Design Automation for Microfluidics-Based Biochips

ACM Journal on Emerging Technologies in Computing Systems

Volumn 1, Issue 3, 2005, Pages 186-223

  Chakrabarty, Krishnendu ^a   Zeng, Jun ^b  

^a Duke University   (United States)

^b European Headquarter and Development Center   (United States)

Author keywords

Algorithms; biochips; Design; design automation; Microfluidics; Performance; Reliability

Indexed keywords

EID: 34249826289     PISSN: 15504832     EISSN: 15504840     Source Type: Journal    
DOI: 10.1145/1116696.1116698     Document Type: Article

References (109)

1. Adamson, A. W. 1990. Physical Chemistry of Surfaces, 5th Ed. Wiley, New York.
2. Anderson, J. D. 1995. Computational Fluid Dynamics: The Basics with Applications. McGraw-Hill, New York.
3. Affymetrix GeneChip(r). http://www.affymetrix.com.
4. Batchelor, G. K. 2000. An Introduction to Fluid Dynamics. University Press, Cambridge, England.
5. Brebbia, C. A. 1978. The Boundary Element Method for Engineers. Pentech Press, London, England.
6. Burns, M. A., Johnson, B. N., Brahmasandra, S. N., Handique, K., Webster, J. R., Krishnan, M., Sammarco, T. S., Man, P. M., Jones, D., Heldsinger, D., Mastrangelo, C. H., and Burke, D. T. 1998. An integrated nanoliter DNA analysis device. Science 282, 484-487.
7. Chatterjee, A. N. and Aluru, N. R. 2005. Combined circuit/device modeling and simulation of integrated microfluidic systems. J. Microelect. Syst. 14, 81-95.
8. Chen, J. Z., Darhuber, A. A., Troian, S. M., and Wagner, S. 2004. Capacitive sensing of droplets for microfluidic devices based on thermocapillary actuation. Lab on a Chip 4, 473-480.
9. 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 IEEE MEMS Conference. IEEE Computer Society Press, Los Alamitos, CA, 32-52.
10. Choi, C.-H., Westin, K. J. A., and Bruer, K. S. 2003. Apparent slip flows in hydrophilic and hydrophobic microchannels. Phys. Fluids 15, 2897-2902.
11. Clough, R. W. 1960. The finite element method in plane stress analysis. In Proceedings 2nd ASCE Conference on Electronic Computation (Pittsburgh, PA). 345-378.
12. CoventorWare−. http://www.coventor.com.
13. Darhuber, A. A., Valention, J. P., Troian, S. M., and Wagner, S. 2003. Thermocapillary actuation of droplets on chemically patterned surfaces by programmable microheater arrays. J. MicroElectroMechanical Syst. 12, 873-879.
14. Deb, N. and Blanton, R. D. 2000. Analysis of failure sources in surface-micromachined MEMS. in Proceedings of International Test Conference. 739-749.
15. Duffy, D. C., Gillis, H. L., Lin, J., Sheppard, N. F., and Kellogg, G. J. 1999. Microfabricated centrifugal microfluidic systems: Characterization and multiple enzymatic assays. Anal. Chem. 71, 4669-4678.
16. Erickson, D. 2005. Towards numerical prototyping of labs-on-chip, modeling for integrated microfluidic devices. J. Microfluidics Nanofluidics, 10.1007/s10404-005-0041-z.
17. Fitzpatrick, D. and Miller, I. 1998. Analog Behavioral Modeling with the Verilog-A Language. Kluwer Academic Publishers, Boston, MA.
18. Gallardo, B. S., Gupta, V. K., Eagerton, F. D., Jong, L. I., Craig, V. S., Shah, R. R., and Abbott, N. L. 1999. Electrochemical principles for active control of liquids on submillimeter scales. Science 283, 57-60.
19. Grayson, A., Shawgo, R., Johnson, A., Flynn, N., Li, Y., Cima, M., and Langer, R. 2004. AbioMEMS review: MEMS technology for physiologically integrated devices. Proc. IEEE 92, 6-21.
20. Harrison, D. J., Fluri, K., Seiler, K., Fan, Z. H., Effenhauser, C. S., and Manz, A. 1993. Micromachining a miniaturized capillary electrophoresis-based chemical analysis system on a chip. Science 261, 895-897.
