Chapter 1: Protolyne™: A Micromachining Process for

Microfluidic Applications

1.1 Introduction
Protolyne is a glass chip prototyping technology provided by Micralyne wherein a
client submits a drawing and receives 5 chips produced with the design. This technology
enables the user to develop a network of bulk-micromachined channels and features with
8 reservoirs in glass substrate for microfluidic applications. The main features of this
technology are:

• the chip consists of two pieces of Schott Borofloat™ glass which are fusion-bonded
together; the dimensions of each glass piece is 16 X 95 X 1.1 mm;
• the top plate has eight 2-mm diameter reservoirs (holes for fluidic connections); their
layout is fixed.
• the bottom plate has the client’s pattern (fixed 20 µm etch depth) and the etch pads
bulk-etched into it. These etch pads consist of 1.5 mm diameter circular pad to be
connected to the etched channels and are also used to align the top and bottom plates

Figure 1-1 shows top and end-on views of Protolyne highlighting the two pieces of glass
and locations of the reservoirs.

4.25 61.5 mm 9.25 Reservoirs

Etched
10 10 (Φ = 2 mm) channels
4.25
7.5 16 mm 2.2
4.25 95 mm
Dimensions in mm. Top View End-on View

Figure 1-1: Top and End-on views of Protolyne.

1.2 Designing with Protolyne

1.2.1 Technology File Description

The technology file to design devices with Protolyne technology has been
developed in L-Edit or MEMSPRO version 3.0 and above. This file is in TDB format
and can be downloaded from CMC's web site. Some layers used in the technology file
are briefly described below:

• Glass Substrate: This represents the bottom glass plate and is represented in grey
outline colour. GDSII number for this layer is 58
• Glass Etch: This layer is used to represent bulk-etched microfeatures (channels,
chambers, etc.) in the glass substrate. It is in solid red colour with GDSII number 46
• Reservoir Etch: This layer is used to etch 1.5-mm diameter circular etch pad on the
glass substrate to align the upper and lower glass plates. Its is in solid blue colour and
has GDSII number 49
• Chip Feature Outline: This layer shows a number of chip features in the top and
bottom plates that serve to guide your design layout. Specifically, the Chip
Perimeter (outer edges of the top and bottom glass pieces), Layout Boundary (box
within which all design features must fit), and Reservoir (outline of the 2-mm
diameter holes in the top plate) features are represented in this layer. The layer is
purple outline colour, GDSII number 58.
• 3-D Fill: This layer is not used in 2D layout and is only used when extracting the
third dimension model. It will be explained later in the manual

If we look at the mask for the bottom plate, it begins with a layout of 1.5-mm
diameter etched pads (blue) with markers for the 2-mm diameter holes on the top glass
layer. These holes are etched in each design:

3 4 Å Port Numbering Æ 5 6

2 1 8 7
Figure 1-2: Layout of Bottom plate.

1.2.2 Important Design Rules and considerations

The use of design rules ensures the highest possibility of successful fabrication.
The design rules for Protolyne evolved through process development, the experience of
Micralyne staff and from the previous Protolyne runs. The design rules are dictated by
the process constraints and individual process steps.
The design rules for Protolyne process are mandatory and violation of these rules
may result in non-functional device. Table 1-1 summarises the design rules for the
Protolyne process.

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 Design Consideration Limit
Etch depth: 20 ±2 µm
Minimum feature size: 6 µm
Minimum feature angle: 90°
Minimum mask line width: 10 µm
Minimum circle diameter: 40 µm
Minimum edge-to-edge channel Greater of 100 µm or
separation (post-etch): 75% of channel width
Minimum dist. from edge of chip: 2 mm
Maximum total channel length: 1m
Maximum total etched area: Quarter of chip
Table 1-1: Summary of design rules for Protolyne process.

