Soft Lithography

Making a valve in PDMS

by Emelie Hilner and Susanne Stefanou
May 13, 2004

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 1. Introduction ____________________________________________
2. Soft Lithography __________________________________________
2.1 Advantages and disadvantages with polydimethylsiloxane (PDMS) ___________________ 3
2.2 The procedure of Soft Lithography _____________________________________________ 4
3. Microfluidics ____________________________________________
3.1 The physical background______________________________________________________ 5
3.2 Methods of moving fluid in microfluidic devices ___________________________________ 6
4. Components ____________________________________________
4.1 Mixers _____________________________________________________________________ 7
4.1.1 Chaotic mixer ____________________________________________________________________ 7
4.2 Valves _____________________________________________________________________ 7
4.2.1 Hydrogels _______________________________________________________________________ 8
4.2.2 Multilayer soft lithography __________________________________________________________ 8
4.3 Laminar flow _______________________________________________________________ 8
5. Applications of micro fluidics and soft lithography_____________________________
5.2 Immunoassay _______________________________________________________________ 9
5.3 Gradient __________________________________________________________________ 10
6. Experimental part __________________________________________
6.1 Experimental setup _________________________________________________________ 11
6.2 Discussion of experiment _____________________________________________________ 12
7. Conclusion _____________________________________________
References ______________________________________________

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1. Introduction

Soft Lithography is a group of non-photolithographic techniques based on self assembly or

replica molding. Soft lithography has many applications and can be used for fabrication of
high quality microstructures and nanostructures. There are many advantages of using soft
lithography. The technique is inexpensive, it can be performed in an normal laboratory
environment without an expensive clean room, it is not diffraction limited, many of the
processes are additive and the waste of materials is minimized [1,2].

The aim of the report is to give a presentation of the area of soft lithography, specifically
replica molding, with PDMS and a brief description of microfluidics. It also presents
applications of the technique and contains an experimental part with a discussion.

2. Soft Lithography

In soft lithography micropatterns are created of self assembled monolayer (SAM) by contact
printing and microstructures are formed in materials by embossing and replica molding.

Contact printing is a method to transfer a pattern to a material due to the contact between the
stamp and the surface of the material. The method allows the creation of many copies of the
pattern and it can be used for patterning large areas and two dimensional structures as well as
three dimensional structures [1,2].

Replica molding is a method to duplicate the pattern of the master. The method can be used
for fabrication of topographically complex, optically functional structures [1,2].

Embossing is another method for transfer a pattern from quartz or metal master to a plastic
sheet. Due to the high temperature and pressure the plastic sheet is being imprinted.
Embossing is a low cost method suitable for devices that do not have to undergo design
changes [1,2].

2.1 Advantages and disadvantages with polydimethylsiloxane (PDMS)

The use of elastomer such as polydimethylsiloxane has many advantages over silicon or glass.
A device with fluidic control needs components that are less stiff than glass or silicon. PDMS
is cheaper than silicon, it is more flexible and it bonds easier to other material than silicon or
glass do [3,4]. PDMS conforms to the surface of the substrate over a large area and can adjust
to surfaces that are non planar. PDMS is a homogenous and optical transparent material down
to about 300 nm. PDMS is waterproof and permeable to gases. The surface properties of
PDMS can easily be changed by exposure of the surface in oxygen plasma. This way PDMS
can bond to other materials that have a wide range of free energies.

Despite all the advantages the use of PDMS provides, there are some problems with PDMS.
Gravity, adhesion and capillary forces stress the features of PDMS leading to collapse which

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defects the created pattern. The adhesion between the stamp and the substrate can also cause
sagging of the structures.

Figure 1a) Collapse of the pattern made in PDMS, b) sagging, c) shrinking [1]

PDMS is a shrinking material which can defect the structure of the pattern. It can also swell
due to chemical reaction with some kind of nonpolar solvents such as toluene. Figure 1
illustrates deformations that can occur in the surface of PDMS.

