Week 1: Let's get it started!
Objective of this week
To discover more in-depth the subject and focus on the design of our chips for different micromixing procedures.
What we did
By reading different articles, we were able to create a literature review and withdraw some information on how to design our chips. We learned how to work together, choose the right parameters, design chips on Clewin and FreeCAD, emboss and assemble chips in the context of neuron chips, and use the tikiwiki as our platform.
Difficulties encountered
What was mostly hard during this week was knowing where to start. There was a lot of literature to review, but thankfully Lorraine had already some knowledge of chips. The second hard thing was working on CleWin and FreeCAD with our computers. Unfortunately, only Lorraine could work on CleWin since Anel and Johanna could not download it because of their Macbooks. Secondly, softwares are sometimes a little too heavy, especially when we add a lot of details. For example, too many constraints on FreeCAD makes your computer so slow that you have the time to go down 3 floors and go back up, and it would still be processing.
This first week was also used to get to know our workspace and colleagues. The OpenLab of Saint-Germain-des-près became our real office, nearly our second home and the help from each group is incredible.
Day-by-day notes
[-]
Monday, February 7th
On our first day, we all met our supervisor, Hugo Salmon to talk for the first time about the project. We were able to understand the different principles we are going to use and set the main goals for the following week. We agreed that we are going to have a group meeting every Monday to see the progress of our work at 9 or 10 am. Dr Salmon explained to us the experimental part of the project, from the engineering and chemistry point of view. We finished our meeting with the list of what he expected us to do for the week.
At the end of the meeting, we decided to discover more deeply our project. Anel downloaded FreeCAD and started some general practices. Lorraine downloaded Clewin and started learning how to use it. Johanna tried to find a way to download Clewin on Mac, which was with no result, and read the two articles given by Dr Salmon.
Dr Salmon provided us with many files that could help us with the design of our chip; and also gave us the confidentiality agreement and the lab rule which we all signed.
Tuesday, February 8th
For the second day, we decided to work altogether but outside of the university. Anel did some literature reviews for micromixers and worked on understanding the dimensions of chips. Johanna worked on the organization with the creation of google drive for the whole team. She organized the different files, read the papers found by Lorraine, and created a template for the schedule since we did not have access yet to the tikiwiki. We all worked on filling it in which was quite tricky since we did not have a clear idea of what we are going to do in detail. Lorraine looked for articles to find instances of acoustic design/passive design. She also worked on basic acoustic design.
Wednesday, February 9th
For this third day, we all looked at how to fabricate a chip with elastomer. We had a quick demo on how to emboss and assemble a chip in the context of a neuron chip with the help of Solène, a PhD student. It was a really valuable experience since it showed us how to produce chips. The three of us got the chance to participate in the production of one of her chips which was very exciting.
For the rest of the day, Anel drew chips, and chambers and decided on their dimensions. She also looked for different pieces of information such as the SHMS size, limiting factors, and angles and did a literature review. Johanna read papers on how to design a microfluidic chip. She learned about positive draft angles and studied the depth and length of the channels. She also wrote the protocol of how to fabricate the chip based on the demo and drew some other designs for the chip. Lorraine formed herself on the use of the thermal press and read two overviews on micromixers.
That day was also the day we discovered tikiwiki! Lorraine played with it to get to know more about the website and how to use it.
Thursday, February 10th
This Thursday, we all worked in the OpenLab. Anel drew passive herringbone micromixers designs and did more practice on the FreeCAD. Johanna first looked for and wrote the protocol for the lithography, then started learning how to use FreeCAD. By the end of the day, she created the first basic design on FreeCAD with the three chambers and the serpentines. Lorraine looked for data in the bibliography on acoustic design. She finished as well the first draft of the basic acoustic design. She then looked for data in the bibliography on passive design.
Friday, February 11th
For this day, we all worked separately. Johanna started the creation of her second design on FreeCAD for passive micromixing and started to work on the tikiwiki template. Lorraine worked on the basic acoustic design and finalized it, before starting the herringbone chip design on Clewin.
Week 2: Ready... set... design!
Objective of this week
The goal of the week was to have our final design on CleWin so we could do the Lithography and to start filling the tikiwiki, especially with the Gantt Chart.
What we did
- Active mixing on FreeCAD
- Herringbone grooves on CleWin
- Advanced on the TikiWiki, creation of the Gantt chart
Difficulties encountered
The difficulties we encountered this week were mainly observed on our different software: FreeCAD and CleWin.
