Description
The translocation of DNA through nanopores is an intensively studied field as it can lead to a new perspective in DNA sequencing. It was first experimentally shown that in a system composed of a nanopore and a DNA in a salt solution, the translocated DNA can modulate the ionic current through the pore. This can be done by means of an externally applied electric field. The current modulation will be studied in detail in subproject C.5. However, it is not clear, whether these ionic current measurements can be used to distinguish each DNA nucleobase.
Additional experiments use electrode built on the nanopore to measure the tunnelling current across the nanopore. In this case, it is not the ions that play a significant role, but the transport properties of the nanopore perpendicular to the translocation direction. It was also proposed, that a functionalization of the nanopore could enhance the tunnelling current measured for each nuclease, leading to an error free read-out of the DNA. A possible candidate for the functionalization could be a diamondoid molecule. The important aspect in a functionalizing nanopore would be the electronic structure of the nanopore-DNA system across which the tunnelling current is flowing. An additional important role is also assigned on the exact geometry and the base orientation in the pore. The orientation of the nucleobase in the pore is prone to thermal fluctuations and the effect of the ionic solution, both of which can change the tunnelling current. In this project, we will focus on diamondoid-functionalized nanopores and hope to shed light in all the important aspects in order to give an insight to experiments. Relevant parameters would be the functionalization molecule, the geometry of the nanopore, as well as the surrounding conditions, the ions and their concentration.
The study would be very demanding as the dynamical properties of a system with many particles needs to be studied. In this respect, we use for our simulations a bottom-up approach using a combination of density-functional-theory (DFT), non-equilibrium Green functions scheme (NEGF), ab initio Molecular Dynamics and classical Molecular Dynamics. We will begin with quantum mechanical simulation of a very small system which contains an electrode or an electrode with a nuclease. Next we will increase the complexity step wise transferring also the effect and characteristics of each step. The main goal would be to study the system in a size which is relevant to the experiments, while remaining precise and realistic. We hope, that our simulations will lead to the main goal which would be the use of a functionalized nanopore in DNA sequencing, but also use our electronic structure-particles coupling scheme to verify and compare with the experiments.