2.2 The procedure of Soft Lithography

The procedure for soft lithography can be visualized in figure 1. To be able to use soft
lithography one must first create a master. The master is used to cast the PDMS stamp or
mold and it is often fabricated with photolithography. To create a master one has to draw the
pattern with a CAD. The pattern is then printed on a transparent sheet of polymer which
represents the photomask. The pattern of this film is then transferred into films of photoresists
coated on silicon substrate using photolithography. The developed pattern can be used as a
master to create the PDMS stamps. [1,2]

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 Idea Designed pattern Mask
CAD
Image
printing Photolitho-
graphy

Structures Stamp or mold Master

Soft lithography Replica

molding

Figure 2 The procedure of soft lithography

3. Microfluidics

Microfluidics is the manipulation of gases and liquids in channels of cross sectional

dimension on the order of 10-100 _m [6]. Microfluidic system has many applications in
biology and chemistry. The ability to create small devices instead of large has a lot of
benefits. The cost to manufacture components is less, smaller amounts of reagents and
solvents are needed, the time of analysis is decreased, the separation efficiency is increased
and the production of harmful biproducts is decreased. Also the miniaturization allows us to
approach the size scale of fundamental biochemical processes.

3.1 The physical background

The creation of components in microscale arise new designs that take advantage of the forces
that work in microscale [5]. Important parameters in microfluidics are laminar flow, diffusion,
fluidic resistant, surface to area ratio and surface tension. In microchannels the flow is often
laminar which means that the fluid has a non-random flow. By calculating the Reynolds
number (Re) one can determine if the flow is laminar or turbulent. To calculate the Reynolds
number one need to know the density _, the viscosity _ and the velocity _ of the fluid but also
the hydraulic diameter Dh according to the formula:

ρυDh
Re =
µ

If the calculated number is lower than 2300 then the flow is laminar otherwise the flow is
turbulent. Because of the laminar flow the mixing between streams flowing in contact with
€ each other occur by diffusion. It is established that when two or more streams are in contact
for long time the amount of diffusion between the streams increases.

A fluid that flows in a microchannel is affected by the fluidic resistance. If the geometry of
the microchannels is circular the resistance can be calculated by the viscosity _ of the fluid,
the microchannel radius r and its length L according to:

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 8µL
R=
πr 4

If the geometry of the microchannels is rectangular the resistance of the channel is calculated
by:
€
12µL
R=
wh 3

Where w is the channel width and h is the channel height and w>>h.

From the above formula it can be established that a long narrow channel exhibit high fluidic
resistance and a short wide channel exhibit low fluidic resistance.

In microchannels the surface area to volume has large effect because one small channel with a
small volume gives a large surface area to volume. Another factor that is important in
microscale is surface tension forces. In microchannel the length fluids travel based on
capillary force become significant.

3.2 Methods of moving fluid in microfluidic devices

A crucial element in a microfluidic system is the transport of the fluid in the channels. There
are two main modes for driving the fluid in a microchannel system. Pressure driven flow and
electrokinetic.

The transport of fluid in microchannels by pressure driven flow needs a pressure drop [4,7].
This drop is often created by applying a positive pressure at the inlet of the channel and
opening the outlet to atmospheric pressure. Another way to establish drop of pressure is to
open the inlet channel to atmospheric pressure while the outlet is connected to a vacuum.
Pressure driven flow can be used for fluid with an assembly of different substance and for
microchannels made of many materials. Pressure drive flow has the disadvantage that it needs
vacuum or external source. Due to the non-uniform velocity profile of the pressure driven
flow in a channel the method needs also a high resolution separation.

Electrokinetic flow involves electrophoresis and electroosmosis. [4,7] In electrophoresis the

movement of the fluid particles is due to their charge in electric field which is balanced by the
viscous drag.

Electroosmosis occurs when the fluid moves in a channel due to an applied electric field.
Since the channel walls are made of materials with charged surface, ions of the opposite
charge will build up next to the walls to balance the charge. If an external electric voltage is
applied to the channel walls these ions will be attracted to the electrode of opposite charge
and start to move. The ions will drag along with them bulk solution as a consequence of the
viscous drag (figure 3). This flow transport will create a flat velocity profile. The fluidic flow
can easily be controlled by switching the voltage on and off. Electroosmosis is efficient for
channels with a diameter less than 0.1 mm.

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 Figure 3 Electroosmotic flow [15]

4. Components

It is possible to make many different kinds of devices based on soft lithography and
microfluidics. In such devices certain components like mixers, valves and pumps are often
needed. Some examples of such components are described below.

4.1 Mixers

Because of the laminar flow in micro channels liquids mix only by diffusion. If active mixing
is needed a mixer must be integrated in the system.

4.1.1 Chaotic mixer

This type of mixer is made by structuring the floor of the channel by grooves in for example a
“staggered herringbone design” [8] (figure 4).

