This page serves as a record of the latest recommended protocols for different processes used for the QBio course. Please feel free to update it with your latest results and experiences.

As a reminder, please use only shared materials and those in the boxes labeled QBio.

Polydimethylsiloxane (PDMS) Casting

Following the steps below yields a cured PDMS device inside a device mold.

Materials & Apparatus

  • PDMS (Sylgard 184, Dow Corning)
  • Device mold or master
  • Thinky mixer
  • Cups for Thinky mixer
  • Dessicator
  • Vacuum pump


  1. Weigh PDMS into a container for the Thinky mixer.
    • A ratio of 10 parts base to 1 part cross-linker is typical. Changing the ratio changes the stiffness of the final device.
    • Approximately 15 to 20 g is sufficient for a single device.
    • You can verify the mixer settings by pressing mode. The typical settings are 30 seconds at 2000 rpm for mixing and 30 seconds at 2200 rpm for de-foaming.
  2. Pour the PDMS onto your device mold.
    • Fill the whole mold to a depth of between 4 and 6 mm.
    • To make a mold from a silicon master, either place the wafer into a petri dish or into a boat made of aluminum foil. Additional PDMS will be required to fill the whole container to the specified depth the first time.
  3. De-gas the PDMS at least until all the bubbles have lifted off the surface of the mold. Place your sample in the desiccator and replace the lid. Turn the timer dial to start the pump running. Remove your device from the desiccator once the device is sufficiently cleared of bubbles.
    • You can periodically release and re-engage the vacuum to pop the bubbles faster.
  4. Place your mold into the oven to cure. Once the device in the mold is fully cured, you can continue to device fabrication
    • Please label the oven with the temperature you are using, and the time your devices will finish baking, so other users will know when they can safely use the oven.
    • If you are baking your devices in a petri dish, please use 65C or less. Cast your device into a hand made foil boat for use at higher temperatures.
    • PDMS will cure in about 2 hours at 80C and roughly 4 hours at 65C, but most devices are cured overnight.
    • Devices cured at different temperatures reach a different final stiffness.

PDMS Device Fabrication

This process starts from a device cured on top of a mold and leaves you with a bonded device which is ready for flow or further processing.

Materials & Apparatus

  • Cured PDMS device mold
  • Bonding substrate
  • Scalpel
  • Biopsy punch (0.75 mm)
  • Isopropanol
  • Sonicator
  • Scotch tape
  • UV-Ozone (UVO) chamber


  1. Cut the PDMS around the edges of the device using a scalpel.
    • It may be necessary to pass the scalpel over the features one additional time to ensure that the PDMS is cut all the way down to the silicon wafer.
    • You can check whether the scalpel is all the way through by looking to see whether you see one or two images of the cuts that you make. When the cut goes all the way through, the actual cut seems to merge with its mirror image seen in the silicon.
    • Leave about 3 mm of space away from your channels and critical features to allow for good bonding.
    • The whole slab should fit on the substrate that serves as the base of your channels. This is typically a 50 mm x 75 mm glass slide, but you can also use a glass cover slip, or another piece of PDMS.
  2. Lift out the PDMS device using the scalpel to lever one edge of the device upwards. Grip the lifted edge and pull evenly and gently to completely remove the device from the mold.
  3. Punch each inlet and outlet using a biopsy punch. Ensure that cores are removed from the holes.
    • Other sizes of punches and tubing are possible. Use 0.75 mm diameter punches with PE/2 tubing, 1/32" tubing, or 20G needles.
  4. Clean the device and the bonding substrate thoroughly using isopropanol and sonication.
    • If the glass slides are extremely dirty, remove macroscopic dirt using isopropanol and lint-free wipes to wipe the dirt away, before doing solvent cleaning.
    • One can also use Scotch tape to lift on pieces of PDMS dirt and dust.
  5. Activate the bonding surfaces of the PDMS device and the bonding substrate. There are two possible methods for this, which are detailed below:
    1. Place the device and the bonding substrate into the UVO chamber with their bonding surfaces exposed for 10 minutes.
      • The plate which holds the devices can be moved by releasing the set screw. Tighten the set screw once the plate is set to the desired height. It should positioned with the black line marked on the column in line with the bottom of the chamber.
    2. Use the corona discharge wand in the fume hood nearest the entrance door. Simply point the wand towards the bonding surfaces of the substrate and run it over the surface with even coverage, using 3 passes over both the halves with a duration of 1 minute each.
  6. Place the two bonding surfaces together starting with one edge and let the PDMS device fall into contact with the bonding substrate.
  7. Bake the device in the oven to complete the bonding process.
    • The current recommended baking time is 65C overnight. Better results have been achieved with 110C for 20 minutes prior to lower the temperature to 65C.

Surface Treatment for Droplet Microfluidics

For droplet microfluidics, the channels should be rendered fluorophilic by coating the surface of the channels with perfluorinated groups. Here, a perfluorinated silane reacts with the surface to achieve the desired surface coating.

Materials & Apparatus

  • Bonded PDMS chip


  1. Punch and bond the device, following the protocol for PDMS-glass chips.
  2. Dilute perfluorinated silane (Heptadecafluoro-1,1,2,2-tetrahydrodecyl trichlorosilane) 1:1000 (V/V) in Novec HFE7500 to a final volume of ~1mL in a glass vial.
  3. Connect the needle and tubing to the syringe, and aspirate the solution into the syringe.
  4. Prime the tubing, holding the tubing outlet above the glass vial, which now serves a waste container.
  5. Connect the syringe to the oil inlet of the first device which is being treated.
  6. Connect tubing to the outlet of the device, making sure that the tubing drains into the waste container. Plug any extra junctions with dead-end tubing.
  7. Press the solution through the device, watching to make sure it fills the droplet making junction completely.
  8. Repeat steps 6 and 7 for each device on the chip.
  9. Rinse all the devices using pure HFE7500, following the same procedure as in steps 6 and 7.
  10. Clean the top of the device with wipes. Seal any contaminated wipes into a plastic bag, labeled as hazardous waste.
  11. Dispose of any liquid collected into the waste container as halogenated hazardous waste.
  12. (Optional) Bake the device for 4 hours at 65C to remove any residual solvent.

Channel Electrode Fabrication


  1. Punch and bond the device, following the protocol for PDMS-glass devices.
  2. Cover a hot plate with aluminum foil and set it to 100C.
  3. For each electrode channel, the metal electrode pin will be inserted into one end, and the other end of the channel serves as a relief hole for excess solder. Press the indium wire solder into each of the electrode holes until the solder melts and starts to flow out of the associated relief hole.
  4. Press the electrode pins into the filled electrode holes. Ensure that the pin is pressed all the way to the bottom of the hole.
  5. Clean the surface of the device using tweezers to scrape away the leftover solder. Wipe away any residue with ispropanol.
  6. Remove the device from the hot plate, apply UV cure adhesive around the electrode pins and cure it (60s at 8mW/cm^2 seems to work). The epoxy serves to hold the electrodes rigidly in place.
  7. Place the device back on the hot plate and allow it to sit for 10 minutes. This allows the solder to liquefy and come back into contact with the pins if the contact was broken during prior handling.
  8. Allow the device to cool slowly, either by removing it and placing it on a surface with low thermal transfer, or by turning off the hot plate, and allowing it to cool back to room temperature.
  9. Dispose of any contaminated wipes in a sealed plastic bag.

Silanization of Molds

To be completed.

Other Protocols

Please provide links or descriptions of protocols that have not been developed or adapted for the facilities available to QBio in the section below.