Based on observation of molecule D's movement, modify the system so that three possible exits exist.
Literal
Molecule D [possessive-の] movement [possessive-の] observation [basis-に基づき], possible exits [subject-が] three exist [purpose-よう] system [target-に] modification [object-を] add.
~に基づき is the formal て-form equivalent of ~に基づいて (based on). 変更を加える means 'to make modifications.' A technical instruction with dense noun-chain modifiers typical of scientific writing.