A low-cost fluid-level synthesis for droplet-based microfluidic biochips integrating design convergence, contamination avoidance, and washing

Abstract

Droplet-based microfluidic biochips (or DMFBs) are rapidly becoming a revolutionizing lab-on-a-chip technology. Numerous application specific protocols bridging the cross-disciplinary fields necessitate DMFBs as their prime need. The main goal at the fluid level is to minimize bioassay schedule length. Also, for a safe assay outcome, contamination among droplet routes must be avoided. Size restriction of a chip and reconfigurable nature of the operational modules in DMFB introduce contaminated cells which necessarily require washing as an urgent need. As the sub-tasks of fluid level possess their own constraints for a successful DMFB design, rip-up and reiteration of sub-tasks may become unavoidable if all of those constraints are not satisfied mutually. To achieve a shorter time for chip realization a crucial need in fluid-level design is to avoid rip-up and re-iteration; hence, design convergence is to be incorporated that collectively considers the fluid-level sub-tasks, instead of solving them individually. Thus, this paper focuses on the fluid level of DMFBs while considering design convergence, contamination avoidance, and washing issues. Obtained results are compared with several existing benchmarks.

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References

  1. 1.

    Agarwal V, Singla A, Samiuddin M, Roy S, Ho TY, Sengupta I, Bhattacharya BB (2017) Reservoir and mixer constrained scheduling for sample preparation on digital microfluidic biochips. In: 2017 22nd Asia and South Pacific design automation conference (ASP-DAC). IEEE, pp 702–707

  2. 2.

    Alistar M, Pop P (2014) Online synthesis for operation execution time variability on digital microfluidic biochips. In: 2014 14th international symposium integrated circuits (ISIC). IEEE, pp 356–359

  3. 3.

    Alistar M, Pop P, Madsen J (2013) Operation placement for application-specific digital microfluidic biochips. In: 2013 Symposium on design, test, integration and packaging of MEMS/MOEMS (DTIP). IEEE, pp 1–6

  4. 4.

    Chakrabarty K (2010) Design automation and test solutions for digital microfluidic biochips. IEEE Trans Circuits Syst I Regul Pap 57(1):4–17

    MathSciNet  Article  Google Scholar 

  5. 5.

    Chakrabarty K, Xu T (2010) Digital microfluidic biochips design automation and optimization. CRC Press, Boca Raton

    Book  Google Scholar 

  6. 6.

    Chakraborty S, Chakraborty S, Das C, Dasgupta P (2016) Efficient two phase heuristic routing technique for digital microfluidic biochip. IET Comput Digit Techn 10(5):233–242

    Article  Google Scholar 

  7. 7.

    Garey MR, Johnson DS (2002) Computers and intractability, vol 29. WH Freeman, New York

    Google Scholar 

  8. 8.

    Grissom DT, Brisk P (2014) Fast online synthesis of digital microfluidic biochips. IEEE Trans Comput Aided Des Integr Circuits Syst 33(3):356–369

    Article  Google Scholar 

  9. 9.

    Hassin R (1992) Approximation schemes for the restricted shortest path problem. Math Oper Res 17(1):36–42

    MathSciNet  Article  Google Scholar 

  10. 10.

    Ho TY (2012) Design automation for digital microfluidic biochips: from fluidic-level toward chip-level. In: 2012 IEEE 11th international conference Solid-state and integrated circuit technology (ICSICT). IEEE, pp 1–4

  11. 11.

    Ho TY, Chakrabarty K, Pop P (2011) Digital microfluidic biochips: recent research and emerging challenges. In: 2011 7th IEEE/ACM/IFIP international conference hardware/software codesign and system synthesis. ACM, pp 335–344

  12. 12.

    Ho TY, Zeng J, Chakrabarty K (2010) Digital microfluidic biochips: a vision for functional diversity and more than moore. In: 2010 IEEE international conference on computer-aided design. IEEE, pp 578–585

  13. 13.

    Keszocze O, Wille R, Ho TY, Drechsler R (2014) Exact one-pass synthesis of digital microfluidic biochips. In: 51st international conference design automation conference. ACM, pp 1–6

  14. 14.

    Liao C, Hu S (2014) Physical-level synthesis for digital lab-on-a-chip considering variation, contamination, and defect. IEEE Trans Nanobiosci 13(1):3–11

    Article  Google Scholar 

  15. 15.

    Luo Y, Chakrabarty K, Ho TY (2015) Hardware/software co-design and optimization for cyberphysical integration in digital microfluidic biochips. Springer, Berlin

    Book  Google Scholar 

  16. 16.

    Maftei E, Pop P, Madsen J (2010) Tabu search-based synthesis of digital microfluidic biochips with dynamically reconfigurable non-rectangular devices. Des Autom Embed Syst 14(3):287–307

    Article  Google Scholar 

  17. 17.

    Maftei E, Pop P, Madsen J (2011) Synthesis of digital microfluidic biochips with reconfigurable operation execution. Ph.D. thesis, Technical University of Denmark, Computer Science and Engineering

  18. 18.

    Maftei E, Pop P, Madsen J (2012) Routing-based synthesis of digital microfluidic biochips. Des Autom Embed Syst 16(1):19–44

    Article  Google Scholar 

  19. 19.

