Hardware Reference
In-Depth Information
5.4
Bioassay-Specific Reservoir Allocation for PCR Biochip
In a typical mixing procedure after DNA amplification, several reagents/samples are
required to be mixed in a certain ratio. The number of mix-split operations depends
on the mixing algorithm and the target ratio. The mixing process is generally
represented by a mixing (or a sequencing) graph G. Figures
3.10
and
5.4
shows
two examples of the sequencing graphs for solution preparation procedures [
27
,
28
].
The sequencing graph of a bioassay is a directed graph. Each node of zero in-degree
in the graph represents a dispensing operation, and each internal node represents
a fluidic operation (e.g., mixing/dilution) [
27
]. The droplet transportation cost in
the PCR should be optimized based on the given sequencing graph of the bioassay,
which requires appropriate allocation of reservoirs to the reagents and scheduling of
mixing/dilution operations as specified in the sequencing graph.
In this section, we will discuss the layout-design algorithm for PCR biochip.
The “electrode ring” structure for low-cost biochip is introduced in Sect.
5.4.1
.
The droplet routing problem on low-cost PCR biochip is introduced in Sect.
5.4.2
.
Section
5.4.3
presents the algorithm of bioassay-specific resource allocation for
PCR biochip.
5.4.1
Electrode Ring on Low-Cost Biochips
The placement algorithm described in Sect.
5.3.3
assigns a location for each of the
devices on a 2D grid. As mentioned in Sect.
5.3.3
, a heater is usually placed at the
center of the layout; reservoirs are placed on the boundary of the biochips. In order
to complete the layout design of the PCR biochip, the positions of electrodes on the
biochips have to be determined, and droplet transportation paths among the devices
need to be created.
In order to reduce the number of electrodes in a typical low-cost biochip, the
output ports of all reservoirs on the layout are connected in a “cycle” consisting
Level 4
C
1
C
2
C
3
Level 3
M
9
M
10
M
11
M
12
R
4
M
8
Level 2
R
2
M
3
M
4
R
3
M
5
R
4
M
6
M
7
Level 1
M
1
R
1
R
2
R
4
R
3
R
4
R
2
R
1
M
2
R
4
Level 0
R
1
R
4
R
1
R
3
Fig. 5.4
An example of the sequencing graph [
28
]
