MATCHIT Matrix for Chemical IT

MATCHIT Publications

The following scientific contributions are based on work that has been performed by members of the MATCHIT Consortium dated from 2010 and onwards.

Peer-reviewed

Journal Articles

1. Life after the Synthetic Cell / Rasmussen, S.. In: Nature, vol. 465 (7297), p. 422 (2010)
2. Detection of Association and Fusion of Giant Vesicles Using Fluorescence-Activated Cell Sorter / Sunami T, Caschera F, Morita Y, Toyota T, Nishimura K, Matsuura T, Suzuki H, Hanczyc MM, Yomo T. Langmuir 26(19), 15098-15103 (2010)
3. DNA-Mediated Self-Assembly of Artificial Vesicles / Hadorn M, Eggenberger Hotz P. PLoS One 5 5(3):e9886 (2010)
4. Enzyme-like replication de novo in a micro-controller / Tangen, U. Artificial life, Fall 2010, Vol. 16, No. 4, pp 311-328 (2010)
5. The Ten Grand Challenges of Synthetic Life / Danchin, A.; de Lorenzo, V.; dos Santos, V.; Krasnogor, N.; Rasmussen; S. & Moya, A.. Porcar, . Systems and Synthetic Biology, 5(1-2): 1–9 (2011)
6. On the Growth Rate of Non-Enzymatic Molecular Replicators / Fellermann, H. & Rasmussen, S. Entropy 13(10), pp 1892-1903 (2011)
7. 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.; Rasmussen, S.; Boncella, J. M.  and Monnard, P.-A.. ChemPhysChem, 12, pp 828-835 (2011)
8. Mode Switching and Collective Behavior in Chemical Oil Droplets / Horibe, N.; Kobayashi, K.; Hanczyc, M. and Ikegami, T.Entropy 2011, 13(3), 709-719 (2011)
9. 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).
10. Programmed Vesicle Fusion Triggers Gene Expression / Caschera F, Sunami T, Matsuura T, Suzuki H,. Hanczyc MM, Yomo T. Langmuir, 27 (21), pp 13082-13090 (2011)
11. Stable Vesicles Composed of Mono- or Dicarboxylic Fatty Acids and Trimethylammonium Amphiphiles / Caschera, F., de la Serna, J. B., Löffler, P.M., Rasmussen, T.E., Hanczyc, M. and Monnard, P.-A.. Langmuir (2011)
12. 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)
13. 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)
14. Replication of Simulated Prebiotic Amphphile Vesicles Controlled by Experimental Lipid Physiochemical Properties / Armstrong, D.L.; Markovitch, O.; Zidovetzki, R. & Lancet, D. Physical Biology, Vol. 8, No 6 (2011)
15. A Self-Replicating Peptide Nucleic Acid. / Plöger, T. A. & von Kiedrowski, G.  arXiv:1112.4952v1 (arXiv e-print) (2011)
16. Improved Large-Scale Liquid-Phase Synthesis and High-Temperature NMR Characterization of Short (F) PNAs / Plöger, T. A. & von Kiedrowski, G. Helvetica Chimica Acta2011, 94(11), 1952–1980 (2011)
17. Nonenzymatic Polymerization of Nucleic Acids from Monomers: Monomer Self-Condensation and Template Directed Reactions / Dörr, M. Löffler, P. M. G. & Monnard, P.-A. Current Organic Synthesis, Vol 9 (6), pp 735-763 (29) (2012).
18. Excess Mutual Catalysis is Required for Effective Evolvability / Markovitch, O. & Lancet, D. Artificial Life, Summer 2012, Vol. 18, No.3, pp 243 - 266 (2012)
19. Is There an Optimal Level of Open-Endedness in Prebiotic Evolution? / Markovitch, O.; Sorek, D.; Lui, L.T.; Lancet, D & Krasnogor, N. Origin of Life and Evolution of Biospheres (2012)
20. Hieracical Unilamellar Vesicles of Controlled Compositional Heterogeneity / Hadorn, M.; Boenzli. E.; Hotz, P.E. & Hanczyc, M.M. PLOSONE (2012)
21. Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets / Hadorn, M.; Boenzli. E.; Sørensen, K.T.; Fellermann, H.; Hotz, P.E. & Hanczyc, M.M. PNAS, 109 (47) (2012)
22. An Oil Droplet Division-Fusion Cycle / Caschera, F.; Rasmussen, S. & Hanczyc, M. ChemPlusChem (2012)
23. Microscale Chemically Reactive Eletronic Agents / McCaskill. J.S; Öhm, J.; Mayr, P.; Cronin, L.; Willner, I.; Hermann, A.; Rasmussen, S.; Stepanek, F.; Packard, N. & Wills, P.R. Old City Publishing (2012)
24. Field programmable chemistry: Integrated chemical and electronic processing of informational molecules towards electronical chemical cells / Wagler, P.F.; Tangen, U.; Maeke, T. & McCaskill, J.S. Biosystems, vol. 109 (1), pp 2-17 (2012)
25. RNA Phosphodiester Bond by Histidine-Containing Dipeptides / Wieczorek, R.; Dörr, M.; Chotera, A.; Luisi, P. L. & Monnard, P.-A. . ChemBioChem, vol. 14, Issue 2, pp 166 (2013)

