Optically controlled self-assembled quantum dots have received substantial attention in the quantum computing area, as techniques for initializing, manipulating, and reading out single spin qubits have been demonstrated in essence. The electron-spin coherence and hole-spin coherence are limited due to noisy quantum effects, and there is a significant need for further evaluation and investigation studies. In this work, the behavior of charge noise and spin noise for a fundamental logic unit of four qubit embedded in an AlAs/GaAs heterostructure is reported based on the modeling and simulation approach in the atomic level to provide a more in-depth analysis and evaluation of quantum noise. The numerical calculations are based on reliable simulation methods, which are consistent with experimental results. The approach presented here can become the basis for scaled-up advanced simulations expanding to larger logical blocks of qubits.