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- Creator:
- Brandt, Daniel, A. and Ridley, Aaron, J.
- Description:
- The research that produced this data focused on conducting a statistical comparison between horizontal winds modeled with GITM and those derived from the accelerometer aboard the GOCE satellite. The winds from GITM and GOCE were compared by constructing their respective probability densities under different levels of geomagnetic activity, and by distributing them as a function of geomagnetic activity, magnetic latitude, magnetic local time, day-of-the-year, and solar radio flux.
- Keyword:
- Thermosphere, GITM, GOCE, Neutral winds, and Thermospheric modeling
- Discipline:
- Science and Engineering
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- Creator:
- Smith, Joeseph P., Gronewold, Andrew D., Read, Laura, Crooks, James L., School for Environment and Sustainability, University of Michigan, Department of Civil and Environmental Engineering, University of Michigan, and Cooperative Institute for Great Lakes Research, University of Michigan
- Description:
- Using the statistical programming package R ( https://cran.r-project.org/), and JAGS (Just Another Gibbs Sampler, http://mcmc-jags.sourceforge.net/), we processed multiple estimates of the Laurentian Great Lakes water balance components -- over-lake precipitation, evaporation, lateral tributary runoff, connecting channel flows, and diversions -- feeding them into prior distributions (using data from 1950 through 1979), and likelihood functions. The Bayesian Network is coded in the BUGS language. Water balance computations assume that monthly change in storage for a given lake is the difference between beginning of month water levels surrounding each month. For example, the change in storage for June 2015 is the difference between the beginning of month water level for July 2015 and that for June 2015., More details on the model can be found in the following summary report for the International Watersheds Initiative of the International Joint Commission, where the model was used to generate a new water balance historical record from 1950 through 2015: https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf. Large Lake Statistical Water Balance Model (L2SWBM): https://www.glerl.noaa.gov/data/WaterBalanceModel/, and This data set has a shorter timespan to accommodate a prior which uses data not used in the likelihood functions.
- Keyword:
- Water, Balance, Great Lakes, Laurentian, Machine Learning, Machine, Learning, Lakes, Bayesian, and Network
- Citation to related publication:
- Smith, J., Gronewald, A. et al. Summary Report: Development of the Large Lake Statistical Water Balance Model for Constructing a New Historical Record of the Great Lakes Water Balance. Submitted to: The International Watersheds Initiative of the International Joint Commission. Accessible at https://www.glerl.noaa.gov/pubs/fulltext/2018/20180021.pdf, Large Lake Statistical Water Balance Model (L2SWBM). https://www.glerl.noaa.gov/data/WaterBalanceModel/, and Gronewold, A.D., Smith, J.P., Read, L. and Crooks, J.L., 2020. Reconciling the water balance of large lake systems. Advances in Water Resources, p.103505.
- Discipline:
- Science and Engineering
-
- Creator:
- Agnit Mukhopadhyay
- Description:
- Conducting quantitative metrics-based performance analysis of first-principles-based global magnetosphere models is an essential step in understanding their capabilities and limitations, and providing scope for improvements in order to enhance their space weather prediction capabilities for a range of solar conditions. In this study, a detailed comparison of the performance of three global magnetohydrodynamic (MHD) models in predicting the Earth’s magnetopause location and ionospheric cross polar cap potential (CPCP) has been presented. Using the Community Coordinated Modeling Center’s Run-on-Request system and extensive database on results from various magnetospheric scenarios simulated for a variety of solar wind conditions, the aforementioned model predictions have been compared for magnetopause standoff distance estimations obtained from six empirical models, and with cross polar cap potential estimations obtained from the Assimmilative Mapping of Ionospheric Electrodynamics (AMIE) Model and the Super Dual Auroral Radar Network (SuperDARN) observations. We have considered a range of events spanning different space weather activity to analyze the performance of these models. Using a fit performance metric analysis for each event, we have quantified the models’ reproducibility of magnetopause standoff distances and CPCP against empirically-predicted observations, and identified salient features that govern the performance characteristics of the modeled magnetospheric and ionospheric quantities.
