Chemical Production and Molecular Computing in Addressable Reaction Compartments

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8493)


Biological systems employ compartmentalisation in order to orchestrate a multitude of biochemical processes by simultaneously enabling “data hiding” and modularisation. In this paper, we present recent research projects that embrace compartmentalisation as an organisational programmatic principle in synthetic biological and biomimetic systems. In these systems, artificial vesicles and synthetic minimal cells are envisioned as nanoscale reactors for programmable biochemical synthesis and as chassis for molecular information processing. We present P systems, brane calculi, and the recently developed chemtainer calculus as formal frameworks providing data hiding and modularisation and thus enabling the representation of highly complicated hierarchically organised compartmentalised reaction systems. We demonstrate how compartmentalisation can greatly reduce the complexity required to implement computational functionality, and how addressable compartments permit the scaling-up of programmable chemical synthesis.


Emulsion Droplet Dissipative Particle Dynamics NAND Gate Reaction Rule Rapid Model Prototype 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Rothman, J.E.: The golgi apparatus: two organelles in tandem. Science 213(4513), 1212–1219 (1981) PMID: 7268428Google Scholar
  2. 2.
    Rothman, J.E.: Mechanisms of intracellular protein transport. Nature 372(6501), 55–63 (1994)CrossRefGoogle Scholar
  3. 3.
    Chaplin, J.C., Russell, N.A., Krasnogor, N.: Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates. Biosystems 109(1), 35–51 (2012)CrossRefGoogle Scholar
  4. 4.
    Amos, M., Dittrich, P., McCaskill, J., Rasmussen, S.: Biological and chemical information technologies. In: Proceedings from the 2nd European Future Technologies Conference and Exhibition 2011 (FET 2011), pp. 56–60. Procedia Computer Science (2011)Google Scholar
  5. 5.
    Monnard, P.A.: Liposome-entrapped polymerases as models for microscale/nanoscale bioreactors. J. Membr. Biol. 191(2), 87–97 (2003)CrossRefGoogle Scholar
  6. 6.
    Noireaux, V., Libchaber, A.: A vesicle bioreactor as a step toward an artificial cell assembly. Proc. Nat. Acad. Sci. USA 101(51), 17669–17674 (2004)CrossRefGoogle Scholar
  7. 7.
    Roodbeen, R., van Hest, J.C.M.: Synthetic cells and organelles: compartmentalization strategies. BioEssays 31(12), 1299–1308 (2009)CrossRefGoogle Scholar
  8. 8.
    Beales, P.A., Vanderlick, T.K.: Specific binding of different vesicle populations by the hybridization of membrane-anchored DNA. J. Phys. Chem. A 111(49), 12372–12380 (2007)CrossRefGoogle Scholar
  9. 9.
    Hadorn, M., Hotz, P.E.: DNA-mediated self-assembly of artificial vesicles. PLoS One 5(3), e9886 (2010)Google Scholar
  10. 10.
    Hadorn, M., Bonzli, E., Fellermann, H., Eggenberger Hotz, P., Hanczyc, M.: Specific and reversible DNA-directed self-assembly of emulsion droplets. Proc. Nat. Acad. Sci. USA 109(47) (2012)Google Scholar
  11. 11.
    Bonifacino, J.S., Glick, B.S.: The mechanisms of vesicle budding and fusion. Cell 116(2), 153–166 (2004)CrossRefGoogle Scholar
  12. 12.
    Richard, A., Marchi-Artzner, V., Lalloz, M.N., Brienne, M.J., Artzner, F., Gulik-Krzywicki, T., Guedeau-Boudeville, M.A., Lehn, J.M.: Fusogenic supramolecular vesicle systems induced by metal ion binding to amphiphilic ligands. Proc. Nat. Acad. Sci. USA 101(43), 15279–15284 (2004) PMID: 15492229Google Scholar
  13. 13.
    Caschera, F., Sunami, T., Matsuura, T., Suzuki, H., Hanczyc, M.: Programmed vesicle fusion triggers gene expression. Langmuir 27(21), 13082–13090 (2011)CrossRefGoogle Scholar
  14. 14.
    Terasawa, H., Nishimura, K., Suzuki, H., Matsuura, T., Yomo, T.: Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules. Proc. Nat. Acad. Sci. USA 109(16), 5942–5947 (2012) PMID: 22474340Google Scholar
  15. 15.
    Waage, P., Gulberg, C.M.: Studies concerning affinity. Journal of Chemical Education 63(12), 1044 (1986)CrossRefGoogle Scholar
  16. 16.
    Paun, G.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)CrossRefzbMATHMathSciNetGoogle Scholar
  17. 17.
    Cardelli, L.: Brane calculi – interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  18. 18.
    Bacci, G., Miculan, M.: Measurable stochastics for brane calculus. Theor. Comp. 431, 117–136 (2012)CrossRefzbMATHMathSciNetGoogle Scholar
  19. 19.
    Fellermann, H., Cardelli, L.: Programmable chemistry in DNA addressable bioreactors. R. Soc. Interface (2014)Google Scholar
  20. 20.
    Cardelli, L.: Strand algebras for DNA computing. Nat. Comput. 10, 407–428 (2011)CrossRefzbMATHMathSciNetGoogle Scholar
  21. 21.
    Weyland, M.S., Fellermann, H., Hadorn, M., Sorek, D., Lancet, D., Rasmussen, S., Fuchslin, R.M.: The MATCHIT automaton: Exploiting compartmentalization for the synthesis of branched polymers. Computational and Mathematical Methods in Medicine, 467428 (December 2013)Google Scholar
  22. 22.
    Varki, A.: Biological roles of oligosaccharides: all of the theories are correct. Glycobiology 3(2), 97–130 (1993) PMID: 8490246Google Scholar
  23. 23.
    Koeller, K.M., Wong, C.: Complex carbohydrate synthesis tools for glycobiologists: enzyme-based approach and programmable one-pot strategies. Glycobiology 10(11), 1157–1169 (2000)CrossRefGoogle Scholar
  24. 24.
    Smaldon, J., Romero-Campero, F.J., Trillo, F.F., Gheorghe, M., Alexander, C., Krasnogor, N.: A computational study of liposome logic: towards cellular computing from the bottom up. Systems and Synthetic Biology 4(3), 157–179 (2010)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.School of Computing ScienceNewcastle UniversityNewcastle upon TyneUnited Kingdom
  2. 2.Complex Systems LabBarcelona Biomedical Research ParkBarcelonaSpain
  3. 3.European Centre for Living TechnologyVeneziaItaly

Personalised recommendations