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CO is commonly used as a tracer of the total gas mass in both the interstellar medium and in protoplanetary disks. Recently there has been much debate about the utility of CO as a mass tracer in disks. Observations of CO in protoplanetary disks reveal a range of CO abundances, with measurements of low CO to dust mass ratios in numerous systems. One possibility is that carbon is removed from CO via chemistry. However, the full range of physical conditions conducive to this chemical reprocessing is not well understood. We perform a systematic survey of the time dependent chemistry in protoplanetary disks for 198 models with a range of physical conditions. We varying dust grain size distribution, temperature, comic ray and X-ray ionization rate, disk mass, and initial water abundance, detailing what physical conditions are necessary to activate the various CO depletion mechanisms in the warm molecular layer. We focus our analysis on the warm molecular layer in two regions: the outer disk (100 au) well outside the CO snowline and the inner disk (19 au) just inside the midplane CO snow line. After 1 Myr, we find that the majority of models have a CO abundance relative to H$_2$ less than $10^{-4}$ in the outer disk, while an abundance less than $10^{-5}$ requires the presence of cosmic rays. Inside the CO snow line, significant depletion of CO only occurs in models with a high cosmic ray rate. If cosmic rays are not present in young disks it is difficult to chemically remove carbon from CO. Additionally, removing water prior to CO depletion impedes the chemical processing of CO. Chemical processing alone cannot explain current observations of low CO abundances. Other mechanisms must also be involved.
CO is thought to be the main reservoir of volatile carbon in protoplanetary disks, and thus the primary initial source of carbon in the atmospheres of forming giant planets. However, recent observations of protoplanetary disks point towards low volat
Based on the interstellar CO/H2 ratio, carbon monoxide-based censuses of protoplanetary disks in Lupus, sigma Orionis, and Chamaeleon I found no disks more massive than the minimum-mass solar nebula, which is inconsistent with the existence of exopla
The $sigma$ Orionis cluster is important for studying protoplanetary disk evolution, as its intermediate age ($sim$3-5 Myr) is comparable to the median disk lifetime. We use ALMA to conduct a high-sensitivity survey of dust and gas in 92 protoplaneta
We study the origin of tail-like structures recently detected around the disk of SU Aurigae and several FU~Orionis-type stars. Dynamic protostellar disks featuring ejections of gaseous clumps and quiescent protoplanetary disks experiencing a close en
We present new Atacama Large Millimeter/submillimeter Array (ALMA) observations for three protoplanetary disks in Taurus at 2.9,mm and comparisons with previous 1.3,mm data both at an angular resolution of $sim0.1$ (15,au for the distance of Taurus).