School of Physical & Mathematical Sciences

Division of Physics & Applied Physics

(PAP339 Physics Lab 3B)

1






PAP339experiment

LabonaChip

Designandbuildyourownmicrofluidicsdevice

Location: Cavitationlab PAP0513

CommonBiolab PAP0514

Supervision: Dr.PedroA.QuintoSu(apedro@ntu.edu.sg)

ManualandIdea: Asst.Prof.Dr.ClausDieterOhl
withhelpfrom
LyeRibinand
AngWenTing

January2009

School of Physical & Mathematical Sciences

Division of Physics & Applied Physics
(PAP339 Physics Lab 3B)

2
1.Abstract
Labonachip (LOC) is the short form for integrated microfluidics devices. This technique
allowsscalingdownfluidtreatmentfromlargetothemicrometerrange.Alreadyworkingexamples
are the gene analysis (Gene Chip) or the polymerase chain reaction, both shrunk down from floor
filling lab spaces to square centimeters or even millimeters. Not only the application side but also
the fluid mechanics on the small scale is highly interesting, e.g. by shrinking the geometry the
volumetosurfaceratioincreasesthusmakingviscous/surfaceforcesdominant.
The LOC experiment will give you the opportunity to peek into fluid mechanics, to gain
experimental skill on creating these small devices, and to study and analyze flow patterns with
photographictechniques.Thestudent maychoose histopic from a setofmicrofluidicdesigns,or if
he likes study literature and chose his own microfluidics design. Below is a collection of five
workableprojects.
Diffusioninlaminarflow
Determinethediffusioncoefficientfromtwoormoreparallelflows.
Atheorypartexists.

MicroPIVofaflowinarectangularchannel
Measureandcomparethevelocityfieldinalaminarchannelflowwiththeanalyticalprofile
(Poiseuilletypeflow).
Available,theorypartmustbeworkedoutorlookedupbyyou.

Deformationofredbloodcells
Studythedeformationofaredbloodcellexposedtonormalandshearstresses.
Theexperimentnotyetavailable.

Microfluidicmixer
Generateaconcentrationgradientbysubsequentdilution
Thetheoryisverysimilartodiffusioninlaminarflow,pleasecontactPedroQuintoSuifyou
wanttoconductthisexperiment.

Flowfocusing
Focusingflowsallowtogeneratemonodispersedmicrobubbles(focusedgasflow)or
droplets(focusedoil/waterflow).
Itwastestedinthelabandshowntowork.Thetheorypartmustbeworkoutbyyou.

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Division of Physics & Applied Physics
(PAP339 Physics Lab 3B)

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2.Introduction
Microfluidics is the study of the behaviour of fluids that are geometrically constrained to a
scale of micrometer and below. At this level, the Reynolds numbers (Re) which compares inertial
forceswithviscousforcesaresmallandtheflowislaminar.Thus,themixingoffluidsbecomesslow
asthereisnoturbulenceandthemixingisgovernedmainlybydiffusion.

Q: What is the definition of the Reynolds number? Estimate the Reynolds number for water in a
channelof100mwidth(doublethethicknessofhair)andflowat1mm/s.

In this experiment, you will be fabricating a microfluidic device in poly(dimethylsiloxane)

(PDMS) by soft lithography. The techniques or recipe to manufacture the device are given in
Chapter3.Detailsontheoryforthevariousprojectscan foundinChapter4.Importantliterature is
statedattheend.
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(PAP339 Physics Lab 3B)

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3.LabonaChipRecipe
Thesubstrateusedinthisexperimentisa75x50x1mmmicroscopeslide.Chemicalsthat
are required are acetone, ethanol, deionised (D.I.) water, MicroChem SU8 2050 Photoresist,
MicroChemSU8DeveloperandSylgard184SiliconeElastomerKit.Equipmentsthatwouldbeused
are sonicator, spin coater, hot plate, stopwatch, UV irradiator, weighing scale, convection oven,
plasmacleaner,syringepumpandopticalmicroscope.Otherthingsthatareneededaregloves,petri
dishes, beakers, compressed air, mask, scissors, box with hole slightly bigger than the size of the
designinthecentre,blacktape,disposablecup,spatula,scotchtape,syringes,18Gand30Gsyringe
needles,metalcutter,rubbertubingandfooddye.
Thegeneraloutlookofthefabricationprocesscanbesummarizedasbelow:

PRECAUTIONS
Alwayshandlethechemicalswithglovesandinthefumehood!
Washyourhandsaftertakingoffgloves!
Disposeanybrokenglassonlyintheglassdisposalbox!
Wastechemicalsshouldbepouredintothechemicalwastebottle!
Whenyouareunsurepleaseask!Allequipmentisresearchequipment,thuspotentially
dangerousandatleastveryexpensive.

