# Introduction
This project studies the effect of hydrodynamic force on colloidal systems. To be specific, how can viscosity of the solvent affect the microstructure and mechanical behavior of the colloidal gels. To achieve this, we perform index matching for synthesized thermoresponsive-functionalized silica particles, and use confocal laser scanner with fast scanning rate to capture three-dimensional structure of the colloidal gel.
# Experiments
## Particles Synthesis
Our target is obtaining functionalized silica particles with designed temperature response, and disperse them into the hydrocarbon medium with proper index matching and controllable and adjustable viscosity.
Also, to have the silica particles work for our confocal setup, we have to use a florescence dye to color the centre part. This requires modification of some of the original steps shown in the paper.
To control the attractive potential, one method is by what we're doing here, change the temperature (and # of these brushes) and use the thermoresponsive properties of the octadecane brushes to adjust repulsion. An alternative method is [[Three-dimensional confocal microscopy of colloids#^9de3c4|using polystyrene]] to control the [[Depletion force|depletion force]], then adjust the attractive potential.
### Silica particles synthesis
Smooth silica particles are synthesized using the [Stöber process](https://en.wikipedia.org/wiki/St%C3%B6ber_process) and functionalized with -NH group. As described in [[Toughening colloidal gels using rough building blocks|paper]], the typical process would be:
- 200 mL ethanol, 18 mL MiliQ (water), 10 mL ammonia; stir in 500 mL glass bottle, 500 rpm.
- Add 12.4 mL TEOS to the solution, wait to react for 24 h. Till here we have the desired size silica particles synthesized using stöber process.
- Add 3.1 mL MAPTMS solution (5% volume friction in ethanol) using syringe pump (2 ml/h), wait to react for 1 h after injection.
- Clean the particles 1x with ethanol and 2x with isopropanol with centrifugation and redispersion steps.
This gives 300 nm diameter silica particles, to adjust particle sizes (our target would be ~micron diameter) different reaction time/temperature/reactant concentration should be considered. The silica particles would have solid structure and with a refractive index being 1.45.
>[!Info]-
>The chemicals applied are:
>TEOS: [Tetraethyl orthosilicate](https://en.wikipedia.org/wiki/Tetraethyl_orthosilicate), formula $\rm Si(OC_{2}H_{5})_{4}$, $\rm C_{2}H_{5}$ may also be written as $\rm Et$, which means the ethyl group.
>![[Tetraethyl_orthosilicate.svg|200]]
>MAPTMS: Trimethoxy\[3-(methylamino)propyl\]silane, this is the chemical brings the -NH group.
>Isopropanol: Isopropyl alcohol; formula $\rm C_{3}H_{8}O$; structure ![[2-Propanol.svg|60]]
>[!Note]- Step-by-step Operations in the Lab
>For our synthesis, although chemicals are the same, but we adapt different amount and therefore different reaction time and particle size. Below is the procedures this project adapt:
>1. Wash the flask with water and ethanol. Use the deionized water to wet all inner surface, and the brush (on a iron wire) to remove the residual silica particles at the bottom of the flask. Wash twice with water, then take ethanol to wash twice again. The waste liquid (water and ethanol) goes into the waste container. Wash the magnetic stir bar in the same procedures. Dry flask and magnetic bar with nitrogen gas.
>2. Take requires chemicals from the pharmacy cabinets, ammonia and ethanol are stored in the further one, and TEOS in stored in the one near 506 entrance.
>3. Find the proper beaker which have the chemical names on them (except for the ethanol one). Take the syringe from the cabinet, also the stopper and the needles. Take pipettes (3 in total, 10 mL, 5 mL and 500 $\mu L$). Find a septa. Remember to put the pipettes back to where they were.
>4. Adjust the beaker to the proper position. Go to the Ar gas cylinder and open the valve (rotate clockwise to open until feel the resistance). Return to the fume hood, find the tube with argon supply, open the valve (check whether the main valve is open before adjusting the regulating valve), insert the gas supply on the upper opening of the flask. Adjust the argon flow rate and look at the small glass bottle as the flow rate indicator.
>5. Use the beaker for temporary storage of the chemicals, in case the large bottle gets contaminated. Pour about 40 mL ethanol into the beaker, use the pipette with 10 mL range, inject 25 mL ethanol from the beaker to the flask, through the side entrance. Place the beaker close enough to the entrance to avoid dipping. After this, dispose the pipette tip to the solid waste buckets.
>6. Similarly, inject required amount (4.75 mL) of ammonia into the flask. Notice the ammonia is easy to get dripped, so get closer. After adding all required chemicals to the flask, put the magnetic bar in, adjust the stirrer to 500 rpm. Then put the septa on the side entrance, block air getting inside.
>7. Take the syringe, remove the piston and place it aside. Screw the stopper to the top of the syringe. Use pipette to add required chemicals and florescence dye into the syringe (15 mL ethanol, 2.5 mL TEOS, 0.25 mL dye). After all chemicals goes into it, put the piston back (don't go deep, just a little bit so air not get compressed too much), mix the liquids, and remove the stopper and push the piston, to remove the air inside the syringe. Leave some air at the top.
