The present work reports on progress in the developments of a multi-thread physical Monte Carlo simulator including molecular effects. Written in C++ language, the simulator tracks each neutron’s history through Monte Carlo steps and relies on parameterized analytical functions for the microscopic neutron cross section rather than extrapolating between values of nuclear data sheets. These functions are organized in a library that may be accessed by simple function calls, eliminating database dependency and pre-simulation data preparation. As a novel feature molecular effects such as excitation and vibration degrees of freedom are considered and implemented and its influence on some simulation results are shown.