Abstract: A computing device including a processor configured to simulate a quantum device at least in part by receiving a single-particle Hamiltonian matrix that describes an initial Hamiltonian operator. The initial Hamiltonian operator may model a plurality of parts of a quantum device. Simulating the quantum device may further include estimating a reduced density matrix associated with a first part, estimating a plurality of eigenvectors and eigenvalues of the reduced density matrix, and generating a transformed Hamiltonian matrix. Generating the transformed Hamiltonian matrix may include transforming the single-particle Hamiltonian matrix into a natural-orbital basis of the first part such that the transformed Hamiltonian matrix has a reduced dimensionality. The natural-orbital basis may be spanned by a subset of the eigenvectors of the reduced density matrix.