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Theoretical Study on Molecular Devices: Proton Transfer, Real-Time Electron Dynamics, and Fast DNA Sequencing

Theoretical Study on Molecular Devices: Proton Transfer, Real-Time Electron Dynamics, and Fast DNA Sequencing
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Functional molecular devices containing molecular mechanical, photonic, and electronic devices play a vital role in nanotechnology. Even though the advances in experimental techniques enable us to measure single molecular properties, many experiments are only based on the intuition without intriguing quantum mechanical understanding. Thus, the theory-based quantum mechanical understanding is essential for the development of current nanotechnology. In this dissertation, we represent a comprehensive theoretical, computational, and methodological study for functional molecular devices. As an application for molecular mechanical devices, we calculate internal proton transfer phenomena in protontated/deprotonated adipic acids. Based on first-principles calculations with Gaussian03 package and the molecular dynamics study with Car-Parinello Molecular Dynamics (CPMD) program, we calculate the ground state and transition state properties with several nuclear configurations. Also, we investigate the pathway of structural changes with DFTB program. As a result, the mechanical transformation allows the internal proton transfer in protonated/deprotonated adipic acids. Molecular photonic devices are related to their excited state property. However, it is well-known that general ground state theories such as the density functional theory cannot describe excitation phenomena properly. Thus, many theories for the exact description of excited states have been developed. In this thesis, we implement the real-time time-dependent density functional theory onto the planewave-based density functional theory program, quantum-ESPRESSO. The well-known fourth-order Suzuki-Trotter time evolution operator is used to describe the real-time evolution of electron density. Especially, we implement the third-order complex Suzuki-Trotter time evolution operator which is twice faster than the fourth-order real Suzuki-Trotter operator and as accurate as the fourth-order one. We represent the numerical accuracy for both time evolution algorithms. Also, the absorption spectrum of an ethylene molecule is calculated and compared with the experimental results. For further research, the coupled electron-nucleus dynamics within the Ehrenfest regime is implemented, and the dissociation of an excited hydrogen molecule is investigated. Finally, with a quantum electron transport code, POSTRANS, and classical molecular dynamics study, we theoretically design an intriguing molecular electronic device, a fast DNA sequencing device based on a graphene nanoribbon. For the future biotechnology such as personal medicines and gene therapy, the development of fast and inexpensive DNA sequencing methods is on demand. Due to the advances in nanotechnology, the coupling between nanotechnology and biotechnology opens a new era for the real-time DNA sequencing. In this thesis, we represent an ultrafast DNA sequencing exploiting well-defined interactions between a graphene nanoribbon and nucleobases, and statistical analysis with our own data-mining approach and 2-dimensional transient autocorrelation.
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