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Supporting data: Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles
- Creator:
- Saldinger, Jacob, Raymond, Matt , Elvati, Paolo, and Violi, Angela
- Description:
- The accurate and rapid prediction of generic nanoscale interactions is a challenging problem with broad applications. Much of biology functions at the nanoscale, and our ability to manipulate materials and purposefully engage biological machinery requires knowledge of nano-bio interfaces. While several protein-protein interaction models are available, they leverage protein-specific information, limiting their abstraction to other structures. Here, we present NeCLAS, a general, and rapid machine learning pipeline that predicts the location of nanoscale interactions, providing human-intelligible predictions. Two key aspects distinguish NeCLAS: coarse-grained representations, and the use of environmental features to encode the chemical neighborhood. We showcase NeCLAS with challenges for protein-protein, protein-nanoparticle and nanoparticle-nanoparticle systems, demonstrating that NeCLAS replicates computationally- and experimentally-observed interactions. NeCLAS outperforms current nanoscale prediction models, and it shows cross-domain validity, qualifying as a tool for basic research, rapid prototyping, and design of nanostructures., Software: - To reproduce all-atom molecular dynamics (MD) NAMD is required (version 2.14 or later is suggested). NAMD software and documentation can be found at https://www.ks.uiuc.edu/Research/namd/, - To reproduce coarse-grained MD simulations, LAMMPS (version 29 Sep 2021 - Update 2 or later is suggested). LAMMPS software and documentation can be found at https://www.lammps.org, - To rebuild free energy profiles, the PLUMED plugin (version 2.6) was used. PLUMED software and documentation can be found at https://www.plumed.org/ , and - To generate force matching potentials, the was used the OpenMSCG software was used. OpenMSCG software and documentation can be found at https://software.rcc.uchicago.edu/mscg/
- Keyword:
- Neural Networks, Proteins, Dimensionality Reduction, Nanoparticles, and Coarse-Graining
- Citation to related publication:
- https://www.biorxiv.org/content/10.1101/2022.08.09.503361v2
- Discipline:
- Science
-
- Creator:
- Towne, Aaron and Dawson, Scott
- Description:
- This dataset contains data from direct numerical simulations of two-dimensional stationary and pitching flat-plate airfoils at Reynolds number 100. The dataset contains time-resolved snapshots of the velocity field, lift and drag coefficients, and airfoil kinematics spanning 40-100 convective time units. Cases include a stationary airfoil and eight different pitching frequencies. All data are stored within hdf5 files, and a Matlab script showing how the data can be read and manipulated is provided. Please see the ‘airfoilDNS_README.pdf’ file for more information. We recommend using the ‘airfoilDNS_example.zip’ file as an entry point to the dataset. and The dataset is part of “A database for reduced-complexity modeling of fluid flows” (see references below) and is intended to aid in the conception, training, demonstration, evaluation, and comparison of reduced-complexity models for fluid mechanics. The paper introduces the flow setup and computational methods, describes the available data, and provides an example of how these data can be used for reduced-complexity modeling. Users of these data should cite the papers listed below.
- Keyword:
- fluid mechanics and aerodynamics
- Citation to related publication:
- Towne, A., Dawson, S., Brès, G. A., Lozano-Durán, A., Saxton-Fox, T., Parthasarthy, A., Biler, H., Jones, A. R., Yeh, C.-A., Patel, H., Taira, K. (2022). A database for reduced-complexity modeling of fluid flows. arXiv:2206.11801. and Dawson, S. T. M., Floryan, D. C., Rowley, C. W., and Hemati, M. S. (2016) Lift enhancement of high angle of attack airfoils using periodic pitching. AIAA Paper 2016-2069.
- Discipline:
- Engineering and Science
-
- Creator:
- Towne, Aaron S. and Lozano-Durán, Adrián
- Description:
- This dataset contains data from two direct numerical simulations of a turbulent zero-pressure-gradient flat-plate boundary layer spanning friction Reynolds numbers from 292 to 728 (BL1) and 488 to 1024 (BL2). The dataset contains time-resolved snapshots of the three-dimensional velocity field for both cases: roughly 10,000 snapshots spanning 20 eddy-turnover times for BL1 and 7,500 snapshots spanning 7 eddy-turnover times for BL2 . Also included for both cases are pre-processed correlations at several wall-normal distances, mean and root-mean-squared velocity and vorticity profiles, several boundary-layer metrics, and time-resolved velocity data in the streamwise-wall-normal plane. All data are stored within hdf5 files, and a Matlab script showing how the data can be read and manipulated is provided. Please see the ‘BLdns_README.pdf’ file for more information. We recommend using the ‘BLdns_example.zip’ file as an entry point to the dataset. and The dataset is part of “A database for reduced-complexity modeling of fluid flows” (see references below) and is intended to aid in the conception, training, demonstration, evaluation, and comparison of reduced-complexity models for fluid mechanics. The paper introduces the flow setup and computational methods, describes the available data, and provides an example of how these data can be used for reduced-complexity modeling. Users of these data should cite the paper listed below.
