2011

Peer-reviewed 2011

Journal Articles
  1. On the Growth Rate of Non-Enzymatic Molecular Replicators. / Fellermann, H. & Rasmussen, S. Entropy 2011, 13(10), 1882-1903 (2011)
  2. Amino Acids Attached to 2'-amino-LNA: Synthesis and Excellent Duplex Stability. / Johannsen, M. W. ; Crispino, L. ; Wamberg, M. C. ; Kalra, N. ; Wengel, J.I: Organic & Biomolecular Chemistry, Vol. 9, Nr. 1, 07.01.2011, pp. 243-252 (2011)
  3. Molecular Logic Gates using Surface-Enhanced Raman.Scattered Light. / Witlicki, E. H.; Johnsen, C.; Hansen, S. W.; Silverstein, D. W.; Bottomley, V. J.; Jeppesen, J. O.; Wong, E. W.; Jensen, L. & Flood, A. H. American Chemical Society Journal, vol. 133, 19 (2011)
  4. Coping With Complexity: Machine Learning Optimization of Cell-Free Protein Synthesis. / Caschera, F. ; Bedau, M. ; Buchanan, A. ; Cawse, J. ; de Lucrezia, D. ; Gazzola, G. ; Hanczyc, M. ; Packard, N.. I: Biotechnology and Bioengineering, Vol. 108, Issue 9, pp 2218-2228 (2011).
  5. Synthesis and Complexation Studies between Trifluoromethylammonium Threads and Dibenzo[24]Crown-8. / Johnsen, C,; Stein, P. C.; Nielsen, K.; Bond, A. D. & Jeppesen, J. O. European Journal of Organic Chemistry, vol. 2011, No. 4, pp 759 - 769 (2011)
  6. Interactions Between Catalysts and Amphiphile Structures and Their Implications for a Protocell Model. / Maurer, S. E.; DeClue, M. S.; Albertsen, A. N.;Dörr, M.; Kuiper, D. S.; Ziock, H.-J.; Rasmussen, S.; Boncella, J. M.; Monnard, P.-A..I: ChemPhysChem, Vol. 12, Issue 4, pp. 828-835 (2011).
  7. Mode Switching and Collective Behavior in Chemical Oil Droplets. / Horibe, N.; Hanczyc, M.; Ikegami, T.I: Entropy, Vol. 13, Nr. 3, pp. 709-719 (2011).
  8. Prebiotically Relevant Mixed Fatty Acid Vesicles Support Anionic Solute Encapsulation and Photochemically Catalyzed Trans-membrane Charge Transport. / Cape, J. L.; Monnard, P.-A.; Boncella, J. M..I: Chemical Science, Vol. 2, pp. 661-667 (2011).
  9. Primitive Membrane Formation, Characteristics and Roles in Emergent Properties of a Protocell. / Maurer, S.E.; Monnard, P.-A. I: Entropy, Vol. 13, pp. 466-484 (2011).
  10. Pyrene Intercalating Nucleic Acids with a Carbon Linker./ Østergaard, M.E.; Wamberg, M.C. & Pedersen, E.B. Nucleosides, Nucleotides and Nucleic Acids, Vol. 30, pp 210-226 (2011)
  11. The Ten Grand Challenges of Synthetic Life. / Porcar, M.; Danchin, A.; de Lorenzo, V.; dos Santos, V.; Krasnogor, N.; Rasmussen; S. & Moya, A. Systems and Synthetic Biology, 5 (1-2), pp 1-9, SpringerLink. (2011)
  12. Stable Vesicles Composed of Mono-or Dicarboxylic Fatt Acids and Trimethylammonium Amphiphiles. / Caschera, F.; Bernadino de la Serna, J.; Löffler, P.M.G.; Rasmussen, T.E.; Hanczyc, M.; Bagatolli, L. & Monnard, P.-A. Langmuir, 27 (23), 14078-14090, dx.doi.org/10.1021/la203057b (2011)
  13. Metabolism and motility in prebiotic structures. / Hanczyc, M.M. Philosophical Transactions of the Royal Society B, vol. 366, no. 1580, pp 2885-2893 (2011)
  14. A Quantitative Analytical Method to Test for Salt Effects on Giant Unilamellar Vesicles / Hadorn, M.; Boenzli, E. & Eggenberger, P. H. Scientific Reports 1 (168) (2011)
