This thesis explores silicon as a platform for dopant-based quantum computation and analog quantum simulation, employing scanning tunneling microscope (STM) lithography to achieve atomically precise device structures. Beginning with a comprehensive review of the device fabrication process and a theoretical introduction to transport in dopant-based nanostructures, this thesis establishes a framework for constructing dopant-based devices where both spin and charge degrees of freedom can be harnessed for quantum information processing. To address the challenge of scalability, automated STM patterning workflows are developed. Algorithms inspired by electronic design automation (EDA) are introduced to accelerate the creation of both atomically precise quantum structures and large-area electrical leads.

The experimental chapters present device architectures for spin readout and analog quantum simulation. Charge sensing and energy-selective spin readout are demonstrated using a donor-dot single electron transistor (SET). Spin relaxation times (T₁) are measured across varying magnetic fields showing relaxation occurs mainly through charge noise enhanced spin-orbital coupling. These results provide a foundation for implementing spin manipulation in the next stage of development. Works on analog quantum simulation include the experimental realization of the two-dimensional Hubbard model using dopant arrays, supported by numerical simulations based on an extended Fermi-Hubbard model. Spin filling in these arrays is further investigated through magnetotransport measurements, revealing a “Hund’s rule” like behavior in electron configurations. In addition, a 32×32 quantum dot array was fabricated to extend the study beyond small systems, enabling the simulation of transport through localized electronic states and the exploration of disorder-induced conduction phenomena.

Finally, I present results on optimized RF reflectometry circuits for charge sensing in a donor-dot SET, achieving a minimum integration time of 600 ns to resolve charge states on a donor cluster. Applied to a 3×3 quantum dot array, these techniques identify site-resolved charge addition lines through distinct capacitive couplings to the leads, enabling unambiguous assignment of electron occupation across the lattice. These studies demonstrate the versatility of atomically precise dopant systems in probing strongly correlated electron physics and advancing silicon-based quantum information processing.