1. Microfluidic Biochips
Application Model
Microfluidic Biochips
Biochemical application is modeled using a sequencing graph G(O, E) that is directed, acyclic and polar.
Set O captures the operations that need to be performed and the associated execution time.
Edge set E captures the dependency constraints.
Biochips are replacing conventional biochemical analyzers and are able to integrate on-chip all the necessary functionalities for biochemical analysis using microfluidics.
In Flow-based biochips, liquid samples of discrete volume flow in the on-chip channel circuitry.
The biochip has two layers (fabricated using soft lithography): flow layer and control layer. The liquid samples are in the flow layer and are manipulated through microvalves created using the air pressurized control layer.
By combining these microvalves, more complex units like mixers, micropumps etc. can be built with hundreds of units being accommodated on one single chip. a
Pressure
source z1
Control layer
Flow layer
Valve va
Fluidic input
Source
Sink
Mix (4)
Mix (5)
Heat (3)
Mix (3)
Heat (2)
Filter (5)
Mix (2) O1 O2 O3 O5 O4 O6 O7 O8 O9
O10
Microvalve
Architecture Model
Detector
Mixer
Filter
In3
In4
In2
In1
Out3
Out2
Out1
The biochip architecture is modeled as a topology graph that captures the
Biochip components (resource constraints)
Biochip inlets/outlets and interconnections between components
Permissible fluid flow (routing) paths and their associated latencies
Biochip: Functional View
Biochip Synthesis z2 z3 z4
In1
In2
In3
In4 z5 z7 z8
z11
Out2
Out3
Out1 v1 v2 v3 v4 v6 v5
Detector
Filter
z10
z12
Mixer z9
z13 z1 z6 v7
Component Library
Currently, researchers manually map the applications onto the valves of the chip which is inefficient, time consuming and would not scale for larger, more complex chips.
Problem: Synthesize the application onto the given chip architecture minimizing the application completion time and satisfying the resource and dependency constraints.
Component
Operational Phases
Execution Time
Mixer
Ip1/ Ip2/ Mix/ Op1/ Op2
0.5s
Filter
Ip/ Filter/ Op1/ Op2
20s
Detector
Ip/ Detect/ Op 5s
Separator
Ip1/ Ip2/ Separate/ Op1/ Op2
140s
Heater
Ip/ Heat/ Op
20ºC/s
Allocation and Placement
We consider that the biochip architecture is given. The allocation and placement is captured by the topology graph based architecture model.
Mixer
The rotary mixer is shown here. It has five operational phases. First two phases (Ip1 and Ip2) are used to move the liquid samples into the mixer. In the next phase (Mix) the samples are mixed, followed by two output phases (Op1 and Op2) removing the mixed sample from the mixer.
It has a typical execution time of 0.5s, but this can vary depending on the application. The exact time is specified by the application designer while specifying the application model.
Binding, Scheduling and Routing
Biochip: Schematic View
List Scheduling-based binding and scheduling heuristic utilized
Since routing latencies are comparable to operation execution times, thus fluid routing (contention aware edge scheduling) is also taken into account (boxes with labels Fx in figure below) along with the operation scheduling (boxes with labels Ox).
As an output, we generate the control sequence for a biochip controller for auto executing the application on the specified biochip.
Mixer1
Mixer2
Mixer3
Heater1
Filter1 16
23.5
42.5 56 1 2 3 4 5 6 7 8 9 10 11 F1 F4 O1
F10 F9 F2 F5 O3
F14 S1 S2 S3
Input
Waste
To other components
F25-1 O6
F15
F14
Pump F3 F6 O4
F19 F3 F6 O2
F19 O7
F19
O10
F23
F19
Conceptual View O5 O8
Waste
Input O9
The proposed model-based approach is expected to reduce human effort, enabling designers to take early design decisions by being able to evaluate their proposed architecture, minimizing the design cycle time and also facilitating programmability and automation.
Schematic View
Contact: Professor Jan Madsen