- Citation to related publication:
- Mukhopadhyay, A., Jia, X., Welling, D. T., & Liemohn, M. W. (2021). Global Magnetohydrodynamic Simulations: Performance Quantification of Magnetopause Distances and Convection Potential Predictions. Frontiers in Astronomy and Space Sciences, 8. https://doi.org/10.3389/fspas.2021.637197
- Discipline:
- Engineering and Science
-
- Creator:
- Revzen, Shai
- Description:
- This repository contains both the data and python3 code that reads this data and reproduces the relevant figures. The code depends on NumPy >1.17 and matplotlib >3.1 and was tested on python 3.8
- Keyword:
- locomotion, slipping, low Reynolds number, walking, and slithering
- Discipline:
- Science and Engineering
-
- Creator:
- Ramasubramani, Vyas
- Description:
- The goal of the work is to elucidate the stability of a complex experimentally observed structure of proteins. We found that supercharged GFP molecules spontaneously assemble into a complex 16-mer structure that we term a protomer, and that under the right conditions an even larger assembly is observed. The protomer structure is very well defined, and we performed simulations to try and understand the mechanics underlying its behavior. In particular, we focused on understanding the role of electrostatics in this system and how varying salt concentrations would alter the stability of the structure, with the ultimate goal of predicting the effects of various mutations on the stability of the structure. There are two separate projects included in this repository, but the two are closely linked. One, the candidate_structures folder, contains the atomistic outputs used to generate coarse-grained configurations. The actual coarse-grained simulations are in the rigid_protein folder, which pulls the atomistic coordinates from the other folder. All data is managed by signac and lives in the workspace directories, which contain various folders corresponding to different parameter combinations. The parameters associated with a given folder are stored in the signac_statepoint.json files within each subdirectory. The atomistic data uses experimentally determined protein structures as a starting point; all of these are stored in the ConfigFiles folder. The primary output is the topology files generated from the PDBs by GROMACS; these topologies are then used to parametrize the Monte Carlo simulations. In some cases, atomistic simulations were actually run as well, and the outputs are stored alongside the topology files. In the rigid_protein folder, the ConfigFiles folder contains MSMS, the software used to generate polyhedral representations of proteins from the PDBs in the candidate_structures folder. All of the actual polyhedral structures are also stored in the ConfigFiles folder. The actual simulation trajectories are stored as general simulation data (GSD) files within each subdirectory of the workspace, along with a single .pos file that contains the shape definition of the (nonconvex) polyhedron used to represent a protein. The logged quantities, such as energies and MC move sizes, are stored in .log files. The logic for the simulations in the candidate_structures project is in the Python scripts project.py, operations.py, and scripts/init.py. The rigid_protein folder also includes the notebooks directory, which contains Jupyter notebooks used to perform analyses, as well as the Python scripts used to actually perform the simulations and manage the data space. In particular, the project.py, operations.py and scripts/init.py scripts contain most of the logic associated with the simulations.
- Keyword:
- Protein assembly, Cryo TEM, Hierarchical Assembly, Monte Carlo simulation, and Coarse-grained simulation
- Citation to related publication:
- Anna J Simon, Vyas Ramasubramani, Jens Glaser, Arti Pothukuchy, Jillian Gerberich, Janelle Leggere, Barrett R Morrow, Jimmy Golihar, Cheulhee Jung, Sharon C Glotzer, David W Taylor, Andrew D Ellington,"Supercharging enables organized assembly of synthetic biomolecules," bioRxiv 323261; doi: https://doi.org/10.1101/323261
- Discipline:
- Science and Engineering
-
- Creator:
- Isaacoff, Benjamin P., Li, Yilai, Lee, Stephen A., and Biteen, Julie S.
- Description:
- This is the experimental data referenced in our manuscript entitled “SMALL-LABS: An algorithm for measuring single molecule intensity and position in the presence of obscuring backgrounds .” These live-cell single-molecule imaging movies were used as a test of the SMALL-LABS single-molecule image analysis algorithm. The dataset comprises two movies; each one is provided both as a .tif stack and as an .avi file. The movie called “low_bg” has a standard low background, and the movie called “high_bg” includes a high fluorescent background produced by an external 488-nm laser.
- Keyword:
- single-molecule, microscopy, image analysis, mirobiology, and bacteria
- Citation to related publication:
- B.P. Isaacoff, Y. Li, S.A. Lee, J.S. Biteen, "SMALL-LABS: Measuring Single-Molecule Intensity and Position in Obscuring Backgrounds." Biophysical Journal, 975-982, 116, 2019. https://doi.org/10.1016/j.bpj.2019.02.006
- Discipline:
- Engineering and Science
-
- Creator:
- Mirshams Shahshahani, Payam
- Description:
- Investigating minimum human reaction times is often confounded by the motivation, training, and state of arousal of the subjects. We used the reaction times of athletes competing in the shorter sprint events in the Athletics competitions in recent Olympics (2004-2016) to determine minimum human reaction times because there's little question as to their motivation, training, or state of arousal. The reaction times of sprinters however are only available on the IAAF web page for each individual heat, in each event, at each Olympic. Therefore we compiled all these data into two separate excel sheets which can be used for further analyses.
