A Field-Programmable Pin-Constrained Digital Microfluidic Biochip Dan Grissom and Philip Brisk...

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Transcript of A Field-Programmable Pin-Constrained Digital Microfluidic Biochip Dan Grissom and Philip Brisk...

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A Field-Programmable Pin-Constrained Digital Microfluidic Biochip Dan Grissom and Philip Brisk University of California, Riverside Design Automation Conference Austin, TX, USA, June 4, 2013 Slide 2 2 Digital Microfluidic Biochips (DMFB) 101 Slide 3 3 Goal Goal: Inexpensive, general-purpose DMFB Why: Affordable/accessible to poor/remote communities Problem: Direct-addressing wire-routing is expensive (m n wires) Pin-constrained devices are application specific ( < m n wires) n m Many PCB Layers Few PCB Layers DA: 100 pins Vs. PC: 28 pins Slide 4 Direct-Addressing Synthesis Pin-Constrained Mapping/Reduction 4 I1 O1 1 123 23 4 5 6 1 7 3 1 2 2 I2 Pin-Constrained Synthesis Problem Application Specific! Slide 5 5 The Solution Solution: Field-programmable, pin-constrained (FPPC) DMFB Generally and field-programmable Reduce pin-count (PCB layers) DMFB Type DAFPPC Dimensions12w 15h # Electrodes180111 # Unique Pins18033 Slide 6 I1 M1 I2 Det1 6 FPPC DMFB Features Complete Synthesis List Scheduling onto discrete resources e.g. 4 mixers, 4 split/store/detect modules Simple, fast left-edge binding I1 [0,1) M1 [1,4) I2 [0,1) Det1 [4,9) Slide 7 7 FPPC DMFB Features (contd) Complete Synthesis (contd) Sequential router (I/O Module, Module Module, Module I/O) Horizontal/vertical routing channels 3-pins per channel Routing cycles Direct-Addressing DMFB (DA) vs. Field-Programmable Pin-Constrained DMFB (FP) Benchmarks Array Dim. # Electrodes Used # Pins Routing Time (s) Operations Time (s) Total Time (s) DAFPDAFPDAFPDAFPDAFPDAFP PCR 15x1912x21285153285430.72.111 11.713.1 In-Vitro 1 15x1912x21285153285430.72.614 14.716.6 In-Vitro 2 15x1912x21285153285431.23.818 19.221.8 In-Vitro 3 15x1912x21285153285431.96.2221823.924.2 In-Vitro 4 15x1912x21285153285431.88.8241925.827.8 In-Vitro 5 15x1912x21285153285432.911.6322534.936.6 Protein Split 1 15x1912x21285153285431.82.971 72.873.9 Protein Split 2 15x1912x21285153285436.26.1106 112.2112.1 Protein Split 3 15x1912x212851532854313.913.5176 189.9189.5 Protein Split 4 15x1912x212851532854332.929.3316 348.9345.3 Protein Split 5 15x1912x252851772854963.661.4670596733.6657.4 Protein Split 6 15x2512x2937520337555161.2127.41156 1317.21283.4 Protein Split 7 15x2512x3137523937563290.3260.6235322762643.32536.6 Avg. Normalized Improvement: ( > 1 is improvement) 1.826.530.681.070.98 10 Experimental Results Negative Impact on Routing Offset by Positive Impact on Operation Time Yields Neutral Effect on Overall Assay Time Slide 11 FPPC DMFB vs. Direct-Addressing DMFB Direct-Addressing DMFB (DA) vs. Field-Programmable Pin-Constrained DMFB (FP) Benchmarks Array Dim. # Electrodes Used # Pins Routing Time (s) Operations Time (s) Total Time (s) DAFPDAFPDAFPDAFPDAFPDAFP PCR 15x1912x21285153285430.72.111 11.713.1 In-Vitro 1 15x1912x21285153285430.72.614 14.716.6 In-Vitro 2 15x1912x21285153285431.23.818 19.221.8 In-Vitro 