Details
| Original language | English |
|---|---|
| Pages (from-to) | 13452-13464 |
| Journal | Physical Chemistry Chemical Physics |
| Volume | 25 |
| Issue number | 19 |
| Publication status | Published - 19 Apr 2023 |
Abstract
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.
ASJC Scopus subject areas
- Physics and Astronomy(all)
- General Physics and Astronomy
- Chemistry(all)
- Physical and Theoretical Chemistry
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In: Physical Chemistry Chemical Physics, Vol. 25, No. 19, 19.04.2023, p. 13452-13464 .
Research output: Contribution to journal › Article › Research › peer review
}
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 -