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Tropopause-penetrating convection is capable of rapidly transporting air from the lower troposphere to the upper troposphere and lower stratosphere (UTLS). Since the vertical redistribution of gases in the atmosphere by convection can have important impacts on the chemistry of the UTLS, the radiative budget, and climate, it has become a recent focus of observational and modeling studies. Despite being otherwise limited in space and time, recent aircraft observations from field campaigns such as the Deep Convective Clouds and Chemistry experiment have provided new high-resolution observations of convective transport. Modeling studies, on the other hand, offer the advantage of providing high-resolution spatially and temporally continuous output related to the physical, dynamical, and chemical characteristics of storms and their environments. While it is currently known that stratosphere-to-troposphere transport and troposphere-to-stratosphere transport are possible, it is not understood what mechanisms are responsible for transport and what impact convection has on UTLS composition. Since the characteristics of simulated convection depend on the chosen model design, the sensitivity of simulated convective transport to the choice of physical (bulk microphysics or BMP and planetary boundary layer or PBL) and chemical parameterizations was examined in the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem). In particular, multiple cases where in situ observations are available from the recent (2012) Deep Convective Clouds and Chemistry (DC3) experiment were simulated. Model output is evaluated using ground-based radar observations of each storm and in situ trace gas observations from two aircraft operated during the DC3 experiment. Model results show measurable sensitivity of the physical characteristics of a storm and the transport of water vapor and additional trace gases into the UTLS to the choice of BMP. The physical characteristics of the storm and transport of insoluble trace gases are largely insensitive to the choice of PBL scheme and chemical mechanism, though several soluble trace gases (e.g., SO2, CH2O, HNO3) exhibit some measurable sensitivity. To evaluate the mechanisms responsible for stratosphere-to-troposphere transport of ozone-rich air, high-resolution simulations of a case with observed stratosphere-to-troposphere transport around the anvil of a mesoscale convective system (MCS) were performed using WRF-Chem. Several hypotheses, which include dynamic instabilities, mass conservation, and ageostrophic circulations driven by pressure perturbations are evaluated. Model results suggest that this transport pathway occurs as a two-step process: (1) downwelling that is driven by mass conservation as the MCS deposits air into the UTLS and (2) differential advection of outflow air in the upper troposphere, which wraps high ozone air around and under the MCS anvil. Dynamic instabilities are not a leading contributor to this transport process. Although WRF-Chem appears to adequately simulate this transport, trajectory calculations indicate that the transported air does not originate above the lapse-rate tropopause (LRT). Since observations showed ozone mixing ratios in excess of 200 ppb (typical of the lower stratosphere), this suggests that the model did not fully represent this transport process. To examine the impact of tropopause-penetrating convection on the chemical composition of the UTLS, two 10-day periods of high frequency, tropopause-penetrating convection over the United States were simulated with WRF-Chem. One period representative of springtime convection (May 18-27, 2011) and one period representative of summertime convection (August 5-15, 2013) were chosen to examine the differences in convective transport between the two seasons. Overall, springtime convection has a larger impact than summertime convection, with a net effect of increasing water vapor in the lower stratosphere and increasing ozone in the upper troposphere. Springtime convection frequently increases the water vapor mixing ratio in the lowermost stratosphere by over 20% while changes in stratospheric water vapor from summertime convection are much lower (~7-11% increase). Increases in the upper tropospheric ozone mixing ratio range from 8-19% from springtime convection and are minimal from summertime convection. Changes in the composition of the UTLS are largely sensitive to the height of the tropopause, with the largest changes being in environments with tropopause heights between 11 and 13 km (typical of springtime environments in the United States). An objective algorithm to detect stratosphere-to-troposphere transport of ozone-rich air shows that while this air occasionally descends in the troposphere around the anvil of convective storms, the air is of upper tropospheric origin and little air comes from the stratosphere. The algorithm suggests that large springtime convective systems in low-tropopause environments are most responsible for this downward transport.