Search Constraints
Filtering by:
Language
English
Remove constraint Language: English
Discipline
Engineering
Remove constraint Discipline: Engineering
« Previous |
1 - 10 of 25
|
Next »
Number of results to display per page
View results as:
Search Results
-
- 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:
- Engineering and Science
- Title:
- Simulation Data associated with the paper: Supercharging enables organized assembly of synthetic biomolecules
-
- 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., Ebert, S.M., and Boyle, K.J. (2017). Development and Validation of a Toddler Manikin for Assessing Belt Fit in Aviation Seats. Technical Report UMTRI-2017-7. University of Michigan Transportation Research Institute, Ann Arbor, MI. https://deepblue.lib.umich.edu/handle/2027.42/140985 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 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
- Title:
- Belt fit Manikin Representing a Two-Year-Old Child
-
- 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, Science, General Information Sources, Health Sciences, and Other
- Title:
- Downloaded IAAF Sprint Results in all Heats for 2004 - 2016 Olympics for both Men and Women
-
- 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:
- Engineering, Science, and Health Sciences
- Title:
- Supporting data and scripts for the paper "Variability in the location of High Frequency Oscillations during prolonged intracranial EEG recordings"
-
- 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
- Citation to related publication:
- Discipline:
- Engineering
- Title:
- TCCIII Near-Wall Flow
-
- 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:
- https://arxiv.org/abs/1701.04389
- Discipline:
- Engineering
- Title:
- Data Files for Real-Time Energy Disaggregation of a Distribution Feeder's Demand
-
- Creator:
- Malik, Hafiz and Khan, Muhammad Khurran, King Saud University
- Description:
- Details of the microphone used for data collection, acoustic environment in which data was collected, and naming convention used are provided here. 1 - Microphones Used: The microphones used to collect this dataset belong to 7 different trademarks. Table (1) illustrates the number of used Mics of different trademarks and models. Table 1: Trademarks and models of Mics Mic Trademark Mic Model # of Mics Shure SM-58 3 Electro-Voice RE-20 2 Sennheiser MD-421 3 AKG C 451 2 AKG C 3000 B 2 Neumann KM184 2 Coles 4038 2 The t.bone MB88U 6 Total 22 2- Environment Description: A brief description of the 6 environments in which the dataset was collected is presented here: (i) Soundproof room: a small room (nearly 1.5m × 1.5m × 2m), which is closed and completely isolated. With an exception of a small window in the front side of the room which is made of glass, all the walls of the room are made of wood and covered by a layer of sponge from the inner side, and the floor is covered by carpet. (ii) Class room: standard class room (6m × 5m × 3m). (iii) Lab: small lab (4m × 4m × 3m). All the walls are made of glasses and the floor is covered by carpet. The lab contains 9 computers. (iv) Stairs: is in the second floor. The place of recording is 3m × 5m (v) Parking: is the college parking. (vi) Garden: is an open space outside the buildings. 3- Naming Convention: This set of rules were followed as a naming convention to give each file in the dataset a unique name: (i) The file name is 19 characters long, and consists of 5 sections separated by underscores. (ii) The first section is of 3 characters indicates the Microphone trademark. (iii) The second section of 4 characters indicates the microphone model as in table (2). (iv) The third section of 2 characters indicates a specific microphone within a set of microphones of the same trademark and model, since we have more than one microphone of the same trademark and model. (v) The fourth section of 2 characters indicates the environment, where Soundproof room --> 01 Class room --> 02 Lab --> 03 Stairs --> 04 Parking --> 05 Garden --> 06 (vi) The fifth section of 2 characters indicates the language, where Arabic --> 01 English --> 02 Chinese --> 03 Indonesian --> 04 (vii) The sixth section of 2 characters indicates the speaker. Table 2: Microphones Naming Criteria Original Mic Trademark and model --> Naming Convenient Shure SM-58 --> SHU_0058 Electro-Voice RE-20 --> ELE_0020 Sennheiser MD-421 --> SEN_0421 AKG C 451 --> AKG_0451 AKG C 3000 B --> AKG_3000 Neumann KM184 --> NEU_0184 Coles 4038 --> COL_4038 The t.bone MB88U --> TBO_0088 For example: SEN_0421_02_01_02_03 is an English file recorded by speaker number 3 in the soundproof room using microphone number 2 of Sennheiser MD-421
- Keyword:
- audio forensic, multimedia forensics, microphone identification, tamper detection, splicing detection, and codec identification
- Citation to related publication:
- http://dx.doi.org/10.1080/00450618.2017.1296186
- Discipline:
- Government, Politics and Law, Engineering, and Science
- Title:
- The KSU-UMD Dataset for Benchmarking for Audio Forensic Algorithms
-
- Creator:
- Grosky, William I. and Ruas, Terry L.
