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- 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:
- Reed, Matthew P., Boyle, K.
- Description:
- This is the first physical anthropomorphic test device to be based both on statistical body shape models as well as 3D printing.
- Keyword:
- Child Belt Fit Manikin
- Citation to related publication:
- Reed, M.P. and Boyle, K.J. (2017). Development of a manikin representing a two‐year‐old child for belt‐fit measurement. Proc. 2017 IRCOBI Conference. Antwerp, Belgium. https://trid.trb.org/view/1486130 and Kim, K.H., Jones, M.L.H., Ebert, S.M., Malik, L., Manary, M.A., Reed, M.P., and Klinich, K.D. (2015). Development of Virtual Toddler Fit Models for Child Safety Restraint Design. Technical Report UMTRI-2015-38. University of Michigan Transportation Research Institute, Ann Arbor, MI.
- Discipline:
- Engineering
-
- 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
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- Creator:
- Moniri, Saman, Xiao, Xianghui, and Shahani, Ashwin J.
- Description:
- The data file is comprised of 22,500 X-ray projections (15 scans of 1500 projections each) recorded during solidification of Al-Ge-Na. The raw data file is in .hdf format and can be reconstructed into .tiff, e.g., by using the TomoPy toolbox in Python.
- Keyword:
- X-ray microtomography, synchrotron, in situ, 4D materials science, irregular eutectic, growth, and solidification
- Citation to related publication:
- Moniri, S., Xiao, X., & Shahani, A. J. (2019). The mechanism of eutectic modification by trace impurities. Scientific Reports, 9(1), 3381. https://doi.org/10.1038/s41598-019-40455-3
- Discipline:
- 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:
- Carlevaris-Bianco, Nicholas , Ushani, Arash , and Eustice, Ryan
- Description:
- This is a large scale, long-term autonomy dataset for robotics research collected on the University of Michigan’s North Campus. The dataset consists of omnidirectional imagery, 3D lidar, planar lidar, GPS, and proprioceptive sensors for odometry collected using a Segway robot. The dataset was collected to facilitate research focusing on longterm autonomous operation in changing environments. The dataset is comprised of 27 sessions spaced approximately biweekly over the course of 15 months. The sessions repeatedly explore the campus, both indoors and outdoors, on varying trajectories, and at different times of the day across all four seasons. This allows the dataset to capture many challenging elements including: moving obstacles (e.g., pedestrians, bicyclists, and cars), changing lighting, varying viewpoint, seasonal and weather changes (e.g., falling leaves and snow), and long-term structural changes caused by construction projects. To further facilitate research, we also provide ground-truth pose for all sessions in a single frame of reference. and A detailed description of the dataset and the methods used to generate it is in the document nclt.pdf. If you use this dataset in your research please cite: Carlevaris-Bianco, N., Ushani, A., Eustice, R. (2021). The University of Michigan North Campus Long-Term Vision and LIDAR Dataset [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/7rnm-6a03
- Keyword:
- Long-term SLAM, place recognition, lidar, computer vision, and field and service robotics
- Citation to related publication:
- Carlevaris-Bianco, Nicholas, et al. “University of Michigan North Campus Long-Term Vision and Lidar Dataset.” The International Journal of Robotics Research, vol. 35, no. 9, Aug. 2016, pp. 1023–1035, doi:10.1177/0278364915614638.
- Discipline:
- Engineering
-
- Creator:
- Sick, Volker , Reuss, David L, and Greene, Mark L
- Description:
- This archive contains data files from spark-ignited homogeneous combustion internal combustion engine experiments. Included are high-resolution two-dimensional two-component velocity fields acquired at two 5 x 6 mm regions, one near the head and one near the piston. Crank angle resolved heat flux measurements were made at a third location in the head. The engine was operated at 40 kPa, 500 and 1300 RPM, motor and fired. Included are in-cylinder pressure measurements, external pressure and temperature data, as well as details on the geometry of the optical engine to enable setups of simulation configurations.
- Keyword:
- combustion, internal combustion engine, heat Transfer, particle image velocimetry, in-cylinder flow, TCC III engine , optical engine, CFD validation, PIV, boundary layer, and turbulence
- Discipline:
- Engineering
-
- Creator:
- Mathieu, Johanna L, Balzano, Laura, and Ledva, Gregory S
- Description:
- This data set contains the relevant time series for constructing and testing electricity load models within the related paper. The files within are a '.mat' file that contains the data and a 'readme.txt' file detailing the contents of the data.
- Keyword:
- Output feedback, Online learning, Machine learning, Real-time filtering, and Energy disaggregation
- Citation to related publication:
- Ledva, G.S., Balzano, L., Mathieu, J.L., 2018. Real-Time Energy Disaggregation of a Distribution Feeder’s Demand Using Online Learning. IEEE Trans. Power Syst. 33, 4730–4740. Accessible at https://arxiv.org/abs/1701.04389 and https://doi.org/10.1109/TPWRS.2018.2800535
- Discipline:
- Engineering
-
- Creator:
- Schiffmann, Philipp, Sick, Volker, and Reuss, David L
- Description:
- This archive contains data files from spark-ignited homogenous combustion internal combustion engine experiments. Included are two-dimensional two-component velocity fields from various measurement planes with maximized field of view, in-cylinder pressure measurements, external pressure and temperature data, as well as details on the geometry of the optical engine to enable setups of simulation configurations. Fired operation was with stoichiometric propane air, 40kPa MAP, at 1300 RPM.
- Keyword:
- TCC III engine, internal combustion engine, particle image velocimetry, in-cylinder flow, turbulence in engines, CFD validation data, cyclic variability, optical engine, combustion variability, and PIV
- Citation to related publication:
- dx.doi.org/10.1177/1468087417720558
- Discipline:
- Engineering
-
- Creator:
- Schiffmann, Philipp, Sick, Volker, and Reuss, David L
- Description:
- This archive contains data files from spark-ignited homogenous combustion internal combustion engine experiments. Included are two-dimensional two-component velocity fields acquired in a small, high-resolution field of view near the spark plug, and images of hydroxyl radical chemiluminescence recording the early flame-kernel growth. Included are in-cylinder pressure measurements, external pressure and temperature data, as well as details on the geometry of the optical engine to enable setups of simulation configurations. Included are tables of one-per-cycle parameters for each test with methane or propane at stoichiometric, dilute limit, lean limit, and rich limit, operation conducted at 40kPa and 1300 RPM.
- Keyword:
- OH* imaging, TCC III engine, internal combustion engine, particle image velocimetry, in-cylinder flow, turbulence in engines, CFD validation data, cyclic variability, early flame kernel growth, optical engine, combustion variability, ignition, and PIV
- Citation to related publication:
- dx.doi.org/10.1177/1468087417720558
- Discipline:
- Engineering