All publications arranged by type and year

Journal Articles

  • Monnard, P. A., Growth and shape transformations of giant phospholipid vesicles upon interaction with an aqueous oleic acid suspension, ACS publications, (2008).
  • Görnerup, O., Nilsson-Jacobi, M., A method for inferring hierarchical dynamics in stochastic processes, Advances in Complex Systems 11, (2008) 1-16. http://arxiv.org/abs/nlin.AO/0703034/
  • Hayden, E., von Kiedrowski, G., Lehman, N., Systems chemistry on ribozyme self-construction: Evidence for anabolic autocatalysis in a recombination network, Angewandte Chemie International Edition, (2008) in press. http://www3.interscience.wiley.com/journal/117943443/tocgroup
  • von Kiedrowski, G., Leslie e. Orgel (1927-2007), Angewandte Chemie International Edition 47, (2008) 2338-9. http://www3.interscience.wiley.com/journal/117943443/tocgroup http://www3.interscience.wiley.com/cgi-bin/fulltext/117932024/PDFSTART
  • Zimmermann, J., Cebulla, M. P. J., Mönninghoff, S., von Kiedrowski, G., Self-assembly of a DNA dodecahedron from 20 trisoligonucleotides with c3h linkers, Angewandte Chemie International Edition 47, (2008) 3626-30. http://www3.interscience.wiley.com/journal/117943443/tocgroup http://www3.interscience.wiley.com/cgi-bin/fulltext/117949756/PDFSTART
  • Görnerup, O., Crutchfield, J. P., Hierarchical self-organization in the finatary process soup, Artificial Life 14, (2008) 245 – 54. http://www.mitpressjournals.org/doi/pdf/10.1162/artl.2008.14.3.14301
  • Knutson, C. et al., Metabolic photo-fragmentation kinetics for a minimal protocell: Rate limiting factors, efficiency, and implications for evolution, Artificial Life 14, (2008) 189-201.
  • Solé, R. V., Valverde, S., Rasmussen, S., Molecular self-assembly with dissipative lattice dynamics (dld) models, Artificial Life submitted, (2008). http://complex.upf.es/index.php?page=30
  • Tangen, U., Enzyme-like replication de novo in a micro-controller environment, Artificial Life submitted, (2008).
  • Sardanyés, J., Error threshold ghosts in a simple hypercycle with error prone self-replication, Chaos, Solitons and Fractals 35, (2008) 313-9. http://complex.upf.es/index.php?page=24
  • Sardanyés, J., Ghosts in high dimensional non-linear dynamical systems: The example of the hypercycle, Chaos, Solitons and Fractals in press, (2008). http://complex.upf.es/index.php?page=22
  • Chemnitz, S., Tangen, U., Wagler, P. F., Maeke, T., McCaskill, J. S., Electronically programmable membranes for improved biomolecule handling in micro-compartments on-chip, Chemical Engineering Journal 135S, (2008) 276-9. http://dx.doi.org/10.1016/j.cej.2007.07.061
  • Monnard, P. Z., HJ, Eutectic phase in water-ice: A self-assembled environment conducive to metal-catalyzed non-enzymatic rna polymerization, Chemistry & Biodiversity Accepted, (2008).
  • Forlin, M. et al., Evolutionary experiments for self-asembling amphiphilic systems, Chemometrics and Intelligent Laboratory Systems, (2008) 153-60.
  • Weronski, P., Jiang, Y., Rasmussen, S., Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine, Complexity 13, (2008) 41547.
  • Theis, M. G., G. et al., Optimal formulation of complex chemical systems with a genetic algorithm, CompPlexUs accepted, (2008).
  • Monnard, P. A., M., D., Ziock, H.-J., Amphiphile nanostructures as model for artificial cell-like entities, Current Nanoscience 4, (2008) 71-87.
  • Monnard, P. A., Ziock, H., DeClue, M., Organic nano-compartments as biomimetic reactors, and protocells, Current Nanoscience 4, (2008) 71-87.
  • Füchslin, R., Maeke, T., McCaskill, J. S., Multipolar reactive dpd: A novel tool for spatially resolved simulations in cell biology, European Physical Journal E (EPJE) submitted, (2008). http://arxiv.org/abs/0705.1445.
  • Solé, R. V., Evolution and self-assembly of protocells, International Journal of Biochemistry and Cell Biology submitted, (2008). http://complex.upf.es/index.php?page=32
  • Zhou, X., Jiang, Y., Rasmussen, S., H., Z., Bridging coarse-grained models by jump-in-sample simulations, J. Chem. Phys 128, (2008) 174107-1 - -7.
  • Eriksson, A., Nilsson Jacobi, M., Nyström, J., Tunstrøm, K., Effective thermostat induced by coarse-graining of spc water, Journal of Chemical Physics 129, (2008) 024106. http://arxiv.org/abs/0802.1157
  • Füchslin, R. M., Eriksson, A., Fellermann, H., Ziock, H., Coarse-graining and scaling in dissipative particle dynamics, Journal of Chemical Physics submitted, (2008). http://arxiv.org/abs/cond-mat/0703682
  • Tamulis, A., Tamulis, V., Quantum mechanical design of molecular electronics or gate for regulation of minimal cell functions, Journal of Computational and Theoretical Nanoscience 5, (2008) 545-53. http://www.ingentaconnect.com/content/asp/jctn/2008/00000005/00000004/art00014?token=0042115d25c5f3b3b47672848773b257b556e6d7b384f58762f67e915d9c234a65
  • Monnard, P. S., J, Metal-ion catalyzed polymerization in the eutectic phase in water-ice: A possible approach to template-directed rna polymerization, Journal of Inorganic Biochemistry 102, (2008) 1104-11.
  • Fontich, E., Sardanyés, J., General scaling law in the saddle-node bifurcation: A complex phase space study, Journal of Physics A: Mathematical and Theoretical 41, (2008) 38230. http://complex.upf.es/index.php?page=23
  • Sardanyés, J., Fontich, E., Replicator dynamics on the phase plane: The role of intraspecific cooperation in competition, Journal of Physics A: Mathematical and Theoretical in press, (2008). http://complex.upf.es/index.php?page=26
  • Melas, V., Pepelyshev, A., Poli, I., Seeking designs for mixture experiments with many ingredients, Journal of Statistical Planning and Inference submitted, (2008).
  • Carletti, T., Serra, R., Poli, I., Villani, M., Filisetti, A., Sufficient conditions for emergent synchronization in protocell models, Journal of Theoretical Biology accepted, (2008).
  • Sardanyés, J., Elena, S., Solé, R. V., Simple quasispecies models for the survival-of-the-flattest effect: The role of space, Journal of Theoretical Biology 250, (2008) 560-8. http://complex.upf.es/index.php?page=20
  • Sardanyés, J., Fontich, E., On the metapopulation dynamics of autocatalytic replicators, Journal of Theoretical Biology submitted, (2008). http://complex.upf.es/index.php?page=27
  • DeClue, M. S. et al., Towards artificial life: Catalytic coupling of information, metabolism, and container in a minimal protocell, (LA-UR 07-2511) submitted, (2008).
  • Bedau, M. A., Is weak emergence just in the mind? , Minds and Machines In press, (2008).
  • Tamulis, A., Quantum mechanical control of artificial minimal living cells, Neuro Quantology Journal 6, (2008). http://www.neuroquantology.com/JOURNAL/index.php/nq/issue/current
  • Eriksson, A., Nilsson Jacobi, M., Nyström, J., Tunstrøm, K., Using force covariance to derive effective stochastic interactions in dissipative particle dynamics, Physical Review E 77, (2008) 016707. http://arxiv.org/abs/0704.3324?context=cond-mat
  • Sardanyés, J., Solé, R. V., Matching allele dynamics and coevolution in a minimal predator-prey replicator model, Physics Letters A 372, (2008) 341-50. http://complex.upf.es/index.php?page=21
  • Macía, J., Solé, R. V., The physics of protocell replication: From fusion to fission, Physics of Life Reviews submitted, (2008). http://complex.upf.es/index.php?page=28
  • Monnard, P. A., The dawn of the rna world: Rna polymerization from monoribonucleotides underprebiotically plausible conditions, Prebiotic Evolution and Astrobiology, eds Jeffrey T. F. Wong, Landes Bioscience, (2008).
  • Tamulis, A., Quantum self-assembly of artificial minimal living cells and molecular electronics control, Viva Origino 36, (2008) 10-9. http://www.origin-life.gr.jp/3602/3602J.html