>8. Connect the injection tube to the syringe, and the needle to the other end of the tube, remove the cap of the needle, and push the piston to get all the airs out of the tube, with the liquid right at the needle. After this use the aluminum foil to cover every parts with liquid with dye go through (flask, syringe, tube). Puncture the needle into the septa.
>9. Take the syringe pump (No.3) from the cabinet, mount the syringe onto the injection position. Select proper syringe size (20 ml) and injection rate (which should be preselected, 20 $\mu L/min$), turn the pump on, and wait for reaction.
>---
>After reaction, cleaning and sample washing:
>1. Check whether the syringe pump reaches the end. Stop stirring and turn off the Ar supply (first the regulation valve, then the valve at the gas cylinder). Remove the septa and stop the gas supply plug. Pour the synthesized sample into two (large) centrifuge tubes, with equal portion. Adjust the mass using plastic pipettes.
>2. Place the two centrifuge tubes into the [centrifuge](https://en.wikipedia.org/wiki/Centrifuge), set 5 mins and 5000 rpm ([revolutions per minute](https://en.wikipedia.org/wiki/Revolutions_per_minute)). This is the beginning of the washing process. Wait until the set speed is reached and not noise/vibration can be notice. Otherwise press stop immediately.
>3. Meanwhile, find ethanol and water for washing, take the stir bar out before washing. Wash the flask with ethanol twice first, use the brush to clean the silica attached to the inner surface. After ethanol, clean the flask with water once without using brash. Wash the magnetic bar with ethanol and water once each also.
>4. Remove the syringe from the syringe pump. Take the needle off from the injection tube connected to syringe (add the cap first), dispose it into the waste box for sharp solids. The syringe may still have some liquids left inside, remove the connected tube from the syringe, pull the piston and let air get inside, connect again, inject the liquids and the air together into the tube, and the other end of the tube goes to the waste tank. Use the air to "wash" the tube, repeat this process several times, until almost no color liquid is visible inside the tube. Put the tube back to the stack and the syringe pump to the drawer.
>6. Fill the flask with water almost full, put the stirrer bar inside. Turn the stirrer on (500 rpm). Go the the cabinet to find KOH (potassium hydroxide), put 5-6 pieces into the flask, wait for (at least) 1 hour for the base to react with the residual silica. Remember to seal the top entrance with a ground glass stopper and the plastic septa for the side one.
>7. The centrifugation should finish. Take the centrifuge tubes and pour the upper liquids (all of them) into the waste tank, then disperse with ethanol, 20 mL each tube.
>8. Use the [vortex mixer](https://en.wikipedia.org/wiki/Vortex_mixer) to do the initial redisperse process, make sure no sedimentation visible at the bottom of the centrifuge tubes. Then place two tubes into the [sonicator](https://en.wikipedia.org/wiki/Sonication), set 5 mins, wait until it finish.
>9. After the sonication gets done, take the tubes out. Then this is one entire washing process. Wash 3 times in total, i.e., centrifugation -> pour the liquids -> add ethanol -> vortex mixer -> sonication -> centrifugation -> pour the liquids -> ... ->sonication. Till the end we get the well-mixed, clean, emulsion-like liquid.
>10. Take a small size centrifuge tube, check its mass, record, the add 500 $\mu L$ sample liquids into the centrifuge tube, weight again and record. Place the tube with lid open in the fume hood for drying. Check the mass of solid sample after.
> ---
> Fictionizing -NH groups on the particle surface. This is done by adding MATPMS solution into the washed particles.
> 1. Use vortex to have the particles well mixed, ensure no sedimentation at the bottom. Record the dried sample mass, then compute the volume fraction and mass percentage. Use the confocal to measure the diameter of the particles. Put the mass percentage into the spreadsheet to compute the required amount for 5% MATPMS solution.
> 2. Find a flask, wash with water and ethanol, pour the sample in, keep stirring. (This reaction prefer water as a catalyst, so in previous washing step a technical grade ethanol is better)
> 3. If have the stock solution, use pipette to get calculated amount into the flask. In the sample 1, it's 0.045 mL. Wait until fully reacted (~1h or more).
> 4. After graft -NH, separate the liquids into 2 15 mL centrifuge tube, centrifuge, pour away ethanol away and add 10 mL isopropanol, vortex, sonicate, centrifuge, etc. Wash three times with isopropanol in total.
>
> Till here we should have properly dispersed -NH grafted silica particles prepared. Next step would be the click reaction.
>[!Tip]-
>- The pipette tips with different size are separated by color, check the color of pipette for their corresponding tips.
>- The following illustrations are for indicating where are the chemicals and instruments are. Red lines for the drawers/cabinets below the operating surfaces (desks/fume hood), the orange lines are the shelves above the operating surfaces.