Books

1. Living Technology: 5 Questions / Bedau, M.; Hansen, P.G.; Parke, E. & Rasmussen, S.. Automatic Press / VIP. p 236 (2010)

Book Chapters

1. 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)

Contributions to Conference Proceedings

1. Designing a Protocell: Attempt at a Systemic Design Linking Information, Metabolism and Container / Maurer, S.E.; Albertsen, A.; Cape, J.; Boncella, J.M.; Spencer, L.; Ziock, H.-J.; Rasmussen, S. and P.-A. Monnard. In Proceedings of the Artificial Life 12 Conference (2010)
2. Doctor in a Cell: Vision and Accomplishments / Gill, B; Kahan-Hanum M; Skirtenko, N; Adar R. and Shapiro E. In Proceedings of the Artificial Life 12 Conference (2010)
3. On the Interplay of Kinetics, Thermodynamics, and Information in Simple Replicating Systems / Corominas-Murtra, B.; Fellermann, H.; Sole, R. and Rasmussen S. In Proceedings of the Artificial Life 12 Conference (2010)
4. 'In Vitro' and 'In Silico' Complementary Studies on the Physical Properties of Prebiotic Compartments / Piedrafita, G.; Shirt-Ediss, B.; Mavelli, F.; Monnard, P.-A. and Ruiz-Mirazo K. In Proceedings of the Artificial Life 12 Conference (2010)
5. Physically Grounded Simulations of a Self-Replicating Chemical Aggregate / Fellermann, H. and Rasmussen S.  In Proceedings of the Artificial Life 12 Conference (2010)
6. The emergence of replication in a digital evolution system using a secondary structure approach / Tangen, U. In Proceedings of the Artificial Life 12 Conference (2010)
7. 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
8. 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)
9. 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)
10. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model /Svaneborg, C.; Fellermann, H. & Rasmussen, S. Proceedings for the DNA18 Conference to appear in Lecture Notes in Computer Science, Vol. 7433, pp 123-134 (2012)

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 (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. 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. (Aug. 2011) Abstract from the 70th Harden Conference on Synthetic Biology: Design and Engineering through Understanding. Staffordshire, UK (2011)
4. Dynamic Bonding Framework for Modeling DNA Chemistry. / Svaneborg, C. SimBioMa, Konstanz, Germany (Sept. 2011)
5. Murine DNA methyltransferase Dnmt3a: probing of DNA-enzyme interactions with benzo[a]pyrene-containing DNA by fluorescence / Minero, G.K.A. DECHEMA Biotransformations 2011, Book of Abstracts (2011)
6. Monitoring and fast analysis of triplex formation / Minero, G.K.A. & McCaskill, J.S. JCS-Ruhr 2011, Book of Abstracts (2011)
7. Integrating Molecular Computation and Material Production in an Artificial Subcellular Matrix / Fellermann, H.; Hadorn, M.; Bönzli, E. & Rasmussen, S. @ Living Machine 2012: The First International Conference on Biomimetic and Biohybrid Systems, Barcelona, Spain, Lecture Notes in Computer Science, pp 343-344, Springer (2012)
8. Protocellular energetics and autonomous functions / Albertsen, A.N.; Maurer, S.E.; Cape, J.;Fellermann, H.; Boncella, J.M.; Ziock, H.J.; Rasmussen, S. & Monnard, P.-A. Proceedings of the 13th International Conference on Synthesis and Simulation of Artificial Life. MIT Press (2012)
9. Mapping the collective intelligence of the Artificial Life XIII stakeholders / Dörr, M.; Schmidt-Petersen, S.; Fellermann, H.; Laursen, L. & Rasmussen, S. Proceedings of the 13th International Conference on Synthesis and Simulation of Artificial Life. MIT Press (2012)
10. A Minimal Artificial Subcellular Matrix / Hadorn, M.; Gil, B.; Svaneborg, C.; Hanczyc, M.M.; Fellermann, H.; Fuchslin, R.; Hotz, P.E.; Kunstmann-Olsen, C.; Lancet, D.; McCaskill, J.; Monnard, P.-A.; Kiedrowski, G.V. & Rasmussen, S. Proceedings of the 13th International Conference on Synthesis and Simulation of Artificial Life. MIT Press (2012)
11. Towards protocellular embedded replication of nucleic acids / Löffler, P.M.G.; Wieczorek, R.;Wamberg, M.; Dörr, M.; Pedersen, P.L.; Svaneborg, C.; Fellermann, H.; Edson, J.B.;  Cape, J.L.;  Ziock, H.J.; Boncella, J.M.; Rasmussen, S. & Monnard, P.-A. Proceedings of the 13th International Conference on Synthesis and Simulation of Artificial Life. MIT Press (2012)
12. How to implement a wetware system able to emulate in silico results / Hadorn, M.; Boenzli, E.; Hanczyc, M.M.; Rasmussen, S. & Hotz, P.E. Proceedings of the 13th International Conference on Synthesis and Simulation of Artificial Life. MIT Press (2012)
13. Is There an Optimal Level of Open-Endedness in Prebiotic Evolution? / Markovitch, O.; Sorek, D.; Lui, L.T.; Lancet, D & Krasnogor, N. Conference Report OQOL12, University of Leister, UK (2012)

