://doi.org/10.1016/j.ins.2020.04.048
- Discipline:
- Other, Science, and Engineering
-
- Creator:
- Ruas, Terry, Grosky, William, and Aizawa, Akiko
- Description:
- This data set is a collection of word similarity benchmarks (RG65, MEN3K, Wordsim 353, simlex999, SCWS, yp130, simverb3500) in their original format and converted into a cosine similarity scale. In addition, we have two Wikpedia Dumps from 2010 (April) and 2018 (January) in which we provide the original format (raw words), converted using the techniques described in the paper (MSSA, MSSA-D and MSSA-NR) (title in this repository), and also the word embeddings models for 300d and 1000d using a word2vec implementation. A readme.txt is provided with more details for each file.
- Keyword:
- multi-sense embeddings, MSSA, word2vec, wikipedia dump, synset, and natural language processing
- Citation to related publication:
- https://doi.org/10.1016/j.eswa.2019.06.026
- Discipline:
- Other
-
- Creator:
- Trung, Huy-Sinh, Liemohn, Michael W, and Ilie, Raluca
- Description:
- The goal of this research was to understand structures where the solar wind plasma contribution to the total plasma was equal to the ionospheric plasma. This simulation was performed over a simulation time of 12 hours for 4 different plasma compositions for 2 different solar wind profiles., The SWMF used the Block Adaptive Tree Solar wind Roe-type Upwind Scheme version 9.20. It can be found at http://csem.engin.umich.edu/tools/swmf/downloads.php. These data can be processed using the simulation code deposited at the Deep Blue Data record indicated in the "Citation to related material" field., and To cite this data set: Trung, H.-S., Liemohn, M., W., Ilie, R. (2019). 12 hour data for magnetospheric simulations for a multifluid plasma for 8 different configurations [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/fwq2-ey41
- Keyword:
- Space Physics, Magnetospheres, and 3D
- Citation to related publication:
- Trung, H.-S., Liemohn, M.W. Ilie, R. (2019). Steady State Characteristics of the Terrestrial Geopause [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/7w13-kq27
- Discipline:
- Science
-
- Creator:
- Li, Yang and Steiner, Allison
- Description:
- WRF-Chem simulation with 1.33 km resolution using the MYJ PBL scheme over the Baltimore-Washington region and WRF-Chem simulation with 1.33 km resolution using the YSU PBL scheme over the Baltimore-Washington region
- Keyword:
- LES, WRF-Chem, vertical mixing, oxidants, boundary layer dynamics
- Citation to related publication:
- Li, Y., Barth, M. C., and Steiner, A. L.: Comparing turbulent mixing of atmospheric oxidants across model scales, Atmospheric Environment, 199, 88-101, https://doi.org/10.1016/j.atmosenv.2018.11.004, 2018.
- Discipline:
- Science
-
- Creator:
- Morales, Annareli
- Description:
- The research that produced this data involves exploring the sensitivity of orographic precipitation to changes in microphysical parameters found in the Morrison microphysics scheme within CM1 model. These microphysical sensitivities are also tested within different environments. The tests can be described as "one-at-a-time" experiments, i.e., an individual parameter is perturbed while keeping the rest constant. Annareli Morales conducted this research for her PhD research while working at the Mesoscale and Microscale Meteorology lab at NCAR in Boulder, CO.
- Keyword:
- Orographic precipitation
- Citation to related publication:
- Morales, A., H. Morrison, and D. Posselt, 2018: Orographic precipitation response to microphysical parameter perturbations for idealized moist nearly neutral flow. Journal of Atmospheric Science, 75, 1933-1953, https://doi.org/10.1175/JAS-D-17-0389.1
- Discipline:
- Science
-
- Creator:
- Burleigh, M.
- Description:
- Brightness from an all-sky imager has been used as a spatiotemporal constraint for auroral inputs selected from in situ rocket measurements which are used to drive the ionospheric model. This method allows for realistic ionospheric forcing that is not captured in traditional "on-off" methods of describing PMAFs. Transient forcing (simulated PMAFs) and steady forcing ("on-off") simulations have been generated for comparison.
