We have developed a kinetic Monte Carlo (kMC) simulator that links atomic migration and binding energies determined primarily from first principles calculations to macroscopic phenomena and laboratory time scales. Input for the kMC simulation is obtained from a combination of ab initio planewave pseudopotential calculations, molecular dynamics simulations, and experimental data. The simulator is validated against an extensive series of experimental studies of the diffusion of B spikes in self-implanted Si. The implant energy, dose, and dose rate, as well as the detailed thermal history of the sample, are included. Good agreement is obtained with the experimental data for temperatures between 750 and 950°C and times from 15 to 255 s. At 1050°C we predict too little diffusion after 105 s compared to experiment: apparently, some mechanism which is not adequately represented by our model becomes important at this temperature. Below 1050°C, the kMC simulation produces a complete description over macroscopic time scales of the atomic level diffusion and defect reaction phenomena that operate during the anneals. This simulator provides a practical method for predicting technologically interesting phenomena, such as transient enhanced diffusion of B, over a wide range of conditions, using energetics determined from first-principles approaches.