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Synthesis of Reliable Digital Microfluidic Biochips using Monte Carlo Simulation

Synthesis of Reliable Digital Microfluidic Biochips using Monte Carlo Simulation. Elena Maftei, Paul Pop , Florin Popen ţ iu Vl ă dicescu Technical University of Denmark. Background & Motivation. Automation. Automation. Automation. Integration. Integration. Integration. Miniaturization.

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Synthesis of Reliable Digital Microfluidic Biochips using Monte Carlo Simulation

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  1. Synthesis of Reliable Digital Microfluidic Biochips using Monte Carlo Simulation Elena Maftei, Paul Pop, Florin Popenţiu Vlădicescu Technical University of Denmark

  2. Background & Motivation Automation Automation Automation Integration Integration Integration Miniaturization Miniaturization Miniaturization Test tubes Robotics Microfluidics Slide soruce: Krish Chakrabarty, Duke University

  3. Microfluidics Droplet-based biochips Continuous-flow biochips (Duke University) 2002 (University of Michigan) 1998 Slide soruce: Krish Chakrabarty, Duke University

  4. Biochip Architecture

  5. Electrowetting on Dielectric

  6. Synthesis: Main Design Tasks Allocation Binding Placement Scheduling

  7. Fault Model • Types of faults: • Permanent • Parametric • Causes: • Particle contamination • Excessive voltage • Coating failure • Assumption: • Same probability for all cells

  8. Fault Tolerance

  9. Design Automation • ILP-based syntehsis • Constraints: • Scheduling and precedence • Resource • Placement • Optimization objective: • Minimize the completion time of the application • Evaluation of a design alternative using MCS • Generate a set of faulty cells • Try to reconfigure the biochip such that the execution time remains the same as for the case with no faults • Reconfiguration done using ILP-based synthesis

  10. Experimental Evaluation • Real-life application • Mixing stage of polymerase chain reaction (PCR)‏ • Assay completion time: 13 s • Experimental setup • ILP: GAMS 21.5, CPLEX 9.130 • SunFire v440 4, UltraSPARC IIIi CPUs, 1,062 MHz and 8 GB RAM • MCS: 5,000 runs with a cell failure probability of 0.999

  11. Contributions and Message • Contributions • ILP-based synthesis of digital microfluidic biochips • Considered permanent cell faults • Message • Labs-on-a-chip can be implemented with digital microfluidics • CAD tools are essential for the design of such biochips

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