- Keyword:
- fluid mechanics, boundary layer, and turbulence
- Citation to related publication:
- Towne, A., Dawson, S., Brès, G. A., Lozano-Durán, A., Saxton-Fox, T., Parthasarthy, A., Biler, H., Jones, A. R., Yeh, C.-A., Patel, H., Taira, K. (2022). A database for reduced-complexity modeling of fluid flows. arXiv:2206.11801.
- Discipline:
- Engineering and Science
-
- Creator:
- Sun, Hu, Ren, Jiaen, Chen, Yang, and Zou, Shasha
- Description:
- Our research focuses on providing a fully-imputed map of the worldwide total electron content with high resolution and spatial-temporal smoothness. We fill in the missing values of the original Madrigal TEC maps via estimating the latent feature of each latitude and local time along the 2-D grid and give initial guess of the missing regions based on pre-computed spherical harmonics map. The resulting TEC map has high imputation accuracy and the ease of reproducing. and All data are in HDF5 format and are easy to read using the h5py package in Python. The TEC map is grouped in folders based on years and each file contains a single-day data of 5-min cadence. Each individual TEC map is of size 181*361.
- Keyword:
- Total Electron Content, Matrix Completion, VISTA, Spherical Harmonics, and Spatial-Temporal Smoothing
- Citation to related publication:
- Sun, H., Hua, Z., Ren, J., Zou, S., Sun, Y., & Chen, Y. (2020). Matrix Completion Methods for the Total Electron Content Video Reconstruction. arXiv preprint arXiv:2012.01618. and Zou, S., Ren, J., Wang, Z., Sun, H., & Chen, Y. (2021). Impact of Storm-Enhanced Density (SED) on Ion Upflow Fluxes During Geomagnetic Storm. Frontiers in Astronomy and Space Sciences, 162.
- Discipline:
- Science
-
Data for Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality
- Creator:
- Li, Qiuyang, Alfrey, Adam, Hu, Jiaqi, Lydick, Nathanial, Paik, Eunice, Liu, Bin, Sun, Haiping, Lu, Yang, Wang, Ruoyu, Forrest, Stephen, and Deng, Hui
- Description:
- This dataset contains raw and source data for all figures generated in the manuscript "Macroscopic Transition Metal Dichalcogenides Monolayers with Uniformly High Optical Quality" The raw data files include '.spe' data, which are spectral data collected by LightField Sofware, and '.dset' and '.vms' files, which are X-ray photoelectron spectroscopy (XPS) data and require CasaXPS to access. The source data files include the processed data that can be directly used for generating the corresponding figures in the manuscript.
- Keyword:
- 2D materials, Exciton-polaritons, and Photonics
- Discipline:
- Science
-
- Creator:
- Towne, Aaron, Yeh, Chi-An., Patel, Het, and Taira, Kunihiko
- Description:
- This dataset contains data from a three-dimensional large eddy simulation of Mach 0.3 flow over a NACA 0012 airfoil at Reynolds number 23,000, which features a transitional boundary layer, separation over a recirculation bubble, and a turbulent wake. The dataset contains 16,000 time-resolved snapshots of the mid-span and spanwise-averaged velocity fields. All data are stored within hdf5 files, and a Matlab script showing how the data can be read and manipulated is provided. Please see the ‘airfoilLES_README.pdf’ file for more information. We recommend using the ‘airfoilLES_example.zip’ file as an entry point to the dataset. and The dataset is part of “A database for reduced-complexity modeling of fluid flows” (see references below) and is intended to aid in the conception, training, demonstration, evaluation, and comparison of reduced-complexity models for fluid mechanics. The paper introduces the flow setup and computational methods, describes the available data, and provides an example of how these data can be used for reduced-complexity modeling. Users of these data should cite the papers listed below.
