Routing-Based Synthesis of Digital Microfluidic Biochips

Routing-Based Synthesis of Digital Microfluidic Biochips 1

Routing-Based Synthesis of Digital Microfluidic Biochips

Elena Maftei, Paul Pop, Jan MadsenTechnical University of Denmark

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Microfluidic Biochips

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Technical Univ. of Denmark

2010

Duke University 2002

Continuous-flow biochips Droplet-based biochips


Microfluidic Biochips

Applications Sampling and real time testing of air/water for

biochemical toxins Detection of adverse atmospheric conditions DNA analysis and sequencing Clinical diagnosis Point of care devices

Advantages: High throughput (reduced sample / reagent consumption) Space (miniaturization) Time (parallelism) Automation (minimal human intervention)

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Outline

Motivation Architecture Typical Design Tasks Problem Formulation Proposed Solution

GRASP-Based Synthesis

Experimental Evaluation Conclusions

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Droplet

Photo-diode

Inputport

Output port

S3:Serum

B:NaOH

R1: Glucose oxidase

R2: Lactate oxidase

Biochip Architecture

Biochip created at Duke University

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Electrowetting on Dielectric

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Operation Area (cells) Time (s) Mixing 2x2 6 Mixing 2x3 5 Mixing 2x4 4

Dilution 2x2 6 Dilution 2x3 5 Dilution 2x4 3 Storage 1x1 –

Module-Based Synthesis: Design Tasks

Scheduling

Binding

Placement

Allocation

S1

S2

S3 B

R1

R2

W

Store

Mixer1

Mixer2

Dil

uter

Detector

Mixer1

Mixer2

Diluter

Store

Detector

O7

O9

O3

O11

O10 O4

1 2

3

4

5 6

7

10

8

9

In S1 In R 1

Mix

Detect

In S2 In B

DiluteIn R 2

Mix

Detect

Source

Sink

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Module-Based Synthesis

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Module-Based SynthesisO7

O8

O9

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O7 1x4

O8 1x4

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O9 2x4

O10 1x4

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Mixing

Droplets can move anywhere

Fixed area: module-based synthesis

Unconstrained:routing-basedsynthesis

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Routing-Based Synthesis

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Routing-Based SynthesisO7

O8

O9

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When will the operations complete?

For module-based synthesis we know the completion time from the module library.

But now there are no modules, the droplets can move anywhere. How can we find out the

operation completion times?

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Characterizing operations

If the droplet does not move: very slow mixing by diffusion

If the droplet moves, how long does it take to complete?

Mixing percentages:p0, p90, p180 ?

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Characterizing operations

We know how long an operation takes on modules

Starting from this, can determine the percentages?

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Decomposing modules

Safe, conservative estimatesp90=0.1%, p180 = -0.5%, p0 =0.29% and 0.58%

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Moving a droplet one cell takes 0.01 s.



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Droplet- vs. Module-Based Synthesis

Module-Based SynthesisRouting-Based Synthesis

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Problem Formulation

Input Application graph Architecture (matrix of electrodes) Library of non-reconfigurable devices

Output Implementation which minimizes application execution

time Droplet routes for all reconfigurable operations Allocation and binding of non-reconfigurable modules from a

library Scheduling of operations

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Proposed Solution

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Proposed Solution

Meet

Execute

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Proposed Solution

Meet

Execute

Minimize the time until the droplet(s)arrive at destination

Minimize the completiontime for the operation

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GRASP-Based Heuristic

Greedy Randomized Adaptive Search Procedure

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For each droplet: Determine possible moves Evaluate possible moves Make a list of

best N possible moves Perform a randomly

chosen possible move

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Experimental Evaluation

Routing-Based Synthesis (RBS) vs. to Module-Based Synthesis* (MBS)

Two real-life applications (the table below) Ten synthetic benchmarks (see the paper)

(*) E. Maftei at al.: Tabu Search-Based Synthesis of Dynamically ReconfigurableDigital Microfluidic Biochips. CASES, 2009 (best paper award)

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Contributions and Message

Message Labs-on-a-chip can be implemented with microfluidics CAD tools are essential for the design of biochips

Contributions Eliminated the concept of “virtual modules” and proposed

a routing-based synthesis approach Proposed a GRASP-based algorithm for showing that

routing-based synthesis leads to significant improvements compared to module-based synthesis

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Discussion

Module-based vs. routing-based Module-based needs an extra routing step between the

modules;Routing-based performs unified synthesis and routing

Module-based wastes space: only one module-cell is used;Routing-based exploits better the application parallelism

Module-base can contain the contamination to a fixed area;

We are extending routing-based to consider contamination

Module-based: nice, useful abstraction? Routing based: too much spaghetti?

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Routing-Based Synthesis of Digital Microfluidic Biochips

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