Abstraction layers for scalable microfluidic biocomputing

Natural Computing

Volumn 7, Issue 2, 2008, Pages 255-275

  Thies, William ^a   Urbanski, John Paul ^b   Thorsen, Todd ^b   Amarasinghe, Saman ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Biological computation; DNA computing; Laboratory automation; Microfluidics; Programming languages; Self assembly

Indexed keywords

COMPUTER AIDED DESIGN; COMPUTER LANGUAGE; CONFERENCE PAPER; DATA ANALYSIS SOFTWARE; GENETIC ALGORITHM; INFORMATION PROCESSING DEVICE; MATHEMATICAL COMPUTING; MICROFLUIDIC ANALYSIS; MOLECULAR COMPUTER; PROCESS DESIGN;

EID: 44249090445     PISSN: 15677818     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11047-006-9032-6     Document Type: Conference Paper

References (49)

1. R Adar Y Benenson G Linshiz A Rozner N Tishby E Shapiro 2004 Stochastic computing with biomolecular automata PNAS 101 9960 9965 10.1073/pnas.0400731101 Adar R, Benenson Y, Linshiz G, Rozner A, Tishby N, Shapiro E (2004) Stochastic computing with biomolecular automata. PNAS 101:9960–9965
2. L Adleman 1994 Molecular computation of solutions to combinatorial problems Science 266 1021 1024 10.1126/science.7973651 Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024
3. Alfred V. Aho RS, Ullman JD (1988) Compilers: principles, techniques, and tools, 2nd edn. Addison-Wesley Publishing Company, pp 561
4. L Allan N Morrice S Brady G Magee S Pathak P Clarke 2003 Inhibition of caspase-9 through phosphorylation at Thr 125 by ERK MAPK Nature Cell Biol 5 647 654 10.1038/ncb1005 Allan L, Morrice N, Brady S, Magee G, Pathak S, Clarke P (2003) Inhibition of caspase-9 through phosphorylation at Thr 125 by ERK MAPK. Nature Cell Biol 5:647–654
5. Batten C, Krashinsky R, Knight JT (2004) A scalable cellular logic technology using zinc-finger proteins. In 3rd workshop on non-silicon computing
6. K Benenson T Paz-Elitzur R Adar E Keinan Z Livneh E Shapiro 2001 Programmable and autonomous computing machine made of biomolecules Nature 414 430 434 10.1038/35106533 Benenson K, Paz-Elitzur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Programmable and autonomous computing machine made of biomolecules. Nature 414:430–434
7. Y Benenson B Gil U Ben-Dor R Adar E Shapiro 2004 An autonomous molecular computer for logical control of gene expression Nature 429 423 429 10.1038/nature02551 Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429:423–429
8. RS Braich N Chelyapov C Johnson PWK Rothemund L Adleman 2002 Solution of a 20-variable 3-SAT problem on a DNA computer Science 296 499 502 10.1126/science.1069528 Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296:499–502
9. DN Breslauer PJ Lee LP Lee 2006 Microfluidics-based systems biology Mol BioSystems 2 97 112 10.1039/b515632g Breslauer DN, Lee PJ, Lee LP (2006) Microfluidics-based systems biology. Mol BioSystems 2:97–112
10. H Chou M Unger S Quake 2001 A microfabricated rotary pump Biomed Microdevices 3 323 330 10.1023/A:1012412916446 Chou H, Unger M, Quake S (2001) A microfabricated rotary pump. Biomed Microdevices 3:323–330
11. SKW Dertinger DT Chiu NL Jeon GM Whitesides 2001 Generation of gradients having complex shapes using microfluidic networks Anal Chem 73 1240 1246 10.1021/ac001132d Dertinger SKW, Chiu DT, Jeon NL, Whitesides GM (2001) Generation of gradients having complex shapes using microfluidic networks. Anal Chem 73:1240–1246
12. H Ellerby S Martin L Ellerby S Naiem S Rabizadeh G Salvesen C Casiano N Cashman D Green D Bredesen 1997 Establishment of a cell-free system of neuronal apoptosis: comparison of premitochondrial, mitochondrial, and postmitochondrial phases Neuroscience 17 6165 6178 Ellerby H, Martin S, Ellerby L, Naiem S, Rabizadeh S, Salvesen G, Casiano C, Cashman N, Green D, Bredesen D (1997) Establishment of a cell-free system of neuronal apoptosis: comparison of premitochondrial, mitochondrial, and postmitochondrial phases. Neuroscience 17:6165–6178
13. M Elowitz S Leibler 2000 A synthetic oscillatory network of transcriptional regulators Nature 403 335 338 10.1038/35002125 Elowitz M, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338