21. Haus, H. A. and Melcher, J. R. 1989. Electromagnetic Fields and Energy. Prentice-Hall, Englewood Cliffs, NJ.
22. Hirsch, C. 1988. Numerical Computation of Internal and External Flows: Fundamentals of Numerical Discretization. Wiley, New York.
23. Hirt, C. W., Amsden, A. A., and Cook, J. L. 1974. An Arbitrary Lagrangian-Eulerian computing method for all flow speeds. J. Comput. Phys. 14, 227-253.
24. Hirt, C. W. and Nichols, B. D. 1981. Volume of fluid (VOF) method for the dynamics of free boundaries. J. Comput. Phys. 39, 201-225.
25. Homsy, A., Koster, S., Eijkel, J. C. T., van den Berg, A., Lucklum, F., Verpoorte, E., and De Rooij, N. F. 2005. A high current density DC magnetohydrodynamic (MHD) micropump. Lab on a Chip 5, 466-471.
26. Hull, H. F., Danila, R., and Ehresmann, K. 2003. Smallpox and bioterrorism: Public-health responses. J. Lab. Clin. Med. 142, 221-228.
27. Ichimura, K., Oh, S., and Nakagawa, M. 2000. Light-driven motion of liquids on a photoresponsive surface. Science 288, 1624-1626.
28. Infineon Electronic DNA Chip. http://www.infineon.com.
29. International Technology Roadmap for Semiconductors (ITRS). http://public.itrs.net/Files/ 2003ITRS/Home2003.htm.
30. Jacobson, S. C., Hergenroeder, R., Koutny, L. B. and Ramsey, J. M. 1994. High-speed separations on a microchip. Anal. Chem. 66, 1114-1118.
31. Jee, A. and Ferguson, F. J. 1993. Carafe: An inductive fault analysis tool for CMOS VLSI circuits. In Proceedings of IEEE VLSI Test Symposium. IEEE Computer Society Press, Los Alamitos, CA, 92-98.
32. Jones, T. B. 1973. Electrohydrodynamic heat pipes. Int. J. Heat Mass Trans. 16, 1045-1048.
33. Jones, T. B. 2002. On the relationship of dielectrophoresis and electrowetting. Langmuir 18, 4437-4443.
34. Jones, T. B., Gunji, M., Washizu, M., and Feldman, M. J. 2001. Dielectrophoretic liquid actuation and nanodroplet formation. J. Appl. Phys. 89, 1441-1448.
35. Kahng, A. B., Mandoui, I., Reda, S., Xu, X., and Zelikovsky, A. Z. 2003. Evaluation of placement techniques for DNA probe array layout. In Proceedings of IEEE/ACM International Conference on Computer Aided Design. ACM, New York, 262-269.
36. Karniadakis, G. and Beskok, A. 2001. Microflows: Fundamentals and Simulation. Springer-Verlag, Berlin, Germany.
37. Kerkhoff, H. G. 1999. Testing philosophy behind the micro analysis system. In Proceedings of SPIE: Design, Test and Microfabrication ofMEMS and MOEMS 3680. 78-83.
38. Kerkhoff, H. G. and Acar, M. 2003. Testable design and testing of micro-electro-fluidic arrays. In Proceedings of IEEE VLSI Test Symposium. IEEE Computer Society Press, Los Alamitos, CA. 403-409.
39. Kerkhoff, H. G. and Hendriks, H. P. A. 2001. Fault modeling and fault simulation in mixed micro-fluidic microelectronic systems. J. Elect. Testing: Theory Appl. 17, 427-437.
40. Kolpekwar, A. and Blanton, R. D. 1997. Development of a MEMS testing methodology. In Proceedings of International Test Conference, 923-931.
41. Landau, L. D. and Lifshitz, E. M. 1960. Electrodynamics of Continuous Media, Addison-Wesley, Reading, MA.
42. Laser, R. D. J. and Santiago, J. G. 2004. A review of micropumps. J. Micromech. Microeng. 14, R35-R64.
43. Lauga, E. and Stone, H. A. 2003. Effective slip in pressure-driven Stokes flow. J. Fluid Mech. 489, 55-77.
44. Leal, L. G. 1992. Laminar Flow and Convective Transport Processes: Scaling Principles and Asymptotic Analysis. Butterworth-Heinemann, Boston, MA.
45. Lion, N., Rohner, T. C., Dayon, L., Aranud, I. L., Damoc, E., Youhnovski, I. N., Wu, Z., Roussel, C., Josserand, J., Jensen, H., Rossier, J., Przyblski, M., and Girault, H. 2003. Microfluidic systems in proteomics. Electrophoresis 24, 3533-3562.