  • Patzke, V., von Kiedrowski, G., Self-replicating systems, Arkivoc 5, (2007) 293-310. http://www.arkat-usa.org/ http://www.arkat-usa.org/get-file/19231/
  • Fellermann, H., Rasmussen, S., Ziock, H. J., Solé, R. V., Life cycle of a minimal protocell: A dissipative particle dynamics study, Artificial Life 13, (2007) 319-45. http://complex.upf.es/index.php?page=16
  • Serra, R., Carletti, T., Poli, I., Synchronization phenomena in surface reaction models of protocells, Artificial Life 13, (2007) 1-16.
  • Miyashita, S., Murata, S., Emerging cell array based on reaction-diffusion, Artificial Life and Robotics 11, (2007) 32-6.
  • Murata, S. M. S., Array based on reaction-diffusion, ‬‬Artificial Life and Robotics 11, (2007) 32-6‬.
  • Miyashita, S., ‬morphogenesis of  3d sheets exploiting a spatial condition, Artificial Life and Robotics‬ 11, (2007) ‬139-44.
  • Weronski, P., Jiang, Y., Rasmussen, S., Molecular dynamics study of small pna molecules in lipid-water system, Biophys. J. 92, (2007) 3081-91.
  • Sardanyés, J., Solé, R. V., Delayed transitions in nonlinear replicator networks: About ghosts and hypercycles, Chaos, Solitons and Fractals 31, (2007) 305-15. http://complex.upf.es/index.php?page=18
  • Sardanyés, J., Solé, R. V., Red queen strange attractors in host-parasite replicator gene-for-gene coevolution, Chaos, Solitons and Fractals 32, (2007) 1666-78. http://complex.upf.es/index.php?page=13
  • Sardanyés, J., Solé, R. V., The role of cooperation and parasites in nonlinear replicator delayed extinctions, Chaos, Solitons and Fractals 31, (2007) 1279-96. http://complex.upf.es/index.php?page=9
  • Tamulis, A., Tsifrinovich, V. I., Tretiak, S., Berman, G. P., Allara, D., Neutral radical molecules ordered in self-assembled monolayer systems for quantum information processing, Chemical Physics Letters 436, (2007) 144 - 9. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TFN-4MSHY29-1&_user=1049315&_rdoc=1&_fmt=&_orig=search&_sort=d&view;=c&_version=1&_urlVersion=0&_userid=1049315&md5;=05d0ce1acabe4bb298cbdd69e56c0770
  • Helvik, T., Lindgren, K., Nordahl, M. G., Continuity of information transport in surjective cellular automata, Communications in Mathematical Physics 272, (2007) 53-74. http://www.springerlink.com/content/162044h13423t1h1/
  • Görnerup, O., Crutchfield, J. P., Primordial evolution in the finitary process soup, Electronic Journal of Theoretical Physics Special Issue 2007 4, (2007). http://www.ejtp.com/specialissue2007.html
  • Carletti, T., Fanelli, D., From chemical equations to evolution: Emergence of species, Europhysics Letters 77, (2007) 18005p1–p6.
  • Wagler, P. F., Hempelmann, W., Programmierbare flüsse in mikrofluidikchips, GIT Labor-Fachzeitschrift, (2007) 736,. http://www.wagler-home.de/publications/svx_media/git0907_736_wagler.pdf
  • Sardanyés, J., Solé, R. V., Chaotic stability in spatially-resolved host-parasite replicators: The red queen on a lattice, International Journal of Bifurcations and Chaos 17, (2007) 589-606. http://complex.upf.es/index.php?page=19
  • Fernando, C., von Kiedrowski, G., Szathmary, E., A stochastic model of nonenzymatic nucleic acid replication: Elongators sequester replicators, Journal of Molecular Evolution 64, (2007) 572-85. http://www.springer.com/life+sci/cell+biology/journal/239 http://springerlink.com/content/5393437r700123r1/fulltext.pdf
  • Macía, J., Solé, R. V., Protocell self-reproduction in a spatially explicit metabolism-vesicle system, Journal of Theoretical Biology 245, (2007) 400-10. http://complex.upf.es/index.php?page=14
  • Tamulis, A., Artificial living cells and nanobiorobots, Mokslas ir Technika (Science and Technology) 12, (2007) 26-8. http://www.ktl.mii.lt/mt/
  • Sen, A., Nielsen, P. E., On the stability of peptide nucleic acid duplexes in the presence of organic solvents, Nucleic Acids Research, (2007) 3367-74. http://nar.oxfordjournals.org/cgi/content/full/35/10/3367
  • Monnard, P. A., Ziock, H. J., Question 9: Prospects for the construction of artificial cells or protocells, Origins of Life and Evolution of Biospheres 37, (2007) 469-72.
  • Tamulis, A., Tamulis, V., Question 9: Quantum self-assembly and photoinduced electron tunneling in photosynthetic systems of artificial minimal living cells, Origins of Life and Evolution of Biospheres 37, (2007) 473-6. http://www.springerlink.com/content/87x5333271jm1288/?p=11a3ed962f4449a89d38275cb822029cπ=32
  • Fellermann, H., Solé, R., Self-replicating nanocells: A physically embodied, information-free scenario, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1803-11.
  • Fellermann, H., Solé, R. V., Minimal model of self-replicating nanocells: A physically embodied information-free scenario, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1803-11. http://complex.upf.es/index.php?page=15
  • Macía, J., Solé, R. V., Synthetic turing protocells: Self-reproducing vesicles through symmetry-breaking instabilities, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1821-9. http://complex.upf.es/index.php?page=10
  • McCaskill, J., Packard, N. H., Rasmussen, S., Bedau, M. A., Evolutionary self-organization in complex fluids, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1763-79. http://journals.royalsociety.org/content/y2k482233q3x8218/?p=6da59ebaac5140d9bc3ac26784a45892π=4 http://www.journals.royalsoc.ac.uk/content/y2k482233q3x8218/fulltext.pdf
  • Monnard, P. A., Luptak, A., Deamer, D. W., Models of primitive cellular life: Polymerases and templates in liposomes, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1741-50.
  • Munteanu, A., Attolini, C., Rasmussen, S., Ziock, H., Solé, R., Generic darwinian selection in catalytic protocell assemblies, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1847-55.
  • Munteanu, A. et al., Generic darwinian selection in protocell assemblies, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 847-1855. http://complex.upf.es/index.php?page=17
  • Rocheleau, T., Rasmussen, S., Nielsen, P., Nilsson Jacobi, M., Ziock, H., Emergence of protocellular growth laws, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1841-5. http://www.santafe.edu/research/publications/workingpapers/06-11-044.pdf
  • Solé, R. V., Munteanu, A., Rodriguez-Caso, C., Macía, J., Synthetic-protocell biology: From reproduction to computation, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1727-39.
  • Solé, R. V., Munteanu, A., Rodriguez-Caso, C., Macía, J., Synthetic protocell biology: From reproduction to computation, Phil. Trans. Roy. Soc. Lond. ser. B 362, (2007) 1727-39. http://complex.upf.es/index.php?page=11
  • Sardanyés, J., Solé, R. V., Spatio-temporal dynamics in simple asymmetric hypercycles under weak parasitic coupling, Physica D 231, (2007) 116-29. http://complex.upf.es/index.php?page=12
  • Valverde, S., Sole, R. V., Bedau, M. A., Packard, N. H., Topology and evolution of technology innovation networks, Physical Review E 76, (2007) 056118-1 – -7. http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id;=PLEEE8000076000005056118000001&idtype;=cvips&gifs;=yes
  • Savage, V. M. et al., Scaling of number, size, and metabolic rate of cells with body size in mammals, Proc. Natl. Acad. Sci. USA 104, (2007) 4718-23.
  • Tamulis, A., Tamulis, V., Quantum self-assembly and photoinduced electron tunneling in photosynthetic system of minimal living cell, Viva Origino 35, (2007) 66-72. http://www.origin-life.gr.jp/3502/3502066/3502066.html
  • Füchslin, R., Maeke, T., Tangen, U., McCaskill, J. S., Evolving inductive generalization via genetic self-assembly, Advances in Complex Systems 9, (2006) 1-29.
