Module placement for fault-tolerant microfluidics-based biochips

ACM Transactions on Design Automation of Electronic Systems

Volumn 11, Issue 3, 2006, Pages 682-710

  Su, Fei ^a,b   Chakrabarty, Krishnendu ^a,b  

^a DUKE UNIVERSITY   (United States)

^b Duke University   (United States)

Author keywords

Biochips; Microfluidics; Module placement; Physical design automation

Indexed keywords

EID: 33748424561     PISSN: 10844309     EISSN: 10844309     Source Type: Journal    
DOI: 10.1145/1142980.1142987     Document Type: Article

References (56)

1. AGNIHOTRI, A. R., ONO, S., LI, G., YILDIZ, M. C., KHATKHATE, A., KOH, C. K., AND MADDEN, P. H. 2005. Mixed block placement via fractional cut recursive bisection. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 24, 748-761.
2. AHN, C. H., CHOI, J.-W., BEAUCAGE, G., NEVIN, J. H., LEE, J.-B., PUNTAMBEKAR, A., AND LEE, J. Y. 2004. Disposable smart lab on a chip for point-of-care clinical diagnostics. In Proceedings of the IEEE 92, 154-173.
3. ANDRONESCU, M., D., DEES, D., SLAYBAUGH, L., ZHAO, Y., CONDON, A., COHEN, C., AND SKIENA, S. 2003. Algorithms for testing that sets of DNA words concatenate without secondary structure. Natural Comput. 2, 391-415.
4. BAZARGAN, K., KASTNER, R., AND SARRAFZADEH, M. 2000a. Fast template placement for reconfigurable computing systems. IEEE Des. Test Comput. 17, 68-83.
5. BAZARGAN, K., KASTNER, R., AND SARRAFZADEH, M. 2000b. 3-D floorplanning: Simulated annealing and greedy placement methods for reconfigurable computing systems. In Design Automation for Embedded Systems 5, 329-338.
6. BÖHRINGER, K. F. 2005. Modeling and controlling parallel tasks in droplet-based microfiuidic systems. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst.
7. BRADLEY, R. AND SKIENA, S. 1997. Fabricated arrays of strings. In Proceedings of the International Conference on Research in Computational Molecular Biology, 57-66.
8. CASOTTO, A., ROMEO, F., AND SANGIOVANNI-VINCENTELLI, A. 1987. A parallel simulated annealing algorithm for the placement of macro-cells. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 6, 838-847.
9. CHANDY, J. A., KIM, S., RAMKUMAR, B., PARKES, S., AND BANERJEE, P. 1997. An evaluation of parallel simulated annealing strategies with application to standard cell placement. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 16, 398-410.
10. CHANG, Y. C., CHANG, Y. W., WU, G. M., AND WU, S. W. 2000. B*-tree: A new representation for non-slicing floorplans. In Proceedings of the IEEE/ACM Design Automation Conference, 458-463.
11. CHATTERJEE, A. N. AND ALURU, N. R. 2005. Combined circuit/device modeling and simulation of integrated microfluidic systems. J. Microelectromechanical Syst. 14, 81-95.
12. CHEN, T.-C. AND CHANG, Y.-W. 2005. Modern floorplanning based on fast simulated annealing. In Proceedings of the ACM International Symposium on Physical Design (ISPD), 104-112.
13. CHO, S. K., FAN, S. K., MOON, H., AND KIM, C. J. 2002. Toward digital microfluidic circuits: creating, transporting, cutting and merging liquid droplets by electrowetting-based actuation. In Proceedings of the IEEE MEMS Conference, 32-52.
14. COELLO, C. 1999. An updated survey of evolutionary multiobjective optimization techniques: State of the art and future trends. In Proceedings of the IEEE Evolutionary Computation Conference, 140-143.