> - **Room 4**:
> ![[Drawing 2023-10-25 13.53.07.excalidraw.svg]]
> A. Ethanol and ammonia; Technical grade liquids (70%);
> B. Technical grade liquids (70%);
>
> - **Room 3**:
> ![[Drawing 2023-10-25 13.52.48.excalidraw.svg]]
> A. Sonicator;
> B. Rheometer;
>
> - **Room 2**:
> ![[Drawing 2023-10-25 12.22.54.excalidraw.svg]]
> A. Sonicator;
> B. Vortex mixer (vortex shaker), centrifuge;
> C. Tube for injection, stoppers;
> D. Syringe pump (No.3);
> E. Scale, plastic pipette;
> F. Needles for syringe;
> G. Clamps;
> H. Base (KOH)
>
> - **Room 1**:
> ![[Drawing 2023-10-25 12.39.29.excalidraw.svg]]
> A. Pipette, small volume pipette tips;
> B. Large volume pipette tips;
> C. TEOS;
>
>- Take care of the liquids inside the needle tube before injection, they can flow very fast (since the volume of the tube is extremely small).
>[!example]- Sample record
>Silica particles by stöber process:
>
>|Date |Sample #|empty centrifuge tube (mg)| mass with sample (mg) |mass dried (mg| volume with sample ($\mu L$)|
>|-|-|-|-|-|-|
>|10.25|1|970|1355|977|500|
>|10.25|2|974|1368|984|500|
>|10.27|3|977|1365|988|500|
>|10.27|4|978|1378|986|500|
>|10.30|5|974|1359|981|500|
>|10.30|6|978|1367|985|500|
>|10.31|7|988|1375|996|500|
>|10.31|8|995|1403|996|500|
>|11.01|9|987|1379|997|500|
>|11.01|10|990|1399|999|500|
>|11.02|11|989|1396|998|500|
>|11.02|12|989|1403|998|500|
>|11.03|13|975|1390|983|500|
>|11.03|14|981|1388|989|500|
>|11.06|15|974|1358|982|500|
>|11.06|16|978|1391|986|500|
>|11.07|17|969|1354| |500|
>|11.07|18|976|1368| |500|
>
>The following table provides required information for functionalization.
>
>|Date |Sample #|Diameter (nm, confocal)|$\Delta$ m (mg)|Weight percentage (g/mL)|
>|-|-|-|-|-|
>|10.25|1|1000|7|0.014|
>|10.25|2|1000|10|0.020|
>|10.27|3|~1000|10|0.020|
>|10.27|4|~1000 (some particles are smaller while some are bigger (~1300)|9|0.018|
>|10.30|5|1000|7|0.014|
>|10.30|6|1000|7|0.014|
>|10.31|7|1400|8|0.016|
>|10.31|8|1400|8|0.016|
>|11.01|9|1100|10|0.020|
>|11.01|10|1100|9|0.018|
>|11.02|11|1200|9|0.018|
>|11.02|12|1200|9|0.018|
>|11.03|13|1400|8|0.016|
>|11.03|14|1400|8|0.016|
>|11.06|15|1500|8|0.016|
>|11.06|16|1500|8|0.016|
>|11.07|17|
>|11.07|18|
>
>>[!Question]
>>Why the total mass with tube for 500 $\mu L$ sample differ this much?
>>Answer: My personal view is, the pipette is not perfectly accurate and a tiny drop could make big different in milligram level.
### Octadecane-alkynoate functionalization
The functionalization is with an alkynoate group following the Fischer esterification process, as described in the paper [[Toughening colloidal gels using rough building blocks]].
- 10 g (1 eq) of octadecanol was dissolved in 70 mL of toluene at 50 $^\circ C$ in a 100 mL roundbottom flask.
- After dissolution, 0.5 g (5% of octadecanol weight) of pTsOH was added to reaction, followed by 2.52 mL (1.1 eq) of propiolic acid.
- A [Dean-Stark trap](https://en.wikipedia.org/wiki/Dean%E2%80%93Stark_apparatus) and a condenser gets installed on the flask, solution heated to 135 $^\circ C$ for 24 h.
- The octadecane-alkynoate was purified by evaporating the toluene and then dissolved in 20 mL of acetone, dropped into iced MiliQ (water) for the octadecane-alkynoate gets prescriptated.
- The suspension was then isolated and dried. (vacuum filter, dried at vacuum, 30 $^\circ C$, 24 h)
>[!Note]-
>- The thermoresponsive behaviour of the particles are provided by the functionalized surface interacting with the medium (in the paper they use [[Temperature-Dependent Nanostructure of an End-Tethered Octadecane Brush in Tetradecane and Nanoparticle Phase Behavior|tetradecane]] or [[Interface–solvent effects during colloidal phase transitions|n-hexadecane]]). This would (potentially) limit the possible choice of the medium. We also have to consider this effective when we do index matching.
> - Not really, see the [[#^522261|answer below]].
>- But since the volume fraction of these -decane could be small, this won't affect the index matching; or the interaction is by some functional groups, we'd better investigate this how the interaction works later.