  • Pankau, W. M., Mönninghoff, S., von Kiedrowski, G., Thermostable and monoconjugable gold clusters with a dodecadentate thioether ligand gripper, Angewandte Chemie International Edition 45, (2006) 1889-92. http://www3.interscience.wiley.com/journal/117943443/tocgroup http://www3.interscience.wiley.com/cgi-bin/fulltext/112464043/PDFSTART
  • Stanciewicz, J., Eckardt, L. H., Meeting review: Chembiogenesis 2005 and systems chemistry, Angewandte Chemie International Edition 45, (2006) 342-4. http://www3.interscience.wiley.com/journal/117943443/tocgroup http://www3.interscience.wiley.com/cgi-bin/fulltext/112224708/PDFSTART
  • Ehrenfreund, P., Rasmussen, S., Cleaves, J., Chen, L., Experimentally tracing the key steps in the origin of life: The aromatic world, Astrobiology 6, (2006) 490-520.
  • Sen, A., Nielsen, P. E., Unique properties of purine/pyrimidine asymmetric pna-DNA duplexes: Differential stabilization of pna-DNA duplexes by purines in the pna strand, Biophys. J. 90, (2006) 1329-37. http://www.biophysj.org/cgi/content/full/90/4/1329
  • Nielsen, P. E., Goranovi_, G., Rasmussen, S., Can (non-biological) life be created de novo? , Biozoom 3, (2006). http://www.biokemi.org/biozoom/2006_3/bz_0306e.htm
  • Tangen, U. et al., An electronically controlled microfluidics approach towards artificial cells., CompPlexUs 3, (2006) 48-57. http://dx.doi.org/10.1159/000094187 http://content.karger.com/ProdukteDB/produkte.asp?doi=10.1159/000094187
  • Munteanu, A., Solé, R. V., Pattern formation in noisy self-replicating spots, International Journal of Bifurcations and Chaos 16, (2006) 3679-85. http://complex.upf.es/index.php?page=7
  • Sardanyés, J., Solé, R. V., Ghosts in the origins of life? , International Journal of Bifurcations and Chaos 16, (2006) 2761-5. http://complex.upf.es/index.php?page=5
  • Hanczyc, M. M., Toyota, T., Ikegami, T., Packard, N., Sugawara, V., Chemistry at the oil-water interface: Self-propelled oil droplets, J. Am. Chem. Soc, (2006).
  • Maxwell, J., Boman, M., Springer, R. W., Narayan, J., Gnanavelu, S., Hyperbaric laser chemical vapor deposition of carbon fibers from the 1-alkenes, 1-alkynes, and benzene, J. Am. Chem. Soc. 128, (2006) 4405-13.
  • Stahl, I., von Kiedrowski, G., Kinetic nmr titration: Including chemical shift information in the kinetic analysis of supramolecular reaction systems such as organic replicators, J. Am. Chem. Soc. 128, (2006) 14014-5. http://pubs.acs.org/journals/jacsat/index.html
  • Tamulis, A., Tamulis, V., Graja, A., Quantum mechanical modeling of self-assembly and photoinduced electron transfer in pna based artificial living organism, Journal of Nanoscience and Nanotechnology 6, (2006) 965-73. http://www.ingentaconnect.com/content/asp/jnn/2006/00000006/00000004/art00008
  • Munteanu, A., Solé, R. V., Phenotypic diversity and chaos in protocell dynamics, Journal of Theoretical Biology 240, (2006) 434-42. http://complex.upf.es/index.php?page=8
  • Sardanyés, J., Solé, R. V., Bifurcations and phase transitions in spatially-extended two-member hypercycles, Journal of Theoretical Biology 243, (2006) 468-82. http://complex.upf.es/index.php?page=4
  • Solé, R. V., Sardanyés, J., Diez, J., Mas, A., Information catastrophe in rna viruses through replication thresholds, Journal of Theoretical Biology 240, (2006) 353-9. http://complex.upf.es/index.php?page=6
  • Rinkevicius, Z., Tamulis, A., Tamuliene, J., Beta-diketo structure for quantum information processing, Lithuanian Journal of Physics 46, (2006) 413-6. http://www.itpa.lt/LFD/Lfz/Turiniai/Turi2006.html#
  • Tamuliene, J., Tamulis, A., Ziriakoviene, A., A., G., Quantum chemical design of two logical functions molecular device, Lithuanian Journal of Physics 46, (2006) 163-7. http://www.itpa.lt/LFD/Lfz/Turiniai/Turi2006.html#
  • Tamulis, A., Tamulis, V., Self-assembling of artificial programmable cells and their growing and control, Mokslas ir Gyvenimas (Science and Life) 12, (2006) 32.
  • Zhou, X., Jiang, Y., Kramer, K., Rasmussen, S., Ziock, H., Hydrodynamics for entropic systems: Space-time compression and pair correlation function approximation, Phys. Rev. E 74, (2006) 35701-1 - -4.
  • Tamuliene, J., Balevicius, M. L., Search for sensitizer to peptide nucleic acid sequence with adenine and guanine bases, Viva Origino 34, (2006) 112-5. http://www.origin-life.gr.jp/3403/3403112/3403112.html
  • Maxwell, J. et al., Process-structure map for diamond-like carbon fibers from ethene at hyperbaric pressures, Advanced Functional Materials 15, (2005) 1077-87.
  • Kindermann, M., Stahl, I. R., M., Pankau, W. M., von Kiedrowski, G., Systems chemistry: Kinetic and computational analysis of a nearly exponential replicator, Angewandte Chemie International Edition 44, (2005) 6750-5. http://www3.interscience.wiley.com/journal/117943443/tocgroup http://www3.interscience.wiley.com/cgi-bin/fulltext/112097104/PDFSTART
  • Nilsson, M., Hierarchical structures in smooth dynamical systems, Artificial Life 11, (2005) 493–512,. http://www.mitpressjournals.org/toc/artl/11/4
  • Achilles, K., von Kiedrowski, G., Kinetic model studies on the chemical ligation of oligonucleotides via hydrazone formation., Bioorg. Med. Chem. Letters 15, (2005) 1229-33. http://www.sciencedirect.com/science/journal/0960894X http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TF9-4F92406-1-1&_cdi=5221&_user=2873218&_orig=search&_coverDate=02%2F15%2F2005&_sk=999849995&view;=c&wchp;=dGLbVlb-zSkWz&md5;=28f3b94fb22e6989ebb62a5cf824e30e&ie;=/sdarticle.pdf
  • Nilsson Jacobi , M., Rasmussen,S., Tunstrøm, K., Modeling the dynamics of a minimal protocell container, International Journal of Astrobiology 4, (2005) 79–89. http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid;=335356&fulltextType;=RA&fileId;=S1473550405002478
  • Ehses, S., Ackermann, J., McCaskill, J. S., Optimization and design of oligonucleotide setup for strand displacement amplification, J Biochem Biophys Methods 63, (Jun 30, 2005) 170-86. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db;=PubMed&dopt;=Citation&list;_uids=15975661
  • Goranovic, G., Sørensen, M. P., Brøns, M., Bruus, H., Electrohydrodynamic and shear-stress interfacial instability of two streaming viscous liquids inside a microfluidic channel, J. Fluid. Mech. Submitted, (2005).
  • Tamuliene, J., Tamulis, A., Quantum mechanical investigations of self-assembled system consisting of peptide nucleic acid, sensitizer, and lipid precursor molecules, Lithuanian Journal of Physics, 45, (2005) 167-74. http://www.itpa.lt/LFD/Lfz/Turiniai/Turi2005.html
  • Gillooly, J. F. et al., The metabolic basis of whole-organism rna and phosphorous content, Proc. Natl. Acad. Sci. USA 102, (2005) 11923-7.
  • Savage, V. M. et al., The predominance of quarter-power scaling in biology, Functional Ecology 18, (2004) 257-82.
  • Lichtensteiger , L., the need to adapt and its implications for embodiment, Lecture Notes in Computer Science LNCS   3139, (2004) ‬98-106.
  • Tamuliene, J., Tamulis, A., Kulys, J., Electronic structure of dodecyl syringate radical suitable for esr molecular quantum computers, Nonlinear Analysis: Modeling and Control 9, (2004) 185-96. http://www.lana.lt/journal/issues.php
  • Rasmussen, S., Chen, L., Stadler, P. F., Stadler, B., Proto-organism kinetics: Evolutionary dynamics of lipid aggregates with genes and metabolism, Orig. Life Evol. Life. 34, (2004) 171-80.
  • Rasmussen, S. et al., Transitions between nonliving and living matter, Science 303, (2004) 963-5.
  • Rasmussen, S. et al., Living and nonliving matter, Science (Letters) 305, (2004) 41-3.
  • Tamulis, A., Tamuliene, J., Tamulis, V., Ziriakoviene, A., Quantum mechanical design of molecular computers elements suitable for self-assembling to quantum computing living systems, Solid State Phenomena, Scitec Publications, Switzerland 97-98, (2004) 175-80.
  • Packard, N. H., Shaw, R. (2005). http://arxiv.org/cond-mat/0412626