Figure 4 Staggered herringbone design [8]

The grooves add a transverse component to the fluid flow and make the liquids “fold” into
each other. This folding makes the effective area larger over which diffusion can occur.
The orientation of the pattern is reversed after each half cycle and after approximately 16
cycles the liquids are completely mixed.

4.2 Valves

Valves are used to control the fluid flow in micro channels and can act as switches.

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4.2.1 Hydrogels

Hydrogels are polymers that change their volume when pH in the surrounding liquid changes.
This property makes them useful for making self-regulated valves for micro channels [9]
(figure 5).

Figure 5 Hydrogel valve [9]

A mixture of monomers and a photoinitiator is allowed to flow into the channel and the
channel is then irradiated with UV- light through a photomask. When exposed to light the
mixture polymerizes and the remaining monomer are removed by flushing the channel with
water. The resolution is good and many different patterns can be made using this method.

The response time of hydrogels is quite slow but this is compensated by the great advantage
of not needing any external control.

4.2.2 Multilayer soft lithography

Multilayer soft lithography, with multiple layers of structures in soft materials, can be used to
fabricate for example valves and peristaltic pumps [10]. A valve can be made by crossing
two channels at right angels to each other. When pressure is applied to the upper channel the
membrane between the channels are deflected downwards and flow in the lower channel is
reduced or shut off. A peristaltic pump can be made by placing many such valves in series
(figure 6).

Figure 6 Peristaltic pump [10]

4.3 Laminar flow

A property of microfluidic channels that are often made use of in devices are the laminar
flow. It can be used to create e.g. concentration gradients [4].

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5. Applications of micro fluidics and soft lithography

There are many biophysical applications of devices based on soft lithography and micro
fluidics such as separation of proteins and DNA, immunoassays and enzymatic assays for
detection, sorting and manipulation of cells, generation of stable molecular gradients for
studying e.g. neurons and many more. We will in this section give some examples of
interesting applications and devices made with soft lithography.

5.1 Multiplexer

The first device is the multiplexer, which makes it possible to individually address 1000
different chambers on a chip [11]. A system of microfluidic channels can be made in two
different layers, one layer of control channels and one layer of flow channels. The channels in
the different layers are at right angels to each other and at the crossings the thin membrane
between the channels can be deflected and act as a hydraulic actuated valve (described
above). If a fluid is made to flow in the control channels at certain pressure the valves will be
actuated and the flow channels will be shut of.

The control channels may vary in width while the width of the flow channels is constant,
which makes a binary control system possible (figure 7). This enables for flow channels to be
controlled by only a few control channels. In one of the devices made by Thorsen, Maerkl and
Quake [4] 20 control channels can control 1024 flow channels.

Figure 7 Multiplexer [11]

Two sets of flow channels controlled by two different multiplexers can be crossed and
suddenly we have a large number of individually addressable chambers. An analogy to this
system is the electrical circuits of a computer memory. Systems of this kind can be used e.g.
to detect Escherichia coli in a sample and for protein crystallization [11].

5.2 Immunoassay

Another interesting device is the parallel, serially dilution immunoassay [12]. The sample
containing antibodies from e.g. HIV+ are sequentially mixed with buffer containing BSA
(bovine serum albumin) and become diluted (figure 8).

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 Figure 8 Parallel, serially dilution immunoassay [12]

The mixing is carried out by chaotic mixers (described above). The different dilutions are
then flowed over stripes with immobilized antigen and the antibodies bind to the antigens.
Fluorescent secondary antibodies can then be used to stain the primary antibodies and by
measuring the intensity of the fluorescence the concentration of bond antibodies. The
fluorescence decreases with increased dilution of the sample in a way specific for the type of
antibody and possible content of antibodies in the sample can be detected.

The stripes with antigen can contain different types of antigens so that the sample can be
analysed for many different antibodies at the same time. This of course saves a lot of time.

5.3 Gradient

A third application is a device that utilizes laminar flow to create a gradient of virus
concentration over immobilized cells [13].

Proteins can be produced by infecting cells with virus. The virus carries the DNA sequence
for the protein and inserts it into the cells DNA so that the protein can be expressed and
collected. The optimal concentration of viruses (called MOI – multiplicity of infections) that
should be used for producing a maximal amount of protein is different for different proteins.
Determining this optimal concentration is done by diluting the virus to different
concentrations, infecting cells and then determining the amount of protein produced.