>[!Info]-
>Octadecanol: [Stearyl alcohol](https://en.wikipedia.org/wiki/Stearyl_alcohol), saturated fatty alcohol (hydrocarbon + OH); formula $\rm CH_{3}(CH_{2})_{16}CH_{2}OH$. ![[1-Octadecanol.svg|500]]
>[Toluene](https://en.wikipedia.org/wiki/Toluene): aromatic hydrocarbon, formula $\rm C_{7}H_{8}$. ![[Toluol.svg]]
>pTsOH: Toluenesulfonic acid-p monohydrate ([p-Toluenesulfonic acid](https://en.wikipedia.org/wiki/P-Toluenesulfonic_acid))
>[Propiolic acid](https://en.wikipedia.org/wiki/Propiolic_acid): formula $\rm HC_{2}CO_{2}H$. ![[Propiolic_acid_Structural_Formula_V.2.svg|120]]
>[!Note]- Step-by-step Operations in the Lab
>We might do this later if we consume all the presynthesized octadecane-alkynoate. This part is left blank temporary.
### Amine-yne click-like-reaction functionalization
With the -NH functionalized silica, we now should add the synthesized octadecane-alkynoate to the surface of those particles. This is illustrated in the [[s41467-023-41098-9.pdf#page=2&selection=266,0,266,38|Figure 1a]] of the paper.
- The octadecane-alkynoate was dissolved in isopropanol at 5 wt% at 40 $^\circ C$. Forming a stock solution.
- To graft 1 g of secondary amine functionalized particles, 1.25 mL of the stock solution was added to a 10 wt% suspension of particles in isopropanol at 40 $^\circ C$, stir for 3 h.
- The functionalized particles were then washed three times with isopropanol, dried in a rotary evaporator, and subsequently in a vacuum oven for 48 h.
>[!Note]- Step-by-step Operations in the Lab
>Take the redispersed silica particles with grafted -NH surface in isopropanol. Check the spreadsheet for the required volume of 5% octadecane-alkynoate solution.(for sample 1, the value should be 0.0732 mL) Add the solution into the suspension in the flask, place it into the sonicator, set the temperature as $40\ ^\circ C$ and time as 3h.
Till here we get the dried, functionalized particles. After redispersion to the index matched fluid, we get the required colloidal gels for confocal experiments.
>[!Question]-
>Why the functionalized group seems to be all octadecane, with the solvent (or dispersion medium) being different decade (n-). What's the range of these functional groups that have the proper thermoresponsive behaviour. Or say, when we do index matching which hydrocarbon solvent can we use?
>
>**Answer**: There is no further requirement for the solvent we apply, any (satisfy our requirements) alkane would be fine. The only requirements is the dispersion medium should be hydrophobic (and alkane automatically satisfy that). But as a reference the lower carbon chains say lower than $C_{14}$, tetradecane, may be used to match the refractive index and control the viscosity. ^522261
### Particles drying with rotavap
[[Rotary evaporator]] (abbr. rotavap), is used for particles drying particles. This device could remove the solvents without making the particles adhere too tightly to the bottom of the container or each other. This feature facilitates the redispersion compared to vacuum oven.
The standard containers are glass vessels developed for such application and are designed to withstand such vacuum level. Flask with ground glass joint is a good choice, who ensure the airtight and can maintain the vacuum level. An alternative is directly connect the centrifuge tube to the device. The plastic tube is not originally designed for this purpose, but should be fine as long as the liquid inside is small.
The powder may still stick at the bottom of the container, use spatula to remove these particles.
>[!Note]- Step-by-step Operations in the Lab
>1. Adjust the vacuum to a desired level. For drying powders dispersed in isopropanol, a good initial valve would be 400-500 mbar.
>2. Press start. The vacuum pump would try to
Dried particles are then transfer to 1.5 mL centrifuge tube for further redispersion. For each sample, the weight of the centrifuge tube with and without particles are measured. And with the silica density (2.65 g/mL), the volume of dispersion medium are calculated, also the total volume with particles dispersed.
A typical value of total volume for 40% volume fraction colloids is 210 mL.
### Glass slide octadecane grafting
To reach the no slip condition, glass slide should be prepared (i.e., octadecane grafting for silica) using the same scheme for particles. Glass slides are first cleaned with soap water, ethanol and dry with nitrogen gas. These prepared glass slides are then placed inside a [plasma cleaner](https://en.wikipedia.org/wiki/Plasma_cleaning), which is as a final cleaning step.
After cleaning, glass slide is placed inside 100 mL MAPTMS solution, which is prepared in advance, and poured inside a sample container with Teflon holder. These Teflon holder may fix the glass slides and ensure they are well separated and do not overlap. The reaction takes 2 hours or longer, then the glass slide is transfer into octadecane-alkynoate solution at 40 $^\circ C$. This reaction should take 3 hours or longer.
## Refractive Index Matching
To avoid the scattering in the confocal scanning, refractive index of the particles and the medium should be the same (or very close).
Under alkane family, we'll try to maximize the viscosity range and ensure the dispersion medium does not crystallize/solidify. The viscosity given in the handbook does not specify for isomers when carbon greater than 9. But we can use the normal one as a reference, and perform measurement on viscometers.
A short script will be applied to perform the data matching. This is expected to be done in this week.
The wavelength should be dependent on the florescence dye, which in our case is 561 nm. But since the confocal scanner works in the [[Ultrafast imaging of soft materials during shear flow#^1b74a1|visible range]], the relative change of refractive index $n_{D}$ would be small. We just use the organic compounds properties in the handbook, not the relative permittivity for fluid. (Although it would be interesting to double-check the result using the $\epsilon_{r}$)
The mixing follows linear mixing law with mole fraction.