Books

  • Bedau, M. A., Cleland, C., The nature of life: Classical and contemporary perspectives from philosophy and science (New York: Cambridge University Press, In press, 2009), pp.
  • Bedau, M. A., Parke, E. C., The prospect of protocells: Social and ethical implications of recreating life (Cambridge: MIT Press, In press, 2009), pp.
  • Baragona, R., Battaglia, F., Poli, I., Evolutionary statistics (Springer, 2008), pp. accepted.
  • Baragona, R., Battaglia, F., Poli, I., Evolutionary statistics for high dimensional data (Springer, 2008), pp.
  • Bedau, M. A., Humphreys, P., Emergence: Contemporary readings in philosophy and science (Cambridge: MIT Press, 2008), pp. http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11341
  • Lindgren, K., Information theory for complex systems — lecture notes. Chalmers university of technology, göteborg, sweden (To be submitted after revision and extension for publication as a book, 2008), pp. ../../../../Global_Publications/InformationTheory-LectureNotes-Lindgren.pdf?ver=0&helpview;=238124&ftype;=0
  • Rasmussen, S. et al., Protocells: Bridging nonliving and living matter (Cambridge: MIT Press, In press, 2008), pp. http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630
  • Rasmussen, S., Mangalagiu, D., Initiativ for videnskab, teknologi og policy. Mouritsen, O. G., Ed., Viljen til visdom (2008), pp.
  • Solé, R. V., Rasmussen, S., Bedau, M. A., Towards the artificial cell. Theme issue of philosophical transactions of the royal society b, Philosophical transactions of the royal society b special issue (Philosophical Transactions of the Royal Society B, 2007), pp. 1723-925. http://journals.royalsociety.org/content/n1p715478p27/

Theses

  • Chemnitz, S., Ph.D.,  "Hybride Mikrofluidiksysteme als programmierbare Umgebung zur Untersuchung biochemischer Modellreaktionen." Univ. Saarland, Advisors: McCaskill, J. S., Seidel, H.(2006).
  • Ehses, S., Ph. D., "Isothermale in vitro Selektion und Amplifikation zur Untersuchung von Evolutionsvorgängen" Ruhr University Bochum, Advisors: McCaskill, J. S., Kiedrowski, G. v. (2005).
  • Rücker, T., Ph.D., "Biomolekulare Informationsverarbeitung in vernetzten Mikroflussreaktoren." University of Bonn, Advisors: McCaskill, J. S., Famulok, M. (2005).
  • Lichtensteiger, L., Ph.D., "Bodies That Think Quickly and Learn Fast:  On the Interdependence of Morphology and Control for Intelligent Behavior." (2004) PhD Thesis,  University of Zurich,  Switzerland.

Book Sections

  • Sardanyés, J., The hypercycle: From molecular to ecosystems dynamics, in Landscape ecology research trends. (2008) pp. Chapter 6, 1-12. http://complex.upf.es/index.php?page=22
  • Bedau, M. A., The evolution of complexity, in Mapping the future of biology: Evolving concepts and theories In Thomas Pradeu, A. B., and Michel Morange, eds., Ed. (Berlin: Springer, In press, 2008).
  • Tamulis, A., Tamulis, V., Ziock, H., Rasmussen, S., Influence of water and fatty acid molecules on quantum photoinduced electron tunnelling in photosynthetic systems of pna based self-assembled protocells”, chapter 2, in Multi-scale simulation methods for nanomaterials R., R., Mohanty, S., Eds. (John Wiley & Sons, Inc.; New Jersey, 2008) pp. 9-28.
  • Tamulis, A., Tamulis, V., Ziock, H., Rasmussen, S., Influence of water and fatty acid molecules on quantum photo-induced electron tunneling in self-assembled photosynthetic centers of minimal protocells, chapter 2, in Multiscale simulation methods for nanomaterials Ross, R. B. a. M., S., Ed. (Wiley, 2008) pp. Chapter 2.
  • Monnard, P. A., The dawn of the rna-world: Non-enzymatic rna polymerization from mono-ribonucleotides under prebiotically plausible conditions, in Prebiotic evolution and astrobiology Lazcano, A. a. W., J.T.F., Ed. (Landes Bioscience, 2008) pp. Chapter 10. in press
  • Bedau, M. A. a. M. T., Social and ethical implications of artificial cells, in The prospect of protocells: Social and ethical implications of the recreation of life In Bedau, M. A. a. P., E. C. , eds., Ed. (Cambridge: MIT Press, In press, 2008).
  • Parke, E. C., Bedau, M. A., The precautionary principle and its critics, in The prospect of protocells: Social and ethical implications of the recreation of life In Bedau, M. A., Parke, E. C. e., Eds. (Cambridge: MIT Press, In press, 2008).
  • Parke, E. C., Bedau, M. A., Introduction to the prospect of protocells, in The prospect of protocells: Social and ethical implications of the recreation of life In Bedau, M. A., Parke, E. C. e., Eds. (Cambridge: MIT Press, In press, 2008).
  • Solé, R. V. et al., Models of protocell replication, in Protocells: Bridging living and non-living matter Rasmussen, S., al., e., Eds. (MIT Press, in press, 2008). http://complex.upf.es/index.php?page=22
  • Parke, E. C., Bedau, M. A., Social and ethical issues concerning protocells, in Protocells: Bridging nonliving and living matter In Rasmussen, S., Bedau, M. A., Chen, L., Deamer, D. , Krakauer, D. C. , Packard, N. H. , Stadler, P. F. , eds., Eds. (Cambridge: MIT Press, In press, 2008). http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630
  • Rasmussen, S. et al., Assembly of a minimal protocell, in Protocells: Bridging nonliving and living matter Rasmussen, S. et al., Eds. (in MIT Press, in press, 2008). http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630, http://www.worldcat.org/oclc/182913278&referer;=brief_results
  • Rasmussen, S., Bedau, M. A., McCaskill, J. S., Packard, N. H., A roadmap to protocells, in Protocells: Bridging nonliving and living matter In Rasmussen, S., Bedau, M. A., Chen, L., Deamer, D. , Krakauer, D. C. , Packard, N. H. , Stadler, P. F., eds., Eds. (Cambridge: MIT Press. In press., 2008). http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630
  • Woodruff, W. H., Energetics, energy flow, and scaling in life and protolife, in Protocells: Bridging nonliving and living matter Rasmussen, S., al., e., Eds. (2008). in press
  • Nilsson-Jacobi, M., Hierarchical dynamics, in Springer's encyclopedia on complex systems. (Springer (to appear), 2008). No link available due to copyright issues
  • Bedau, M. A., Une vue fonctionnelle de la cellule vivante minimale (a functional view of minimal cellular life), in Comment définir la vie? In H. Bersini and J. Reisse, e., Ed. (Paris: Vuibert, 2007) pp. 5-13. http://www.decitre.fr/livres/Comment-definir-la-vie-Les-reponses-de-la-biologie-de-l-intelligence-artificielle-et-de-la-philosophie-des-sciences.aspx/9782711748655
  • Bedau, M. A., What is life?, in A companion to the philosophy of biology In S. Sarkar and A. Plutynski, e., Ed. (New York: Blackwell, 2007) pp. 455-71. http://www.blackwellpublishing.com/book.asp?ref=9781405125727&site;=1
  • Bedau, M. A., Artificial life, in Handbook of the philosophy of biology In M. Matthen and C. Stephens, e., Ed. (Amsterdam: Elsevier, 2007) pp. 585-603. http://www.elsevier.com/wps/find/bookdescription.cws_home/711119/descript
  • Jiang, Y., Travis, B., Knutson, C., Zhang, J., Weronski, P., Numerical methods for protocell simulations, in Protocells: Bridging nonliving and living matter Rasmussen, S. et al., Eds. (Cambridge: MIT Press, 2007). in press
  • McCaskill, J. S., Evolutionary microfluidic complementation towards artificial cells, in Protocells: Bridging nonliving and living matter Rasmussen, S. et al., Eds. (MIT Press, 2007). http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630
  • Mouritsen, O. G., Jakobsen, A. F., Forming the essential template for life: The physics of lipid self-assembly, in Protocells: Bridging nonliving and living matter Rasmussen, S. et al., Eds. (MIT Press, in press, 2007). http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid;=11630
  • Buchanan, A., Gazzola, G., Bedau, M. A., Evolutionary design of a model of self-assembling chemical structures, in Systems self-assembly: Multidisciplinary snapshots In N. Krasnogor, S. G., D. Pelta and J.L. Verdegay, eds., Ed. (Amsterdam: Elsevier, 2007) pp. 79-100. Elsevierhttp://www.elsevier.com/wps/find/bookdescription.cws_home/714277/description#description
  • Serra, R., Carletti, T., Poli, I., Filisetti, A., The growth of populations of protocells, in Towards a general theory of emergence G., M., A., A. P., Eds. (Singapore: World Scientific, 2007) pp. in press.
  • Pankau, W.-M. et al., Replicatable nanoscaffolded multimodularity – a chemical perspective, in Functional synthetic receptors Hamilton, A., Schrader, T., Eds. (Wiley, 2006).
  • Bedau, M. A. et al., Evolutionary design of a ddpd model of ligation, in Lecture notes in computer science 3871, V., Ed. (Springer, 2005) pp. 201-12.

