Modeling and Simulation of Charge Transport Through Nanoscale Nucleic Acid Structures

Abstract

Understanding and controlling the electrical conductivity of nucleic acids has gained more interest in the past decade. Measuring DNA conductance for sensing biological processes, developing new sequencing techniques, and future molecular device applications have led to an interest in its electrical properties. Further, DNA Origami exploits the self-assembly property of DNA to create complex three-dimensional architectures. This technique helps build nanoscale structures bottom-up instead of the top-down approach currently used in nanoelectronics. Therefore, understanding how charge transports through nucleic acids can help engineer a new class of biosensors and nanoelectronics. The difficulties in explaining experiments arise because the system is at the nanoscale, exists in a solvent environment and is floppy. Therefore, the atomic details of the molecule have a substantial impact on the results. This thesis focuses on the theory and modeling of quantum charge transport through nucleic acid structures using Green’s function method. First, we discuss the development of the model for elastic and inelastic electron scattering. We show that the weak coupling between the DNA bases is untreatable with first-order perturbation approximation. Hence, the phenomenological Büttiker probe method is developed to be used on DNA structures instead of the commonly used self-consistent NEGF method to include scattering. Next, we discuss the energy-dependent decoherence model, where the decoherence decays from the molecular orbitals of the system. We demonstrate that using the real and imaginary parts of the self-energy in this model is critical to obtaining the correct integration of the density of states. With the developed models, we study the following electrical-based applications in the metal-DNA-metal junction setup: (1) detection of single-base mismatch; (2) DNA doping through intercalation to modulate the conductance; (3) using the sequence to engineer DNA heterostructures; (4) understanding perpendicular charge transport in DNA lying on a gold substrate. This thesis demonstrates that the model can explain experiments and help simulate unexplored paths. However, further work is required to model large DNA Origami structures and include contact atoms to the ab-initio methods to help study the current-voltage characteristics, expanding the scope of the DNA applications.