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The power of parallel supercomputing resources has progressed to the point where first-principles calculations involving systems up to 10³ atoms are feasible, allowing ab initio exploration of increasingly complex systems such as amorphous networks, nanostructures, and large defect clusters. Expansion of our fundamental understanding of modified Si-based materials is paramount, as these materials will likely flourish in the foreseeable cost-driven future in diverse micro- and nanotechnologies. Here, density-functional theory calculations within the generalized gradient approximation are applied to refine configurations of Si-based materials generated from Metropolis Monte Carlo simulations and study their resultant structural properties. Particular emphasis is given to the contributions of strain and disorder on the mechanical, optical, and electronic properties of modified Si-based materials in which aspects of compositional variation, phase, strain scheme, morphology, native defect incorporation, and quantum confinement are considered. The simulation strategies discussed are easily extendable to other semiconductor systems.