Aquacore: a programmable architecture for microfluidics

ABSTRACT

Advances in microfluidic research has enabled lab-on-a-chip (LoC) technology to achieve miniaturization and integration of biological and chemical analyses to a single chip comprising channels, valves, mixers, heaters, separators, and sensors. These miniature instruments appear to offer the rare combination of faster, cheaper, and higher-precision analyses in comparison to conventional bench-scale methods. LoCs have been applied to diverse domains such as proteomics, genomics, biochemistry, virology, cell biology, and chemical synthesis. However, to date LoCs have been designed as application-specific chips which incurs significant design effort, turn-around time, and cost, and degrades designer and user productivity. To address these limitations, we envision a programmable LoC (PLoC) and propose a comprehensive fluidic instruction set, called AquaCore Instruction Set (AIS), and a fluidic microarchitecture, called AquaCore, to implement AIS. We present four key design aspects in which the AIS and AquaCore differ from their computer counterparts, and our design decisions made on the basis of the implications of these differences. We demonstrate the use of the PLoC in a range of domains by hand-compiling real-world microfluidic assays in AIS, and show a detailed breakdown of the execution times for the assays and an estimate of the chip area.

REFERENCES

• 1: Agilent Lab-on-a-chip Products, http://www.chem.agilent.com/Scripts/PCol.asp?lPage=50.
• 2: Caliper Life Sciences, LabChip Products, http://www.caliperls.com/technology_partners/microfluidic/.
• 3: P. Auroux et al. Micro total analysis systems. 2. Analytical standard operations and applications. Analytical Chemistry, 74(12):2637--2652, 2002.
• 4: R. G. Blazej, P. Kumaresan, and R. A. Mathies. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. Proceedings of the National Academy of Sciences (PNAS), 103(19):7240--7245, 2006.
• 5: J. Adam Butts , Gurindar S. Sohi, Characterizing and predicting value degree of use, Proceedings of the 35th annual ACM/IEEE international symposium on Microarchitecture, November 18-22, 2002, Istanbul, Turkey
• 6: N. A. Cellar and R. T. Kennedy. A capillary-pdms hybrid chip for separations-based sensing of neurotransmitters in vivo. Lab on a Chip, 6(9):1205--1212, June 2006.
• 7: E. Clark, J. Fanguy, and C. Henry. High-throughput multi-analyte screening for renal disease using capillary electrophoresis. Pharmaceutical and Biomedical Analysis, 25(5--6):795--801, 2001.
• 8: K. Wayne Currenta , Kelvin Yuka , Charles McConaghy , Peter R. C. Gascoyne , Jon A. Schwartz , Jody V. Vykoukal , Craig Andrews, A High-Voltage Integrated Circuit Engine for a Dielectrophoresis-based Programmable Micro-Fluidic Processor, Proceedings of the 2005 International Conference on MEMS,NANO and Smart Systems, p.153-158, July 24-27, 2005 [doi>10.1109/ICMENS.2005.15]
• 9: P. Dittrich, K. Tachikawa, and A. Manz. Micro total analysis systems. Latest advancements and trends. Analytical Chemistry, 78(12):3887--908, 2006.
• 10: C. Goll et al. Microvalves with bistable buckled polymer diaphragms. Micromechanics and Microengineering, 6(1):77--79, 1996.
• 11: W. Grover et al. Development and multiplexed control of latching pneumatic valves using microfluidic logical structures. Lab on a Chip, 6:623--631, 2006.
• 12: E. Hasselbrink, T. Shepodd, and J. Rehm. High-pressure microfluidic control in lab-on-a-chip devices using mobile polymer monoliths. Analytical Chemistry, 74(19):4913--4918, 2002.
• 13: E. T. Lagally, C. A. Emrich, and R. A. Mathies. Fully integrated pcr-capillary electrophoresis microsystem for dna analysis. Lab on a Chip, 1(2):102--107, Oct. 2001.
• 14: C.-C. Lee et al. Multistep Synthesis of a Radiolabeled Imaging Probe Using Integrated Microfluidics. Science, 310(5755):1793--1796, 2005.
• 15: K. Mogensen, H. Klank, and J. Kutter. Recent developments in detection for microfluidic systems. Electrophoresis, 25(21-22):3498--512, 2004.
• 16: N. Nguyen and S. Wereley. Fundamentals and Applications of Microfluidics. Artech House, 2002.
• 17: K. Oh et al. World-to-chip microfluidic interface with built-in valves for multichamber chip-based PCR assays. Lab on a Chip, 5:845--850, 2005.
• 18: J. Pan, D. VerLee, and M. Mehregany. Latched valve manifolds for efficient control of pneumatically actuated valve arrays. In Proceedings of the International Conference on Solid State Sensors and Actuators, volume 2, pages 817--820, 1997.
• 19: M. Pollack, A. Shenderov, and R. Fair. Electrowetting-based actuation of droplets for integrated microfluidics. Lab on a Chip, 2(1):96--101, 2002.
• 20: D. Reyes et al. Micro total analysis systems. 1. Introduction, theory, and technology. Analytical Chemistry, 74(12):2623--2636, 2002.
• 21: K. Shaikh et al. A modular microfluidic architecture for integrated biochemical analysis. Proceedings of the National Academy of Sciences (PNAS), 102(28):9745--9750, 2005.
• 22: V. Srinivasan et al. A digital microfluidic biosensor for multianalyte detection. In Proceedings of the 16th Annual IEEE International Conference on Micro Electro Mechanical Systems, pages 327--330, 2003.
• 23: F. Su, K. Chakrabarty, and R. Fair. Microfluidics-Based Biochips: Technology Issues, Implementation Platforms, and Design-Automation Challenges. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 25(2):211--223, 2006.
• 24: W. Thies et al. Abstraction layers for scalable microfluidic biocomputers. In International Meeting on DNA Computing, Seoul, Korea, June 2006.
• 25: M. Unger et al. Monolithic Microfabricated Valves and Pumps by Multilayer Soft Lithography. Science, 288(5463):113--116, 2000.
• 26: J. P. Urbanski et al. Digital microfluidics using soft lithography. Lab on a Chip, 6(1):96--104, Jan 2006.
• 27: T. Vilkner, D. Janasek, and A. Manz. Micro total analysis systems. Recent developments. Analytical Chemistry, 76(12):3373--85, 2004.

INDEX TERMS

Primary Classification:
  C. Computer Systems Organization
  C.0 GENERAL
      Subjects: Instruction set design (e.g., RISC, CISC, VLIW)

Additional Classification:
  C. Computer Systems Organization
  C.0 GENERAL
      Subjects: System architectures

General Terms:
Design

Keywords:
fluidic, fluidic microarchitecture, instruction set, microfluidics, programmable lab on a chip