One of the computers, where we were designing on FreeCAD, crashed due to the high number of constraints. We also had some drawing errors in on design. On CleWin we had to work on the dimensions of the designs which was tricky.
Day-by-day notes
[-]
Monday, February 14th
Today we had our weekly meeting with our supervisor Hugo Salmon. We presented our design, got some feedback and set up the plan for the following week. We worked mostly on FreeCAD to model by designing the herringbone patterns on the basic design. We also designed herringbone grooves on CleWin and modified our existing charts.
Tuesday, February 15th
We all went to the room to see the CNC machine in the morning. Our afternoon can be divided into 3 main "work". We got trained for CNC machining, to understand the constraints of the milling and the way to reduce the stress on the mill tip. We worked fully on the template of the tikiwiki, to understand how everything is working and to have a template so we can fill it daily. We then started to fill it. Finally, we designed passive microfluidic channel on CleWin.
Wednesday, February 16th
This Wednesday, we worked on the literature review for acoustic properties and setup. We learned how to create a Gantt chart in excel and the tikiwiki. We then started filling the tikiwiki by writing the one-page report of the previous week, and the day-by-day report.
In the afternoon, we had a meeting with our supervisor to discuss designs: they needed to be shrunk down. New passive and active micromixers were designed with this new constraint taken into account.
Thursday, February 17th
We worked on the FreeCAD protocol to optimize the serpentine and increase the herringbone for the bigger mile size. We continued working on the tikiwiki, and the designs on CleWin. The designs are layered out on the soft mask during a meeting with Hugo Salmon. We then designed more curved acoustic channel with varying parameters.
Friday, February 18th
We finalised 2 designs: simple channel with herringbone, and serpentine with herringbone. Lorraine went to the cleanroom to produce the master mold using photolithography. Only the first layer was completed.
For the tikiwiki, after discovering that it was easy to edit the Gantt chart without having to log in, we tried to create a template on a google sheet. We created the gallery and added some pictures. We also modified our page "meet the team" to add our supervisor Hugo Salmon.
Week 3: It's getting real
Objective of this week
Our main objectives this week were:
- Test the transducer with the generator, amplifier, and oscilloscope
- Emboss and assemble our chips
- Test the mixing of our chip prototypes.
What we did
- Moved the CNC machine in the Open Lab
- Profilometry of our channels,
- Set up the circuit with the transducer, generator, amplifier, and oscilloscope,
- Thermoformed three of our chips,
- Assembly and mixing/flow test in the first three chips prototypes, with contact with the Petri dish and with a flat FlexDym surface.
- Work on the tikiwiki.
Difficulties encountered
This week we did not have any problems. The main difficulties were setting up the circuit with the transducer, and studying the flow in our chips. When our chips were stuck to the petri dish, we had some leakage in the chambers under our chip. To solve this problem, we assembled our chip with a flat FlexDym surface. The flow ended up being better, without any leakage. The third problem was the syringe. We used two syringes manually (held by two different people) so the pressure was different and both colours we used as fluids were not equal.
Day-by-day notes
[-]
Monday, February 21th
Common: Meeting with our supervisor Hugo Salmon. Photoshoot for the tikiwiki "Meet the group" section.
Anel: Work on FreeCAD.
Johanna: Sum up for the Day by day report and weekly report, work on the logo, Gantt chart, tikiwiki
Lorraine: Protocol with Francisco, day by day report, put the layout, work on the logo
Tuesday, February 22th
Common:Installation of the CNC machine into the OpenLab room.
Anel & Johanna: Clean room characterisation with profilometry and microscope pictures of channels.
Lorraine: Placing the new chip designs for acoustic mixing on a layout for hard mask printing.
Wednesday, February 23th
Anel: setting up the transducer, evaluate frequencies, comparing with literature (circular transducer 41mm)
Johanna: Helped Anel with the set-up of the transducer and the use of the oscilloscope. Work on the TikiWiki template, organisation of the website and design of the new logo on the iPad using Notability.
Lorraine: Looking for a new colour chart for the tiki wiki. Logo agreed-upon design is made in vectors using illustrator and photoshop.
Thursday, February 24th
Morning:
Johanna & Lorraine: Thermoforming three acoustic and simple chip.
Afternoon:
Anel & Lorraine: assembly and mixing test in the first three chip prototypes.