Conference Proceedings

  • Miyashita, S., Hotz, M. P. E., in IEEE International Conference on Mechatronics‭ (‬ICM‭). (2007). in press
  • Rasmussen, S., Mangalagiu, D., Ziock, H., How do European and U.S. Energy sectors address climate change? paper presented at the 2008 Academy of Management Annual Meeting, Anaheim, California, USA 2008.
  • Serra, R., Villani, M., A CA model of spontaneous formation of concentration gradients paper presented at the ACRI 2008, Berlin: Springer Lecture Notes in Computer Science 2008.
  • Kelly, C., McMullin, B., O’Brien, D., Enrichment of interaction rules in a string-based artificial chemistry paper presented at the The Eleventh International Conference on the Simulation and Synthesis of Living Systems, ALIFE-08, Winchester 2008. ../../../../Global_Publications/kellyALifeXI.pdf?ver=0&helpview;=238124&ftype;=0
  • Forlin, M., Poli, I., De March, D., Slanzi, D., Serra, R., Model-based evolutionary designs for biological complex systems experimentation paper presented at the European Conference on Complex Systems JECCS08 2008.
  • Forlin, M., Poli, I., De March, D., Slanzi, D., Serra, R., Model-based evolutionary designs for biological complex systems experimentation paper presented at the European Conference on Complex Systems, JECCS08 2008. http://www.jeruccs2008.org/
  • Slanzi, D., Forlin, M., De March, D., Poli, I., Probabilistic networks for high dimensional biochemical systems paper presented at the European Conference on Complex Systems, JECCS08 2008. http://www.jeruccs2008.org
  • Rasmussen, S., Mangalagiu, D., Ziock, H., How do european and u.S. Energy sectors address climate change? : A comparative study of the role of corporate social responsibility paper presented at the International Energy Workshop, Paris 2008.
  • Packard, N., Exploration and exploitation in complex experimental designs paper presented at the MITSOCS Mathematics In The Science Of Complex Systems, Venice 2008.
  • Poli, I., Complex systems experimental designs paper presented at the MITSOCS, Mathematics In The Science Of Complex Systems 2008.
  • Tamulis, A., Quantum mechanical interpretation of origin of life paper presented at the Proceedings of annual science conference of Faculty of Natural Sciences of Vilnius University 2008.
  • Slanzi, D., Poli, I., De March, D., Forlin, M., Bayesian networks for high-dimensional experiments paper presented at the Proceedings of Bayesian Analysis of High dimensional Data, CRiSM Workshop 2008. http://www2.warwick.ac.uk/fac/sci/statistics/crism/news/workshops/
  • De March, D., Forlin, M., Slanzi, D., Poli, I., Predictive neural networks for designing experiments paper presented at the Proceedings of Wivace 2008 2008.
  • Serra, R., Carletti, T., Poli, I., Filisetti, A., Synchronization phenomena in internal reaction models of protocells paper presented at the Proceedings of Wivace 2008 2008.
  • Carta, D. et al., Functionalization of organosilane substrate to bind biomolecules: Aging paper presented at the VI workshop on Sol-Gel, Lecce 2008.
  • Miyashita, S., Hadorn, M., Eggenberger Hotz, P., Water floating self-assembling agents paper presented at the The 1st KES Symposium on Agent and Multi-Agent Systems, Wroclaw, Poland 2007. in press
  • Monnard, P. A., Ziock, H., Eutectic phase in water-ice: A self-assembled environment conducive to metal-catalyzed non-enzymatic rna polymerization paper presented at the accepted Topical review for the special issue of Chemistry and Biodiversity, XIII ICBIC 2007.
  • McMullin, B., Kelly, C., O’Brien, D., Multi-level selectional stalemate in a simple artificial chemistry paper presented at the Advances in Artificial Life, 9th European Conference (ECAL-07), Lisbon 2007. ../../../../Global_Publications/ecal-2007-camera-ready.pdf?ver=0&helpview;=238124&ftype;=0
  • Carletti, T., Fanelli, D., Evolution of a population of protocells: Emergence of species paper presented at the BIOMAT 2006: International Sysposium on Mathematical and Computational Biology 2007.
  • Filisetti, A., Serra, R., Carletti, T., Poli, I., Villani, M., Synchronization phenomena in protocell models paper presented at the BIOMAT 2007, International Symposium on Mathematical and Computational Biology 2007.
  • Tamulis, A., Tamulis, V., Quantum mechanical modeling of artificial minimal living cells paper presented at the book of abstracts of 37th Lithuanian national physics conference 2007.
  • Tamulis, A., Tamulis, V., Quantum mechanical self-assembling of artificial minimal cells and control by molecular electronics and spintronics logical devices paper presented at the book of abstracts of COST D27 Final Evaluation conference “Prebiotic Chemistry and Early Evolution”, Inter – University Center, Dubrovnik, Croatia 2007.
  • Kelly, C., McMullin, B., O’Brien, D., Mitchell, G. G., P., S. d. F., The evolution of complexity in a multi-level artificial chemistry paper presented at the European Conference on Complex Systems, ECCS-07, Dresden 2007. http://cssociety.org/tiki-index.php?page=ECCS07-219
  • Forlin, M., Poli, I., De March, D., Packard, N., Serra, R., Evolving the experimental design for amphiphilic systems paper presented at the European Symposium on Nature-inspired Smart Information Systems 2007.
  • Rasmussen, S., Mangalagiu, D., Ziock, H., Bollen, J., Bollen, J., Collective intelligence for decision support in very large stakeholder networks : The future us energy system paper presented at the IEEE Symposium on Artificial Life, ALIFE '07 2007.
  • Kelly, C., McMullin, B., O’Brien, D., Mitchell, G. G., P., S. d. F., Preliminary steps toward artificial protocell computation paper presented at the International Conference on Morphological Computation 2007. ../../../../Global_Publications/morph-comp-2007.pdf?ver=0&helpview;=238124&ftype;=0
  • Miyashita, S., Hadorn, M., Eggenberger Hotz, P., Tribolon – water floating self-assembling units paper presented at the International Conference on Morphological Computation, Venice Italy 2007. in press
  • Serra, R., Carletti, T., Poli, I., Surface–reaction models of protocells paper presented at the International Symposium on Mathematical and Computational Biology BIOMAT2006 2007.
  • Tangen, U., From evolving software towards models of dynamically self-assembling processing systems paper presented at the Proceedings of ECCS 2006 2007.
  • Fellermann, H., Rasmussen, S., Ziock, H., Solé, R., A simple model of self-replicating protocells paper presented at the Proceedings of the 4th Annual Conference on Foundations of Nanoscience 2007.
  • Miyashita, S., Hadorn, M., Eggenberger Hotz, P., Water floating active units paper presented at the ROBOMEC 2007, Japan 2007. in press
  • Forlin, M., De March, D., Slanzi, D., Poli, I., A predictive evolutionary approach to design biochemical experiments, risk and prediction paper presented at the SIS 2007.
  • Slanzi, D., Poli, I., De March, D., Forlin, M., Bayesian networks for detecting relevant variable interactions for biochemical experiments, risk and prediction paper presented at the SIS 2007.
  • Slanzi, D., Trevisan, M., Villanova, L., Palù, G., Poli, I., Bayesian analysis of cytomegalovirus infection from microarray data, risk and prediction paper presented at the SIS 2007.