Posters

1. Knitting a Protocell / Maurer, S.E. @ The 12th International Conference on Synthesis and Simulation of Artificial Life (AlifeXII), Odense, Denmark (2010)
2. Using LEGO Mindstorm to create an affordable open-source liquid handling robot / Barnkob, M.S. and Hanczyc M.M. @ The 12th International Conference on Synthesis and Simulation of Artificial Life (AlifeXII), Odense, Denmark (2010)
3. Attempt at a Systemic Design of a Protocell: Linking Information, Metabolism and Container / Albertsen, A.N. @ Challenges in Chemical Biology, Manchester, UK (2011)
4. Excess mutual catalysis is required for effective evolvability / Markovitch, O. @ The Eleventh European Conference on Artificial Life (ECAL11) Paris, France (2011) - Voted in 2^nd place by the conference participants
5. Evolutionary Attributes of Simulated Prebiotic Metabolic Network / Markovitch, O. & Lancet, D. @ The Eleventh European Conference on Artificial Life (ECAL11) Paris, France (2011)
6. High Self-Catalysis Leads to Evolutionary Dead-End / Markovitch, O. & Lancet, D. @ Origins 2011, Montpellier, France (2011)
7. Electronically switchable DNA hybridization via triplex interactions / Minero, G.K.A.; Wagler, P.F. & McCaskill, J.S. @ The 18th international conference on DNA Computing and molecular Programming, DNA18 (2012)
8. Selection in populations of compositional assemblies / Markovitch, O. @ Gordon Research Conference on the Origin of Life, TExas, USA, Jan., 2012

Non-Peer-Reviewed

Invited Articles and Encyclopedias

1. Om at skabe en celle fra bunden. / Pedersen, P.L. & Rasmussen, S. Kaskelot, pp 12-15 (2011)
2. Aspekter af liv, information, virkelighed og fysik / Rasmussen, S. Kvant, no. 2 (pp 25-28) (2011)
3. Fra syntetisk liv til levende teknologi / Svaneborg, C.;  Albertsen, A.N.; Fellermann, H. & Rasmussen, S. Aktuel Naturvidenskab (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)

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)

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.

Other

1. Programmable DNA self-assembly of three-dimensionally defined nano objects / Svaneborg, C. Internet publication.
2. Simulation of non-enzymatic DNA replication chemistry / Svaneborg, C. Internet publication.
3. DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (excess oil) / Svaneborg, C. Internet publication
4. DPD Simulation of coarsening dynamics of oil-surfactant-water mixtures (surfactant) / Svaneborg, C. Internet publication
5. Computer Simulation of the Thermal Motion of poly-AT DNA under Standard Conditions / Svaneborg, C. Internet publication

Science Policy

1. Syntesebiologi: Debatoplæg  / Rasmussen, S; Lindberg Møller, B.; Christensen, G.; Vedelsby, J.; Horst, M.; Holm, S. & Breck, T. The Danish Board of Technology (30 pp) (May 2011)
2. Syntesebiologi til debat: Ny udvikling inden for bio- og genteknologi Fra rådet til tinget. Teknologirådets nyhedsbrev til Folketinget. / Rasmussen, S; Lindberg Møller, B.; Christensen, G.; Horst, M.; Andreasen, M.; Holm, S. & Breck, T. The Danish Board of Technology
3. POLICY PAPER COMMISSIONED BY THE DANISH BOARD Of TECHNOLOGY: Synthetic Biology. Discussion Paper / Rasmussen, S; Lindberg Møller, B.; Christensen, G.; Vedelsby, J.; Horst, M.; Holm, S. & Breck, T. The Danish Board of Technology (30 pp) (May 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)