This thesis focuses on evaluating atmospheric chemistry and transport models’ capability in simulating the chemistry and dynamics of power plant plumes, evaluating their strengths and weaknesses in predicting air quality trends at regional scales, and exploring air quality trends in an urban area. First, the Community Mutlti-scale Air Quality (CMAQ) model is applied to simulate the physical and chemical evolution of power plant plumes (PPPs) during the second Texas Air Quality Study (TexAQS) in 2006. SO2 and NOy were observed to be rapidly removed from PPPs on cloudy days but not on cloud-free days, indicating efficient aqueous processing of these compounds in clouds, while the model fails to capture the rapid loss of SO2 and NOy in some plumes on the cloudy day. Adjustments to cloud liquid water content (QC) and the default metal concentrations in the cloud module could explain some of the SO2 loss while NOy in the model was insensitive to QC. Second, CMAQ is applied to simulate the ozone (O3) change after the NOx SIP Call and mobile emission controls in the eastern U.S. from 2002 to 2006. Observed downward changes in 8-hour O3 concentrations in the NOx SIP Call region were under-predicted by 26%–66%. The under-prediction in O3 improvements could be alleviated by 5%–31% by constraining NOx emissions in each year based on observed NOx concentrations while temperature biases or uncertainties in chemical reactions had minor impact on simulated O3 trends. Third, changes in ozone production in the Houston area is assessed with airborne measurements from TexAQS 2000 and 2006. Simultaneous declines in nitrogen oxides (NOx=NO+NO2) and highly reactive Volatile Organic Compounds (HRVOCs) were observed in the Houston Ship Channel (HSC). The reduction in HRVOCs led to the decline in total radical concentration by 20-50%. Rapid ozone production rates in the Houston area declined by 40-50% from 2000 to 2006, to which the reduction in NOx and HRVOCs had the similar contribution. Houston petrochemical and urban plumes largely remained in a strong VOC-sensitive regime of ozone formation and maintained high Ozone Production Efficiency (OPE: 5-15).