- After an initial search, most of the alkane does not show a refractive index larger than 1.45, when they are liquid. One anomalously large refractive index is 2,2,3,3-Tetramethylbutane ($\rm C_{8}H_{18}$), it has a 1.47 refractive index, but it is solid at room temperature. It would be possible to dissolve this high index alkane into some low index ones, and match $n_{D}$ of silica.
- Or if we go to the long chain alkane, like 2,6,10,15,19,23-Hexamethyltetracosane (squalane), $\rm C_{30}H_{62}$, it has a refractive index of 1.453 and being liquid at room temperature.
- Another alternative is using alkene or alkyne for refractive index matching. If they show [[Mechanical response of colloidal system|nonlinear effective]], then use the linear regime only. But since they are all simple hydrocarbon, they should behave in the Newtonian regime only.
In the project, we will use the third method, i.e., index matching with any hydrocarbon.
- The best candidates for index matching would be having refractive index **very close to 1.45**, but two or three liquids show a huge range of viscosity. This would make the system have higher precision on index matching without losing the wide range for viscosity adjustment.
- aromatic compounds seem to have higher refractive index. They can be used to increase the refractive index. Alkane with less carbon can be used to decrease the $n_{D}$.
- It would be better to use some well studied hydrocarbons for dispersion medium, so it is possible to find some rheological properties as reference.
- There are more hydrocarbons with low viscosity, so it would be better to find those with high viscosity first, then adjust the refractive index by picking less viscous fluids.
- We'll have three different viscosity, with a difference of 2 orders of magnitude, namely 1, 10, 100 $\rm mPa\ s$. If Squalane at 5 $^\circ C$ cannot reach 100 mPa s, then we may use the viscosity 0.6, 6, 60 mPa s.
>[!example]- Dispersion Medium Candidates
>
>#### High viscosity hydrocarbons:
>| Name | Formula |$0\ ^\circ C$ Viscosity (mPa s) | Refractive index | Toxic | Env hazard| Health hazard|
>|------|--------|------------------|------------------|---------|--------|-----------|
>|2,6,10,15,19,23-Hexamethyltetracosane (Squalane)|C30H62|115.0|1.4530| | | |
>|cis-Decahydronaphthalene|C10H18| 5.645 |1.4810| yes | yes | yes |
>|trans-Decahydronaphthalene (more stable)|C10H18|3.243|1.4695| yes | yes | yes |
>|Tridecane| C13H28 |2.909 | 1.4256 | | | yes |
>|Dodecane|C12H26|2.277|1.4210| | | yes |
>|Undecane|C10H24|1.707|1.4164| | | yes |
>
>#### Low viscosity hydrocarbons:
>
>| Name | Formula |$0\ ^\circ C$ Viscosity (mPa s) | Refractive index | Toxic | Env hazard| Health hazard|
>|------|--------|------------------|------------------|---------|--------|-----------|
>|1-Pentene|C5H10|0.241|1.3715| | yes | yes |
>|2-Methyl-2-butene|C5H10| 0.255| 1.3778| | yes | yes |
>|Pentane|C5H12|0.274|1.3575| | yes | yes |
>|Isopentane|C5H12|0.277|1.3537| | yes | yes |
>|1-Hexene|C6H12|0.326|1.3852| | | yes |
>|Neopentane|C5H12|~0.3|1.3476| | yes | |
>|2,5-Dimethylhexane|C8H18| ~0.6 |1.3925| |yes | yes|
>|Octane|C8H18|0.700|1.3944| | yes|yes|
>|Decane|C10H22|1.277|1.4090| | |yes|
>
>**Notice: neopentane is a gas at room temperature (mp -16, bp 9.5).** And a general issue for low viscosity hydrocarbon is that they are health hazardous ( **Aspiration hazard, category 1**: may be fatal if swallowed and enters airways).
>
>#### High refractive index hydrocarbons:
>
>| Name | Formula |$0\ ^\circ C$ Viscosity (mPa s) | Refractive index | Toxic | Env hazard| Health hazard|
>|------|--------|------------------|------------------|---------|--------|-----------|
>|trans-1,3,5-Hexatriene|C6H8| unknown (comp~0.3)|1.5135| | | yes |
>|cis-1,3,5-Hexatriene|C6H8|unknown (comp~0.3)|1.4577| | | yes |
>|Indan|C9H10|2.230|1.5378| | | yes |
>|1,3,5-Cycloheptatriene (Tropilidene)|C7H8| (~1)|1.53| yes | | yes |
>|1-Methylnaphthalene|C11H10|(~3)|1.617| | yes | yes |
>|1,4-Cyclohexadiene|C6H8|(~0.6)|1.4725| | | |
>
>#### Refractive index near 1.45 hydrocarbons:
>
> |Name| Formula |$0\ ^\circ C$ Viscosity (mPa s) | Refractive index | Toxic | Env hazard| Health hazard|
> |------|--------|------------------|------------------|---------|--------|-----------|
> |2,6,10,15,19,23-Hexamethyltetracosane (Squalane)|C30H62|115.0|1.4530| | | |
> |Bicyclo[4.1.0]heptane (Norcarane)| C7H12| unknown (comp~0.5)|1.4564| - | - | - |
> |Cycloheptene|C7H12|unknown (comp~1)|1.4552| | | |
> |Cycloheptane|C7H14|(~1)|1.4436| | | yes |
> |Decylcyclohexane (mp -1.72)|C16H32| unknown (comp~6)|1.4534| - | - | - |
> |Methylenecyclohexane|C7H12|unknown (comp~0.8)|1.4523| | | yes |
> |1,3-Cyclopentadiene (Pyropentylene)|C5H6|unknown (comp~0.3)|1.4440| yes | | |
> |Limonene|C10H16|0.8462 (25 ℃)|1.4730| | yes| ?|
> |2,5-Norbornadiene (requires stabilization)|C7H8|(~1)|1.4702| | | |
Based on above candidates, we selected limonene as the low viscosity dispersion medium and squalane as the high viscosity dispersion medium. They are not toxic and have relatively high boiling point. Hopefully the viscosity range could satisfy our requires, i.e., 2 orders of magnitude. The refractive index will be adjusted with some low carbon alkane.
