In this study we report on manipulation of nucleation by means of periodic modulation of the growth rate, R, during molecular beam epitaxial growth of Si on Si(l11). We have found that the bilayer (BL)-by-BL growth can be improved by applying the R-modulation synchronized with the nucleation and that the phase of reflection high-energy electron diffraction (RHEED) intensity oscillations can be shifted independently of the bilayer (BL) deposition. A beating phenomenon of the RHEED oscillations was observed, which can be attributed to the superimposed effects of the R-modulation and the regular BL-by-BL growth. We have used the phenomenological correspondence between the surface step density and the RHEED oscillations as a basis to discuss the growth. By employing a kinetic solid-on-solid Monte Carlo model without vacancies and overhangs all significant experimental features could be simulated.