Date of Graduation

8-2017

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Microelectronics-Photonics (PhD)

Degree Level

Graduate

Department

Microelectronics-Photonics

Advisor/Mentor

Tung, Chao-Hung Steve

Committee Member

Nair, Arun K.

Second Committee Member

Kim, Jin-Woo

Third Committee Member

Li, Jiali

Keywords

DNA sequencing; First-Principle simulation; Numerical simulation; One dimensional carbon

Abstract

resolution at the single nucleotide level when developing DNA sequencers. The purpose of this research was to numerically study the electrical properties associated with the interaction between 1D carbon chain, known as carbyne, and ssDNA. First, the electrical properties of the carbyne chain were calculated. Second, the electrical properties of the carbyne chain were calculated in the presence of different ssDNA bases. Analyzing the differences between the two cases led to determining the effects of these different bases on the electrical properties. The numerical simulation approach conducted in this research was based on the first-principle simulation. The first-principle simulation was based on using density functional theory (DFT) and non-equilibrium Green’s functions (NEGF). The electrical properties investigated in this study included the density of states and the transmission probability functions that were used to calculate the electrical current. The study showed that the electrical response of the chain in the presence of each base is distinguishable. In particular, the chain current increased by 3.3 μA in the presence of base A at 0.6 V. In contrast, the current decreased by 41.1 μA, 14.7 μA, and 25.6 μA in the presence of bases C, T, and G, respectively. Moving bases A and C to different locations showed different electrical responses due to having O, NH2, and CH at different distances from the chain. A force model was developed to describe the force interaction between the chain and these groups. The force trend showed a similar trend to the electrical current when compared at -0.85 V. Different orientations of the bases influenced the electrical properties in a different way. For two different orientations, parallel and perpendicular to the chain axis, base A showed 0.0776 mA difference in the electrical current at 0.6 V. Base C, G, and T showed 0.0325 mA, 0.0426 mA, and 0.00305 mA difference, respectively. More importantly, this work contributes to the knowledge of the nano device based DNA sequencing technique and enables further progress toward ultrafast, low cost, label-free, and high-resolution DNA sequencing devices.

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