- Keyword:
- Poleward moving auroral forms, High-latitude ionosphere, Ionospheric modeling, Transient forcing, PMAF, GEMINI-TIA, and RENU2
- Citation to related publication:
- Burleigh, M., Zettergren, M., Lynch, K., Lessard, M., Moen, J., Clausen, L., Kenward, D., Hysell, D., and Liemohn, M. (2019). Transient ionospheric upflow driven by poleward moving auroral forms observed during the Rocket Experiment for Neutral Upwelling 2 (RENU2) campaign. Geophysical Research Letters. (Submitted).
- Discipline:
- Science
-
Galaxy Shape Catalogs for Dark Energy Survey Science Verification (DES-SV) Data - Additional Regions
- Creator:
- Das, Rutuparna and Dark Energy Survey (DES)
- Description:
- This dataset is associated with the University of Michigan Dept. of Physics dissertation titled "Shedding Light on the Dark: Exploring the Relation Between Galaxy Cluster Mass and Temperature Through Weak Gravitational Lensing" by Rutuparna Das. It is also associated with a paper, currently in preparation, by Das et al (details to be added once paper is submitted/accepted)., This work contains information about shapes of galaxies observed by the Dark Energy Survey (DES) during its Science Verification (SV) run. The official DES SV shape catalog has already been released to the public (see details in Jarvis et al. (2016), henceforth called "J16"). This work follows the methods presented in J16, and contains shapes from areas of the sky that were not processed as part of the official DES-SV catalog but were necessary for the work presented in the aforementioned dissertation. Each catalog contains information for galaxies in a 80′ × 80′ cutout centered at a given galaxy cluster., Note that these catalogs are not entirely analogous to the official DES-SV catalog. For one, we only measure shapes for galaxies, as stars and other objects were not needed for the dissertation. Our catalogs also only extend to a magnitude of 24 in r-band, whereas a small fraction of the objects in the official Im3shape catalog are dimmer (see Figure 29 of J16)., We also include other information necessary for weak lensing studies. Aside from all fields from Im3shape and noise bias calibration (listed and described in J16), these catalogs contain columns for object positions (“ra_gold”, “dec_gold”) and magnitudes in various filters (“mag_detmodel_g”, “mag_detmodel_r”, “mag_detmodel_i”, “mag_detmodel_z”) from the SVA1-Gold catalog ( https://des.ncsa.illinois.edu/releases/sva1/docs/docs-gold). Additionally, we include mean redshift measurements from two DES photo-z measurement pipelines, TPZ and DESDM Neural Network (“z_TPZ”, “z_DESDMnn”) (more details in Sanchez et al. (2014))., and References: Jarvis, M., Sheldon, E., Zuntz, J., et al. 2016, Monthly Notices of the Royal Astronomical Society, 460, 2245. Sanchez, C., Carrasco Kind, M., Lin, H., et al. 2014, Monthly Notices of the Royal Astronomical Society, 445, 1482.
- Keyword:
- weak lensing, galaxy clusters, galaxy shapes, cluster cosmology, Dark Energy Survey, DES, and galaxy shape catalogs
- Discipline:
- Science
-
- Creator:
- Gerber, Elisabeth R., Morenoff, Jeffrey D., Ostfeld, Mara C., Sand, Sharon L., and Fan, Yucheng
- Description:
- Survey topics included: Household Composition, Residence and Housing Status; Health, Social Determinants of Health, Long COVID, Mental Health; Disability; Perceptions of Neighborhood; Transportation mode; Financial Precarity; Perception of Control; Voting; Employment; Demographics. This data file contains 673 Ypsilanti residents' close-ended responses. The full dataset will be published on ICPSR.
- Keyword:
- Ypsilanti, MI, Household composition, Housing status, Health, Long COVID symptom, Mental health, Disability, Perceptions of neighborhood, Transportation mode, Perceptions of control, Voting, Financial precarity, Employment, and Demographics
- Discipline:
- News and Current Events and Social Sciences