Simulation and Design Files for "Intrinsic Twist and Scaffold Continuity Govern the Conformational Dynamics of DNA Origami Nanosheets"

This dataset contains the simulation files used in the study“Intrinsic Twist and Scaffold Continuity Govern the Conformational Dynamics of DNA Origami Nanosheets.”All simulations were performed using the coarse-grained oxDNA model to investigate how intrinsic twist and lattice continuity (seamed vs. seamless designs) shape the conformational free-energy landscape of DNA origami nanosheets. The repository is organized into two main categories—Seamed and Seamless—corresponding to different scaffold routing architectures. Each design variant includes: • caDNAno design files Blueprints used to generate each nanosheet architecture. • Equilibrium simulation data Initial and final configurations, oxDNA input files, mean structures, RMSD/RMSF data, and total energy outputs (no trajectory files). • WHAM free-energy reconstruction files 100 colvars files per system, associated metadata, and WHAM results.For structures pulled in both directions, top_wham and bot_wham folders are provided. • Complete umbrella-sampling dataset (one representative case) For the seamed–main design pulled in the bottom-closing direction, full umbrella-sampling files are included:100 initial and final configurations, window energies, order-parameter time series, and mutual trap files for all windows. All other systems include the full preparation, equilibrium, and WHAM data, but omit large umbrella-sampling trajectories to keep the dataset compact. The complete example demonstrates the full workflow required to reproduce the analysis. For questions, please contact: Reza Soheilifard ([e-mail]).