  • Chemnitz, S., Tangen, U., Wagler, P. F., Maeke, T., McCaskill, J. S., Electronically programmable membranes for improved biomolecule handling in micro-compartments on-chip paper presented at the 9th International Conference on Microreaction Technology (IMRET 9) 2006.
  • Eriksson, A., Görnerup, O., Nilsson Jacobi, M., Rasmussen, S., Quasi-species and aggregate dynamics paper presented at the Artificial Life X, Proceedings of the tenths conference on the simulation and synthesis of living systems 2006.
  • Carletti, T., Fanelli, D., Evolution of a population of protocells: Emergence of species paper presented at the BIOMAT 2006: International Sysposium on Mathematical and Computational Biology 2006.
  • Serra, R., Carletti, T. P., I., Surface–reaction models of protocells paper presented at the BIOMAT 2006: International Sysposium on Mathematical and Computational Biology 2006. World Scientific Publishing Company(http://eproceedings.worldscinet.com/9789812708779/9789812708779_0003.html).
  • Tamulis, A., Tamulis, V., Quantum processes in photosynthetic systems of artificial minimal cells paper presented at the book of abstracts of conference “Chembiogenesis 2006”, Barcelona, Spain 2006.
  • Tamulis, A., Abstract of presentation „basic questions about the origin of life“, question 9: Artificial life paper presented at the book of abstracts of International School on Complexity – 4th Course, Italy, Erice 2006.
  • Tamulis, A., Tamulis, V., Measure of complexity and photoinduced electron tunneling in photosynthetic systems of pna based self-assembled protocells paper presented at the book of abstracts of Third Annual Meeting COST Action P10 Physics of Risk & Workshop on Complex System Science, Vilnius Lithuania 2006. http://physrisk.itpa.lt/index.php?option=com_content&task;=view&id;=29&Itemid;=56
  • Theis, M., Gazzola, M., Forlin, M., Poli, I., Hanczyc, M., Bedau, M., Optimal formulation of complex chemical systems with a genetic algorithm paper presented at the ECCS06 online Proceedings 2006. http://sbsxnet.sbs.ox.ac.uk/complexity/complexity_PDFs/ECCS06/Conference_Proceedings/Conference%20proceedings.pdf
  • Goranovic, G., Rasmussen, S., Nielsen, P. E., Artificial life forms in microfluidic computers paper presented at the Proc. MicroTAS 2006, Tokyo Japan 2006. http://www.memphys.sdu.dk/publication/show_attachment.php?File_ID=126.
  • Nilsson Jacobi, M., Quotient manifold projections and hierarchical dynamics paper presented at the Proceeding of ECCS06 2006. http://arxiv.org/abs/math-ph/0606016/
  • Eriksson, A., Görnerup, O., Nilsson Jacobi, M., Rasmussen, S., Quasi-species and aggregate dynamics paper presented at the Proceedings of ALife X 2006. http://arxiv.org/abs/q-bio.PE/0511044/
  • Schroer, J. P., Lindgren, K., Simulation of higher-order self-assembly paper presented at the Proceedings of ECCS06 2006. ../../../../Global_Publications/selfassembly_ECCS06_Chalmers.pdf?ver=0&helpview;=238124&ftype;=0
  • Kelly, C., McMullin, B., O'Brien, D., On protocell “computation”, paper presented at the Proceedings of the European Conference on Complex Systems (ECCS-06), Oxford 2006. http://cssociety.org/tiki-index.php?page=ECCS06-152
  • Miyashita, S., Hotz, M. P. E., Morphogenetic evolution of 3d sheets exploiting a spatial constraint paper presented at the Proceedings of the IEEE World Congress on Computational Intelligence (CEC) 2006.
  • Carletti, T., Protocells under the chemoton hypothesis may evolve paper presented at the Proceedings of Wiva 3 2006. (http://laral.istc.cnr.it/wiva3/atti/wiva3/home.htm)
  • Serra, R., Carletti, T., Poli, I., Emergent synchronization in protocell models paper presented at the Proceedings of Wiva 3 2006. http://laral.istc.cnr.it/wiva3/atti/wiva3/presentazioni/SerraCarlettiPoli.pdf
  • Forlin, M., Poli, I., De March, D., Packard, N., Serra, R., Evolving complex biochemical experimentation paper presented at the Proceedings of Wiva 4 2006. (http://laral.istc.cnr.it/wiva3/atti/wiva3/home.htm
  • Serra, R., Carletti, T., Poli, I., Emergent synchronization in protocell models paper presented at the Proceedings of Wiva 5 2006.
  • Gazzola, G., Buchanan, A., Packard, N. H., Bedau, M. A., Catalysis by self-assembled structures in emergent reaction networks paper presented at the submitted to ECAL2007 for publication in LNCS 2006.
  • Tamuliene, T., Tamulis, A., Nielsen, P., Quantum mechanical investigations of flexibility of e and e(ag) nucleobases paper presented at the book of abstracts of 36th Lithuanian National Physics Conference, Vilnius 2005.
  • Tamulis, A., Tamulis, V., Variety of self-replicating complex living system based on quantum information paper presented at the book of abstracts of conference “Chembiogenesis 2005”, Venice, Italy 2005.
  • Tangen, U., Wagler, P.F., Chemnitz, S, Goranovic, G, Maeke, T., McCaskill, J. S., An electronically controlled microfluidics approach towards artificial cells paper presented at the European Conference on Complex Systems 2005. http://complexite.free.fr/ECCS05/proceedingsECCS05.pdf
  • McCaskill, J. S., Ehses, S. et al., Stationary chemical gradient reactors in the search for artificial cells paper presented at the MicroTas 2005 Boston 2005.
  • Wagler, P. F. et al., Dynamical multiphase structures in the microsystem approach to artificial cells paper presented at the MicroTas 2005 Boston 2005.
  • Achim, V. et al., Electrohydrodynamic stability analysis of two-phase flows in confining microsystems paper presented at the Proc. Computational Problems in Physics (CPiP) workshop 2005, Helsinki, Finland 2005.
  • Wagler, P., Tangen, U, Maeke, T, Chemnitz, S, Jünger, M and McCaskill, J.S., Molecular systems on-chip (msoc) - steps forward for programmable biosystems paper presented at the SPIE: Smart Structures and Materials 2004 (San Diego, CA, USA) 2005.
  • Tamuliene, J., Balevicius, M. L., Tamulis, A., Search of suitable sensitizers paper presented at the book of abstracts International conference on “ Structure and Spectroscopy” held in Vilnius , September 2004.
  • Goranovic, G., Sørensen, M. P., Brøns, M., Bruus, H., Electrohydrodynamic stability of two –phase microflows, paper presented at the Proc. MicroTAS 04, Malmö, Sweden 2004.
  • Tarapore, D., Lungarella, M., Gomez, G., Fingerprinting agent-environment interaction via information theory paper presented at the Proc. of the 8th Conf. on Intelligent Autonomous Systems (IAS'04) 2004.
  • Helvik, T., Lindgren, K., Nordahl, M.G., Local information in one-dimensional cellular automata paper presented at the Proceedings for ACRI-2004, Cellular Automata: 6th International Conference on Cellular Automata for Research and Industry 2004. http://books.google.com/books?hl=sv&lr;=&id;=qQs6hyZdzVkC&oi;=fnd&pg;=PA121&ots;=oPT6oBX7Tx&sig;=NRl7ulhSBcbMJLIv3e4zgSCI2Qs
  • Lindgren, K., Eriksson, A., Eriksson, K.-E., Flows of information in spatially extended chemical dynamics paper presented at the Proceedings for Artificial Life 9 2004. uploaded on ../../../../Global_Publications/ALife9_Lindgren_2004.pdf?ver=0&helpview;=238124&ftype;=0
  • Serra, R., Carletti, T., Poli, I., Villani, M., Filisetti, A., Conditions for emergent synchronization in protocells paper presented at the European Conference on Complex Systems ECCS07. Dresden (http://vwitme011.vkw.tu-dresden.de/TrafficForum/dresden/oral.html)