- Citation to related publication:
- Towne, A., Dawson, S., Brès, G. A., Lozano-Durán, A., Saxton-Fox, T., Parthasarthy, A., Biler, H., Jones, A. R., Yeh, C.-A., Patel, H., Taira, K. (2022). A database for reduced-complexity modeling of fluid flows. arXiv:2206.11801. and Yeh, C.-A. and Taira, K. (2019) Resolvent-analysis-based design of airfoil separation control. Journal of Fluid Mechanics, 867:572–610.
- Discipline:
- Science and Engineering
-
- Creator:
- Bougher, Stephen W. and Roeten, Kali J.
- Description:
- The NASA MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft, which is currently in orbit around Mars, has been taking daily (systematic) measurements of the densities and temperatures in the upper atmosphere of Mars between about 140 to 240 km above the surface. Wind measurement campaigns are also conducted once per month for 5-10 orbits. These densities, temperatures and winds change with time (e.g. season, local time) and location, and sometimes fluctuate quickly. Global dust storm events are also known to significantly impact these density, temperature and wind fields in the Mars thermosphere. Such global dust storm period measurements can be compared to simulations from a computer model of the Mars atmosphere called M-GITM (Mars Global Ionosphere-Thermosphere Model), developed at U. of Michigan. This is an ongoing detailed comparison between direct global dust storm period measurements in the upper atmosphere of Mars and simulated MGITM fields and is important because it can help to inform us what physical processes are acting on the upper atmosphere during such large dust events. Since the global circulation plays a role in the structure, variability, and evolution of the atmosphere, understanding the processes that drive the winds in the upper atmosphere of Mars also provides key context for understanding how the atmosphere behaves as a whole system. A basic version of the M-GITM code can be found on Github as follows: https:/github.com/dpawlows/MGITM [less] About 4 months of Neutral Gas and Ion Mass Spectrometer (NGIMS) measurements of densities and winds have been made by the MAVEN team during the summer of 2018 (Elrod et al., 2019; Roeten et al 2022). For this specialized archive (Elrod et al. 2023), one reference measurement interval during this 2018 global dust storm (30-31 August 2018) is selected for detailed study of helium distributions (Elrod et al. 2023). The Mars conditions for this last of nine intervals have been used to launch corresponding M-GITM code simulations, yielding 3-D neutral density, temperature and wind fields for comparison to these NGIMS measurements. This last interval is used to provide M-GITM datacubes to explicitly extract the helium density (plus corresponding temperatures and neutral winds) along the trajectory of each orbit path between 140 and 240 km . A general README file is also provided for this Deep Blue Data archive detailing the contents of each file, while also summarizing the inputs and outputs of the M-GITM code simulations for this study.
- Keyword:
- Mars , NASA MAVEN spacecraft, Mars Thermosphere, Global Dust Strom of 2018, and Helium distribution
- Citation to related publication:
- Elrod, M. K., S. W. Bougher, K. Roeten, R. Sharrar, J. Murphy, Structural and Compositional Changes in the Upper Atmosphere related to the PEDE-2018 Dust Event on Mars as Observed by MAVEN NGIMS, Geophys. Res. Lett., (2019). doi: 10.1029/2019GL084378. and Elrod, M. K., S. W. Bougher, K. Roeten and K. Arnold, Surprising Decrease in the Martian He Bulge during PEDE-2018 and Changes in Upper Atmospheric Circulation, J. Geophysical Research, (2023), doi:XXX
- Discipline:
- Science
-
- Creator:
- Zelditch, Miriam L. and Swiderski, Donald L.
- Description:
- Each row in the file contains the museum ID (museum where the specimen is located and the accession number), the species name, and the values for centroid size, followed by the x,y coordinates for each landmark. Any program that can read in a csv file can read this file.
- Keyword:
- Shape, Sciuridae, mandibles
- Citation to related publication:
- Zelditch, M.L., Swiderski, D.L. The Predictable Complexity of Evolutionary Allometry. Evol Biol (2022). https://doi.org/10.1007/s11692-022-09581-1
- Discipline:
- Science
-
- Creator:
- Szuromi, Matthew P. and Stacey, William C.
- Description:
- The data and scripts are meant to show how burster dynamics determine response to a single biphasic stimulus. The files include data which show trends in the propensity of termination for different burster types and the MATLAB scripts used to generate this data. The MATLAB scripts also allow the user to generate their own data sets for alternative bursting paths and stimulus parameter combinations. Furthermore, they allow the user to visually examine the effects of single stimuli in the voltage timeseries and in state space. How the user can access these features of the script is described in the file "ReadMe.pdf."
