We aim to perform simulation-aided design for a DNA sequencing device, based on MoS2/graphene heterostructures. We plan to simulate DNA sequencing in the prototypical heterostructure devices with the nanopore and nanopath using classical molecular dynamics simulations of DNA translocation through the pore under the effect of the environment. Our simulation-aided design would be investigated for a more realistic DNA sequencing devices under the effect of the environment, which will consider a setup with thousands of atoms using atomistic simulations. In this manner, we are able to analyse the nucleobase trajectories and the interaction between the nucleobases and the nanopore/nanopath. Using state-of-the-art electronic transport calculation, we can evaluate the performance of MoS2/graphene device for the purpose of DNA sequencing. We are confident that our work fills an immediate need in a rapidly expanding field: i.e., the application of two-dimensional nanomaterials to DNA sequencing for which a thorough and comprehensive theoretical underpinning is of crucial importance.