15. CONG, J., HUANG, H., AND YUAN, X. 2005. Technology mapping and architecture evaluation for k/m-macrocell-based FPGAs. ACM Trans. Des. Autom. Electro. Syst. 10, 3-23.
16. CONG, J. AND LIM, S. 2004. Retiming-Based timing analysis with an application to mincut-based global placement. IEEE Trans. Comput. Aided Des. Integrated Circ. Syst. 23, 1684-1692.
17. DING, J., CHAKRABARTY, K., AND FAIR, R. B. 2001. Scheduling of microfluidic operations for reconfigurable two-dimensional electrowetting arrays. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 20, 1463-1468.
18. EDMONDS, J., GRYZ, J., LIANG, D., AND MILLER, R. J. 2003. Mining for empty spaces in large data sets. Theoretical Computer Science 296, 435-452.
19. GAREY M. AND JOHNSON, D. 1979. Computers and Intractability - A Guide to the Theory of NP-Completeness. Freeman, New York.
20. GRIFFITH, E. AND AKELLA, S. 2005. Performance characterization of a reconfigurable planar array digital microfluidic system. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst.
21. GUO, P.-N., CHENG, C.-K., AND YOSHIMURA, T. 1999. An O-tree representation of nonslicing floorplan and its applications. In Proceedings of the ACM/ IEEE Design Automation Conference, 268-273.
22. HANDA, M. AND VEMURI, R. 2004. A fast algorithm for finding maximal-empty rectangles. In Proceedings of the Design, Automation and Test in Europe Conference and Exhibition (DATE), 744-745.
23. INTERNATIONAL TECHNOLOGY ROADMAP FOR SEMICONDUCTOR (ITRS). http://public.itrs.net/Files/-2003ITRS/Home2003.htm.
24. JONES, T. B., GUNJI, M., WASHIZU, M., AND FELDMAN, M. J. 2001. Dielectrophoretic liquid actuation and nanodroplet formation. J. Appl. Phys. 89, 1441-1448.
25. KAHNG, A. B., MANDOIU, I. I., REDA, S., XU, X., AND ZELIKOVSKY, A. Z. 2005. Computer-Aided optimization of DNA array design and manufacturing. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst.
26. LIN, J. M. AND CHANG, Y. W. 2001. TCG: A transitive closure graph-based representation for nonslicing floorplans. In Proceedings of the IEEE/ACM Design Automation Conference, 764-769.
27. MCCLUSKEY, P. 2002. Design for reliability of micro-electro-mechanical systems (MEMS). In Proceedings of the IEEE Electronic Components and Technology Conference, 760-762.
28. MELTZER, S. 1998. PCR in Bioanalysis. Humana Press, Totowa, N.J.
29. MUKHERJEE, T. AND FEDDER, G. K. 1998. Design methodology for mixed-domain systems-on-a-chip [MEMS design]. In Proceedings of the IEEE VLSI System Level Design Conference, 96-101.
30. MURATA, H., FUJIYOSHI, K., NAKATAKE, S., AND KAJITANI, Y. 1995. Rectangle-packing-based module placement. In Proceedings of the IEEE International Conference on CAD, 472-479.
31. PAIK, P., PAMULA, V. K., AND FAIR, R. B. 2003. Rapid droplet mixers for digital microfluidic systems. Lab on a Chip 3, 253-259.
32. PFEIFFER, A. J., MUKHERJEE T., AND HAUAN, S. 2005. Synthesis of multiplexed biofluidic microchips. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst.
33. POLLACK, M. G. 2001. Electrowetting-Based Microactuation of Droplets for Digital Microfluidics. PhD thesis, Duke University.
34. POLLACK, M. G., SHENDEROV, A. D., AND FAIR, R. B. 2002. Electrowetting-Based actuation of droplets for integrated microfluidics. Lab on a Chip 2, 96-101.
35. REED, M. L. AND LYE, W. K. 2004. Microsystems for drug and gene delivery. In Proceedings of the IEEE 92, 56-75.
36. SAIT, S. AND YOUSSEF, H. 1995. VLSI Physical Design Automation: Theory and Practice, IEEE Press, New York.