46. MacCormack, R. W. and Paullay, A. J. 1972. Computational efficiency achieved by time splitting of finite difference operators, AIAA Paper, 72-154.
47. Mantooth, H. A. and Giegenbaum, M. 1995. Modeling with an Analog Hardware Description Language. Kluwer Academic Publishers, Boston, MA.
48. Manz, A., Harrison, D. J., Verpoorte, E. M. J., Fettinger, J. C., Paulus, A., Ludi, H., and Widmer, H. M. 1992. Planar chips technology for miniaturization and integration of separation techniques into monitoring systems-Capillary electrophoresis on a chip. J. Chromatogr. 593, 253-258.
49. McDonald, P. W. 1971. The computation of transonic flow through two-dimensional gas turbine cascades. ASME Paper 71-GT-89.
50. Maxwell, J. C. 1879. On stresses in rarified gases arising from inequalities of temperature. Phil. Trans. R. Soc. Lond. 170, 231-256.
51. Melcher, J. R. and Taylor, G. I. 1969. Electrohydrodynamics: a review of the role of interfacial shear stresses. Ann. Rev. Fluid Mech. 1, 111-146.
52. Melcher, J. R. 1981. Continuum Electromechanics, Section 3.7, The MIT Press, Boston, MA.
53. Mutlu, S., Svec, F., Mastrangelo, C. H., Fretcht, J. M. J., and Gianchandani, Y. B. 2004. Enhanced electro-osmosis pumping with liquid bridge and field effect flow rectification. in Proceedings of IEEE MEMS Conference. 850-853.
54. Nanogen NanoChip(r). http://www.nanogen.com.
55. Navier, C. L. M. H. 1823. M’emoire sur les lois du mouvement des fluides. M’emoires de l’Acad’emie Royale des Sciences de l’Institut de France 6, 389-440.
56. Nguyen, N.-T. and Huang, X. 2005. Thermocapillary effect of a liquid plug in transient temperature fields. Japan. J. Appl. Phys. 44, 1139-1142.
57. Paik, P., Pamula, V. K., and Fair, R. B. 2003. Rapid droplet mixers for digital microfluidic systems. Lab on a Chip 3, 253-259.
58. Pan, F., Kubby, J., and Chen, J. 2002. Numeircal simulation of fluid-structure interaction in a MEMS diaphragm drop ejector. J. Micromech. Microeng. 12, 70-76.
59. Pohl, H. A. 1978. Dielectrophoresis: The Behaviour of Neutral Matter in Nonuniform Electric Fields, Cambridge university Press, Cambridge, England.
60. Pollack, M. G. 2001. Electrowetting-Based Microactuation of Droplets for Digital Microfluidics. Ph.D. dissertation. Duke University.
61. Pollack, M. G., Fair, R. B., and Shenderov, A. D. 2000. Electrowetting-based actuation of liquid droplets for microfluidic applications. Appl. Phys. Lett. 77, 1725-1726.
62. 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.
63. Prins, M. W. J., Welters, W. J. J., and Weekamp, J. W. 2001. Fluid control in multichannel structures by electrocapillary pressure. Science 291, 277-280.
64. Probstein, R. F. 1994. Physicochemical hydrodynamics. Wiley, New York.
65. Rudnyi, E. B. and Korvink, J. G. 2002. Review: Automatic Model Reduction for Transient Simulation of MEMS-based Devices. Sensors Update 11, 3-33.
66. Sammarco, T. S. and Burns, M. A. 1999. Thermocapillary pumping of discrete droplets in microfabricated analysis devices. AI Che J. 45, 350-366.
67. Saville, D. A. 1977. Electrokinetic effects with small particles. Ann. Rev. Fluid Mech. 9, 321-337.
68. Schulte, T. H., Bardell, R. L., and Weigl, B. H. 2002. Microfluidic technologies in clinical diagnostics. Clinica Chimica Acta 321, 1-10.
69. Schwartz, J. A., Vykoukal, J. V., and Gascoyne, P. R. C. 2004. Droplet-based chemistry on a programmable micro-chip. Lab on a Chip 4, 11-17.
70. Senturia, S. D. 1998. CAD challenges for microsensors, microactuators, and microsystems. Proc. IEEE 86, 1611-1626.
