Model elements of an executable model, representing a physical system, are partitioned into one or more linear portions and one or more nonlinear portions. Simulating behavior of the physical system, by executing the model, includes, for each of multiple simulation time intervals, for a first nonlinear portion, computing a correlation matrix characterizing noise associated with one or more ports of the model. A scattering matrix corresponds to a portion of the physical system represented by the first nonlinear portion without accounting for any noise within the portion of the physical system. The correlation matrix is derived from the scattering matrix based on noise within the portion of the physical system. Noise sources representing noise within the portion of the physical system are identified based on the correlation matrix. At least one characteristic of noise associated with each noise source is computed, and noise characteristics are output at selected ports.