This procedure can be done faster and simpler with microfluidics using laminar flow to create
a virus concentration gradient over cells that has been attached to a surface (figure 9). The
concentration gradient is created as the virus mixes with medium by diffusion at the
boundary. The protein expression within the channel can then be observed using fluorescence
since the PDMS from which the channel is made is optically transparent.

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 Figure 9 Channel for infecting cells [13]

6. Experimental part

Our experiment was to try to build and test a valve made in PDMS. The type of diaphragm
valve that we wanted to build consists of tree parts molded in PDMS [14] as figure 10
illustrates.

Figure 10a) The valve consists of three parts b) Operational principle of the valve [14]

The middle part of the valve is a thin membrane that can be deflected by liquid pressure so
that liquid can only flow in the forward direction. The valve can be used to control fluid flow
in e.g. a microfluidic system on a chip.

6.1 Experimental setup

PDMS prepolymer were mixed with hardener in proportions 9:1. The mixture was then
inserted into a vacuum chamber until it was degassed, because any air bubbles causes
unwanted cavities in the structure. PDMS was then spun onto cleaned silicon wafers at 400
rpm during 30 s. The wafers were baked at 80°C for 60 min. The thin PDMS membranes
were then peeled of. The thickness of the membranes was measured to approximately 300 _m.

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The channel structures were designed with a CAD program and were printed on a plastic
transparency with high resolution printer. The transparency was used as a photomask to create
masters for replica molding.

The masters were made using contact print UV lithography. First the silicon wafers were
baked at 200°C for 5 min to remove water from their surface. Then they were washed with
isopropanol and acetone and a layer of resist, SU-8, was spun onto the wafers. The resist was
then prebaked at 95°C for 6 min. The resist was exposed to UV light through the mask for 5-7
s and was thereafter baked again at 95°C and cooled down slowly to around 60°C. The
structures were then developed in SU-8 developer and the wafers were washed with distilled
water. After this procedure the masters were finished.

Unfortunately the structures were destroyed in the development step as a result of the fact that
the resist detached from the wafers (figure 11).

Figure 11 Destroyed structure on wafer (lighter areas are detached resist)

If the structures would have been useful the next step would be to use the masters as
templates for replica molding with PDMS.

The idea was then to bond these structures together with the membrane to form the valve. The
bonding was supposed to be done by exposing the different PDMS parts to oxygen plasma.

The finished valve was supposed to be tested by making a pressure driven flow of water pass
through it with the help of a syringe pump. It was also supposed to be tested in a way to
establish if the flow were inhibited when driven in the reverse direction through the valve.

6.2 Discussion of experiment

The experiment didn’t turn out as expected because we failed to make masters for molding
the channel structures of the valve. The sources of failure might have been that the mask was
too transparent to UV light at the areas that were thought to be dark. This caused the resist to
be exposed to some extent at these areas as well as the structures. Another cause of failure
could be the exposure time because there were uncertainties about the optimal time. Poor

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adhesion of resist is yet another cause of failure. This may be caused by the small amount of
water that always exists on the surface of a wafer.

To improve the adhesion wafers could have been baked at higher temperature and for longer
time before the washing to remove the water. Another solution could be to add some sort of
adhesion promoter to the resist before it is spun onto the wafer. The proper exposure time of
the resist could be found by testing different times before the actual experiment is done. A
chrome mask instead of the transparency could give a better result, but are more expensive
and difficult to make.

7. Conclusion

Soft Lithography techniques together with microfluidic systems have proved to be important
for many biophysical applications. Soft lithography has been around for quite a long time and
is continuously improved. In the future we believe it will become even more important for
fast, simple analyzing and for research. However there are still technical challenges to be
solved.

In order for soft lithography to compete with other lithographic techniques the resolution must
be improved to be able to make smaller structures but also the properties of the PDMS.

PDMS is an elastomeric material which causes channels to sag or shrink and sets boundaries
to the shape and aspect ratio (height/width) of channels when features become small. Another
problem with PDMS is its surface chemistry. Nonspecific adsorption may occur when
working with biological samples and therefore it is important to develop a method to modify
the surface.

Although Soft Lithography with PDMS must overcome its problems it still has advantages
over more common techniques for the type of applications presented in this paper. The fact
that it is less expensive and does not need clean room facilities, once the master is made, is a
contribute factor for the success of the technique in the future.

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