3 15x1912x21285153285431.96.2221823.924.2 In-Vitro 4 15x1912x21285153285431.88.8241925.827.8 In-Vitro 5 15x1912x21285153285432.911.6322534.936.6 Protein Split 1 15x1912x21285153285431.82.971 72.873.9 Protein Split 2 15x1912x21285153285436.26.1106 112.2112.1 Protein Split 3 15x1912x212851532854313.913.5176 189.9189.5 Protein Split 4 15x1912x212851532854332.929.3316 348.9345.3 Protein Split 5 15x1912x252851772854963.661.4670596733.6657.4 Protein Split 6 15x2512x2937520337555161.2127.41156 1317.21283.4 Protein Split 7 15x2512x3137523937563290.3260.6235322762643.32536.6 Avg. Normalized Improvement: ( > 1 is improvement) 1.826.530.681.070.98 11 Experimental Results Neutral Effect Considered Positive Because of Electrode/Pin-Count Reduction Slide 12 12 Pin-Constrained Comparison Multiplexed Immunoassay DMFB PCR Assay DMFB Protein Dilution Assay DMFB Multi-Functional DMFB Xu's Pin-Constrained Results vs. Luo's Pin-Constrained Results BenchmarkArray Dim. # Electrodes Used # PinsTotal Time (s) XuLuoXuLuo PCR15x156214222030 In-Vitro 115x155925217390 Protein Split 315x15542620150170 Multi-Function15x15813727150170 Total Assay Times for Increasing Field-Prog., Pin-Constrained Array Size Array Dim. #Module (Mix/SSD) # Electrodes Used # Pins Total Time(s) PCRIn-Vitro 1Protein Split 3 12x92/3622318.5919.00- 12x123/4892715.8917.26- 12x154/61113312.8816.56- 12x185/71333913.0016.60189.65 12x216/91534313.0816.60189.53 Pin-usage for FPPC design on par with optimized PC DMFBs FPPC can perform general assays vs. optimized PCs 3 specific assays Blah 2 Slide 13 13 Pin-Constrained Comparison Multiplexed Immunoassay DMFB PCR Assay DMFB Protein Dilution Assay DMFB Multi-Functional DMFB Xu's Pin-Constrained Results vs. Luo's Pin-Constrained Results BenchmarkArray Dim. # Electrodes Used # PinsTotal Time (s) XuLuoXuLuo PCR15x156214222030 In-Vitro 115x155925217390 Protein Split 315x15542620150170 Multi-Function15x15813727150170 Total Assay Times for Increasing Field-Prog., Pin-Constrained Array Size Array Dim. #Module (Mix/SSD) # Electrodes Used # Pins Total Time(s) PCRIn-Vitro 1Protein Split 3 12x92/3622318.5919.00- 12x123/4892715.8917.26- 12x154/61113312.8816.56- 12x185/71333913.0016.60189.65 12x216/91534313.0816.60189.53 Slide 14 New DMFB design Pin-constrained design Inexpensive Field-programmable Execute a general assay Can buy an inexpensive, off-the-shelf device and run desired assay Design facilitates different DMFB and module sizes Best of both worlds Similar assay times and flexibility to recent direct- addressing DMFBs Similar pin-counts to recent pin-constrained designs More details & results in the paper/poster 14 Conclusion Slide 15 15 Slide 16 16 Experimental Results FPPC DMFB vs. Direct-Addressing DMFB Slide 17 17 I1 [0,1) O1 [4,5) M1 [1,4) I2 [0,1) I2 O1 M1 I1 I2 O1 M1 I1 O1 M1 I2 Scheduling I1 I2 O1 PlacementRouting 1 123 23 4 5 6 1 7 3 1 2 2 Pin-Mapping Slide 18 18 Traditional Pin-Constrained Synthesis Direct-Addressing Synthesis Pin-Constrained Mapping/Reducing Slide 19 19 I1 O1 1 123 23 4 5 6 1 7 3 1 2 2 I2 Pin-Constrained Example Slide 20 20 Experimental Results FPPC DMFB vs. Direct-Addressing DMFB Slide 21 21 Pin-Constrained Example