71. Shapiro, B., Moon, H., Garrell I. 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 IEEE MEMS Conference. IEEE Computer Society Press, Los Alamitos, CA, 201-205.
72. Smits, J. G. 1990. Piezoelectric micropump with three valves working peristaltically. Sensors and Actuators A 21, 304-306.
73. Srinivasan, V. 2005. A Digital Microfluidic Lab-on-a-Chip for Clinical Diagnostic Applications, Ph.D. dissertation. Duke University.
74. Srinivasan, V., Pamula, V. K., and Fair, R. B. 2004. An integrated digital microfluidic lab-on-a-chip for clinical diagnostics on human physiological fluids. Lab on a Chip 4, 310-315.
75. Srinivasan, V., Pamula, V. K., Pollack, M. G., and Fair, R. B. 2003a. A digital microfluidic biosensor for multianalyte detection. In Proceedings of IEEE MEMS Conference. IEEE Computer Society Press, Los Alamitos, CA, 327-330.
76. Srinivasan, V., Pamula, V. K., Pollack, M. G., and Fair, R. B. 2003b. Clinical diagnostics on human whole blood, plasma, serum, urine, saliva, sweat, and tears on a digital microfluidic platform. in Proceedings of Micro Total Analysis Systems, 1287-1290.
77. Stone, H. A., Stroock, A. D., and Aidari, A. 2004. Engineering flows in small devices: microfluidics toward a lab-on-a-chip. Ann. Rev. Fluid Mech. 36, 381-411.
78. Su, F. and Chakrabarty, K. 2004. Architectural-level synthesis of digital microfluidics-based biochips. In Proceedings of IEEE/ACM International Conference on Computer Aided Design. IEEE Computer Society Press, Los Alamitos, CA, 223-228.
79. Su, F. and Chakrabarty, K. 2005a. Design of fault-tolerant and dynamically-reconfigurable microfluidic biochips. In Proceedings of Design, Automation and Test in Europe (DATE) Conference. 1202-1207.
80. Su, F. and Chakrabarty, K. 2005b. Unified high-level synthesis and module placement for defecttolerant microfluidic biochips. In Proceedings of IEEE/ACM Design Automation Conference, ACM, New York, 825-830.
81. Su, F. and Chakrabarty, K. 2005c. Defect tolerance for gracefully-degradable microfluidics-based biochips. In Proceedings of IEEE VLSI Test Symposium. IEEE Computer Society Press, Los Alamitos, CA, 321-326.
82. Su, F., Chakrabarty. K., and Pamula, V. K. 2005a. Yield enhancement of digital microfluidics-based biochips using space and local reconfiguration. in Proceedings of Design, Automation and Test in Europe (DATE) Conference. 1196-1201.
83. Su, F., Ozev, S., and Chakrabarty, K. 2003. Testing of droplet-based microelectrofluidic systems. In Proceedings of IEEE International Test Conference. IEEE Computer Society Press, Los Alamitos, CA, 1192-1200.
84. Su, F., Ozev, S., and Chakrabarty, K. 2004a. Test planning and test resource optimization for droplet-based microfluidic systems. in Proceedings of European Test Symposium. 72-77.
85. Su, F., Ozev, S. and Chakrabarty, K. 2004b. Concurrent testing of droplet-based microfluidic systems for multiplexed biomedical assays. In Proceedings of IEEE International Test Conference. IEEE Computer Society Press, Los Alamitos, CA, 883-892.
86. Su, F., Ozev, S. and Chakrabarty, K. 2005b. Ensuring the operational health of droplet-based microelectrofluidic biosensor systems. IEEE Sensors J. 5, 763-773.
87. Swart, N. R., Bart, S. F., Zaman, M. H., Mariappan, M., Gilbert, J. R., and Murphy, D. 1998. AutoMM: Automatic generation of dynamic macromodels for MEMS devices. In Proceedings of 11th IEEE International Workshop on Micro Electromechanical Systems (Heidelberg, Germany). IEEE Computer Society Press, Los Alamitos, CA, 178-183.
