Computational fluid dynamics simulations of a flow reactor provided 3D spatial distributions of its temperature and flow profiles and abundances of sulfuric acid, nitrogeneous base, and the acid-base clusters formed from them. Clusters were simulated via their kinetic formation and decomposition involving sulfuric acid and base molecules. Temperature and flow profiles and the base and sulfuric acid distributions are characterized and the latter is compared to mass spectrometer measurements. Concentrations of simulated clusters of sulfuric acid with either NH3 or dimethylamine were compared to experimentally measured particle concentrations. Cluster thermodynamics were adjusted to better the agreement between simulated and experimental results. Free energies of acid-base clusters derived here are also compared to recent quantum chemistry calculations. Sensitivities to the thermodynamics were explored with a 2D laminar flow simulation and the abundance of large clusters was most sensitive to the thermodynamics of the smallest cluster, consisting of 1 base and 1 acid. Comparisons of this model to the computational fluid dynamics models provide verification of the implemented cluster chemistry. A box model was used to calculate nucleation rates for the conditions of other experimental work, and to provide predictions of nucleation for typical atmospheric conditions.