This readme.txt file was generated on 04/24/2023 by Runfang Mao. ----------------------------------------- GENERAL INFORMATION ----------------------------------------- Suggested Dataset Citation: Mao, Runfang; Dorfman, Kevin D. (2023). Data for Diffusion of knots in nanochannel-confined DNA molecules. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/j1rp-kr98. 1. Title of Dataset: Data for Diffusion of knots in nanochannel-confined DNA molecules 2. Author Information Principal Investigator Contact Information Name: Kevin D. Dorfman Institution: University of Minnesota Address: Email: dorfman@umn.edu ORCID: 0000-0003-0065-5157 Associate or Co-investigator Contact Information Name: Runfang Mao Institution: University of Minnesota Address: Email: mao00112@umn.edu ORCID: 0000-0002-8753-2477 3. Date of data collection (single date, range, approximate date) 2022/05/01--2023/04/24 4. Geographic location of data collection (where was data collected?): University of Minnesota, Minneapolis, MN 55455 5. Information about funding sources that supported the collection of the data: This work was supported by National Science Foundation through award CBET-2016879. Computational resources were provided by the Minnesota Supercomputing Institute. 6. Overview of the data (abstract): This data set contains the input and data files from the LAMMPS package used for the MD simulation. This data set also contains the output file and python script used to plot the figures in "Diffusion of knots in nanochannel-confined DNA molecules" by Runfang Mao. With this dataset, users should be able to regenerate and reproduce all the output and figures that appeared in the paper. ----------------------------------------- SHARING/ACCESS INFORMATION ----------------------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Was data derived from another source? No 3. Links to publications that cite or use the data: Mao, R., & Dorfman, K. (2023). Diffusion of knots in nanochannel-confined DNA molecules. Bulletin of the American Physical Society. https://doi.org/10.1063/5.0151025 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use -------------------------------------------------- FOLDER AND FILE DESCRIPTION -------------------------------------------------- The data set is split into the subdirectories 'Initial_config', that contains the input and data file to perform MD simulations, and 'Figures' corresponding to each figure in the main paper. For example, the data and script associated with Figure2 is in 'Figures/Fig2_knotlocation' directories. The subdirectories "Figures/Fig2_knotlocation/analyzed_data" contains the data for reproducing the Figures while the plot_fig2.py is the script used for plotting Figure 2. Below are the descriptions of how the files are organized in each subdirectory. - 'Figures/Fig1_configuration: This subdirectory contains the initial configuration used for generating knotted DNA chain in figure 1. - 'Figures/Fig2_knotlocation: This subdirectory contains the data and script used for generating Figure2. The "analyzed_data" subdirectory contains the data for reproducing plot Figure 2. The "raw_data" subdirectory contains an example MD trajectory "rerun.xyz" and an output example of knot location "BU_knot_L500.input" from Kymoknot package for analyzing knot location. - 'Figures/Fig3_structural_characterization: This subdirectory contains the data and script used for generating Figure3. The subdirectory "3a_histogram_size" contains the data and script used for generating the histogram of Figure 3a while the subdirectory "3b_size" contains the data and script used for generating Figure 3b. - 'Figures/Fig4_unknotting_time: This subdirectory contains the data and script used for generating the Figure 4 associated with the mean-square-displacement. The script plot_fig4a and plot_fig4b are used for reproducing Figure 4a and Figure 4b respectively. - 'Figures/Fig5_MSD: This subdirectory contains the data and script used for generating the Figure 5. The script plot_fig5a and plot fig5b are used for plotting the unknotting time from MD simulation and the theory from knot region breathing and self-reptation at small Nknot/L limit and sensitive Nknot/L limit, respectively. - 'Initial_config/lammps_dat: LAMMPS data file used for performing simulation. For example, L100_p1.dat is the data file for chain length L = 100. The subscript p1-p341 denote the different uncorrelated configurations for L = 100 one can choose from. - 'Initial_config/lammps_run: LAMMPS input file used for performing simulation. ----------------------------------------- METHODOLOGICAL INFORMATION ----------------------------------------- Description of methods used for collection/generation of data: - The data were generated using the LAMMPS software. Information about the LAMMPS package is available on https://www.lammps.org. - The knot output file is generated using Kymoknot Package. Information about Kymoknot package is available on http://kymoknot.sissa.it. ----------------------------------------- File-SPECIFIC INFORMATION ----------------------------------------- 1. File List A. Filename: L{#}_p{*}.dat Short description: data file for LAMMPS MD simulation. For MD simulation, {#} is replaced by a number in the filename (ex. 100, 200, 300, 400, 500, 600 ), where the chain contour length is L = 100, 200, 300, 400, 500, 600. {*} is replaced by a number, denoting the different uncorrelated configurations for L = 100, 200, 300, 400, 500, 600. B. Filename: L{#}_p{*}.in Short description: Input file for MD simulation. Associated with input parameter file L{#}_p{*}.dat with the same {#} and {*} value.