88. Tezduyar, T. E., Behr, M., Mittal, S., and Liou, J. 1992a. New strategy for finite element computations involving moving boundaries and interfaces. The deforming-spatial-domain/space-time procedure. I. The concept and the preliminary numerical tests, Comput. Meth. Appl. Mech. Eng. 94, 339-351.
89. Tezduyar, T. E., Behr, M., Mittal, S., and Liou, J. 1992b. New strategy for finite element computations involving moving boundaries and interfaces. The deforming-spatial-domain/space-time procedure. II. Computation of free-surface flows, two-liquid flows, and flows with drifting cylinders. Comput. Meth. Appl. Mech. Eng. 94, 353-371.
90. Thompson, J. F. 1984. A survey of grid generation techniques in computational fluid dynamics. AIAA J. 22, 1505-1523.
91. Thorsen, T., Maerkl, S., and Quake, S. 2002. Microfluidic large-scale integration. Science 298, 580-584.
92. Tseng, Y.-T., Tseng, F.-G., Chen, Y.-F. and Chieng, C.-C. 2004. Fundamental studies on microdroplet movement by Marangoni and capillary effects. Sensors and Actuators A: Physical 114, 292-301.
93. Turner, M. J., Clough, R. W. Martin, H. C. and Topp, L. P. 1956. Stiffness and deflection analysis of complex structures. J. Aeronaut. Sci. 23, 805-824.
94. Turowski, M., Chen, Z., and Przekwas, A. 2001. Automated generation of compact models for fluidic microsystems. Anal. Integ. Circuits Signal Proc. 29, 27-36.
95. Valentino, J. P., Troian, S. M., and Wagner, S. 2005. Microfluidic detection and analysis by integration of thermocapillary actuation with a thin-film optical waveguide. Appl. Phys. Letters 86, 184101:1-3.
96. Venkatesh, S. and Memish, Z. A. 2003. Bioterrorism: a new challenge for public health. Int. J. Antimicro. Agents 21, 200-206.
97. Verheijen, H. J. J. and Prins, M. W. J. 1999. Reversible electrowetting and trapping of charge: Model and experiments. Langmuir 15, 6616-6620.
98. Verpoorte, E. and De Rooij, N. F. 2003. Microfluidics meets MEMS. Proc. IEEE 91, 930-953.
99. Vykoukal, J., Schwartz, J. A., Becker, F. F., and Gascoyne, P. R. C. 2001. A programmable dielectric fluid processor for droplet-based chemistry. in Proceedings of Micro Total Analysis Systems. 72-74.
100. Wang, Y., Lin, Q., and Mukherjee, T. 2005a. Composable behavioral models and schematic-based simulation of electrokinetic lab-on-a-chips. Accepted for publication in IEEE Trans. CAD.
101. Wang, Y., Lin, Q., and Mukherjee, T. 2005b. A model for laminar diffusion-based complex electrokinetic passive micromixers. Lab On a Chip 5, 877-887.
102. Washizu, M. 1998. Electrostatic actuation of liquid droplets for microreactor applications. IEEE Trans. Industry Appl. 34, 732-737.
103. Wixforth, A. and Scriba, J. 2002. Nanopumps for programmable biochips. GIT Labor-Fachzeitschrift (May), pp. 231-232, (See also http://www.advalytix.de.)
104. Xie, J., Shih, J., Lin, Q., Yang, B., and Tai, Y.-C. 2004. Surface micromachined electrostatically actuated micro peristaltic pump. Lab on a Chip 4, 495-501.
105. Zeng, J., Banerjee, D., Deshpande, M., Gilbert, J., Duffy, D., and Kellogg, G. 2000. Design analyses of capillary burst valves in centrifugal microfluidics. In Micro Total Analysis Systems, Kluwer Academic Publishers, Enschede, The Netherlands, 579-582.
106. Zeng, S., Chen, C.-H., Mikkelson, J. C., and Santiago, J. G. 2001. Fabrication and characterization of electroosmotic micropumps. Sens. Act. B (Chemical) 79, 107-114.
107. Zeng, J. and Korsmeyer, F. T. 2004. Principles of droplet electrohydrodynamics for lab-on-a-chip. Lab on a Chip 4, 265-277.
108. Zhang, T., Chakrabarty, K., and Fair, R. B. 2002. Microelectrofluidic Systems: Modeling and Simulation, CRC Press, Boca Raton, FL.
109. Zoval, J. V. and Madou, M. J. 2004. Centrifuge-based fluidic platforms. Proc. IEEE 92, 140-153.