Substrate
Cleaning
PhotoResist
SpinCoating
SoftBake Development
PostExposure
Bake
UVExposure
PDMS
Preparation
PDMSCuring
PDMS
Bonding
School of Physical & Mathematical Sciences
Division of Physics & Applied Physics
(PAP339 Physics Lab 3B)

Nextyoufindthestepstobuildyourowndeviceusingasanexamplethediffusioninlaminar
flowexperiment.Pleasereadcarefullyoncefullythroughallstepsbeforeyoustart.Thentry
toanswerthequestions.Iftheanswersarenotinthemanualpleaseusegoogleoraskyour
supervisor.

Q: Withwhattypeofmaterialdoestheliquidcomeintocontact?
Whatdoesbondingmeanandhowisitachieved?
WhatexactlyisSU8?Isitapositiveornegativephotoresist?Whoinventedit?
Howexpensiveis1literofSU8?Whyisyellowlightimportant?
Whatfixestheglassplateontheaxisofthespincoater?
WhendoyoupunchholesforthePDMSsupplylines(before/afterbonding)?

1. DesignthemaskusingtheprogramCleWin3.1accordingtothefollowingspecifications:
a. Widthofchannelsconnectingreservoirs1and2shouldbe50m.
b. Widthofmainchannelconnectingtoreservoir3shouldbe100m.
c. Lengthofmainchannelconnectingtoreservoir3shouldbeatleast10000m.
d. Markingsatleast200mabovethemainchanneltoreflectthedistance.
andsendittoProfClausforapprovaltobefabricated.SU8isanegativephotoresistso
themaskshouldbedarkfield.

Fig.4.1:DarkFieldMask
2. Cutthemasktothesizeofthesubstratewiththedesigninthecentre.
3. Retrievethephotoresistfromtherefrigeratorandplaceitinawaterbathfor3hrbefore
opening (this is to minimize condensation of water vapour that may contaminate the
photoresist). The photoresist must not be exposed to white light or it would be
destroyed!
4. Clean the substrate by immersing it in a petri dish of acetone, suspended in the
sonicatorfor15min.RepeatwithethanolandD.I.water.
Reservoir1
Reservoir2
Reservoir3
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Fig.4.2:ElmaS15HElmasonicSonicator
5. Blowdrythesubstratewiththecompressedairanddehydrateitbyheatingitonthehot
plateat65Cfor5minandallowittocooldownfor15minbeforeproceeding.

Fig.4.3:SchottM6CatHotPlate
6. Programthespincoaterwiththefollowingspincycle:
a. 100rpmfor1sat300rpm
2

b. 200rpmfor1sat300rpm
2

c. 300rpmfor1sat300rpm
2

d. 400rpmfor1sat300rpm
2

e. 500rpmfor11sat300rpm
2

f. 1600rpmfor35sat300rpm
2

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Fig.4.4:SPSSpin150SpinCoater
7. Mountthesubstrateinthecentreofthespincoaterandswitchonthevacuumpump.
8. Pourasmallamountofphotoresist(coveringabout10%ofthesurface)onthecentreof
thesubstrate.Pourslowlyatalowheighttominimizetheintroductionofairbubbles.
Returnthephotoresisttotherefrigeratorafteruse!
9. Startthespinprogram.
10. Switchoffthevacuumpumpandremovethesample.
11. Place the sample on the hot plate with the coating facing up and subject it to the
followingheatcycle:
a. 45Cfor30s
b. 65Cfor3min
c. 80Cfor30s
d. 95Cfor13min
e. 80Cfor30s
f. 65Cfor30s
g. 45Cfor30s
h. Roomtemperaturefor15min
12. Place the mask on the side of the sample that is not coated with the photoresist.
Position the mask such that the design does not coincide with any uneven features in
thecoatingandtapeiton.
13. Place the sample with the coated side facing down in the box on the face that is
opposite the hole. Position the sample such that the design coincides with the hole
viewedfromabovethehole.Placeanothermicroscopeslideontopofthemask(thisis
to make sure the mask is flat on the substrate) and tape it securely to the box. All
photoresist except the part that coincides with the design should be covered with the
tape.
14. ClosetheboxandplaceitintheUVirradiatorwiththeholefacingup.