- Keyword:
- Epilepsy, Stimulation, Modelling, Dynamics, Seizure, and Dynamotype
- Citation to related publication:
- (PROVISIONAL) Optimization of Ictal Aborting Stimulation Using the Dynamotype Taxonomy
- Discipline:
- Health Sciences, Engineering, and Science
-
- Creator:
- Huber, Daniel E
- Description:
- The files here provide monthly averaged soil NOx emissions (units of ng N m^-2 s^-1) for the contiguous United States on a 0.25 degree x 0.25 degree grid for the years 2011-2020 .
- Keyword:
- soil NOx, soil emissions, biogenic emissions, and agricultural emissions
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Paleontology, Nondestructive Evaluation Laboratory, Ford Motor Company, and Jones, Martin
- Description:
- Reconstructed CT slices for a right tusk of Loxodonta africana (University of Michigan Museum of Paleontology catalog number UMMP_VP_118186) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_000.tif) is the XYZ origin. Metadata as produced by the Aracor system are included in *.IM$LA text files in IM$LA.zip.
- Keyword:
- Paleontology, CT, Elephantidae, UMMP, University of Michigan Museum of Paleontology, and a4f83cc6-09f2-0032-8a09-60ea798f787c
- Citation to related publication:
- Cherney, M., et al. (in prep)
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:216417 (Acarichthys heckeli (Müller & Troschel, 1849)). Raw Dataset includes 2401 TIF images (each 632 x 853 x 1 voxel at 0.02187606 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:216417 (Acarichthys heckeli (Müller & Troschel, 1849)). Reconstructed Dataset includes 1972 TIF images (each 632 x 853 x 1 voxel at 0.021876 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Perciformes, Cichlidae, Acarichthys heckeli (Müller & Troschel, 1849), 1889117016, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1889117016 and DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252706 (Eigenmannia viricens). Raw Dataset includes 1801 TIF images (each 637 x 456 x 1 voxel at 0.05305043 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252706 (Eigenmannia viricens). Reconstructed Dataset includes 1945 TIF images (each 637 x 456 x 1 voxel at 0.053050 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Gymnotiformes, Sternopygidae, Eigenmannia viricens, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Reconstructed Dataset includes 2000 TIF images (each 888 x 988 x 1 voxel at 0.029451 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Raw Dataset includes 1601 TIF images (each 888 x 988 x 1 voxel at 0.02945109 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Hemiodontidae, Bivibranchia bimaculata, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252559 (Cyphocharax fowleri) - Skull. Reconstructed Dataset includes 1217 TIF images (each 1433 x 1028 x 1 voxel at 0.017592 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252559 (Cyphocharax fowleri) - Skull. Raw Dataset includes 1801 TIF images (each 1433 x 1028 x 1 voxel at 0.01759157 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Curimatidae, Cyphocharax fowleri, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata) - Skull. Reconstructed Dataset includes 1851 TIF images (each 1221 x 1165 x 1 voxel at 0.016589 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata) - Skull. Raw Dataset includes 2401 TIF images (each 1221 x 1165 x 1 voxel at 0.01658923 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Hemiodontidae, Bivibranchia bimaculata, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252559 (Cyphocharax fowleri). Raw Dataset includes 1801 TIF images (each 544 x 834 x 1 voxel at 0.03868037 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252559 (Cyphocharax fowleri). Reconstructed Dataset includes 2000 TIF images (each 544 x 834 x 1 voxel at 0.038680 mm resolution, derived from 1801 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Curimatidae, Cyphocharax fowleri, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Raw Dataset includes 2401 TIF images (each 374 x 555 x 1 voxel at 0.03162589 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Reconstructed Dataset includes 1729 TIF images (each 374 x 555 x 1 voxel at 0.031626 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Hemiodontidae, Bivibranchia bimaculata, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Raw Dataset includes 2401 TIF images (each 521 x 643 x 1 voxel at 0.04052231 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Reconstructed Dataset includes 1970 TIF images (each 521 x 643 x 1 voxel at 0.040522 mm resolution, derived from 2401 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Hemiodontidae, Bivibranchia bimaculata, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Raw Dataset includes 1601 TIF images (each 630 x 347 x 1 voxel at 0.04505992 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:fish:252549 (Bivibranchia bimaculata). Reconstructed Dataset includes 2000 TIF images (each 630 x 347 x 1 voxel at 0.045060 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Actinopterygii, Characiformes, Hemiodontidae, Bivibranchia bimaculata, computed tomography, X-ray, 3D, and DiceCT
- Citation to related publication:
- DiceCT for Fishes: Recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes https://doi.org/10.1111/jfb.15320
- Discipline:
- Science