2011
Peer-reviewed 2011
Journal Articles
- On the Growth Rate of Non-Enzymatic Molecular Replicators. / Fellermann, H. & Rasmussen, S. Entropy 2011, 13(10), 1882-1903 (2011)
- 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)
- 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)
- 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).
- 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)
- 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).
- 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).
- 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).
- 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).
- 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)
- 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)
- 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)
- Metabolism and motility in prebiotic structures. / Hanczyc, M.M. Philosophical Transactions of the Royal Society B, vol. 366, no. 1580, pp 2885-2893 (2011)
- 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)
- 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
- 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)
- 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)
- Acid/Base Controllable Molecular Recognition. / Nielsen, K.; Bähring, S. & Jeppesen, J. O. Chemistry: A European Journal, vol. 17, no. 39, pp 11001 - 11007 (2011)
- Self-assembling scenarios of block-copolymer stars, C. Koch, C. N. Likos, A. Z. Panagiotopoulos, Federica Lo Verso, Molecular Physics 109, 3049-3060 (2011)
- 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
- Membrane self-assembly processes: steps towards the first cellular life. Monnard, P.-A. & Deamer, D. W., Minimal cells (2011).
Contributions to Conference Proceedings
- 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)
- 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)
- 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)
- 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
- 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
- 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)
- 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)
- 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)
- 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)
- 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)
- Dynamic Bonding Framework for Modeling DNA Chemistry. / Svaneborg, C. SimBioMa, Konstanz, Germany (Sept. 2011)
- 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.
- 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
- 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.
- Dipeptide Catalysed Prebiotic Polymerization of RNA. / R. Wieczorek, P.L. Luisi & P.-A. Monnard. @ ISSOL 2011, Montpellier, France. July 3-8, 2011
- 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
- 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
- Attempt at a Systemic Design of a Protocell: Linking Information, Metabolism and Container./ Albertsen, A.N. @ Challenges in Chemical Biology, Manchester, UK. Aug. 2011
- 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
- What can we learn from simulation? / Svaneborg, C. @ Invited talk Dynacorp, Anacapri, Italy (July 2011)
Non-peer-reviewed 2011
Public Service Publications
- 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)
- 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)
- 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)
- 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
- Structure and the Synthesis of Life. Hanczyc, M.M. Architectural Design (February, 2011)
- Om at skabe en celle fra bunden. Pedersen, P.L. & Rasmussen,S. Kaskelot, pp 12-15 (2011)
- Aspekter af liv, information, virkelighed og fysik. / Rasmussen, S. Kvant, no. 2 (pp 25-28) (2011)
- Fra syntetisk liv til levende teknologi. / Svaneborg, C.; Albertsen, A.N.; Fellermann, H. & Rasmussen, S. Aktuel Naturvidenskab (Sept. 2011)
Book Chapters
- Membrane Self-assembly Processes: Steps Towards the First Cellular Life. / Monnard, P.-A. & Deamer, D. PP 123-153 in: Minimal Cells. Springer (2011)
- 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
- 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)
- Dynamic Bonding Framework for Modelling DNA Chemistry. Svaneborg, C. Abstract from SimBioMa, Konstanz, Germany (Sept. 2011)
- 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)
- Non-Enzymatic Biopolymerization Reactions Supported by Heterogeneous Media. / Monnard, P.-A. Abstract from The European Genomics Meeting 2011, Roma, Italy (October 9, 2011)
Posters
- 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)
- DNA Dynamics and Self-Assembly of Soft Condensed Matter / Svaneborg, C. @ SimBioMa, Konstanz, Germany (Sept. 2011)
Other
- Dynamic Bonding and Asymmetric Bond Extensions for the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). / Svaneborg, C. Softwareprogramme.
- Programmable DNA self-assembly of three-dimensionally defined nano objects. / Svaneborg, C. Internet publication.
- Simulation of non-enzymatic DNA replication chemistry. / Svaneborg, C. Internet publication.
- DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (excess oil). / Svaneborg, C. Internet publication
- DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (surfactant). / Svaneborg, C. Internet publication
- Computer Simulation of the Thermal Motion of poly-AT DNA under Standard Conditions. / Svaneborg, C. Internet publication