  15. Non-enzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self-Condensation and Template-directed Reactions. / Dorr, M.; Loffler, P.M.G. & Monnard, P.-A.. Current Organic Synthesis (2011) - Accepted
  16. Programmed Vesicle Fusion Triggers Gene Expression. / Caschera, F.; Sumani, T.; Matsuura, T.; Suzuki, H.; Hanczyc, M. & Yomo, T.. Langmuir 27(21), pp 13082 - 13090 (2011)
  17. Influence of geometry on hydrodynamic focusing and long-range fluid behavior in PDMS microfluidic chips. / Kunstmann-Olsen, C.; Hoyland, J. & Rubahn, H.-G. Microfluidics and Nanofluidics (2011)
  18. Acid/Base Controllable Molecular Recognition. / Nielsen, K.; Bähring, S. & Jeppesen, J. O. Chemistry: A European Journal, vol. 17, no. 39, pp 11001 - 11007 (2011)
  19. Self-assembling scenarios of block-copolymer stars, C. Koch, C. N. Likos, A. Z. Panagiotopoulos, Federica Lo Verso, Molecular Physics 109, 3049-3060 (2011)
  20. Interactions between polymer brush-coated spherical nanoparti cles: The good solvent case, Federica Lo Verso, L. Yelash, S. A. Egorov, K. Binder, Journal of Chemical Physics 135, 214902/1-214902/10 (2011) Selected for publication in the Virtual Journal of Biological Physics Research, issue of December 15 (2011)  
Book Chapters
  1. Membrane self-assembly processes: steps towards the first cellular life. Monnard, P.-A. & Deamer, D. W., Minimal cells (2011).
Contributions to Conference Proceedings
  1. A Review of one Approach to Bottom-up Assembly of Minimal Life. / Rasmussen, S.; Monnard, P.-A,; Hanczyc, M.; Albertsen, A.N.; Bönzli, E.; Caschera, F.; Dörr, M.; Fellermann, H.; Jørgensen, W. H.; Löffler, P.M.G.; Maurer, S.E.; Nielsen, K.A.; Pedersen, P.L.; Svaneborg, C.; Wamberg, M.C.; Wieczorek, R. & Ziock, H.J.. Proceedings of the Eleventh European Conference on the Synthesis of Simulation of Living Systems, ECAL 2011. MIT Press (2011)
  2. Encapsulated Multi-vesicle Assemblies of Programmable Architecture: Towards Personalized Healthcare. / Hadorn, M. & Hotz, P.E..in Biomedical Engineering Systems and Technologies, edited by A. Fred, J. Filipe, & H. Gamboa (Springer-Verlag Berlin, Berlin, 2011), Vol. 127, pp. 141-151 (2011)
  3. Machine Learning for Drug Design, Molecular Machines and Evolable Artificial Cells. / Cashera, F.; Hanczyc, M. & Rasmussen, S. Proceedings of the 13th Annual Conference Companion on Genetic and Evolutionary Computation (GECCO 11). ACM, New York (2011)
  4. Assembling Living Materials and Engineering Life-like Technologies. / Rasmussen, S.; Albertsen, A.N.; Fellermann, H.; Pedersen, P.l.; Svaneborg, C. & Ziock, H.J..Proceedings of the 13th Annual Conference Companion on Genetic and Evolutionary Computation (GECCO 11). ACM, New York (2011) 15
  5. Biological and Chemical Information Technologies. / Amos, M.; Dittrich, P.; McCaskill, J. & Rasmussen, S. Proceedings from the 2nd European Future Technologies Conference and Exhibition 2011 (FET 11) - Procedia Computer Science 7, pp 56-60, Elsevier (2011)
Conference Abstracts/Extended Abstracts
