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Microfluidic Biochips
Application Model

• 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.

• 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.

Microvalve
Architecture Model

• 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
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.

O1
F1
F4
F10
F9
F14
O3
F2
F5
O6
F25-1
F15
F14
Pump
F19
O4
F3
F6
F19
O2
F3
F6
O7
F19
F19
O10
F23
Conceptual View
O5
O8
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
Email Jan_at_imm.dtu.dk