Manuscripts or Incomplete References

  • Caschera, F. et al., Predictive exploration of drug formulation space using model-based high throughput experimentation. (2008).
  • Goranovic, G., Sorensen, M., Brøns, M., Bruus, H., Interfacial instabilities of two viscous liquids in couette-poiseuille flow in the limit of small reynolds numbers. (2008), vol. preprint.
  • Pepelyshev, A., Poli, I., Melas,V., Uniform coverage designs for mixture experiments. (2008), vol. submitted.
  • Carletti, T., Stability, mutations and evolution in a population of chemotons. (2007), vol. preprint.

Reports

  • Tangen, U., “Declaration of the external interface between the ng_biopro-software and another external control-program, version 0.49 enhanced command 's'” (2008). https://134.147.93.67/bmcmyp/Data/PACE/Working_Area/Movement_simulator/BioPRO_Software/ext_interface.pdf
  • Serra, R., Carletti, T., Poli, I., Villani, M., Filisetti, A., “Conditions for emergent synchronization in protocells” (2008).
  • Serra, R., Villani, M., “Spontaneous formation of density gradiente” (2008).
  • Bagheri-Maurer, J., Wagler, P. F., “How to fill fpfa chip modules, version 30 may '07: Operations-manual (how to use the fpfa and biomodule resp.)” (2007). https://134.147.93.67/bmcmyp/Data/PACE/Working_Area/Movement_simulator/BioPRO_Software/FPFA_use_manual.pdf
  • Maeke, T., “Hardware-manual of bio@fox, biopro-hardware-manual revision 0.13” (2007). https://134.147.93.67/bmcmyp/Data/PACE/Working_Area/Movement_simulator/BioPRO_Software/biopro_hw_manual.pdf
  • Tangen, U., “User's-manual of biopro-software, users- and programmers-manual version 0.2” (2007). https://134.147.93.67/bmcmyp/Data/PACE/Working_Area/Movement_simulator/BioPRO_Software/biopro_user_manual.pdf
  • Bedau, M. et al., “Evolutionary design of a ddpd model of ligation” (2006).
  • Forlin, M. et al., “Modelling evolutionary experimental designs for complex chemical systems” (2006).
  • Serra, R., Carletti, T., Poli, I., “Synchronization phenomena in surface-reaction models of protocells” (2006).
  • Agostinelli, C., Cucina, D., Poli, I., “A simulation platform for an electric field particle dynamics (efpd)” (Dep. of Statistics, Univ. Ca’ Foscari of Venice, 2005).
  • Minerva, T., Poli, I., “Evo-stat: Evolutionary statistical modeling, technical report and software, dep. Of social, cognitive and quantitative science” (Univ. of Modena and Reggio Emilia, 2005).


Seminars, Lectures and Conference Presentations

2007-8

Bedau, M.A.: Simulations in artificial life. Keynote address, Third Models and Simulations Conference, University of Virginia, 5-7 March 2009, Charlottesville.

Bedau, M.A.: The second creation: social and ethical implications of recreating life in the laboratory. Invited presentation, Roskilde Science Sunrise Conference, 13-15 August 2008, Roskilde, Denmark.

Bedau, M.A.: 100x more efficient discovery and optimization for high-throughput screening. Oral presentation, 3rd Assay Development and Screening Technologies Conference, San Francisco, 5-6 June 2008.

Bedau, M.A.: Artificial cells: the second creation of life. Invited seminar, European School for Molecular Medicine, IFOM-IEO Campus, Milan, 28 April 2008.

Bedau, M.A.: Pluralism about emergence. Invited lecture, Workshop on Emergence, Erice, Italy, 12-16 April 2008.

Bedau, M.A.: Creating life. Invited lecture, Darwin Day Symposium on the Origins and Early Evolution of Life, National Evolutionary Synthesis Center, Duke University, February 2008.

Bedau, M.A.: A roadmap to minimal chemical life. Invited lecture, Conference on Defining Life, CNRS, Paris, 5 February 2008.

Bedau, M.A.: Can a unique definition of life be formulated? Round table with Mark Bedau, Hugues Bersini, Patrick Forterre, Antonio Lazcano, Pier Luigi Luisi, Alvaro Moreno, Radu Popa, and Bruce Weber, Conference on Defining Life, CNRS, Paris, 5 February 2008.

Bedau, M.A.: Evolutionary search for complex chemical systems. Invited colloquium, Chemistry Department, Reed College, 20 September 2007.

Bedau, M.A.: Weak emergence. Contributed talk, International Society for the History, Philosophy, and Social Studies of Biology, Exeter, England, 29 July 2007.

Bedau, M.A.: Pluralism about emergence. Contributed talk, International Society for the History, Philosophy, and Social Studies of Biology, Exeter, England, 28 July 2007.

Bedau, M.A.: The unsolved mystery of why evolution is so creative. Invited keynote lecture, European Conference of Computing and Philosophy (ECAP 2007), University of Twente, Netherlands, 21-23 July 2007.

Bedau, M.A.: A defense of pluralism about emergence. Invited lecture, conference on Emergence in Science and Philosophy, Catholic University of the Sacred Heart, Milan, Italy, 19-21 June, 2007. 

Bedau, M.A.: The creative evolution of technology. Invited lecture, International Conference on Living Technology, European Center for Living Technology, Venice, Italy, 25-26 May 2007.

Bedau, M.A.: Statistical models for evolutionary design of complex chemistry. Invited presentation, Workshop on Embodied Evolution, European Center for Living Technology, Venice, Italy, 15-16 May 2007.

Bedau, M.A.: Living technology: scientific prospects, practical applications, and social implications. Invited Engineering, Technology, and Culture lecture, University of Illinois, Urbana-Champaign, 11 April 2007.

Eggenberger Hotz, P, Füchslin, R. M., Hadorn, M., Miyashita,. S.: PACE: Artificial Cells as Building Blocks for Modular Robotic Systems,  Poster presentation ‘20 Years Artificial Intelligence Lab, 2007.

Filisetti, A., Serra, R., Carletti, T., Poli, I., Villani, M.: Synchronization phenomena in protocell models. BIOMAT2007, International Symposium on Mathematical and Computational Biology, 2007.

Forlin, M., Poli, I., De March, D., Packard, N., Serra, R.: Evolving the experimental design for amphiphilic systems, European Symposium on Nature-inspired Smart Information Systems, (www.nisis.de), Malta. 2007.

Forlin, M., Poli, I., De March, D., Slanzi, D., Serra, R.: Model-based evolutionary designs  for biological complex systems experimentation, European Conference on Complex Systems, JECCS08, 2008.

Füchslin, R. M.: Dynamic compartmentalization using mpRDPD, Invited lecture PACE Summer School, May 2008, San Servolo, Italy. 

Füchslin, R. M.: Patterns, Circuits, Inductive Generalization, Evolution: Towards Realistic Models, Invited lecture PACE Summer School, May 2008, San Servolo, Italy. 

Füchslin, R. M.: Patterns, Circuits, Inductive Generalization, Evolution: Towards Realistic Models, Talk at the AILab, Zürich Univ. Dec. 2007.

Füchslin, R. M.: Evolutionary Algorithms for Self-Assembling Systems: Simulations as a Tool for Optimizing Optimization, ODES workshop, 15. 7. 2007, Venice.

Görnerup, O., A method for inferring hierarchical dynamics in stochastic processes, ECLT workshop, March, 2008.

