TY - JOUR

T1 - Exploring the dynamics of DNA nucleotides in graphene/h-BN nanopores

T2 - insights from ab initio molecular dynamics

AU - Kiakojouri, Ali

AU - Frank, Irmgard

AU - Nadimi, Ebrahim

N1 - Funding Information: The authors thank the German Federal Ministry of Education and Research, BMBF, and the Iranian Ministry for Science, Research and Technology, MSRT, for partial financial support. Computational resources were provided by the North German Supercomputing Alliance (Norddeutscher Verbund für Hoch- und Höchstleistungsrechnen – HLRN) project nic00061.

PY - 2023/4/19

Y1 - 2023/4/19

N2 - Nanopore devices based on graphene and h-BN heterostructures show outstanding electrical and physical characteristics for high throughput label-free DNA sequencing. On top of their suitability for DNA sequencing with the ionic current method, G/h-BN nanostructures are promising for DNA sequencing by employing the in-plane electronic current. The influence of the nucleotide/device interaction on the in-plane current has been widely explored for static-optimized geometries. Therefore, it is essential to investigate the dynamics of the nucleotides within the G/h-BN nanopores to gain a comprehensive view of their interaction with the nanopores. In this study, we investigated the dynamic interaction between nucleotides and nanopores in horizontal graphene/h-BN/graphene heterostructures. The insulating h-BN layer, where the nanopores are implemented, changes the in-plane charge transport mechanism into the quantum mechanical tunneling regime. We employed the Car-Parrinello molecular dynamics (CPMD) formalism to investigate the interaction of the nucleotides with nanopores in a vacuum as well as in an aqueous environment. The simulation was performed in the NVE canonical ensemble with an initial temperature of 300 K. The results indicate that the interaction between the electronegative ends of the nucleotides and the atoms at the nanopore edge is essential for the dynamic behavior of the nucleotides. Moreover, water molecules have a substantial effect on the dynamics and interactions of the nucleotides with nanopores.

AB - Nanopore devices based on graphene and h-BN heterostructures show outstanding electrical and physical characteristics for high throughput label-free DNA sequencing. On top of their suitability for DNA sequencing with the ionic current method, G/h-BN nanostructures are promising for DNA sequencing by employing the in-plane electronic current. The influence of the nucleotide/device interaction on the in-plane current has been widely explored for static-optimized geometries. Therefore, it is essential to investigate the dynamics of the nucleotides within the G/h-BN nanopores to gain a comprehensive view of their interaction with the nanopores. In this study, we investigated the dynamic interaction between nucleotides and nanopores in horizontal graphene/h-BN/graphene heterostructures. The insulating h-BN layer, where the nanopores are implemented, changes the in-plane charge transport mechanism into the quantum mechanical tunneling regime. We employed the Car-Parrinello molecular dynamics (CPMD) formalism to investigate the interaction of the nucleotides with nanopores in a vacuum as well as in an aqueous environment. The simulation was performed in the NVE canonical ensemble with an initial temperature of 300 K. The results indicate that the interaction between the electronegative ends of the nucleotides and the atoms at the nanopore edge is essential for the dynamic behavior of the nucleotides. Moreover, water molecules have a substantial effect on the dynamics and interactions of the nucleotides with nanopores.

UR - http://www.scopus.com/inward/record.url?scp=85158898802&partnerID=8YFLogxK

U2 - 10.1039/d3cp00416c

DO - 10.1039/d3cp00416c

M3 - Article

C2 - 37132153

AN - SCOPUS:85158898802

VL - 25

SP - 13452

EP - 13464

JO - Physical Chemistry Chemical Physics

JF - Physical Chemistry Chemical Physics

SN - 1463-9076

IS - 19

ER -