The present work focuses on a new ab initio-based collision model for calculating collision cross-sections from the data generated using the quasi-classical trajectory (QCT) method. A large number of trajectories were run on state-of-the-art potential energy surfaces to get the collision cross-section data. The model is expected to be better than the existing phenomenological collision models and produce more realistic results for studying re-entry flows. The new model is employed in the in-house direct simulation Monte Carlo (DSMC) code and used to study the effect of the collision models on Couette flow simulations and steady shock structure flow. The results are compared with those employing the widely used variable hard sphere (VHS) model.