Add SU example note

content/Double Layer.md

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+---
+title: PDMS Fabrication - Single Layer
+draft: false
+tags:
+  - su
+  - pdms
+---
+
+## Wafer silanization
+
+1. Before each fabrication make sure all silicon wafers are silanized using chlorotrymethylsilane (TMCS).
+2. Add 1 mL of TMCS in a small cap and place it inside a container where the wafers are stored. Place the container inside a fume hood for approximately 15 min.
+3. When finished, leave the equimpent inside the fume hood for a few more min, to make sure the entire TMCS has evaporated before.
+
+Wafers are now ready to be used.
+
+## Fabrication
+
+### Introduction
+
+This protocol is about the fabrication of a double-layer chip design (flow & control layer). During this procedure you need to make sure that your working place (PDMS lab) is very clean and avoid any distractions in order to not contaminate your materials. Try to minimize the interactions with your colleagues and always wear gloves and a mask. 
+
+### Materials
+
+- Silicone elastomer kit (SYlgard 184)
+- Curing agent
+- Vacuum desiccator
+- Vacuum pump
+- Silicon wafer (mold)
+- Regular oven
+- Air gun
+- Petri Dishes made of glass
+- Sterile disposable scalpels
+- Aluminium foil
+- Scotch crystal tape (19 mm x 32.9 mm)
+- Pasteur pipettes plastic - 5 ml
+- 0.8 mm hole punch or syringe
+- Tweezers
+- Spin Coater
+
+### Procedure
+
+#### Flow layer fabrication using elastomer and curing agent in ratio 20:1
+
+ 1. Carefully pour **20 g** PDMS elastomer from its container into a clean Petri dish and then using a plastic pasteur pipette add **1 ml ** curing agent into the Falcon. Other applicable volumes are **30:1.5** and **40:2**.
+ 2. Using the plastic pasteur pipette mix the mixture well for at least 5 min.
+ 3. Using tweezers hold the flow layer mold from its edges avoiding the designs and use an air gun to clean it.
+ 4. Place it into an aluminum foil (or into a Petri dish made of glass and covered with aluminum foil with a satiflying diameter).
+ 5. Degas PDMS mixture for approximately **25 min** inside the vacuum desiccator using a vacuum pump.
+ 6. Place the wafer inside the spin coater (with no foil!) and pour the PDMS mixture carefully onto its center.
+ 7. While degasing, set the parameters of the spin coater to **2000 rpm** for **1 min**. Turn on the vacuum. Spin coat the mixture. Note that the higher speed the less pressure is required to close the valves but it is also easier to collapse the membrane. It is very important to check the position of the wafer inside the spin coater to avoid an unevenly spreading of the mixture. Adjust the position until the wafer is centered. You have to be quick in steps 5-7 to avoid the solidification of the mixture.
+ 8. Preheat the oven at **90°C** for 5 min.
+ 9. Using the oven pan place the PDMS flow layer on the mid floor inside the oven and bake it at **90°C** for **30 min** (make sure that the surface is straight).
+10. Remove from the oven.
+
+#### Control layer fabrication using elastomer and curing agent in ratio 5:1
+
+1. Carefully pour **40 g** PDMS elastomer from its container into a clean Petri dish and then using a plastic pasteur pipette add **8 g** curing agent into the Falcon. Other applicable volumes are **50:1**.
+2. Using the plastic pasteur pipette mix the mixture well for at least 5 min.
+3. Using tweezers hold the control layer mold from its edges avoiding the designs and use an air gun to clean it.
+4. Place it into an aluminum foil (or into a Petri dish made of glass and covered with aluminum foil with a satiflying diameter).
+5. Place the aluminum foil with the wafer on a straight surface and pour the PDMS mixture on top of the wafer.
+6. Degas mixture for approximately **25 min** inside the vacuum desiccator using a vacuum pump.
+7. Preheat the oven at **90°C** for 5 min.
+8. Using the oven pan place the PDMS control layer on the mid floor inside the oven and bake it at **90°C** for **30 min** (make sure that the surface is straight).
+9. Remove from the oven and using a sharp scalpel cut out the two PDMS designs.
+10. Place the two designs on a clean surface preferably with holes on it and then create holes for inlets and outlets using a **0.8 mm** hole puncher or a syringe. Only the control layer is punched in this step!
+
+## Alignment & bonding of the two layers
+
+### Procedure
+
+1. Manually align the control layer onto the flow layer using a stereomicroscope; markers placed around the main structure of the device can aid the alignment process. Align directly on the flow layer wafer! Don't spend more than 5 min per alignment!
+2. Bond the two layers by baking them at **90°C** for **1.5 hr**.
+3. Cut and peel each chip (flow & control layer) from the molds.
+4. Place each chip on a clean surface and then create holes for inlets and outlets using a 0.8 mm hole puncher or a syringe (penetrate all the way through the PDMS device).
+5. Protect PDMS surfaces from dust using scotch tape and store them in a clean Petri dish.
+
+## References
+
+1. [Volpetti et al. (2017). A microfluidic biodisplay. ACS synthetic biology](https://pubs.acs.org/doi/10.1021/acssynbio.7b00088)
+2. [Dénervaud et al (2013). A chemostat array enables the spatio-temporal analysis of the yeast proteome. PNAS](https://www.pnas.org/doi/abs/10.1073/pnas.1308265110)

content/PDMS Design.md

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-
 ---
 title: PDMS Design Iterations
 draft: false

content/Single Layer.md

@@ -53,3 +53,8 @@ This protocol is about the fabrication of a chip design (flow or control layer).
 9. Remove from the oven and using a sharp scalpel cut out the two PDMS designs.
 10. Place the two designs on a clean surface preferably with holes on it and then create holes for inlets and outlets using a 0.8 mm hole puncher or a syringe (penetrate all the way through the PDMS device).
 11. Protect PDMS surfaces from dust using scotch tape and store them in a clean Petri dish.
+
+## References
+
+1. [Volpetti et al. (2017). A microfluidic biodisplay. ACS synthetic biology](https://pubs.acs.org/doi/10.1021/acssynbio.7b00088)
+2. [Dénervaud et al (2013). A chemostat array enables the spatio-temporal analysis of the yeast proteome. PNAS](https://www.pnas.org/doi/abs/10.1073/pnas.1308265110)