Johanna: Work on the TikiWiki (Generality) and assistance with the assembly and mixing test Anel & Lorraine did.
Friday, February 25th
Anel: Protocols and reading on chip assembly
Johanna & Lorraine: Work on the Gantt chart, assembly of the chips with a flat surface and mixing test in the first three chip prototypes.
Lorraine:Report to Hugo salmon on the results of the chip assembly
Johanna: Work on the TikiWiki (Price, generality, lab notebook, pictures, contact us)
Week 4: Game on!
Objective of this week
Our main objectives this week were:
- Fabricate a new and improved mold for the active channel
- Finish the fabrication of the passive mold
- Find a method to mold piezo elements during chip fabrication for better embedding inside the chip
- Replicate our flow experiment with FlexDym on glass or polystyrene
What we did
- Create the molds
- Try to close newly fabricated chip on glass and polystyrene
Difficulties encountered
There are several problems encountered with the adhesion of Flexdym on glass with and without a transducer in between. The glass/flexdym adhesion is very weak, therefore a lot of leaks are present. The idea was to use a 37 °C oven for 30-40 mins to improve adhesion and prevent leaks. There are several possible solutions discussed, such as (1) using extra weight, (2) increasing baking temperature, (3) possibility of magnetic field use, (4) glass surface treatment (either chemical with plasma, coatings, or mechanical with fine sandpaper. Another problem faced is with photolithography with the soft mask.. (1) quality of printing due to bubbles, (2) alignment problem: conclusion herringbone structures are not good.
Day-by-day notes
[-]
Monday, February 28th
Tuesday, March 1st
Lorraine: photolithography in the cleanroom for the second layer of the passive design and using the new hard mask for the passive design.
Anel&Johanna: Run some flow experiments with the chips we have and a syringe pusher in the biophysics lab. We did the experiments on flexdym+petri dish; and flexdym+glass.
Wednesday, March 2nd
Tikiwiki protocols
Lorraine: second day at the clean Room
Thursday, March 3rd
Update of the protocol for the photolithography.
Experiment:
- Chip embossment with a round piezo buzzer or glass of the same dimensions as the piezo rectangular buzzer.
- Preparation of epoxy and PDMS for counter molds.
Friday, March 4th
PDMS unmolding
Experiments with active micromixers and colours, without the piezo, to check for leakage and if there is a nice flow.
Week 5: Let's mix it up!
Objective of this week
Our main objectives this week were:
- Try to find a solution to prevent FlexDym on glass chips from leaking
- Emboss more ships with piezo embed
What we did
- Emboss more ships with piezo embed
- used blocks made of FlexDym at inputs to try to fix the leaking theorized to be caused by the tube insertion
Difficulties encountered
Due to the soldering points of the round piezo buzzer, they could not face down with their ceramic component flat against the glass.
Our chip design did not take this into account, making it very difficult to embed them. We decided to mainly focus on the acoustic designs that could work with the rectangular piezo.
The blocks helped prevent the tubing from stretching and damaging the chip causing leaking but the blocks were unsticking, causing leakage themselves.
Day-by-day notes
[-]
Monday, March 7th
Experience: Piezo+ active micromixers+ colors+ petri dish or glass.
Since there was still leakage when the chip was on the glass, we've decided to do it on a petri dish, just to see if the adherence was due to the material difference.
Results: Without the piezo, the flow was good when the chip was on a petri dish, with no leakage. However, we couldn't do it with piezo--> leakage.
Ordering magnets to try and fix the flexdym on the glass issue.
Tuesday, March 8st
Cleaning the chips in the morning and embossment of new chips.
Experiments of serpentine and active micromixer (one channel) on polystyrene+ colours.
Results: Good flow for active micromixer
Wednesday, March 9nd
Anel:
Lorraine: attempt at pressing more chips but there were technical difficulties with the SubLym thermopress, after trying troubleshooting we decided to stop for the day and wait for the machine to get fixed before trying more.
Johanna:
Thursday, March 10rd
Embossment of new chips?
Johanna: Prezi
Lorraine: pressing of three types of chips, the curved acoustic with a diameter of 27 mm, the herringbone designs and block to try and fix the leakage at the inputs
Friday, March 11th
Johanna: Prezi
Anel
Lorraine: plasma hydrolyzing of chips, adding blocks and baking, flow test to see if the leakage and bubbles problem were resolved
Week 6: !
Objective of this week
- Start the poster
- See some mixing between DPDMS and fitC, under the fluorescent microscope for passive micromixers.
