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COVID-19 has raised new challenges for transportation in the post-pandemic era. The social distancing requirement, with the aim of reducing contact risk in public transit, could exacerbate traffic congestion and emissions. We propose a simulation tool to evaluate the trade-offs between traffic congestion, emissions, and policies impacting travel behavior to mitigate the spread of COVID-19 including social distancing and working from home. Open-source agent-based simulation models are used to evaluate the transportation system usage for the case study of New York City. A Post Processing Software for Air Quality (PPS-AQ) estimation is used to evaluate the air quality impacts. Finally, system-wide contact exposure on the subway is estimated from the traffic simulation output. The social distancing requirement in public transit is found to be effective in reducing contact exposure, but it has negative congestion and …