Fig.4.5:UvitecUVIrradiator
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15. SubjecttheboxtoUVirradiationat99.99mWfor28min.
16. Removethesamplefromtheboxanddetachallcomponentstapedtoit.
17. Place the sample on the hot plate with the coating facing up and subject it to the
followingheatcycle(thestructurebecomesvisibleatthisstage):
a. 45Cfor30s
b. 65Cfor1min
c. 80Cfor30s
d. 95Cfor9min
e. 80Cfor30s
f. 65Cfor30s
g. 45Cfor30s
h. Roomtemperaturefor15min
18. Immersethesamplewiththecoatingfacingupinapetridishofdeveloperfor6min.
19. Cleanthesamplewithfreshdeveloper,followedbyethanolandD.I.water.
20. Blowdrythesamplewiththecompressedair.
Congratulations!Themastermoldhasbeenfabricated!

Fig.4.6:MasterMold
21. Prepare about 33g of PDMS by mixing the base and curing agent in the weight ratio of
10:1 in a cup and stirring it. Stir slowly to minimize the introduction of air bubbles.
PDMShasapotlifeof2hratroomtemperaturesostoreitinarefrigeratorifitisnot
inuse!
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Fig.4.7:SetraEL410SWeighingScale
22. Place the cup of PDMS in the convection oven and switch on the vacuum pump for 30
mintodegasit.
23. Tape around the edges of the master mold tightly with the structure facing up (this
createsaboxtoholdthePDMS).
24. Pour the PDMS onto the master mold. Pour slowly at a low height to minimize the
introductionofairbubbles.Saveabout10%ofthePDMSforlateruse!
25. Place the sample in the convection oven and turn the heat control knob to 2.5 (the
temperature would fluctuate about 65C with this setting). Retrieve the sample after
checkingthatthePDMShashardened(about1hrlater).

Fig.4.8:FisherScientificIsotempVacuumOvenModel280AwithWelchDryFastUltraModel2032VacuumPump
26. Cleananewsubstratewiththeprocessesdescribedinsteps4and5.
27. Cuta18Gneedletomaketheendblunt.
28. Cut3piecesoftubingabout30cmlong.
29. Carefully peel the cured PDMS off the master mold (the negative impression of the
structurehasbeenembeddedinthePDMS).
30. Cut the PDMS around the structure (this is to make the PDMS smaller to improve
handling).
31. Puncture holes in the centre of the 3 reservoirs with the blunt needle. Puncture
carefullybytwistingtheneedleinslowly!
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32. Insert the 3 tubing into the holes. Make sure that the tubing does not extend beyond
thehole!
33. PlacethePDMSwiththestructurefacingupandthesubstrateintheplasmacleaner.

Fig.4.9:HarrickPlasmaPlasmaCleaner
34. Switchonthevacuumpumpandtheplasmaforabout1min.Theplasmacontrolknob
shouldbesettooff!
35. Turn the vent valve about 1/8 of a turn counterclockwise and turn the plasma control
knob to medium for about 10 s (there should be a purplish discharge glow in the
chamber).
36. Turn the plasma control know to off, switch off the vacuum pump and turn the vent
valvecompletelycounterclockwise.
37. OpentheplasmacleanerafterventingandquicklyplacethePDMSonthecentreofthe
substrateandpressmanuallytoremoveairbubbles.ThePDMS would notbondto the
glassiftheyarenotplacedincontactwithin1minofplasmacleaning!
38. FillasyringewithamixtureoffooddyeandD.I.waterwiththeratioof1:5andattacha
30Gneedletoit.
39. Testtherobustnessofthesystembyinjectingthemixtureintoeachtubing.
a. Ifthemixturedoesnotflowthroughthechannelsandflowbetweenthetubing
andthePDMSontothesurfaceinstead,thetubingdidnotfilltheholesproperly.
Apply some PDMS around the tubing and repeat step 25 and check the
robustnessofthesystemagain.
b. If the mixture leaks along the channel, the PDMS was not bonded properly to
theglass.Cleanthesubstrateagainwiththeprocessesdescribedinsteps4and
5.DothesameforthePDMSbutwithoutacetoneasitwoulddestroythePDMS.
Startoverfromstep33andchecktherobustnessofthesystemagain.
Congratulations!Themicrofluidicdevicehasbeenfabricated!
School of Physical & Mathematical Sciences
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11

Fig.4.10:MicrofluidicDevice
40. FillasyringewithD.I.waterandattacha30Gneedletoit.

Thenextstepsareespeciallyforthelaminarflowexperimentsandmayvaryfortheothers

41. Programthe syringepumptopump at 60l/min (other settingssuch asthe brand,the

volumes of the syringes and the volume of fluid to be pumped must be set
appropriately).

Fig.4.11:kdScientificSyringePump
42. Mount the syringes on the syringe pump, insert the syringe of mixture into the tubing
connected to reservoir 1 and insert the syringe of water into the tubing connected to
reservoir2.

