The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision and reaction cross sections. However, total cross sections are often determined from extrapolations of relatively lowtemperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic re-entries. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For re-entry flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. Therefore, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the collision pairs for conditions expected in hypersonic shocks. For the N2-N2 pair, a new potential energy surface is developed using the ReaxFF method, and the internal energy relaxation process is also studied usingMD/QCT. TheMD/QCT-computed reaction probabilities exhibited better physical behavior and predicted less dissociation than the baseline total collision energy (TCE) reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model was validated by good agreement of computed equilibrium reaction rates to experimental shock-tube data. The MD/QCT-computed total cross sections were found to agree well with established variable hard sphere (VHS) total cross sections. The MD/QCT total cross sections and reaction probabilities were then used in a DSMC computation of a 1D 5 km/s shock. The DSMC results using the MD/QCT models predicted approximately 7.5% less dissociation and a slightly thicker shock than those using baseline TCE/VHS models.