Yes. Start by submitting an application for the first program you are applying to, and then submit your other application(s) using the same account and login information. You will need to upload all the required application components and pay a separate application fee for each application you submit.
If you are admitted to more than one program, you may enroll in only one. You can apply to the second program (as a dual degree option) after you have completed at least one semester. See the Graduate Student Handbook for details.