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Microfluidic Chips

Microfluidic Biochips: Design, Programming, and Optimization Bill Thies Joint work with Vaishnavi Ananthanarayanan, J.P. Urbanski , Nada Amin , David Craig, Jeremy Gunawardena , Todd Thorsen , and Saman Amarasinghe Indian Statistical Institute March 2, 2011. Microfluidic Chips.

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Microfluidic Chips

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  1. Microfluidic Biochips: Design, Programming, and OptimizationBill ThiesJoint work with Vaishnavi Ananthanarayanan, J.P. Urbanski, Nada Amin, David Craig, Jeremy Gunawardena, Todd Thorsen, and Saman AmarasingheIndian Statistical InstituteMarch 2, 2011

  2. Microfluidic Chips • Idea: a whole biology lab on a single chip • Input/output • Sensors: pH, glucose, temperature, etc. • Actuators: mixing, PCR, electrophoresis, cell lysis, etc. • Benefits: • Small sample volumes • High throughput • Geometrical manipulation • Portability • Applications: • Biochemistry - Cell biology • Biological computing 10x real-time 1 mm

  3. Application to Rural Diagnostics DxBox U. Washington,Micronics, Inc., Nanogen, Inc. Targets: - malaria (done) - dengue, influenza,Rickettsial diseases, typhoid, measles (under development) CARD Rheonix, Inc. Targets: - HPV diagnosis - Detection of specific gene sequences Disposable EntericCard PATH,Washington U.Micronics, Inc., U. Washington Targets: - E. coli, Shigella, Salmonella, C. jejuni

  4. Moore’s Law of Microfluidics:Valve Density Doubles Every 4 Months Source: Fluidigm Corporation (http://www.fluidigm.com/images/mlaw_lg.jpg)

  5. Moore’s Law of Microfluidics:Valve Density Doubles Every 4 Months Source: Fluidigm Corporation (http://www.fluidigm.com/didIFC.htm)

  6. Current Practice: Manage Gate-Level Details from Design to Operation • For every change in the experiment or the chip design: fabricate chip 2. Operate each gate from LabView 1. Manually draw in AutoCAD

  7. Abstraction Layers for Microfluidics Silicon Analog Protocol Description Language - architecture-independent protocol description C Fluidic Instruction Set Architecture (ISA) - primitives for I/O, storage, transport, mixing x86 Pentium III,Pentium IV chip 1 chip 2 chip 3 transistors, registers, … Fluidic Hardware Primitives - valves, multiplexers, mixers, latches

  8. Abstraction Layers for Microfluidics Contributions Protocol Description Language - architecture-independent protocol description BioCoder Language [J.Bio.Eng. 2010] Optimized Compilation [Natural Computing 2007] Fluidic Instruction Set Architecture (ISA) - primitives for I/O, storage, transport, mixing Demonstrate Portability [DNA 2006] Micado AutoCAD Plugin [MIT 2008, ICCD 2009] chip 1 chip 2 chip 3 Digital Sample Control Using Soft Lithography [Lab on a Chip ‘06] Fluidic Hardware Primitives - valves, multiplexers, mixers, latches

  9. Droplets vs. Continuous Flow • Digital manipulation of droplets on an electrode array [Chakrabarty, Fair, Gascoyne, Kim, …] • Pro: • Reconfigurable routing • Electrical control • More traction in CAD community Source: Chakrabarty et al, Duke University • Continuous flow of fluids (or droplets) through fixed channels [Whitesides, Quake, Thorsen, …] • Pro: • Smaller, more precise sample sizes • Made-to-order availability [Stanford] • More traction in biology community

  10. Primitive 1: A Valve (Quake et al.) Control Layer 0. Start with mask of channels Flow Layer

  11. Primitive 1: A Valve (Quake et al.) Control Layer 1. Deposit pattern on silicon wafer Flow Layer

  12. Primitive 1: A Valve (Quake et al.) Control Layer 2. Pour PDMS over mold - polydimexylsiloxane: “soft lithography” Thick layer (poured) Thin layer (spin-coated) Flow Layer

  13. Primitive 1: A Valve (Quake et al.) Control Layer 3. Bake at 80° C(primary cure), then release PDMS from mold Flow Layer

  14. Primitive 1: A Valve (Quake et al.) Control Layer 4a. Punch hole in control channel4b. Attach flow layer to glass slide Flow Layer

  15. Primitive 1: A Valve (Quake et al.) Control Layer 5. Align flow layer over control layer Flow Layer

  16. Primitive 1: A Valve (Quake et al.) Control Layer 6. Bake at 80° C (secondary cure) Flow Layer

  17. Primitive 1: A Valve (Quake et al.) 7. When pressure is high, controlchannel pinches flow channel toform a valve Control Layer pressure actuator Flow Layer

  18. Primitive 2: A Multiplexer (Thorsen et al.) flow layer control layer Bit 2 Bit 1 Bit 0 1 1 1 0 0 0 • Control lines can cross flow lines • - Only thick parts make valves Output 7 Output 6 Output 5 Input Output 4 • Logic is not • complimentary • To control n flow lines, • need 2 log2 n control lines Output 3 Output 2 Output 1 Output 0

