Database Design Regarding a Relationship for Patient Visit
In the long run, thinking in terms of tiers and of ID numbers is more likely to hurt you rather than help you.  At the start, use ID numbers only for those things that don't carry their identity with themselves. Studies should carry their identity with themselves; that is, their names should almost certainly be unique. Patients (people) don't carry their identity with themselves; there are many people named "John Smith".

My guess at primary keys is in parens. Foreign keys should be obvious.  

Studies (study_name)
Patients (patient_id)
StudyPatients (study_name, patient_id)
Visits (study_name, patient_id, visit_timestamp)
PhysicalExam (study_name, patient_id, visit_timestamp)
ClinicalExam (study_name, patient_id, visit_timestamp)


It's not clear whether you need any additional columns to identify rows in PhysicalExam and in ClinicalExam. It doesn't look like it on first glance, though. Later, if there's sufficient interest and if I have enough time, I'll write this in SQL.