Massive Parallel Digital Micro fluidic Biochip Architecture for Automating Large-Scale Biochemistry Assays

Document Type : Article

Authors

1 Department of Computer Science and Engineering, Shahid Beheshti University, G.C., Tehran 1982963113, Iran

2 Department of Computer Engineering, Mahdishahr Branch, Islamic Azad University, Mahdishahr, Iran

Abstract

Micro/Nano fluidic biochips are used to automate the clinical diagnosis, DNA sequencing, automated drug discovery and real time bio-molecular recognition. One of attractive usages of biochips is Lab-on-chip (LOC). Lab-on-Chip technology is a promising replacement for biomedical and chemical apparatus. Two main types of micro fluidic based biochips are used: continuous-flow based and digital micro fluidic biochips (DMFB). In DMFBs, liquids, in the form of droplets, are controlled independently and concurrently over a two dimensional array of cells (or electrodes).Digital micro fluidic biochips provide high ability to con gure and fault tolerance.
In this paper, a new architecture for DMFB with purpose of balancing among the parameters of flexibility, efficiency, cost, and completion time of biological experiments, is presented. In the new architecture, a FPGA-based structure is used, which increase flexibility and paralellizing assay operations. Experiments show
that, the execution time of scheduling, routing, and simulation are improved in comparison with FPPC architecture about 2.54%, 18.76% and 12.52%, respectively in cost of 21% overhead in the number of controlling pins.

Keywords

Main Subjects


References
1. Iliescu, C., Taylor, H., Avram, M., Miao, J., and
Franssila, S. \A practical guide for the fabrication of
micro
uidic devices using glass and silicon", Journal
of Biomicro
uidics, 6(2), pp. 16505-16516 (2012).
2. Zeng J. \Design automation methods and tools for
micro
uidics-based biochips", In Electronics and Electrical
Engineering, Springer, Netherlands (2006).
3. Srinivasan, V., Pamula, V., and Fair, R. \An integrated
digital micro
uidic lab-on-a-chip for clinical
diagnostics on human physiological
uids", Lab on a
Chip Journal, 4(5), pp. 310-315 (2004).
4. Sista, R., Hua, Z., Thwar, P., Sudarsan, A., Srinivasan,
V., Eckhardt, A., Pollack, M., and Pamula, V. \Development
of a digital micro
uidic platform for point of
care testing", Lab on a Chip Journal, 8(12), pp. 2091-
2104 (2008).
5. Su, F. and Chakrabarty, K. \High-level synthesis
of digital micro
uidic biochips", ACM Journal on
Emerging Technologies in Computing Systems, 3(4),
pp. 16-48 (2008).
3474 A. Haddad et al./Scientia Iranica, Transactions D: Computer Science & ... 25 (2018) 3461{3474
6. Grissom, D. and Brisk, P. \A eld-programmable pinconstrained
digital micro
uidic biochip", ACM/IEEE
Design Automation Conference, pp. 1-9 (2013).
7. Xu, T. and Chakrabarty, K. \Broadcast electrodeaddressing
for pin-constrained multi-functional digital
micro
uidic biochips",Proceedings of Design Automation
Conference, pp. 173-178 (2008).
8. Grith, E.J. and Akella, S. \Coordinating multiple
droplets in planar array digital micro
uidic system",
International Journal of Robotics Research, 4(11), pp.
933-949 (2005).
9. Dhar, S., Drezdon, S., and Maftei, E. \Digital micro
uidic
biochip for malaria detection", Technical Report,
Duke University (2008).
10. Maftei, E., Pop, P., and Madsen, J. \Tabu searchbased
synthesis of dynamically recon gurable digital
micro
uidic biochips", Proceedings of the International
Conference on Compilers, Architecture, and Synthesis
for Embedded Systems, pp. 195-204 (2009).
11. Xu, T. and Chakrabarty, K. \Droplet-trace-based
array partitioning and a pin assignment algorithm for
the automated design of digital micro
uidic biochips",
Proceedings of IEEE/ACM CODES+ISSS, pp. 112-117
(2006).
12. Gupta, M.N. \Multi-Board digital micro
uidic biochip
synthesis with droplet crossover optimization", MSc
Thesis, University of Cincinnati (2014).
13. Su, F., Chakrabarty, K., and Fair, R.B. \Micro
uidicsbased
biochips technology, issues, implementation
platforms, and design-automation challenges", IEEE
Transactions on Computer-Aided Design of Integrated
Circuits and Systems, 25(2), pp. 211-223 (2006).
14. Jones, T.B. \Dielectrophoretic liquid actuation and
nanodroplet formation", Application Physicl Journal,
89(2), pp. 1441-1448 (2001).
15. Pollack, M.G. \Electrowetting-based microactuation of
droplets for digital micro
uidics", PhD. Thesis, Duke
University (2001).
16. Chakrabarty, K. \Digital micro
uidic biochips: A
vision for functional diversity and more than moore",
International Conference on VLSI Design, pp. 452-457
(2010).
17. Grissom, D. and Brisk, P. \Fast online synthesis of
generally programmable digital micro
uidic biochips",
In Proceedings of CODES+ISSS, pp. 413-422 (2012).
18. Taajobian, M. and Jahanian, A. \Higher
exibility of
recon gurable digital micro/nano
uidic biochips using
an FPGA-inspired architecture", Scientia Iranica.
Transactions F, Nanotechnology, 23(3), pp. 1554-156
(2016).
19. Maftei, E. \Synthesis of digital micro
uidic biochips
with recon gurable operation execution", PhD Thesis,
Technical University of Denmark (2011).
20. Grissom, D. \Design of topologies for interpreting
assays on digital micro
uidic biochips", PhD. Thesis,
Riverside: University of California (2014).
21. Grissom, D. and Brisk, P. \A high-performance online
assay interpreter for digital micro
uidic biochips", In
The Proceedings of Great Lakes Symposium on VLSI,
pp. 103-106 (2012).

Volume 25, Issue 6
Transactions on Computer Science & Engineering and Electrical Engineering (D)
November and December 2018
Pages 3461-3474