Abstract This study introduces a novel, browser-based simulation framework designed to model the dynamic interactions of atmospheric molecules specifically O, N, and CO, under varying thermodynamic conditions. Utilizing a simplified three-body system, the tool correlates proportional changes in heat and barometric pressure with molecular displacement and velocity over time. The model incorporates principles from kinetic molecular theory and classical mechanics, including conservation of momentum, to simulate real-time behavior through user-controlled environmental parameters. Preliminary results reveal emergent behaviors such as acceleration variance, motion damping, and resonance-like oscillations when thermodynamic inputs fluctuate sinusoidally. While intentionally simplified, the simulation provides meaningful qualitative insights and serves as both an educational platform and a prototype for scientific hypothesis generation. Future iterations will integrate empirical data, inter-molecular forces, and higher-order environmental factors, offering a lightweight alternative to resource-intensive molecular dynamics software.