Use of solid film nanopore in which DNA is threaded through for efficient DNA sequencing devices has various practical issues concerned with nucleobase motion that should be controlled. Translocation rate and different orientation of nucleobases, stochastic motion of single-strand DNA through a nanopore introduce definite amount of noise into the signal defining interaction of nucleobase and nanopore. We propose to consider the single layer graphene nanopore as a two-way interaction scanning device.
The interaction forces between pore and base are structure dependent, even within orientation and noise average over a base, and can be evaluated. The appropriate translocation rate of the base molecule provide a time-dependent function of interaction change inside of interaction interval of each individual base with graphene nanopore. In such case transient characteristics of the individual bases can be used for identification of the bases. The forces between bases and graphene nanopore of 1.5nm diameter are calculated as interaction characteristics of bases. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases and graphene are of the MM2/MM3 type although the possibility of the Van der Waals interaction only can also be considered. The noise of the force signal due to orientation of the bases in the pore is evaluated and base-dependent interaction recognition is considered relative to the magnitude of the AFM signal in the non-contact mode. The time-dependent in-plane for graphene transient force signal resolution for different bases is probed. Possibility of base identification by combination of transient in-plane force taken as orientation averaged signal is studied. Obtained results can simultaneously give additional information for the electronic transport calculations with possible transient base orientations relative to the edge of pore in graphene.