- Keyword:
- minimum reaction time, sprinter, Olympics, Athletics, sex difference, starting block, and false start
- Citation to related publication:
- Mirshams Shahshahani P, Lipps DB, Galecki AT, Ashton-Miller JA (2018) On the apparent decrease in Olympic sprinter reaction times. PLoS ONE 13(6): e0198633. https://doi.org/10.1371/journal.pone.0198633
- Discipline:
- Engineering, Health Sciences, Science, Other, and General Information Sources
-
- Creator:
- Nguyen, Thanh H., Wright, Mason, Wellman, Michael P., and Singh, Satinder
- Description:
- In this work , we study the problem of allocating limited security countermeasures to protect network data from cyber-attacks, for scenarios modeled by Bayesian attack graphs. We consider multi-stage interactions between a network administrator and cybercriminals, formulated as a security game. We propose parameterized heuristic strategies for the attacker and defender and provide detailed analysis of their time complexity. Our heuristics exploit the topological structure of attack graphs and employ sampling methods to overcome the computational complexity in predicting opponent actions. Due to the complexity of the game, we employ a simulation-based approach and perform empirical game analysis over an enumerated set of heuristic strategies. Finally, we conduct experiments in various game settings to evaluate the performance of our heuristics in defending networks, in a manner that is robust to uncertainty about the security environment.
- Keyword:
- Empirical Game-Theoretic Analysis, Multi-stage Security Games, Attack Graph, Game Theory, and Moving Target Defense
- Citation to related publication:
- Nguyen, T. H., Wright, M., Wellman, M. P., & Singh, S. (2017). Multi-stage attack graph security games: Heuristic strategies, with empirical game-theoretic analysis. In MTD 2017 - Proceedings of the 2017 Workshop on Moving Target Defense, co-located with CCS 2017 (Vol. 2017-January, pp. 87-97). Association for Computing Machinery, Inc. https://doi.org/10.1145/3140549.3140562
- Discipline:
- Science and Engineering
-
- Creator:
- Gliske, Stephen V and Stacey, William C
- Description:
- This data is part of a large program to translate detection and interpretation of HFOs into clinical use. A zip file is included which contains hfo detections, metadata, and Matlab scripts. The matlab scripts analyze this input data and produce figures as in the referenced paper (note: the blind source separation method is stochastic, and so the figures may not be exactly the same). A file "README.txt" provides more detail about each individual file within the zip file.
- Keyword:
- hfo, high frequency oscillation, ripple, fast ripple, blind source separation, non-negative matrix factorization, and temporal variability
- Citation to related publication:
- Stephen V. Gliske, Zachary T. Irwin, Cynthia Chestek, Garnett L. Hegeman, Benjamin Brinkmann, Oren Sagher, Hugh J. L. Garton, Greg A. Worrell, William C. Stacey. "Variability in the location of High Frequency Oscillations during prolonged intracranial EEG recordings." Nature Communications. https://doi.org/10.1038/s41467-018-04549-2
- Discipline:
- Science, Engineering, and Health Sciences
-
- Creator:
- Mathews, Elizabeth and Verhoff, Frank
- Description:
- Each pdf is an electronic version of the paper output for each experiment. Each text file is the electronic version of the data on the computer cards for each experiment. These text files are directly readable by Excel. Once in Excel, the data can be manipulated as desired. Additional information is in the theses.
- Keyword:
- Two Liquid Phase Processes, Droplet Size and Concentration, Population Balances, and Dispersed Phase Mixing
- Citation to related publication:
- Ross, S. L. (1971). Measurements and models of the dispersed phase mixing process (Doctoral dissertation). Retrieved from http://hdl.handle.net/2027.42/136886 and Verhoff, F. H. (1969). A study of the bivariate analysis of dispersed phase mixing (Doctoral dissertation). Retrieved from http://hdl.handle.net/2027.42/137651
- Discipline:
- Science and Engineering