It is worth noting that, limonene is a trick liquid, who can react with oxygen and form auto-oxidation product. Although this reaction is relatively slowly (~weeks), one should still notice that limonene stored for a long time could have contents change. Storage with antioxidants or in low temperature could eliminate the oxidation, which is reported in this [[Influence of an anti-oxidant on the formation of allergenic compounds during auto-oxidation of d-limonene|paper]].
In the [[L0047_EU_6N.pdf|SDS]], it is suggested to store under argon atmosphere, avoid light. Consider our short time use, we will just keep it in the fume hood.
## Measurements before Rheoconfocal
### Particles size measurements by confocal microscope
To get an approximation on the particles size, in order to fill the spreadsheet for functionalization, we should first place the sample under confocal microscope and make measurements. An alternative way is using [[Dynamic light scattering]], which also gives the hydrodynamic radius.
The measurements under confocal, without the rheometer part is straightforward, the primary is the operations could be complicated, since parts have merely no communications between each other.
>[!Note]- Step-by-step Operations in the Lab
>1. Open the door, turn on the light for the room and notice sign outside. Write required information in the log book.
>2. Turn switches on for different parts, there is an order, but not very important:
> 1. Laser main switch, rotate the key, and the switches with selected wavelength
> 2. microscope, switch at the back side
> 3. Confocal scanner, the big box close to computer
> 4. Camera
> 5. Computer, the password is written on the sticky note under the monitor
>3. Take the objective lens (100x oil is the one we typically use) and oil, also the extension out. Screw the lens to the extension, remove the cap for microscope protection, then mount (insert from top to bottom, and screw) the entire thing onto the confocal. Drip some oil on the top of objective lens.
>4. Prepare sample, take the holder out from the confocal stage (which is original stored in the accessory area), pick a glass slide and install it in the center of the sample holder. Drip one drop of sample on it, wait till the dispersion medium fully evaporated. Then take the viscosity matched fluid and have a dip on the sample (we typically use [glycerol](https://en.wikipedia.org/wiki/Glycerol), whose refractive index is approximately 1.45).
>5. Place the stage on the confocal (press hard!), turn the confocal operation mode to L100, adjust the height until the slide contact with the lens oil. This typically corresponds to the piezo stage height at around 4600-4800 $\mu m$.
>6. Open the software HC and imagej. In HC, switch on the laser (laser 4, the wavelength is wrong but that's the correct one) with 50% power, turn the main control on. Then on the glass slide a laser spot should be noticeable. Use HC to adjust stage to get the best focus, in imagej press capture to take photos. When taking photos it is suggested to change the laser power to 100% for better contrast. Use the metal piece to block the light.
>7. Save the captured images to the desired folder. Use imagej to add scale bar, make measurements or do postprocessing. To do this, first press `ctrl`+`shift`+`p` to change the property, modify the unit to micrometer by typing *um*, then change the pixel related length to 0.065. This valve is dependent on the objective lens we selected, and this value is only correct for the 100x objective. Use the line tool to draw a line and press `ctrl`+`k` to see the grayscale intensity profile, which reads the particle diameter.
>8. If changing the sample, **low the piezo stage (lens)**, take the sample holder out, then repeat from 4. Remember to add more oil before install the holder back.
>9. Turn off laser (by closing the software) and the computer, take off the sample stage and remove the glass slide. **Always remember to lower the lens before taking off the sample holder!** Then turn off all switches in an inverse order. Remove the objective lens. (Place it back to the plastic cylinders once take it out and unscrew from the extension) Use a tissue or paper for lens cleaning to wrap off the oil, then do this one more time using ethanol. The ethanol is inside the same drawer where the lenses are kept. Finally place everything back. Check if we put the glycerol bottle or any other chemicals back or not.
>10. Remember to write the checkmark after everything finish. Turn off both lights before leaving the room.
Captured images are saved to the directory in the server. Use `Process` > `Batch` > `Macro...` in imagej to convert the units and add scale bar. Save the output file in .jpg.