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Fig.4.12:ExperimentalSetup
43. Placethesampleundertheopticalmicroscope,runthesyringepumpandtakepictures
alongthemainchannelwherethemixingtakesplace.
44. Analyzethecolorgradientinthedirectiontransverseofthefluidflowalongthechannel
andcomparewiththediffusionequations.
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(PAP339 Physics Lab 3B)

13
4.Theorypart

4.1Theoryfordiffusioninalaminarflow
The diffusion equation is a partial differential equation which describes concentration
fluctuations in a fluid undergoing diffusion. It is derived from the continuity equation which states
that a change in density in any part of a system is due to inflow and outflow of material and
effectively, no material is created or destroyed. If the diffusion coefficient is independent of the
concentration,thediffusionequationislinearandcanbeexpressedas,
) , (
) , (
2
t c D
t
t c
r
r
=

where c istheconcentrationat ) , ( t r and Disthediffusioncoefficient.

Fig.2.1:SchematicDrawingofYjunction
To solve the diffusion equation, we consider the y directional diffusion equation in the
centerofthechannel(x0)
2
2
y
c
D
t
c

(1)
Rearranging,
2
2
y
c
D U
z
c
m

(2)
where
m
U isthemaximumofthefluidvelocity.
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Thispartialdifferentialequationcanbesolvedusingsimilaritysolutions.Therefore,wedefinea
dimensionlessvariable
) , , ( D t y f =
zD
U
y
tD
y
m
= =
ExpressingtheoperatorsfromEq.(2)ingives:
z d
dc
z
c

z D z
U y
z
m
2 2
3

= =

and
2
2
2
2
2

y d
c d
y
c

zD
U
y
m
=

.
InsertingtheseexpressionsintoEq.(2)leadstothefollowingnondimensionalequation.
0
2
2
2
= +

d
dc
d
c d
(3)
Note,thatthepartialderivativesaregone.
Aneducatedguessforthesolutiontothisordinarydifferentialequationfor c ()isthe
followingfunction:
( ) [ ] k erf c + = 1
2
1
(4)
Theerrorfunctionisdefinedas
( )
2 2
z
e z erf
dz
d

=

where k isaconstant.
InsertingEq.(4)into(3)definestheconstantk:
4
1
2
= k
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Andthesolutiontothediffusionequationis:

+ =
D
U y
erf c
m
2 2
1
2
1

To analyze the diffusion profile along the channel, we introduce a dimensionless

concentration,
min max
min ~
c c
c c
c

=
where
min
c and
max
c aretheminimumandmaximumconcentrationsrespectively.Evidently,

>
<
= = =
0 y , 1
0 y , 0
) 0 (
max
min
c
c
t c
forthechannelat ) 0 ( < y carryingwaterandthechannelat ) 0 ( > y carryingthedye.
If we define the thickness ofthe diffusion zone y as the length between ) 2 . 0
~
( = c y and
) 8 . 0
~
( = c y ,wecansolveitbyapproximatingtheslopeofthegraphof c
~
against y tobelinearat
) 0 ( = y ,
0 y ,
~ ~
=

dy
c d
y
c

zD
U y
m
m
e
zD
U
dy
c d
4
2
2
1
~

=

c
U
zD
y
m
~
2

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(PAP339 Physics Lab 3B)

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Roughexampleoftheevaluationofthediffusionconstant

( )
m
U
zD
y

44 . 1
2

6
10 0204 . 0 44 . 1


m
U
D

s m U
m
/ 2 . 0
s m D / 10 02 . 9
2 10

Pleaseincludeinyourcalculationtheerroranalysisandstatetheerrorofeachmeasuredquantity.
Graph of Diffusion Thickness ^ 2 against Axial Distance
y =0.0204x +25.035
0
50
100
150
200
250
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000
Axi al Di stance (mi crons)
D
i
f
f
u
s
i
o
n

T
h
i
c
k
n
e
s
s

^

2
(
m
i
c
r
o
n
s
^
2
)
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(PAP339 Physics Lab 3B)

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5.References
[1] R. K. Shah & A. L. London. (1978). Laminar Flow Forced Convection In Ducts. New York:
AcademicPress.
[2] J. Cooper Macdonald et al. Fabrication of Microfluidic Systems in
Poly(dimethylsiloxane),Electrophoresis21,2000,pp.2740.
[3] Rustem F. Ismagilov et al. Experimental and Theoretical Scaling Laws for Transverse
Diffusive Broadening in Twophase Laminar Flows in Microchannels, Applied Physics
Lettersvol.76no.17,2000,pp.23762378.
[4] Yi Futing et al. A New Method for Fabrication of SU8 Structures with a High Aspect
Ratio Using a MaskBack Exposure Technique, Chinese Journal of Semiconductors vol.
25no.1,2004,pp.2629.