Time-dependent CO depletion during the formation of protoplanetary disks
  Understanding the gas abundance distribution is essential when tracing star formation using molecular line observations. Changing density and temperature conditions cause gas to freeze-out onto dust grains, and this needs to be taken into account when modeling a collapsing molecular cloud. This study aims to provide a realistic estimate of the CO abundance distribution throughout the collapse of a molecular cloud. We provide abundance profiles and synthetic spectral lines which can be compared to observations. We use a 2D hydrodynamical simulation of a collapsing cloud and subsequent formation of a protoplanetary disk as input for the chemical calculations. From the resulting abundances, synthetic spectra are calculated using a molecular excitation and radiation transfer code. We compare three different methods to calculate the abundance of CO. Our models also consider cosmic ray desorption and the effects of an increased CO binding energy. The resulting abundance profiles are compared to observations from the literature and are found to agree well. The resulting abundance profiles agree well with analytic approximations, and the corresponding line fluxes match observational data. Our developed method to calculate abundances in hydrodynamical simulations should greatly aid in comparing these to observations, and can easily be generalized to include gas-phase reaction networks. 
C. Brinch, R. J. van Weeren, and M. R. Hogerheijde