This project aims at exploring theoretically, by ﬁrst principles methods, the viability of next generation high-throughput and low-cost DNA squencing protocols utilizing nanopore-based technology. DNA sequencing technology is of fundamental importance to genome research which in turn has a tremendous impact to the development of new medical diagnostics and treatments, molecular medicine, agriculture, evolutionary biology, etc. Nanopore DNA sequencing oﬀers a promising high-throughput and low-cost ”third generation” technology that will be able to sequence a diploid mammalian genome for $1,000 within 24 hours, which will make routine and personal geneitic medical applications feasible and revolutionize genetic medicine. However, theoretical work is needed to answer some fundamental and critical questions at the heart of the technical challenges of nanopore DNA sequencing methods. In this project, by combining Molecular Dynamics simulations, Electronic Structure Theory and Quantum Transport, we will design and build atomic models for various nanopore devices, simulate the electric ﬁeld-driven translocation of DNA molecules through the pores, analyze the mutual interaction between the DNA and the pores and investigate how the ionic and transverse electrical currents during the DNA translocation can be employed to decode the DNA sequence. Results from this project will provide valuable insights into the mechanism of nanopore sequencing and guidance to device design, thus accelerating the development of such a technology. The proposed investigation represents the theoretical side of a medium-scale European program for nanopores DNA sequencing with partners from Germany, Switzerland, Serbia and Israel (nanoDNAsequencing: NanoTools for Ultra Fast DNA Sequencing; Grant agreement no.: 214840).