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Design Automation for Embedded Systems

, Volume 14, Issue 3, pp 287–307 | Cite as

Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable non-rectangular devices

  • Elena MafteiEmail author
  • Paul Pop
  • Jan Madsen
Article

Abstract

Microfluidic biochips are replacing the conventional biochemical analyzers, and are able to integrate on-chip all the necessary functions for biochemical analysis. The “digital” microfluidic biochips are manipulating liquids not as a continuous flow, but as discrete droplets, and hence they are highly reconfigurable and scalable. A digital biochip is composed of a two-dimensional array of cells, together with reservoirs for storing the samples and reagents. Several adjacent cells are dynamically grouped to form a virtual device, on which operations are performed. So far, researchers have assumed that throughout its execution, an operation is performed on a rectangular virtual device, whose position remains fixed. However, during the execution of an operation, the virtual device can be reconfigured to occupy a different group of cells on the array, forming any shape, not necessarily rectangular. In this paper, we present a Tabu Search metaheuristic for the synthesis of digital microfluidic biochips, which, starting from a biochemical application and a given biochip architecture, determines the allocation, resource binding, scheduling and placement of the operations in the application. In our approach, we consider changing the device to which an operation is bound during its execution, to improve the completion time of the biochemical application. Moreover, we devise an analytical method for determining the completion time of an operation on a device of any given shape. The proposed heuristic has been evaluated using a real-life case study and ten synthetic benchmarks.

Keywords

Microfluidics Biochips Reconfigurability Synthesis 

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References

  1. 1.
    Advanced Liquid Logic (2010) http://www.liquid-logic.com/technology.html
  2. 2.
    Bazargan K, Kastner R, Sarrafzadeh M (2000) Fast template placement for reconfigurable computing systems. IEEE Des Test Comput 17(1):68–83 CrossRefGoogle Scholar
  3. 3.
    Chakrabarty K, Su F (2006) Digital microfluidic biochips: synthesis, testing, and reconfiguration techniques. CRC Press, Boca Raton CrossRefGoogle Scholar
  4. 4.
    Chakrabarty K, Zeng J (2005) Design automation for microfluidics-based biochips. ACM J Emerg Technol Comput Syst 1(3):186–223 CrossRefGoogle Scholar
  5. 5.
    Chakrabarty K, Zeng J (2006) Design automation methods and tools for microfluidic-based biochips. Springer, Berlin CrossRefGoogle Scholar
  6. 6.
    Cho M, Pan DZ (2008) A high-performance droplet router for digital microfluidic biochips. In: Proceedings of international symposium on physical design, pp 200–206 Google Scholar
  7. 7.
    Dick RP, Rhodes DL, Wolf W (1998) TGFF: task graphs for free. In: Proceedings of the sixth international workshop on hardware/software codesign, pp 97–101 Google Scholar
  8. 8.
    Fair RB (2007) Digital microfluidics: is a true lab-on-a-chip possible? Microfluid Nanofluid 3(3):245–281 CrossRefGoogle Scholar
  9. 9.
    Glover F, Laguna M (1997) Tabu search. Kluwer Academic, Dordrecht zbMATHGoogle Scholar
  10. 10.
    Maftei E, Paul P, Madsen J, Stidsen T (2008) Placement-aware architectural synthesis of digital microfluidic biochips using ILP. In: Proceedings of the international conference on very large scale integration of system on chip, pp 425–430 Google Scholar
  11. 11.
    Maftei E, Paul P, Madsen J (2009) Tabu search-based synthesis of dynamically reconfigurable digital microfluidic biochips. In: Proceedings of the compilers, architecture, and synthesis for embedded systems conference, pp 195–203 Google Scholar
  12. 12.
    Micheli GD (1994) Synthesis and optimization of digital circuits. McGraw-Hill Science, New York Google Scholar
  13. 13.
    Paik P, Pamula VK, Fair RB (2003) Rapid droplet mixers for digital microfluidic systems. Lab Chip 3:253–259 CrossRefGoogle Scholar
  14. 14.
    Pollack MG, Shenderov AD, Fair RB (2002) Electrowetting-based actuation of droplets for integrated microfluidics. Lab Chip J 2:96–101 CrossRefGoogle Scholar
  15. 15.
    Ren H, Srinivasan V, Fair RB (2003) Design and testing of an interpolating mixing architecture for electrowetting-based droplet-on-chip chemical dilution. In: Proceedings of the international conference on transducers, solid-state sensors, actuators and microsystems, pp 619–622 Google Scholar
  16. 16.
    Silicon Biosystems (2010) http://www.siliconbiosystems.com
  17. 17.
    Su F, Chakrabarty K (2004) Architectural-level synthesis of digital microfluidics-based biochips. In: Proceedings of international conference on computer aided design, pp 223–228 Google Scholar
  18. 18.
    Su F, Chakrabarty K (2005) Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In: Proceedings of the 42nd annual conference on design automation, pp 825–830 Google Scholar
  19. 19.
    Su F, Chakrabarty K (2006) Module placement for fault-tolerant microfluidics-based biochips. ACM Trans Des Autom Electron Syst 11(3):682–710 CrossRefGoogle Scholar
  20. 20.
    Su F, Hwang W, Chakrabarty K (2006) Droplet routing in the synthesis of digital microfluidic biochips. In: Proceedings of design, automation and test in Europe, vol 1, pp 73–78 Google Scholar
  21. 21.
    Thorsen T, Maerkl S, Quake S (2002) Microfluidic largescale integration. Science 298:580–584 CrossRefGoogle Scholar
  22. 22.
    Xu T, Chakrabarty K (2007) Integrated droplet routing and defect tolerance in the synthesis of digital microfluidic biochips. In: Proceedings of design automation conference, pp 948–953 Google Scholar
  23. 23.
    Yuh P-H, Yang C-L, Chang Y-W (2004) Temporal floorplanning using the T-tree formulation. In: Proceedings of international conference on computer aided design, pp 300–305 Google Scholar
  24. 24.
    Yuh P-H, Yang C-L, Chang Y-W (2006) Placement of digital microfluidic biochips using the T-tree formulation. In: Proceedings of design automation conference, pp 931–934 Google Scholar
  25. 25.
    Yuh P-H, Yang C-L, Chang Y-W (2007) Placement of defect-tolerant digital microfluidic biochips using the T-tree formulation. ACM J Emerg Technolog Comput Syst 3(3). doi: acm.org/10.1145/1295231.1295234
  26. 26.
    Yuh P-H, Yang C-L, Chang Y-W, Chen H-L (2007) Temporal floorplanning using three dimensional transitive closure subGraph. ACM Trans Des Autom Electron Syst 12(4). doi: acm.org/10.1145/1278349.1278350

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Technical University of DenmarkKgs. LyngbyDenmark

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