    Maftei E, Pop P, Madsen J (2013) Module-based synthesis of digital microfluidic biochips with droplet-aware operation execution. ACM J Emerg Technol Comput Syst 9(1):2

    Article  Google Scholar 

  20. 20.

    O’neal K, Grissom D, Brisk P (2017) Resource-constrained scheduling for digital microfluidic biochips. ACM J Emerg Technol Comput Syst 14(1):7

    Google Scholar 

  21. 21.

    Pan I, Samanta T (2015) Advanced strategy for droplet routing in digital microfluidic biochips using aco. In: Handbook of research on swarm intelligence in engineering, pp 252–284. IGI Global

  22. 22.

    Pollack M, Shenderov A, Fair R (2002) Electrowetting-based actuation of droplets for integrated microfluidics. Lab Chip 2(2):96–101

    Article  Google Scholar 

  23. 23.

    Roy P, Howladar P, Bhattacharjee R, Rahaman H, Dasgupta P (2013) A new cross contamination aware routing method with intelligent path exploration in digital microfluidic biochips. In: 2013 8th International conference on Design & technology of integrated systems in nanoscale era (DTIS). IEEE, pp 50–55

  24. 24.

    Roy S, Mitra D, Bhattacharya BB, Chakrabarty K (2012) Congestion-aware layout design for high-throughput digital microfluidic biochips. ACM J Emerg Technol Comput Syst 8(3):17

    Article  Google Scholar 

  25. 25.

    Sinnen O (2007) Task scheduling for parallel systems, vol 60. Wiley, New York

    Book  Google Scholar 

  26. 26.

    Su F, Chakrabarty K (2004) Architectural-level synthesis of digital microfluidics-based biochips. In: 2004 IEEE/ACM international conference on computer-aided design. IEEE Computer Society, pp 223–228

  27. 27.

    Su F, Chakrabarty K (2005) Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In: 2005 42nd International conference on design automation conference. ACM, pp 825–830

  28. 28.

    Su F, Chakrabarty K (2008) High-level synthesis of digital microfluidic biochips. ACM J Emerg Technol Comput Syst 3(4):1

    Article  Google Scholar 

  29. 29.

    Su F, Zeng J (2007) Computer-aided design and test for digital microfluidics. IEEE Des Test Comput 24(1):60–70

    Article  Google Scholar 

  30. 30.

    Tang J, Ibrahim M, Chakrabarty K, Karri R (2017) Secure randomized checkpointing for digital microfluidic biochips. IEEE Trans Comput Aided Des Integr Circuits Syst 30(6):1119–1132

    Article  Google Scholar 

  31. 31.

    Wang Q, Shen Y, Yao H, Ho TY, Cai Y (2014) Practical functional and washing droplet routing for cross-contamination avoidance in digital microfluidic biochips. In: 2014 51st ACM/EDAC/IEEE design automation conference. IEEE, pp 1–6

  32. 32.

    Wille R, Keszocze O, Drechsler R, Boehnisch T, Kroker A (2015) Scalable one-pass synthesis for digital microfluidic biochips. IEEE Des Test 32(6):41–50

    Article  Google Scholar 

  33. 33.

    Windh S, Phung C, Grissom DT, Pop P, Brisk P (2017) Performance improvements and congestion reduction for routing-based synthesis for digital microfluidic biochips. IEEE Trans Comput Aided Des Integr Circuits Syst 36(1):41–54

    Article  Google Scholar 

  34. 34.

    Yao H, Wang Q, Shen Y, Ho TY, Cai Y (2016) Integrated functional and washing routing optimization for cross-contamination removal in digital microfluidic biochips. IEEE Trans Comput Aided Des Integr Circuits Syst 35(8):1283–1296

    Article  Google Scholar 

  35. 35.

    Yuh PH, Yang CL, Chang YW (2006) Placement of digital microfluidic biochips using the t-tree formulation. In: 2006 43rd International conference on design automation conference. ACM, pp 931–934

  36. 36.

    Zhao Y, Chakrabarty K (2010) Synchronization of washing operations with droplet routing for cross-contamination avoidance in digital microfluidic biochips. In: 2010 47th International conference on design automation conference. ACM, pp 635–640

  37. 37.

    Zhao Y, Chakrabarty K (2012) Cross-contamination avoidance for droplet routing in digital microfluidic biochips. IEEE Trans Comput Aided Des Integr Circuits Syst 31(6):817–830

    Article  Google Scholar 

  38. 38.

    Zhao Y, Chakrabarty K (2013) Cross-Contamination Avoidance for Droplet Routing. In: Design and testing of digital microfluidic biochips. Springer, New York, NY

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Acknowledgements

Funding was provided by the Visvesvaraya fellowship for Ph.D. scheme under Ministry of Electronics and Information Technology of the Government of India.

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Correspondence to Arpan Chakraborty.

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This work was supported by the Visvesvaraya fellowship for Ph.D. scheme under Ministry of Electronics and Information Technology of the Government of India.

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Chakraborty, A., Datta, P. & Pal, R.K. A low-cost fluid-level synthesis for droplet-based microfluidic biochips integrating design convergence, contamination avoidance, and washing. Des Autom Embed Syst 22, 315–346 (2018). https://doi.org/10.1007/s10617-018-9215-2

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Keywords

  • Contamination
  • Design automation
  • Microfluidics
  • NP-complete
  • One-pass synthesis
  • Washing