- Troubleshoot a way to add the piezo to the active micromixers set-up.
What we did
(Draft)
We had a presentation on Monday with our supervisor and other people from the lab to see our « advancement » in the project.
Poster: Structure, introduction, objective.
We gathered the results that we got for the moment: Profilometry on R to get the graphs.
Experiments with passive micromixers and colours.
Experiments with passive micromixers and fluorescence.
Increased the flow until leakage.
Difficulties encountered
One of the difficulties we encountered this week was setting up the fluorescent microscope. The visualisation of fluorescent on the computer ended up being possible with the help of our supervisor. However, the images we got from it were not the best to collect results. We ended up taking pictures directly from the microscopes with an iPhone 13.
Secondly, it was a stressful week because we still couldn’t set up the active micromixers yet. We tried to find a solution to add the piezo to the set-up for the active micromixers, while still troubleshooting how to get rid of the leakage. In the end, we focused ourselves more on the passive micromixers since the adherence with the passive wasn’t such a big problem.
Day-by-day notes
[-]
Monday, March 14th
Presentation day
We tried to do experiments with the fluorescent confocal microscope. However, we weren't able to set up the microscope to visualize the fluorescence.
Tuesday, March 15st
Cleaning of the chips.
Work on the poster and introduction
Lorraine: hydrolyzing and baking chips that were opened after cleaning. Mixing test with herringbone
Wednesday, March 16nd
Work on the poster and introduction and objectives.
Lorraine: preparing the schematics of thermopressing and flow experiment for the poster
Thursday, March 17rd
Experiments with the confocal microscope and passive micromixers + block+colors. We also added an output.
Results: Bubble and leakage.
Friday, March 18th
Cleaning, new chip embossment.
Experiments with the fluorescence confocal microscope + passive micromixers.
Results: We observed mixing.
We then increased the flow until seeing a leakage.
Week 7: !
Objective of this week
The objectives of this week were to:
- Find an optimal set-up for the active micromixers under the fluorescent microscope.
- See mixing with active micromixers.
- Continue working on the poster.
- Collect some results with the fluorescence
What we did
This week, we focused our experiments on only one design for the active micromixer. You will find in the protocol section of our tikiwiki the steps to set up the active micromixer. We then observed the fluorescence with the fluorescent microscope and took pictures with an iPhone 13. We then measured the fluorescence intensity to justify mixing, with image G. Once we have collected all the raw data from image G, we used R to graph the fluorescent intensity.
Difficulties encountered
To find the optimal set-up for the piezo so that it doesn’t induce leakage for the active micromixers. —> To find the optimal positions of the magnets on the set-up.
Day-by-day notes
[-]
Monday, March 21th
Cleaning and setting up the active micromixer on glass (one channel).
We then run some experiments under the fluorescent microscope. We tried to find a solution to include the piezo in the setup. A bad fixing of the piezo led to a detachment of the chip from the glass.
Tuesday, March 22th
Set-up of active micromixers under the fluorescent microscope, with magnets.
Cleaning of passive chips.
Wednesday, March 23th
Experiment: fluorescent microscope+ active micromixer+ glass+ magnets+ piezo.
Result: There was mixing. The more we waited, the better the bubbles were.
Thursday, March 24th
Experiments in the same conditions for both active and passive micromixers.
Results: There was mixing.
Friday, March 25th
Work on the poster
Work on R to obtain the graphs for profilometry and fluorescent intensity.
Week 8: !
Objective of this week
- Synthesise liposomes
- Work on the poster
What we did
- Calculation to see the number of liposomes etc…
- Lipids preparation
- Experiments with active and passive micromixers.
- NTA
Difficulties encountered
- Leakage with active micromixers. So we focused on passive only.
Day-by-day notes
[-]
Monday, March 28th
Experiments in the same conditions for active and passive micromixers.
Results: Leakage for active (we don't know why).
Mixing for passive, however, we noticed a big bubble in the last channels.
Tuesday, March 29th
Experiments in the same conditions for active and passive micromixers.
Results: Leakage for active (we don't know why).
Great mixing for passive.
Wednesday, March 30th
Work on the poster.
Synthesis of lipids preparation.
Thursday, March 31th
Experiments with passive and lipids preparation. We collected the samples and then used a filter to have our final sample for NTA.
Friday, March 1th
NTA
Sorting of our chips and materials.
Final meeting with Hugo.