Add SU example note

content/Alignment and Bonding.md

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+---
+title: PDMS Alignment and Bonding
+draft: false
+tags:
+  - su
+  - pdms
+---
+
+## Introduction
+
+There are two main ways that are used in the team for bonding PDMS devices to glass slides.
+  - Plasma treatment of the two surfaces to be bonded (PDMS chip & glass slide). This yields the optimal results regarding the bonding strength. 
+  - Overnight baking (90°C, > 16 hr) of the two surfaces to be bonded (PDMS chip & _epoxy-coated_ (ideally) glass slide)
+
+This protocol describes the microwave oven-based plasma treatment method used by the team. The glass slide may be epoxy-coated and may have cells/spores spotted on it.
+
+## Preparation
+
+1. After fabrication all chips are very carefully stored in a Petri dish which has been cleaned using the air gun and EtOH. Before plasma treatment this Petri dish will not be opened again.
+2. As you arrive in the plasma treatment lab, put on gloves and spray them with EtOH.
+3. All equipment and surfaces you will work on have to be sterilized with EtOH, not including the slide, the aluminium foil and the chip. When you sterilize the jar wait for the ethanol to completely evaporate before you start.
+4. Place a piece of aluminium foil inside the sterilized jar, preferably with arcs, because it makes it easier to spark the plasma.
+
+## Plasma treatment
+
+1. Carefully remove the chip and the slide from the Petri dish and the box, while trying to minimize the exposure of the other ones to dust. Remove any dust particles using scotch tape.
+2. Place the chip on the slide with the patterned side facing up and then place them inside the jar, with the empty side of the slide facing the aluminium foil. If you do otherwise the PDMS will be burned.
+3. Evacuate the jar at a pressure range of **2-6 mbar**.
+4. Place the jar inside the microwave and set the power to **100% (800 watts)**. 
+5. Wait until the plasma sparks and after no longer than **2 sec** stop the microwave. 
+
+## Procedure
+
+1. Remove the jar from the microwave as quick as possibly, remove the slide and chip from it and on the previously empty side of the slide, successively (and not all at once!) bond the surface of the patterned side of the chip. This prevents air to be trapped between the two surfaces.
+2. Apply mild pressure for about 5 min on the whole surface of the chip. 
+3. Check the results by looking at the chip against a black background (e.g. black paper) or gently trying to remove the chip from the slide. If you cannot remove the chip you have successfully bonded it to the slide. Note that the chip is still functional if only the pattered part of the PDMS is bonded. 
+
+## Notes
+
+1. Everything you do, try to do it as quickly, and at the same time carefully, as possible. This also minimizes surface exposure to dust during preparation and plasma treatment. 
+2. The bonding process is immediate. If after  several minutes the chip has not bonded at all, the process failed and cannot be repeated.
+1. When you test the results of the bonding, if only a part of the surface was not bonded, after some extra minutes of pressure it may bond.
+1. Some of the team's observations show that for best results, the chips have to be fabricated and bonded during the same day, preferably as fast as possible after their fabrication.
+
+## References
+
+1. [How to succeed with glass PDMS plasma bonding, Elveflow](https://www.elveflow.com/microfluidic-reviews/soft-lithography-microfabrication/soft-lithography-glass-pdms-bonding/)
+2. [Barnes et al. (2021). Plasma generation by household microwave oven for surface modification and other emerging applications. American Journal of Physics](https://aapt.scitation.org/doi/full/10.1119/10.0002706)
+3. [Lab 6A: PDMS Microfluidics: O2 Plasma Treatment ](https://www.youtube.com/watch?v=fMUemBZ0k5Q&t=23s&ab_channel=MITOpenCourseWare)

content/index.md

@@ -12,3 +12,4 @@ See the [documentation](https://quartz.jzhao.xyz) for how to get started.
 - [[Single Layer]] - PDMS chip fabrication
 - [[Double Layer]] - PDMS chip fabrication
 - [[PDMS Design]] - PDMS chip design iterations
+- [[Alignment and Bonding]] - PDMS Alignment and Bonding