1.2.3 Important design considerations

Let’s go through an example to illustrate how one might layout a simple design
and not break the design rules above; upon opening the technology file, we start with the
layout shown in Figure 1-3a

Drawing tools

Layers to select

(a)

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 Pattern to etch in glass – Draw using this red layer (GDS II # 46)

Reservoir etch pad in blue layer (GDS II # 49)

Outline of chip perimeter, layout boundary and reservoir outlines

(top plate) in purple “Chip Feature Outline” layer (GDS II # 58)

(b)

Figure 1-3: Protolyne Technology File.

For clarity, we will remove the text, position the chip horizontally, and zoom in
on the chip – note the different layers that are highlighted in Figure 1-3b. The user
should draw his/her desired pattern using the red layer entitled “Glass Etch” (GDS II #
46). According to the design rule, only the objects created in this layer will be subjected
to a 20 µm-deep glass etch step during processing at Micralyne - all other areas will be
left intact.
We’ll draw a simple pattern with a few fluidic features in L-Edit/MEMS Pro.
Purposely included will be some features that do not conform to Protolyne design rules,
for illustrative purposes. (Please note that, in the design that follows, Micralyne does not
imply or suggest any functionality; the design is being used solely for the purpose of
illustrating how a given design can, or cannot, be drawn into a mask and fabricated using
Protolyne).
In the example shown in Figure 1-4, we want to bring two reagents together in a
Y-junction, have them mix along a meandering channel, react in a larger chamber, and
finally be injected into and separated in a longer separation channel.

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 Y-Intersection

Figure 1-4: Example layout for a microfluidic device.

Let’s look at some of the features of the layout of this design. Figure 1-5(a) shows the
90° Y-intersection (grid dots every 250 µm). All the angles are ≥ 90°, and thus
acceptable.

135° 135°

90° 90° angle & 10 µm line

width- OK

(a) (b)
Figure 1-5: (a) The 90° Y-Channel. (b) Enlarged view of the Y-Channel.

If we zoom in further (grid dots every µm) as shown in Figure 1-5 (b), we can see that the
line width is at the minimum 10 µm, and is thus acceptable. We will discuss acute
angles more with a second example later.
Another consideration to bear in mind is the pre- and post-etch appearance of the
features being designed (Figure 1-6). The Y-intersection shown here is drawn as opaque
in a CAD program, each Y branch being 10 µm wide; the Y will translate into a
transparent pattern in the mask during photolithographic patterning. Wet chemical
isotropic etching of the glass with hydrofluoric acid will begin with an opening exactly
the shape of the Y above, and will remove glass directly below and also beyond the edges
of the pattern. The portion removed during a 20-µm etch from beyond the edges of, for
example, a 1-mm segment of a 10 µm mask line channel would be two quarter-cylinders
of glass, 1 mm in length and 20 µm in radius, one on either side of the channel.

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 Mask layout

Close-up of
channel in
10 µ m = W mask line mask file

W mask line
Masking Layers
Window in
Borofloat glass masking layers
substrate to be etched before etching

Etch 20 µ m,
bond top plate

W channel = 50 µ m
D-shaped
d channel cross-
d = 20 µ m section in
finished device

Figure 1-6: Pre and post appearance of the feature being designed.

Let’s pan out and consider a larger area of the chip; see layout in Figure 1-7.
Several features can be seen: the Y-intersection, three meandering sections, a wide
reaction channel, and a cross intersection. Outside of the layout are two boundaries in
purple (GDS #58). The outer boundary is the “chip footprint”, and shows the actual outer
dimensions of the glass device. The inner boundary is the limit to which any design
features may extend; designs outside of this boundary infringe upon the 2-mm minimum
distance from the chip edge that must be maintained. Note that the channels from the
lower two (blue) reservoirs extend close to, but not beyond the layout boundary, and are
thus acceptable.

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 Figure 1-7: Details of different parts of the design (Y-channel, meander, reaction
channel).