14. D Erickson D Li 2004 Integrated microfluidic devices Anal Chim Acta 507 11 26 10.1016/j.aca.2003.09.019 Erickson D, Li D (2004) Integrated microfluidic devices. Anal Chim Acta 507:11–26
15. Z Ezziane 2006 DNA Computing: applications and challenges Nanotechnology 17 173 198 10.1088/0957-4484/17/2/R01 Ezziane Z (2006) DNA Computing: applications and challenges. Nanotechnology 17:173–198
16. Farfel J, Stefanovic D (2005) Towards practical biomolecular computers using microfluidic deoxyribozyme logic gate networks. In proceedings of the 11th international meeting on DNA computing, 38–54
17. D Faulhammer AR Cukras RJ Lipton LF Landweber 2000 Molecular computation: RNA solutions to chess problems PNAS 97 4 1385 1389 10.1073/pnas.97.4.1385 Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Molecular computation: RNA solutions to chess problems. PNAS 97(4):1385–1389
18. PRC Gascoyne JV Vykoukal JA Schwartz TJ Anderson DM Vykoukal KW Current C McConaghy FF Becker C Andrews 2004 Dielectrophoresis-based programmable fluidic processors Lab Chip 4 299 309 10.1039/b404130e Gascoyne PRC, Vykoukal JV, Schwartz JA, Anderson TJ, Vykoukal DM, Current KW, McConaghy C, Becker FF, Andrews C (2004) Dielectrophoresis-based programmable fluidic processors. Lab Chip 4:299–309
19. A Gehani J Reif 1999 Micro flow bio-molecular computation Biosystems 52 197 216 10.1016/S0303-2647(99)00048-9 Gehani A, Reif J (1999) Micro flow bio-molecular computation. Biosystems 52:197–216
20. WH Grover RA Mathies 2005 An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing Lab Chip 5 1033 1040 10.1039/b505840f Grover WH, Mathies RA (2005) An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. Lab Chip 5:1033–1040
21. W Gu X Zhu N Futai BS Cho S Takayama 2004 Computerized microfluidic cell culture using elastomeric channels and Braille displays PNAS 101 45 15861 15866 10.1073/pnas.0404353101 Gu W, Zhu X, Futai N, Cho BS, Takayama S (2004) Computerized microfluidic cell culture using elastomeric channels and Braille displays. PNAS 101(45):15861–15866
22. JW Hong SR Quake 2003 Integrated nanoliter systems Nature BioTechnol 21 10 1179 1183 10.1038/nbt871 Hong JW, Quake SR (2003) Integrated nanoliter systems. Nature BioTechnol 21(10):1179–1183
23. Johnson C (2006) Automating the DNA computer to solve n-variable 3-SAT problems. In Proceedings of the 12th international meeting on DNA computing, 360–373
24. RD King KE Whelan FM Jones PGK Reiser CH Bryant SH Muggleton DB Kell SG Oliver 2004 Functional genomic hypothesis generation and experimentation by a robot scientist Nature 427 247 252 10.1038/nature02236 King RD, Whelan KE, Jones FM, Reiser PGK, Bryant CH, Muggleton SH, Kell DB, Oliver SG (2004) Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 427:247–252
25. H Kitano 2002 Computational systems biology Nature 420 206 210 10.1038/nature01254 Kitano H (2002) Computational systems biology. Nature 420:206–210
26. Knight T, Sussman G (1998) Cellular gate technology. In Proceedings of the 1st international conference on unconventional models of computation
27. F Lin W Saadi SW Rhee S-J Wang S Mittalb NL Jeon 2004 Generation of dynamic temporal and spatial concentration gradients using microfluidic devices Lab Chip 4 164 167 10.1039/b313600k Lin F, Saadi W, Rhee SW, Wang S-J, Mittalb S, Jeon NL (2004) Generation of dynamic temporal and spatial concentration gradients using microfluidic devices. Lab Chip 4:164–167
28. MS Livstone R Weiss LF Landweber 2006 Automated design and programming of a microfluidic DNA computer Nat Comput 5 1 13 1114.68044 10.1007/s11047-005-3803-3 2208808 Livstone MS, Weiss R, Landweber LF (2006) Automated design and programming of a microfluidic DNA computer. Nat Comput 5:1–13
29. Fluidigm Corportaion (2006) Fluidigm glossary-Moore’s Law. Website. http://www.fluidigm.com/gloss_mlaw.i.ht
30. JS McCaskill 2001 Optically programming DNA computing in microflow reactors BioSystems 59 125 138 10.1016/S0303-2647(01)00099-5 McCaskill JS (2001) Optically programming DNA computing in microflow reactors. BioSystems 59:125–138