```
run("Set Scale...", "distance=1 known=0.065 unit=um");
run("Scale Bar...", "width=5 height=8 font=12 color=White background=None location=[Lower Right] bold overlay");
```
The particle size measurements were performed and estimated during doing this characterization, and provided in sample record callout in [[#Silica particles synthesis]] section. The following images are converted jpg files.
>[!Example]- Captured images
>sample 1 ![[SiO2_20231025_1.jpg]]
>
>sample 2 ![[SiO2_20231025_sample2_1.jpg]]
>
>sample 3 ![[SiO2_20231027_sample3_2.jpg]]
>
>sample 4 ![[SiO2_20231027_sample4_1.jpg]]
>
>sample 5 ![[SiO2_20231030_sample5_1.jpg]]
>
>sample 6 ![[SiO2_20231030_sample6_3.jpg]]
>
>sample 7 ![[SiO2_20231031_sample7_2.jpg]]
>
>sample 8 ![[SiO2_20231031_sample8_2.jpg]]
>
>sample 9 ![[SiO2_20231031_sample9_2.jpg]]
>
>sample 10 ![[SiO2_20231031_sample10_2.jpg]]
>
>sample 11 ![[SiO2_20231031_sample11_2.jpg]]
>
>sample 12 ![[SiO2_20231031_sample12_3.jpg]]
>
>sample 13 ![[SiO2_20231031_sample13_1.jpg]]
>
>sample 14 ![[SiO2_20231031_sample14_1.jpg]]
>
>sample 15 ![[SiO2_20231031_sample15_1.jpg]]
>
>sample 16 ![[SiO2_20231031_sample16_3.jpg]]
### Fluid viscosity by rheometer
The rheometer can be used to measure viscosity data in several different modes. By changing the geometry, people may perform measurements for different types of materials from very non-viscous fluid to viscoelastic polymers. The typically applied geometries include:
- Cone and plate
- Parallel plate
- Couette geometry, or concentric cylinder
Generally speaking, the larger the contact area, the higher the precision of the measurement. And for less viscous liquids, the precision is more important, since the valves are very low and small deviation would have huge impact on the measured results. This means that during the measuring, low-torque limit could easily be reached. For more contents on rheometers, see the [[Rheometer]] page in the characterization directory.
In this project, we use CP 50-1 geometry. As illustrated in the figure in the [[Rheometer#Geometry|geometry]] section, we have a cone-and-plate geometry. Here the number 50 means the radius is 50 mm, and 1 indicates the angle of the cone is 1 degree.
For the project, the primary measurements take 41 points under log scale, with shear rate varies from $0.001$ to $10\ \frac{1}{s}$. The stress is recorded and, therefore, viscosity is calculated from Newtonian model. The initial temperature is set to $25\ ^\circ C$, and after a cycle the temperature would be adjusted to $5\ ^\circ C$ lower. The measurement finish after 5 cycles.
> [!failure]-
> For squalane, the results are reasonable good. At $5\ ^\circ C$ the viscosity is approximately over $80\ mPas$. Each cycle takes around 5000s. The entire measurement takes about 1 day (working hour).
> However, if the liquid has low viscosity, e.g., 70% 30% volume ratio for tetradecane and squalane, the reaching of stable values takes an extremely long time. For each cycle more than 9000s is required. This makes it impossible to get one measurement in one day (working hour).
> One option is to decrease the points, especially in low strain rate regime. Or, use different geometry. It is also possible change the direction of temperature variation, let it go from 5 to 25 Celsius, so we can have the rheometer run at midnight.
>>[!success]
>>We modified the total points to 21, change the waiting time to 150 s, and make the temperature change to the other direction.
>[!Note]- Step-by-step Operations in the Lab
>1. Turn on the rheometer and the water bath. Remember to press `ok` in the thermostat to turn it on.
>2. Open the software, in the panel click `initialization`.
>3. Click `measuring system` -> `service function`. Start adjustment of drive inertia.
>4. Insert geometry, wait for recognition (a checkmark will be displayed).
>5. Click `zero gap`.
>6. Adjust geometry inertia and motor in `service function`.
>7. Put the geometry at 60 mm position (sample loading position).
>8. Load sample (650 $\mu L$), trim the edges, press `stop` the rotate the geometry. Make the gap fully filled.
### Dynamic light scattering
[[Dynamic light scattering]] is used to accurately measure the particle size and dispersity. See the characterization page for theoretical information. For the instrument applied in this project, particle size can be directly read from the software. The raw data is also provided so one could calculate the results for each measurement.
>[!Notice]-
>For the instrument in D floor, pay attention to the follow aspects:
>- Inside the DLS chamber, toluene is filled for refractive index matching. Since we are measuring the diffusion profile and compute the autocorrelation function, it is of great importance checking whether the autocorrelation function shows only a random profile. If not, report immediately.
>- For the same reason, the outer surface of the glass vials should be clean, and does not introduce any contamination into the toluene bath. Before placing the vial into the instrument, always rinse the surface with toluene. This is done by picking a syringe, connect a filter, the rinse the outer surface. Then dry the outer surface, rinse with toluene again.