We’ll next zoom in on the left edge of the large rectangular reaction chamber,
circled in the figure above, occurring after the mixing meanders (grid dots at 25 µm), see
Figure 1-8

Figure 1-8: Enlarged view of meander and reaction chamber connection area.
The square chamber is 250 µm wide. An alternate design is shown in Figure 1-9 with an
“inside” acute (45°) angle, which is not allowed, and an “outside” acute (45°) angle,
which is permitted. Inside and outside refer to whether the acute angle is inside the (red)
feature drawn, or outside.

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 Inside 45° angle - Unacceptable

Two outside 45° angles = inside 315° angles formed

with thinner channel - OK

Figure 1-9: When inside acute angles are less than 90.

If an acute angle were desired, the design could be modified slightly by ‘blunting’
the corner, as shown in Figure 1-10b. Note that the new right-angle side added to the
polygon must meet the minimum feature size of 6 µm; in this case, it is 10 µm (grid dots
at 5 µm):

(a) (b)
Figure 1-10: (a) Unacceptable "inside” acute angle. (b) Acceptable 10µm "blunted”
corner.
Another variation on this chamber might have a rounded entrance and exit (Figure 1-11).
If the diameter of any such curve is ≤ 40 µm, the object will be unacceptable:

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 (a) (b)
Figure 1-11: (a) Unacceptable 30µm circle feature. (b) Acceptable 50 µm circle feature.

Next, let’s examine the channel meanders. Recall that after etching, the
separation of the closest edges must be the greater of 100 µm or 75% of the etched
channel width. In other words, the closest edges must be 100 µm apart for an etched
channel width of up to 133 µm (line width of up to 93 µm on the mask); for an etched
channel width greater than 133 µm, 75% that width must separate the channels.
As a first example (Figure 1-12a), let’s consider the smallest case, a meander with
10 µm line-width channels (grid dots at 50 µm). After the 20 µm etch, the channels will
be 50 µm wide, and must have 100 µm between them, so their centre-to-centre separation
must be 150 µm.

(a) (b)
Figure 1-12: (a) Smaller meander. (b) Larger meander.

A second example (Figure 1-12b) from our sample chip is a larger channel
meander with 160 µm line width, which will yield 200 µm wide channels that must be
separated by 150 µm, so their centre-to-centre spacing must be 350 µm.
Note that the total length of all the channels must not exceed 1 m. Also, the total
etched surface area must not exceed ¼ of the surface area of the 16 mm X 95 mm =
1520 mm2 surface area.

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1.2.4 Other general design considerations

Finally, a few other general comments will be helpful in ensuring that your design
is acceptable and manufactured without error:

1. If using Micralyne’s template L-Edit file, be sure not to modify the cell
entitled: “chip and port template”. This cell is intended to act as guide for
design, however, modification of the cell is likely to result in designs being
misplaced/misaligned w.r.t. the fixed positions of the reservoirs. Also, when
designing in the “Customer design cell”, be sure not to modify the position of
the instance of “chip and port template”, nor ungroup it. If you wish to have
the individual components, instance the “chip and port template” cell a second
time (0 translation in x and y) and ungroup it.

2. Use the proper design tool for the shape you are drawing. For example, when
drawing a long, thin 10 µm line with many vertices that will become a
microfluidic channel once etched, do not use a freeform polygon tool, use a
wire (L-Edit) or polyline (AutoCAD) tool. This will greatly lessen the chance
of having erroneous width irregularities (e.g. zero width). It’s also much
faster to draw. When using such a tool, use butt ends and layout joins, or
round ends and joins if the radius of curvature is 20 µm or greater. Rounded
features are more difficult to manufacture, and an excessive number of such
features may cause the design to be unsuitable for the Protolyne programme.

3. Features should have neither sub-µm dimensions nor be spaced with fractional
µm spacings. For example:
• two squares that are 77 µm on a side and spaced 81 µm apart are
acceptable, but;
• two squares that are 77.5 µm on a side and spaced 81 µm apart are
not acceptable, and;
• two squares that are 77 µm on a side and spaced 81.3 µm apart are also
not acceptable.

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