  19. Primitive 2: A Multiplexer (Thorsen et al.) flow layer control layer Bit 2 Bit 1 Bit 0 1 1 1 0 0 0 • Control lines can cross flow lines • - Only thick parts make valves Output 7 Output 6 Output 5 Input Output 4 • Logic is not • complimentary • To control n flow lines, • need 2 log2 n control lines Output 3 Output 2 Output 1 Output 0 Example: select 3 = 011

  20. Primitive 2: A Multiplexer (Thorsen et al.) flow layer control layer Bit 2 Bit 1 Bit 0 1 1 1 0 0 0 • Control lines can cross flow lines • - Only thick parts make valves Output 7 Output 6 Output 5 Input Output 4 • Logic is not • complimentary • To control n flow lines, • need 2 log2 n control lines Output 3 Output 2 Output 1 Output 0 Example: select 3 = 011

  21. Primitive 2: A Multiplexer (Thorsen et al.) flow layer control layer Bit 2 Bit 1 Bit 0 1 1 1 0 0 0 • Control lines can cross flow lines • - Only thick parts make valves Output 7 Output 6 Output 5 Input Output 4 • Logic is not • complimentary • To control n flow lines, • need 2 log2 n control lines Output 3 Output 2 Output 1 Output 0 Example: select 3 = 011

  22. Primitive 3: A Mixer (Quake et al.) 1. Load sample on bottom 2. Load sample on top 3. Peristaltic pumping Rotary Mixing

  23. Primitive 4: A Latch (Our contribution) • Purpose: align sample with specific location on device • Examples: end of storage cell, end of mixer, middle of sensor • Latches are implemented as a partially closed valve • Background flow passes freely • Aqueous samples are caught Sample Latch

  24. Primitive 4: A Latch (Our contribution) • Purpose: align sample with specific location on device • Examples: end of storage cell, end of mixer, middle of sensor • Latches are implemented as a partially closed valve • Background flow passes freely • Aqueous samples are caught Sample Latch

  25. Primitive 5: Cell Trap • Several methods for confining cells in microfluidic chips • U-shaped weirs - C-shaped rings / microseives • Holographic optical traps - Dialectrophoresis • In our chips: U-Shaped Microseives in PDMS Chambers Source: Wang, Kim, Marquez, and Thorsen, Lab on a Chip 2007

  26. Primitive 6: Imaging and Detection • As PDMS chips are translucent,contents can be imaged directly • Fluorescence, color, opacity, etc. • Feedback can be used todrive the experiment

  27. Abstraction Layers for Microfluidics Protocol Description Language - architecture-independent protocol description Fluidic Instruction Set Architecture (ISA) - primitives for I/O, storage, transport, mixing chip 1 chip 2 chip 3 Fluidic Hardware Primitives - valves, multiplexers, mixers, latches

  28. Driving Applications 1. What are the best indicators for oocyte viability? • With Mark Johnson’s andTodd Thorsen’s groups • During in-vitro fertilization, monitor cell metabolites and select healthiest embryo for implantation 2. How do mammalian signal transduction pathways respond to complex inputs? • With Jeremy Gunawardena’sand Todd Thorsen’s groups • Isolate cells and stimulate with square wave, sine wave, etc.

  29. Driving Applications 1. What are the best indicators for oocyte viability? • With Mark Johnson’s andTodd Thorsen’s groups • During in-vitro fertilization, monitor cell metabolites and select healthiest embryo for implantation 2. How do mammalian signal transduction pathways respond to complex inputs? • With Jeremy Gunawardena’sand Todd Thorsen’s groups • Isolate cells and stimulate with square wave, sine wave, etc. Video courtesy David Craig

  30. CAD Tools for Microfluidic Chips • Goal: automate placement, routing, control of microfluidic features • Why is this different than electronic CAD?

  31. CAD Tools for Microfluidic Chips • Goal: automate placement, routing, control of microfluidic features • Why is this different than electronic CAD? 1. Control ports (I/O pins) are bottleneck to scalability • Pressurized control signals cannot yet be generated on-chip • Thus, each logical set of valves requires its own I/O port 2. Control signals correlated due to continuous flows  Demand & opportunity for minimizing control logic pipelined flow continuous flow

  32. Our Technique:Automatic Generation of Control Layer

  33. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA

  34. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA

  35. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA

  36. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves

  37. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves

  38. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing

  39. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing

  40. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports

  41. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports

  42. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports

  43. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports 5. Generate an interactive GUI

  44. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports 5. Generate an interactive GUI

  45. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports 5. Generate an interactive GUI

  46. Our Technique:Automatic Generation of Control Layer 1. Describe Fluidic ISA 2. Infer control valves 3. Infer control sharing 4. Route valves to control ports 5. Generate an interactive GUI

  47. 1. Describe a Fluidic ISA • Hierarchical and composable flow declarations Sequential flow P1 P2 AND-flow F1Λ F2 OR-flow F1 \/ F2 Mixing mix(F) Pumped flow pump(F) P1 P2 F1 F2 F1 F1 or F2 F2 F F

  48. 1. Describe a Fluidic ISA

  49. 1. Describe a Fluidic ISA mix-and-store (S1, S2, D) { 1. in1 top  out 2. in2 bot  out 3. mix(top bot-left bot-right  top) 4. wash  bot-right  top  bot-left  store } 50x real-time

  50. 2. Infer Control Valves

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