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The difficulty in assessing interactions between atmospheric particles and clouds is due in part to the chemical complexity of the particles and to the wide range of length and timescales of processes occurring simultaneously during a cloud event. The new Cloud-Resolving Model with Organics (CRM-ORG) addresses these interactions by explicitly predicting the formation, transport, uptake, and re-release of surrogate organic compounds consistent with the volatility basis set framework within a nonhydrostatic, three-dimensional cloud-resolving model. CRM-ORG incorporates photochemical production, explicit condensation/evaporation of organic and inorganic vapors, and a comprehensive set of four different mechanisms describing particle formation from organic vapors and sulfuric acid. We simulate two deep convective cloud events over the Amazon rain forest in March 1998 and compare modeled particle size distributions with airborne observations made during the time period. The model predictions agree well with the observations for Aitken mode particles in the convective outflow (10-14 km) but underpredict nucleation mode particles by a factor of 20. A strong in-cloud particle formation process from organic vapors alone is necessary to reproduce even relatively low ultrafine particle number concentrations (similar to 1500 cm(-3)). Sensitivity tests with variable initial aerosol loading and initial vertical aerosol profile demonstrate the complexity of particle redistribution and net gain or loss in the cloud. In-cloud particle number concentrations could be enhanced by as much as a factor of 3 over the base case simulation in the cloud outflow but were never reduced by more than a factor of 2 lower than the base. Additional sensitivity cases emphasize the need for constrained estimates of surface tension and affinity of organic vapors to ice surfaces. When temperature-dependent organic surface tension is introduced to the new particle formation mechanisms, the number concentration of particles decreases by 60% in the cloud outflow. These uncertainties are discussed in light of the other prominent challenges for understanding the interactions between organic aerosols and clouds. Recommendations for future theoretical, laboratory, and field work are proposed.