We have developed a three-dimensional particle based simulator with a coupled molecular dynamics routine that avoids the "double-counting" of the long-range portion of the Coulomb force. As opposed to drift-diffusion based simulators, the Monte Carlo simulator can accurately model high field transport in semiconductor devices, while enabling the real-space treatment of the interactions, including multi-ion and particle contributions, through the coupled molecular dynamics scheme. The inclusion of the electron-electron and electron-ion interactions was shown to play an important role in device simulations. The drain current for MOSFET devices was significantly decreased when the Coulomb forces were added. Using this simulator, random dopant ions in the channel have shown to create fluctuations in the drain current of deep sub-micron MOSFETS as well as fluctuations in the device threshold voltage.