  1. Bottom Up Assembly of Minimal Life. / Rasmussen, S.; Monnard, P.-A,; Hanczyc, M.; Albertsen, A.N.; Bönzli, E.; Caschera, .; Dörr, M.; Fellermann, H.; Jørgensen, W. H.; Löffler, P.M.G.; Maurer, S.E.; Nielsen, K.A.; Pedersen, P.L.; Svaneborg, C.; Wamberg, M.C.; Wieczorek, R. & Ziock, H.J. Abstract from the 6th Danish Conference on Biotechnology and Molecular Biology: Synthetic Biology and Cell Factories. Vejle, Denmark (May 2011)
  2. Dynamic Bonding Framework for Modeling DNA Chemistry. Svaneborg, C. Abstract from the 6th Danish Conference on Biotechnology and Molecular Biology: Synthetic Biology and Cell Factories. Vejle, Denmark (May 2011)
  3. Attempt at a Systemic Design of a Protocell: Connecting information, Metabolism and Container. / Albertsen, A.N.; Maurer, S.E.; Cape, J.; Edson, J.B.; Rasmussen, S.; Ziock, H.J.; Boncella, J.M. & Monnard, P.-A.. ISSOL 2011, Montpellier, France. (July 3-8, 2011)
  4. A Review of one Approach to Bottom Up Assembly of Minimal Life. / Rasmussen, S.; Monnard, P.-A,; Hanczyc, M.; Albertsen, A.N.; Bönzli, E.; Caschera, F.; Dörr, M.; Fellermann, H.; Jørgensen, W. H.; Löffler, P.M.G.; Maurer, S.E.; Nielsen, K.A.; Pedersen, P.L.; Svaneborg, C.; Wamberg, M.C.; Wieczorek, R. & Ziock, H.J.. Proceedings of the Eleventh European Conference on the Synthesis of Simulation of Living Systems, ECAL 2011. MIT Press (2011)
  5. Bottom Up Assembly of Minimal Life. / Rasmussen, S. Abstract from the 70th Harden Conference on Synthetic Biology: Design and Engineering through Understanding. Staffordshire, UK (Aug. 2011)
  6. Dynamic Bonding Framework for Modeling DNA Chemistry. / Svaneborg, C. SimBioMa, Konstanz, Germany (Sept. 2011)
  7. Heterogeneous Self-Assembled Media for Bipolymerization. / Monnard, P.-A. ESF-COST High-level Research Conference on Systems Chemistry III. Crete, Greece. October 23-28, 2011.
  8. Exploring Single Chain Amphipile Self-Assembly and Their Possible Roles in Light Transduction./ Monnard, P.-A. COST CMO703 Systems Chemistry WG03. Crete, Greece (October 28-30, 2011)
Posters
  1. A Scenario for a Genetically Controlled Fission of Artificial Vesicles. / E. Bönzli; M. Hadorn; M.G. Jørgensen; P.H. Eggenberger; M. Hanczyc & T. Yomo.@ The 6th Danish Conference on Biotechnology and Molecular Biology: Synthetic Biology and Cell Factories. Vejle, Denmark, May 2011.
  2. Dipeptide Catalysed Prebiotic Polymerization of RNA. / R. Wieczorek, P.L. Luisi & P.-A. Monnard. @ ISSOL 2011, Montpellier, France. July 3-8, 2011
  3. Eutectic phases in water-ice : an efficient medium for biopolymerization. / Monnard, P.-A.; Dörr, M.; Löffler, P.M.G. & Wieczorek, R. @ ISSOL 2011, Montpellier, France. July 3-8, 2011
  4. Template Directed Oligomer Ligation in Eutectic Phases in Water-Ice. / Dörr, M.; Löffler, P.M.G.; Wieczorek, R. & Monnard, P.-A. @ ISSOL 2011, Montpellier, France. July 3-8, 2011
  5. Attempt at a Systemic Design of a Protocell: Linking Information, Metabolism and Container./ Albertsen, A.N. @ Challenges in Chemical Biology, Manchester, UK. Aug. 2011
  6. Genetically controlled fusion, exocytosis and fission of artificial vesicles - a roadmap. / Bonzli, E.; Hadorn, M.; de Lucrezia, D.; Jørgensen, M.G. Eggenberger Hotz, P.; Hanczyc, M & Yomo, T. @ Synthesizing Life and Biological Systems, Osaka, Japan. October 24-26, 2011.