>- Also, to ensure the inner liquids have proper diffusivity get measured, rinse the inside of the vial too.
>- When placing the vial inside the instrument, do not press hard or insert too fast, which could cause the vial hit the bottom and break inside the instrument. If the holder is too loose or too tight, use the tightening tool for adjustment.
>- Remember to turn the water bath on. DLS relies on the measurement of the diffusivity, which is temperature dependent. Not being at 25 Celsius could lead to huge deviations from the actual values.
>[!Failure]-
>DLS was tried for functionalized particles, dispersed in tetradecane at $60 ^\circ C$. However, the autocorrelation function signal is not significant (~0.5) and fitted particle size is about 10000 nm, which is far larger than our synthesized particles.
>
>Two possible reasons: 1. The samples are too dilute; 2. Particles aggregated.
## Rheoconfocal measurement
The setup of the rheoconfocal is described in the [[Ultrafast imaging of soft materials during shear flow|paper]]. The shear cell of the rheoconfocal is a parallel-plates geometry with 11 mm radius and adjustable gap between plates. For 100 $\mu m$ gap, the total volume would be 72.03 $\mu L$. If the gap between parallel-plates is 300 $\mu m$, then for one single sample only one measurement could be done.
Two glass slides, one with diameter of 22 mm and one with 35 mm were prepared in advance, as described in [[#Glass slide octadecane grafting]] section. The 22 mm slide is stuck on the special geometry, with 35 mm as the plate on the stage.
The samples are loaded between two pre-functionalized glass slides. Camera was adjusted to have the same frame rate as the the scanning of liquid lens. This is done by a calibration before capturing images.
The rheometer should run a constant strain rate test under different test time to see startup flow behavior, constant strain sweeps at multiple temperatures, for obtaining storage modulus and loss modulus, $G'$ and $G''$; amplitude sweeps under different temperature to see yielding behavior with temperature dependence (thermal responsive behavior).
The liquid lens is calibrated using prefabricated pillars with known size on the glass slide.
### High background viscosity: particles dispersed in squalane
Sample 1 is dispersed in squalane, and the volume fraction is controlled to 20%. The sample has an appearance of highly viscous gel, with almost no fluidity. Tip sonication was used to ensure well dispersion of silica particles. The total volume of this sample is approximately 500 $\mu L$.
The sample was loaded between the plates, with a gap of 150 $\mu m$. The gap is well filled for loaded sample.
Due to refractive index change (compared to tetradecane), the thermal responsive behaviour is different from the paper. AT low temperature, the particles form a weak gel, while at high temperature, the gel is stronger. This is the same for our previously measured results for sample 2 (test sample, particles dispersed in 30% squalene and 70% tetradecane).
$G'$ and $G''$ is obtained for constant strain oscillation test. The test is set at 5, 15, 25, 35, 45, 55 $^\circ C$. After the temperature is set, 20 mins waiting time is applied to ensure there is enough time for the system to reach the temperature and undergo any structural changes. the camera then start to scan the sample at a 0.67 volume/s rate, capturing ~700 $\mu m$ z-axis depth in the gel. after scanning, an oscillating shear strain of 0.1% amplitude is applied, with 1 Hz constant frequency. 60 points is captured, with 10 s duration. The total time for this oscillating strain test is 600 s.
For captured scanning, number 1-6 are increase temp, 7-12 are decrease temp, 13-15 are startup flow.
### Medium background viscosity: particles dispersed in tetradecane and squalane
# Preliminary Data Analysis
## Viscosity Data
The viscosity of fluids are measured, as shown in figure below. It is worth noting that we did not do rigorous testing for refractive index, therefore the image at this stage does not show the actual viscosity of fluids used in rheoconfocal experiments.
![[viscosity_2.png]]
In above figure, the semi-transparent red color area indicate the low torque limit.
> [!code]- Code for viscosity plot
>
> ```python
> # -*- coding: utf-8 -*-
> """
> Created on Mon Nov 13 13:22:22 2023
>
> """
> import pandas as pd
> import matplotlib.pyplot as plt
> import os
> import numpy as np
> from matplotlib.lines import Line2D
> '''
> # Globle color determination
> COLOR = '#8a8a8a'
> plt.rcParams['text.color'] = COLOR
> plt.rcParams['axes.labelcolor'] = COLOR
> plt.rcParams['xtick.color'] = COLOR
> plt.rcParams['ytick.color'] = COLOR
> '''
>
> # Constants
> F_tau = 30581.462 # Torque in Nm
> T_min = 100e-9 # Minimum torque, possibly to be measured
> CP_angle = 1 * np.pi / 180 # Cone angle in radians
> Geometry_R = 25e-3 # Radius in meters
> density = 1 # Density, assumed to be 1
> Re_crit = 4 # Critical Reynolds number
>
> def eta_lim(shear_rate):
> return F_tau * T_min / shear_rate * 1000 # 1000 to convert mPas to Pas
>
> def eta_lim_3(shear_rate):
> return (CP_angle ** 3 * Geometry_R ** 2 * density * shear_rate) / Re_crit * 1000
>
> # Define a color palette for your labels
> label_color_map = {
> '$25 ^\circ C