Files accompanying the paper 'Controlling DNA-RNA strand displacement kinetics with base distribution' (https://doi.org/10.1073/pnas.2416988122).

'FFS_scripts' contains all files used for forward flux sampling simulations. Different sequences can be run by simply changing the sequences within .top files. Full results are can be found in the Supplementary Information.

'VMMC_scripts' includes input and output files used for MC simulations for determining energy landscapes. Within these directories, sequences are referred to as 'slow', 'medium', 'flat' and 'fast', which corresponds to sequences 1a, 1b, 1d and 1g respectively.