37. SAKANUSHI, K. AND KAJITANI, Y. 2000. The quarter-state sequence (Q-sequence) to represent the floorplan and applications to layout optimization. In Proceedings of the Asia Pacific Conference Circuits and Systems 829-832.
38. SARHAFZADEH, M. AND WONG, C. K. 1996. An Introduction to VLSI Physical Design. McGraw-Hill, New York.
39. SECHEN C. 1988. VLSI Placement and Global Routing Using Simulated Annealing. Kluwer Academic, Boston, Mass.
40. SECHEN,C. AND SANGIOVANNI-VINCENTELLI, A. 1985. The TimberWolf placement and routing package. IEEE J. Solid-State Circuits 20, 510-522.
41. SHAPIRO, B., MOON, H., GARRELL, R. AND KIM, C. J. 2003. Modeling of electrowetted surface tension for addressable microfluidic systems: Dominant physical effects, material dependences, and limiting phenomena. In Proceedings of the IEEE Conference MEMS, 201-205.
42. SRINIVASAN, V., PAMULA, V. K., POLLACK, M. G., AND FAIR, R. B. 2003. Clinical diagnostics on human whole blood, plasma, serum, urine, saliva, sweat, and tears on a digital microfluidic platform. In Proceedings of the μTAS, 1287-1290.
43. SU, F. AND CHAKRABARTY, K. 2004. Architectural-level synthesis of digital microfluidics-based biochips. In Proceedings of the IEEE International Conference on CAD, 223-228.
44. SU, F., OZEV, S., AND CHAKRABARTY, K. 2003. Testing of droplet-based microelectrofluidic systems. In Proceedings of the IEEE International Test Conference, 1192-1200.
45. SU, F., OZEV, S., AND CHAKRABARTY, K. 2004. Concurrent testing of droplet-based microfluidic systems for multiplexed biomedical assays. In Proceedings of the IEEE International Test Conference, 883-892.
46. TANG, X., TIAN, R., AND WONG, D. F. 2001. Fast evaluation of sequence pair in block placement by longest common subsequence computation. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 20, 1406-1413.
47. TANG, X. T. AND WONG, D. F. 2001. FAST-SP: A fast algorithm for block based on sequence pair. In Proceedings of the Asia and South Pacific Design Automation Conference, 521-526.
48. VERPOORTE, E. AND DE ROOIJ, N. F. 2003. Microfluidics meets MEMS. In Proceedings of the IEEE 91, 930-953.
49. WANG, X., WHITE, J., KANAPKA, J., YE, W., AND ALURU, N. 2005. Algorithms in FastStokes and its application to micromachined device simulation. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst.
50. WHITE, J. 2004. CAD challenges in BioMEMS design. In Proceedings of the IEEE / ACM Design Automation Conference, 629-632.
51. YANG, P. AND CHERN, J. 1993. Design for reliability: The major challenge for VLSI. In Proceedings of the IEEE 55, 730-744.
52. YOUNG, E. F. Y., CHU, C. C. N., AND SHEN, Z. C. 2003. Twin binary sequences: A nonredundant representation for general nonslicing floorplan. IEEE Trans. Comput. Aided Des. Integrated Circuits Syst. 22, 457-469.
53. YUH, P. H., YANG, C. L., AND CHANG, Y. W. 2004a. Temporal floorplanning using the T-tree formulation. In Proceedings of the IEEE International Conference on CAD, 300-305.
54. YUH, P. H., YANG, C. L., CHANG, Y. W., AND CHEN, H. L. 2004b. Temporal floorplanning using 3D-subTCG. In Proceedings of the Asia and South Pacific Design Automation Conference, 725-730.
55. ZENG, J. AND KORSMEYER, F. T. 2004. Principles of droplet electrohydrodynamics for lab-on-a-chip. Lab on a Chip 4, 265-277.
56. ZHANG, T., CHAKRABARTY, K., AND FAIR, R. B. 2002. Microelectrofluidic Systems: Modeling and Simulation. CRC Press, Boca Raton, Fla.