To gain better understanding and develop an integrated model of sensor function, we employed molecular dynamics (MD) simulations. Our goal was to first characterize stable binding modes between a carefully selected group of analytes and ssDNA-SWCNT conjugates. We then sought to identify analyte-sensor interaction parameters that correlate with experimentally measured optical responses. From binding interactions, we identified two primary modes of association between analytes and ssDNA-SWCNT conjugates: stacking on ssDNA bases and stacking on nanotube surfaces. In both cases, we found that molecular charge strongly influenced the stacking stability of the molecules, which explains the sensor's pH dependence observed experimentally. Specifically, positively charged substituents (amines) strongly interact with ssDNA phosphate groups, affecting both stability of binding and binding residence times.