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The two-photon absorption (TPA), the free-carrier absorption (FCA), and the carrier plasma effect play important roles in Si-based photonic devices. These effects have been incorporated directly into a finite-difference time-domain (FDTD) simulator for the first time. To check the validity of the FDTD simulator, it has been applied to the simulation of nonlinear transmission of an ultrashort optical pulse in a short Si high-index-contrast waveguide. The results are consistent with those shown in the literature. The cause of the slight negative slope transmission has been explained as follows. Since the TPA-induced FCA makes the pulse-shape asymmetric, a pulse with a higher optical input intensity tends to have a longer tail. Therefore, a stronger optical pulse is subject to FCA for a longer period, resulting in the negative differential transmission.