Methods, computing systems, and computer-readable media for multi-scale modeling. The method includes determining a first matrix for a plurality of fine cells of a model based at least in part on a physical property value represented by respective fine cells, identifying one or more overlapped cells of the plurality of fine cells that are part of at least two of the plurality of subdomains, and determining a second matrix. Determining the second matrix includes determining an intermediate product by multiplying the first matrix by a prolongation matrix, which includes predicting a row of zeros in the intermediate product for the plurality of fine cells that are not the one or more overlapped cells and are not part of the at least two of the plurality of subdomains that include the one or more overlapped cells. Determining the second matrix also includes multiplying the intermediate product by a restriction matrix.