We present three-dimensional simulations of a protoplanetary disk subject to the effect of a nearby (0.3pc distant) supernova, using a time-dependent flow from a one dimensional numerical model of the supernova remnant (SNR), in addition to constant peak ram pressure simulations. Simulations are performed for a variety of disk masses and inclination angles. We find disk mass-loss rates that are typically 1e-7 to 1e-6 Msol/yr (but peak near 1e-5 Msol/yr during the instantaneous stripping phase) and are sustained for around 200 yr. Inclination angle has little effect on the mass loss unless the disk is close to edge-on. Inclined disks also strip asymmetrically with the trailing edge ablating more easily. Since the interaction lasts less than one outer rotation period, there is not enough time for the disk to restore its symmetry, leaving the disk asymmetrical after the flow has passed. Of the low-mass disks considered, only the edge-on disk is able to survive interaction with the SNR (with 50% of its initial mass remaining). At the end of the simulations, disks that survive contain fractional masses of SN material up to 5e-6. This is too low to explain the abundance of short-lived radionuclides in the early solar system, but a larger disk and the inclusion of radiative cooling might allow the disk to capture a higher fraction of SN material.
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