nach oben

Natural Computing

Erschienen in:

01.06.2008

Abstraction layers for scalable microfluidic biocomputing

verfasst von: William Thies, John Paul Urbanski, Todd Thorsen, Saman Amarasinghe

Erschienen in: Natural Computing | Ausgabe 2/2008

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

Microfluidic devices are emerging as an attractive technology for automatically orchestrating the reactions needed in a biological computer. Thousands of microfluidic primitives have already been integrated on a single chip, and recent trends indicate that the hardware complexity is increasing at rates comparable to Moore’s Law. As in the case of silicon, it will be critical to develop abstraction layers—such as programming languages and Instruction Set Architectures (ISAs)—that decouple software development from changes in the underlying device technology. Towards this end, this paper presents BioStream, a portable language for describing biology protocols, and the Fluidic ISA, a stable interface for microfluidic chip designers. A novel algorithm translates microfluidic mixing operations from the BioStream layer to the Fluidic ISA. To demonstrate the benefits of these abstraction layers, we build two microfluidic chips that can both execute BioStream code despite significant differences at the device level. We consider this to be an important step towards building scalable biological computers.

Vorheriger Artikel Automating the DNA computer: solving n-Variable 3-SAT problems

Nächster Artikel Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

lg n denotes log₂ n.

Alternately, BioStream supports a global error tolerance ε that applies to all concentrations.

Adar R, Benenson Y, Linshiz G, Rozner A, Tishby N, Shapiro E (2004) Stochastic computing with biomolecular automata. PNAS 101:9960–9965CrossRef

Adleman L (1994) Molecular computation of solutions to combinatorial problems. Science 266:1021–1024CrossRef

Alfred V. Aho RS, Ullman JD (1988) Compilers: principles, techniques, and tools, 2nd edn. Addison-Wesley Publishing Company, pp 561

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 5:647–654CrossRef

Batten C, Krashinsky R, Knight JT (2004) A scalable cellular logic technology using zinc-finger proteins. In 3rd workshop on non-silicon computing

Benenson K, Paz-Elitzur T, Adar R, Keinan E, Livneh Z, Shapiro E (2001) Programmable and autonomous computing machine made of biomolecules. Nature 414:430–434CrossRef

Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429:423–429CrossRef

Braich RS, Chelyapov N, Johnson C, Rothemund PWK, Adleman L (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296:499–502CrossRef

Breslauer DN, Lee PJ, Lee LP (2006) Microfluidics-based systems biology. Mol BioSystems 2:97–112CrossRef

Chou H, Unger M, Quake S (2001) A microfabricated rotary pump. Biomed Microdevices 3:323–330CrossRef

Dertinger SKW, Chiu DT, Jeon NL, Whitesides GM (2001) Generation of gradients having complex shapes using microfluidic networks. Anal Chem 73:1240–1246CrossRef

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

Elowitz M, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338CrossRef

Erickson D, Li D (2004) Integrated microfluidic devices. Anal Chim Acta 507:11–26CrossRef

Ezziane Z (2006) DNA Computing: applications and challenges. Nanotechnology 17:173–198CrossRef

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

Faulhammer D, Cukras AR, Lipton RJ, Landweber LF (2000) Molecular computation: RNA solutions to chess problems. PNAS 97(4):1385–1389CrossRef

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 4:299–309CrossRef

Gehani A, Reif J (1999) Micro flow bio-molecular computation. Biosystems 52:197–216CrossRef

Grover WH, Mathies RA (2005) An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. Lab Chip 5:1033–1040CrossRef

Gu W, Zhu X, Futai N, Cho BS, Takayama S (2004) Computerized microfluidic cell culture using elastomeric channels and Braille displays. PNAS 101(45):15861–15866CrossRef

Hong JW, Quake SR (2003) Integrated nanoliter systems. Nature BioTechnol 21(10):1179–1183CrossRef

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

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 427:247–252CrossRef

Kitano H (2002) Computational systems biology. Nature 420:206–210CrossRef

Knight T, Sussman G (1998) Cellular gate technology. In Proceedings of the 1st international conference on unconventional models of computation

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 4:164–167CrossRef

Livstone MS, Weiss R, Landweber LF (2006) Automated design and programming of a microfluidic DNA computer. Nat Comput 5:1–13MATHCrossRefMathSciNet

Fluidigm Corportaion (2006) Fluidigm glossary - Moore’s Law. Website. http://www.fluidigm.com/gloss_mlaw.i.ht

McCaskill JS (2001) Optically programming DNA computing in microflow reactors. BioSystems 59:125–138CrossRef

Neils C, Tyree Z, Finlayson B, Folch A (2004) Combinatorial mixing of microfluidic streams. Lab Chip 4:342–350CrossRef

Ouyang Q, Kaplan PD, Liu S, Libchaber A (1997) DNA solution of the maximal clique problem. Science 278:446–449CrossRef

Paik P, Pamula V, Fair R (2003) Rapid droplet mixers for digital microfluidic systems. Lab Chip 3:253–259CrossRef

Pisanti N (1998) DNA computing: a survey. Bull EATCS 64:171–187

Pollack M, Fair R, Shenderov A (2000) Electrowetting-based actuation of liquid droplets for microfluidic applications. Appl Phys Lett 77(11):1725–1726CrossRef

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

Sia SK, Whitesides GM (2003) Microfluidic devices fabricated in poly(dimethylsiloxane) for biological studies. Electrophoresis 24:3563–3576CrossRef

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

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

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

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

Thorsen T, Maerkl S, Quake S (2002) Microfluidic large scale integration. Science 298:580–584CrossRef

Urbanski JP, Thies W, Rhodes C, Amarasinghe S, Thorsen T (2006) Digital microfluidics using soft lithography. Lab Chip 6:96–104CrossRef

van Noort D (2005) A programmable molecular computer in microreactors. In Proceedings of the 11th international meeting on DNA computing, 365–374

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

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

Winfree E (2003) DNA computing by self-assembly. The Bridge 33(4):37–38

Winfree E, Liu F, Wenzler L, Seeman N (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–544CrossRef

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

Titel: Abstraction layers for scalable microfluidic biocomputing
verfasst von: William Thies
John Paul Urbanski
Todd Thorsen
Saman Amarasinghe
Publikationsdatum: 01.06.2008
Verlag: Springer Netherlands
Erschienen in: Natural Computing / Ausgabe 2/2008
Print ISSN: 1567-7818
Elektronische ISSN: 1572-9796
DOI: https://doi.org/10.1007/s11047-006-9032-6

Springer Professional

Abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"

Weitere Artikel der Ausgabe 2/2008

Combining self-healing and proofreading in self-assembly

Spiking neural P systems with extended rules: universality and languages

Foreword

Automating the DNA computer: solving n-Variable 3-SAT problems

On the complexity of graph self-assembly in accretive systems

Unravel four hairpins!