You can go upstairs using the stairs behind the counter in the main lobby. If you have already talked to Proctor Quinlan of the Brotherhood of Steel, you'll find several technical documents in the filing cabinets here so make sure to check them all out. There's also a master-locked double-door in the middle of the second floor. There's also a Nuka-Cola Quantum on the kitchen to the SW.
Once done looting the place, follow Molly to the Clean Room. Mandatory lockdown will be implemented which will force you to find a way to escape the lab. The sidequest of the same title will become available as well.
Ground floor, storage room west: Sample 3111 on the shelf. There's also a Hazmat Suit and two metal containers in the same room.
Ground floor beside PCA machine: Sample 11317
Ground floor, laboratory west: Sample 413 on the low shelf beside the beaker and beaker stands. In the following room, you'll find Sample 65 on a table between two machines. In the same room, you can use the Novice terminal to unlock the Isotope Containment Room with a Glowing One inside.
Isotope Containment: In the ground floor, north, kill the glowing one inside then retrieve the U-238 canister from the shelf. This is a highly irradiated room so don't linger for long. This is one of the key items for the experiment.
Second floor, eastern room: There's a chem station in the small room and Sample 49 on the table beside a skeleton. From there, you can go up the fallen ceiling as a ramp then follow the ceiling path to reach the western room.
Second floor, western room: Kill the feral ghoul in the same room. You can get Sample 611 beside the terminal. Examine Bergman's terminal. If you selected to override the security, all robots, including Molly will become hostile. If you destroyed Molly, don't forget to loot the CPL key from her wreckage. Also, the quest will be tagged as “Completed” but the main objective which is to “Complete the Research Project” will still remain active. You can use it to open the master-locked door in the second floor lobby. On the table beside the terminal, there's also a Radioactive Containment Password holotape. (This can be used on the locked containment room in the ground floor; worthless if you already lockpicked it.) Leave the room by opening it using the terminal. You may also need to destroy the turrets if you overridden the security systems.
Once done, head back to the Polymer Coating Applicator, starting from the left, place sample 3111 and sample 611 to the right. Next insert the isotope sample on the small holder to the right. Use the terminal again then scan the loaded reagents. Then select “Run Loaded Fabrication Routine”.
Wait for the fabrication to finish then go to the nearby dispenser and pick up your prize: The Peizonucleic Power Armor Chest.
Head to the second floor and unlock the room. Kill the director inside and get the issue of Massachusetts Surgical Journal on the director's table. There's also a fusion core in one of the broken displays in the corner of the room.