31. C Neils Z Tyree B Finlayson A Folch 2004 Combinatorial mixing of microfluidic streams Lab Chip 4 342 350 10.1039/b314962e Neils C, Tyree Z, Finlayson B, Folch A (2004) Combinatorial mixing of microfluidic streams. Lab Chip 4:342–350
32. Q Ouyang PD Kaplan S Liu A Libchaber 1997 DNA solution of the maximal clique problem Science 278 446 449 10.1126/science.278.5337.446 Ouyang Q, Kaplan PD, Liu S, Libchaber A (1997) DNA solution of the maximal clique problem. Science 278:446–449
33. P Paik V Pamula R Fair 2003 Rapid droplet mixers for digital microfluidic systems Lab Chip 3 253 259 10.1039/b307628h Paik P, Pamula V, Fair R (2003) Rapid droplet mixers for digital microfluidic systems. Lab Chip 3:253–259
34. N Pisanti 1998 DNA computing: a survey Bull EATCS 64 171 187 Pisanti N (1998) DNA computing: a survey. Bull EATCS 64:171–187
35. M Pollack R Fair A Shenderov 2000 Electrowetting-based actuation of liquid droplets for microfluidic applications Appl Phys Lett 77 11 1725 1726 10.1063/1.1308534 Pollack M, Fair R, Shenderov A (2000) Electrowetting-based actuation of liquid droplets for microfluidic applications. Appl Phys Lett 77(11):1725–1726
36. Ren H, Srinivasan V, Fair R (2003) Design and testing of an interpolating mixing architecture for electrowetting-based droplet-on-chip chemical dilution. Proceedings of the 12th international conference on solid state sensors, actuators, and microsystems, 619–622
37. SK Sia GM Whitesides 2003 Microfluidic devices fabricated in poly(dimethylsiloxane) for biological studies Electrophoresis 24 3563 3576 10.1002/elps.200305584 Sia SK, Whitesides GM (2003) Microfluidic devices fabricated in poly(dimethylsiloxane) for biological studies. Electrophoresis 24:3563–3576
38. Somei K, Kaneda S, Fujii T, Murata S (2005) A microfluidic device for DNA tile self-assembly. In Proceedings of the 11th international meeting on DNA computing, 325–335
39. Su F, Chakrabarty K (2004) Architectural-level synthesis of digital niicrofluidics-based biochips. In Proceedings of the 2004 international conference on computer aided design, 223–228
40. Su F, Chakrabarty K (2005) Unified high-level synthesis and module placement for defect-tolerant microfluidic biochips. In Proceedings of the 42nd design automation conference 825–830
41. Thies W, Urbanski JP, Thorsen T, Amarasinghe S (2006) Abstraction layers for scalable microfluidic biocomputers. In Proceedings of the 12th international meeting on DNA computing, 308–323
42. T Thorsen S Maerkl S Quake 2002 Microfluidic large scale integration Science 298 580 584 10.1126/science.1076996 Thorsen T, Maerkl S, Quake S (2002) Microfluidic large scale integration. Science 298:580–584
43. JP Urbanski W Thies C Rhodes S Amarasinghe T Thorsen 2006 Digital microfluidics using soft lithography Lab Chip 6 96 104 10.1039/b510127a Urbanski JP, Thies W, Rhodes C, Amarasinghe S, Thorsen T (2006) Digital microfluidics using soft lithography. Lab Chip 6:96–104
44. van Noort D (2005) A programmable molecular computer in microreactors. In Proceedings of the 11th international meeting on DNA computing, 365–374
45. van Noort D, Gast F-U, McCaskill JS (2002) DNA computing in microreactors. In Proceedings of the 8th international meeting on DNA computing, 33–45
46. van Noort D, Zhang B-T (2004) PDMS valves in DNA computers. In: SPIE international symposium on smart materials, nano-, and micro-smart systems, pp 214–220
47. E Winfree 2003 DNA computing by self-assembly The Bridge 33 4 37 38 Winfree E (2003) DNA computing by self-assembly. The Bridge 33(4):37–38
48. E Winfree F Liu L Wenzler N Seeman 1998 Design and self-assembly of two-dimensional DNA crystals Nature 394 539 544 10.1038/28998 Winfree E, Liu F, Wenzler L, Seeman N (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544
49. Yamamoto M, Matsuura N, Shiba T, Kawazoe Y, Ohuchi A (2002) Solutions of shortest path problems by concentration control. In Proceedings of the 7th international meeting on DNA computing, 203–212