Other
  1. What can we learn from simulation? / Svaneborg, C. @ Invited talk Dynacorp, Anacapri, Italy (July 2011)

Non-peer-reviewed 2011

Public Service Publications
  1. Syntesebiologi - debatoplæg. / Lindberg Møller, B.; Christensen, G.; Horst, M.; Vedelsby, J.; Andreasen, M.; Rasmussen, S; Holm, S. & Breck, T. The Danish Board of Technology(May, 2011)
  2. Synthetic Biology. Discussion Paper. / Lindberg Møller, B.; Christensen, G.; Horst, M.; Vedelsby, J.; Andreasen, M.; Rasmussen, S; Holm, S. & Breck, T. The Danish Board of Technology (30 pp) (May 2011)
  3. Syntesebiologi til debat. Ny udvikling inden for bio. og genteknologi. / Lindberg Møller, B.; Christensen, G.; Horst, M.; Vedelsby, J.; Andreasen, M.; Rasmussen, S; Holm, S. & Breck, T. The Danish Board of Technology - Fra rådet til tinget nr. 281 (June, 2011)
  4. Synthetic Biology: Challenges and debate. Newsletter. / Rasmussen, S; Lindberg Møller, B.; Christensen, G.; Horst, M.; Andreasen, M.; Holm, S. & Breck, T. The Danish Board of Technology (June 2011)
Invited Articles and Contributed Encyclopedias
  1. Structure and the Synthesis of Life. Hanczyc, M.M. Architectural Design (February, 2011)
  2. Om at skabe en celle fra bunden. Pedersen, P.L. & Rasmussen,S. Kaskelot, pp 12-15 (2011)
  3. Aspekter af liv, information, virkelighed og fysik. / Rasmussen, S. Kvant, no. 2 (pp 25-28) (2011)
  4. Fra syntetisk liv til levende teknologi. / Svaneborg, C.; Albertsen, A.N.; Fellermann, H. & Rasmussen, S. Aktuel Naturvidenskab (Sept. 2011)

Book Chapters
  1. Membrane Self-assembly Processes: Steps Towards the First Cellular Life. / Monnard, P.-A. & Deamer, D. PP 123-153 in: Minimal Cells. Springer (2011)
  2. Wet Artificial Life: The Creation of Artificial Living Systems. / Fellermann, H. In: Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Springer, Heidelberg (2011)

Conference Abstracts/Extended Abstracts
  1. Dynamic Bonding Framework for Modelling DNA Chemistry. Svaneborg, C. Abstract from the 6th Danish Conference on Biotechnology and Molecular Biology: Synthetic Biology and Cell Factories. Vejle, Denmark (May 2011)
  2. Dynamic Bonding Framework for Modelling DNA Chemistry. Svaneborg, C. Abstract from SimBioMa, Konstanz, Germany (Sept. 2011)
  3. Thermodynamics and kinetics of protocells: Toward a quantitative theory of early life. / Fellermann, H.; Corominas, B.; Solé, R. & Rasmussen, S.. @ ECCS 11, Austria (September 2011)
  4. Non-Enzymatic Biopolymerization Reactions Supported by Heterogeneous Media. / Monnard, P.-A. Abstract from The European Genomics Meeting 2011, Roma, Italy (October 9, 2011)

Posters
  1. DNA Dynamics and Self-Assembly of Soft Condensed Matter. / Svaneborg, C. @ The 6th Danish Conference on Biotechnology and Molecular Biology: Synthetic Biology and Cell Factories. Vejle, Denmark (May 2011)
  2. DNA Dynamics and Self-Assembly of Soft Condensed Matter / Svaneborg, C. @ SimBioMa, Konstanz, Germany (Sept. 2011)

Other
  1. Dynamic Bonding and Asymmetric Bond Extensions for the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). / Svaneborg, C. Softwareprogramme.
  2. Programmable DNA self-assembly of three-dimensionally defined nano objects. / Svaneborg, C. Internet publication.
  3. Simulation of non-enzymatic DNA replication chemistry. / Svaneborg, C. Internet publication.
  4. DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (excess oil). / Svaneborg, C. Internet publication
  5. DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (surfactant). / Svaneborg, C. Internet publication
  6. Computer Simulation of the Thermal Motion of poly-AT DNA under Standard Conditions. / Svaneborg, C. Internet publication