Molecular Line Emission from Planet-Forming Disks with ALMA

The physical and chemical conditions in the protoplanetary disk set the initial conditions for planet formation. Constraining the properties of disks is of key importance for understanding how planets assemble.
Observations of molecular lines in disks provide valuable information on disk properties. This thesis presents ALMA observations, analysis and modelling of molecular line emission from four disks that all exhibit evidence for forming planets. Using the first-ever observations of 13C17O in protoplanetary disks, the CO gas mass of the HD 163296 and HL Tau disks are robustly constrained. The new masses are a factor of 2-10 times higher than existing estimates using C18O, and highlight the potential gravitational instability of the HL Tau disk. Analysis of the radial distribution of HCO+ and H13CO+ in the HD 97048 disk reveals a low ratio that can be explained via chemical fractionation. This indicates that the gas temperature in the outer disk is low (approx. 10 K) despite this disk being hosted by an A-type star. Both silicon and sulphur bearing volatiles are observed to be significantly depleted in disks, similar to dark clouds. Multiple lines of SO and SiO are targeted towards HD 100546 and HD 97048. The detection of the shock tracer SO in the HD 100546 disk is attributed to either a disk wind or a circumplanetary disk. Complementary chemical modelling reveals the molecular carriers of S and Si in the two sources, and predicts SiS as tracer of S and Si in disks. This thesis shows that 13C17O is a robust tracer of disk gas mass, HCO+ isotopologue emission may trace reservoirs of cold gas in typically warm disks, and Si and S bearing molecules are useful probes of shock induced structures such as circumplanetary disks.