- Description:
- This dataset was used for a proof-of-concept of fixed lexical chain approach for semantic information retrieval.
- Keyword:
- fixed lexical chains
- Citation to related publication:
- Ruas, T. L., & Grosky, W. I. (2017). Exploring and expanding the use of lexical chains in information retrieval. Ann Arbor: University of Michigan. Retrieved from the Deep Blue institutional repository website: http://dx.doi.org/10.3998/2027.42/136659
- Discipline:
- Engineering
- Title:
- Semantic-Based Document Retrieval Using Spatial Distributions of Concepts
-
- Creator:
- Jones, Monica L.H.
- Description:
- These manikins represent body shape models for children weighing 9 to 23 kg in a seated posture relevant to child restraint design. The design of child restraints is guided in part by anthropometric data describing the distributions of body dimensions of children. However, three-dimensional body shape data have not been available for children younger than three years of age. These manikins will be useful for assessing child accommodation in restraints. The SBSM can also provide guidance for the development of anthropomorphic test devices and computational models of child occupants. The sampled manikins were predicted for a range of torso length and body weight dimensions. The SBSM model was exercised for two torso lengths and nine body weights to obtain 18 body shapes. The 3D shape models can be downloaded in a standard mesh format (PLY). Each body shape is accompanied by predicted landmark locations and standard anthropometric variables.
- Keyword:
- Child anthropometry, Child restraint system, Statistical body shape model, and Anthropomorphic testing device (ATD)
- Citation to related publication:
- http://childshape.org/toddler/manikins/ Jones, M.L.H., Klinich, K.D., Ebert, S.M., Malik, L., Manary, M.A., and Reed, M.P. (2015). A Pilot Study of Toddler Anthropometry and Posture in Child Restraint Systems. Short Communications from AAAM's 59th Annual Scientific Conference, Traffic Injury Prevention, 16:sup2, S240-S243, DOI: 10.1080/15389588.2015.1073071
- Discipline:
- Engineering
- Title:
- Three-Dimensional Body Shape Manikins of Young Children for Child Restraint Design
-
- Creator:
- Jones, Monica L.H.
- Description:
- This study evaluated the performance of a video-based intervention for improving the belt fit obtained by drivers. Previous laboratory studies have demonstrated that some drivers position their seat belts suboptimally. Specifically, the lap portion of the belt may be higher and farther forward relative to the pelvis than best practice, and the shoulder portion of the belt may be outboard or inboard of mid-shoulder. A video was developed to present the most important aspects of belt fit best practices, with emphasis on the lap belt. The video demonstrated how a seat belt should be routed with respect to an individual’s anatomy to ensure a proper fit. The three key belt fit concepts conveyed in the video were: 1) Lap belt low on hips, touching the thighs. 2) Shoulder belt crossing middle of collarbone. 3) Belt snug, as close to bones as possible. Additional context about the ability to achieve to good belt fit, such as opening a heavy coat or adjusting the height adjusters on the B-pillar behind the windows, were also presented.
- Keyword:
- Safety, Seatbelt Fit, Intervention, and Evaluation
- Citation to related publication:
- Jones, M.L.H., Ebert, S.M., Buckley, L., Park, J., and Reed, M.P. (2016). Evaluating an Intervention to Improve Belt Fit for Drivers. Technical Report UMTRI 2016-12. University of Michigan Transportation Research Institute, Ann Arbor, MI. Reed, M.P., Ebert-Hamilton, S.M. and Rupp, J.D. (2012). Effects of obesity on seat belt fit. Traffic Injury Prevention, 13(4):364-372. https://doi.org/10.1080/15389588.2012.659363 Reed, M.P., Ebert, S.M. and Hallman, J.J. (2013). Effects of driver characteristics on seat belt fit. Stapp Car Crash Journal, 57:43-57. Jones, M.L.H., Ebert, S.M., and Reed, M.P. (2015). Effects of High Levels of Obesity on Driver Seat Belt Fit. Advancing Transportation Leadership and Safety Technical Report ATLAS-2015-016. University of Michigan Transportation Research Institute, Ann Arbor, MI.
- Discipline:
- Engineering
- Title:
- A Video-Based Intervention to Improve Belt Fit
- « Previous
- Next »
- 1
- 2
- 3