Kelly, C., McMullin, B., O'Brien, D., Mitchell, G.G. Speroni di Fenizio, P.:  The Evolution of Complexity in a Multi-Level Artificial Chemistry.Poster presentation at European Conference on Complex Systems (ECCS-07), Dresden, Germany, 2007

Lindgren, K.: Flows of information in chemical pattern formation, talk at Modelling Complex Biological Systems in the Context of Genomics, Evry, 3 May, 2007.

Lindgren, K.: Quantifying spatial structure in dynamical systems — from microscopic reversibility to macroscopic irreversibility, talk at Max Planck Institute for Mathematics in the Sciences, Leipzig, Nov. 2007.

Lindgren, K.: Self-replicating patterns: dynamics, energy, and information, talk at Joint Nordic Astrobiology and Swedish Astrobiology Network Meeting, Stockholm, Nov. 6-7, 2007.

Lindgren, K.: Self-replicating patterns and information dynamics, AlbaNova and Nordita Colloqium, Stockholm, Febr. 7, 2008.

Lindgren, K.: A dynamical systems route to complexity, lecture at ECLT Summer School Blueprint for an artificial cell, ECLT, 8 May, 2008.

Lindgren, K.: Quantifying spatial structure in symbol sequences — identifying correlations and local information, talk at Statistical Semantics of Genomes: From Sequence to Function, Evry, May 27-29, 2008.

McCaskill, J.: Complementation Systems for Genetic Self- assembly, ECLT International Conference on Living Technology, Venice, May 2007 

McCaskill, J.: Living Technology: Complementing Evolution and Self-assembly, invited seminar, Microsoft Research Labs, Cambridge, May 2007

McCaskill, J.: Programmable artificial cell evolution, PACE, invited presentation, Complex Research Projects Forum at ECCS 08, Dresden, October 2007, Position Paper available at:  http://cordis.europa.eu/fp7/ict/fet-proactive/cosiict-ws-oct07_en.html#presentations

McCaskill, J.: Directing evolutionary self-organisation, invited lecture, Para Limes Conference ‘Science without boundaries’, October 2007

McCaskill, J.: Alternative bio-inspired ICT’s, FET Workshop on alternative bio-inspired ICT’s, Brussels, February 2008

McCaskill, J.: Autopoietic vesicular protocells by mprDPD, ECLT Protocell Modelling Workshop, Venice, March 2008

McCaskill, J.: Evolvable electronic chemical cells and programmable chemistry for ICT: Theoretical background, PACE/ECLT Summer School, Blueprint for an Artificial Cell, San Servolo, Venice, 4-17th May 2008.

McCaskill, J.: Physics of genetically-programmable self-organizing systems: towards artificial chemical cells for intelligent microscopic construction. FIAS, Frankfurt, July 2008

McMullin, B.: A computational approach to What is life?, PACE/ECLT Summer School, Blueprint for an Artificial Cell, San Servolo, Venice, 4-17th May 2008.

McMullin, B.: Evolving Computation in Protocells: Harder than it might seem! Protocell Modelling Workshop. ECLT, Venice, 10-12 March 2008

Nilsson Jacobi, M.: Dynamical hierarchies, ECCS07 in Dresden, October 2007.

Nyström, J., Potts-based simulation model for physically self-assembling units, ECLT workshop, March, 2008.

Packard, N.: Exploration and Exploitation in Complex Experimental Designs MITSOCS, Mathematics In The Science Of Complex Systems, workshop organized at ECLT, 2008.

Packard, N.: Genetic algorithms and evolutionary computation, Chemical Genetic Algorithms, PACE/ECLT Summer School, Blueprint for an Artificial Cell, San Servolo, Venice, 4-17th May 2008.

Poli, I.: Complex Systems Experimental Designs, MITSOCS, Mathematics In The     Science Of Complex Systems (workshop organized at ECLT), 2008.

Poli, I.: Combinatorial experimental designs and statistical models, PACE/ECLT Summer School, Blueprint for an Artificial Cell, San Servolo, Venice, 4-17th May 2008.

Slanzi, D., Forlin, M. , De March, D., Poli, I.: Probabilistic networks for high dimensional biochemical systems, European Conference on Complex Systems, JECCS08, 2008.

Slanzi, D., Poli, I., De March, D. and Forlin, M.: Bayesian Networks for High-dimensional Experiments, International Conference on Bayesian Analysis of High dimensional Data, CRiSM Workshop , Warwick, UK, 2008.

Slanzi, D., Poli, I., De March, D. and Forlin, M.: Bayesian Networks for Detecting Relevant Variables Interactions for Biochemical Experiments, Risk and Prediction, SIS, Venezia, 2007.

Tamulis, A.: Quantum Mechanical Self-Assembling of Artificial Minimal Cells and Control by Molecular Electronics and Spintronics Logical Devices, COST D27 Final Evaluation conference Prebiotic Chemistry and Early Evolution, Inter – University Center, Dubrovnik, Croatia, May 11 - 13, 2007. 

Tamulis, A.: Quantum mechanical modeling of artificial minimal living cells, 37th Lithuanian national physics conference, June 11-13, 2007. 

Tamulis, A.: invited lecture, Quantum Mechanical Self-assembling of Artificial Minimal Cells and Control by Molecular Electronics and Spintronics Logical Devices, in international Nanotechnology School on Nanostructured materials for biosensors and medicine, 2008, February 18-22, School place: Klaipeda hotel, L. Stuokos–Guceviciaus street 3, Vilnius.  

Tamulis, A.: Quantum Self-Assembly of Artificial Living Cell and Molecular Electronics Control of Photosynthesis and Gene Dehybridization, presentation at European Center For Living Technology Workshop on Protocell Modelling, March, 10-12, 2008, Venice.  

Tamulis, A.: invited lecture, Quantum mechanical processes of self-assembly, photosynthesis and control of artificial living cells, Workshop of „Biomedicine Physics and Nanophotonics Studies Center, 2008-04-29, Hotel Best Western „Naujasis Vilnius, Konstitucijos ave. No 14, Vilnius, Lithuania.  

Tamulis, A.: invited lecture, Quantum mechanical self-assembly of artificial living cells, photosynthesis and control, International conference on „Innovative Medicine, May 22-24, 2008, Hotel „ARTIS, Liejyklos str. No 11/25, Vilnius, Lithuania.  

Tamulis, A.: Quantum Mechanical Modeling of Artificial Minimal Living Cells, in Cell Model Systems Summer School CNR, Rome, 8-13 June, 2008. 

Tangen, U.: On striving for open-ended evolution to improve the means for optimization-problems in the field of engineering. Embodied Evolution Workshop, ECLT Venice, 2007.

Tangen, U. Enzyme-like replication de novo in a micro-controller environment, ProtoCell-Modelling-Workshop ECLT,Venice, 2008.

Tangen, U. Evolutionary self organization of digital systems, ECLT-Summerschool, Venice, 2008.

Tangen, U.: Enzyme-like replication de novo in a micro-controller environment GWAL-2008 (German Workshop on Artificial Life) Keynote-Lecture, Leipzig, 2008.

Wagler, P.F.: Microfluidics as a tool for designing artificial cells, ECLT Summerschool Blueprint for an Artificial Cell (May 4-17 2008 in Venice).

Wagler, P.F.: Electronically programmable membranes and improved biomolecule handling on microfluidic biochips, Micro and Nano Technologies (MiNaT) Congress in Stuttgart, Germany, June 2007.

 

Nystrom, J., Higher-order self-assembly through morphological growth of artificial cells  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.

Serra, R., Conditions for syncronization  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.

Shaw, R., Flow on shapes  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.

Tamulis, A., Quantum self-assembly of artificial living cell and molecular electronics control of photosynthesis and gene de-hybridization  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.

Tangen, U., Evolutionary information generation and stabilization of a protocell  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.

Tunstrom, K., Coarse graining of united atoms fluid  (2008) paper presented at the Protocell Modelling Workshop, European Centre for Living Technology, Minich, 10/03/2008.


2006-7

Bedau, M.A: Evolutionary design of complex chemical systems. Invited keynote lecture, Adaptation in Artificial and Biological Systems (AISB’06), University of Bristol, Bristol, England, 3 April 2006.

Bedau, M.A: Automated design of artificial life forms from scratch. Invited plenary presentation, 7th German Workshop on Artificial Life, Jena, Germany, 26-28 July 2006.

Bedau, M.A: Protocells illustrate NBIC convergence and its social and ethical implications. Presentation at a Workshop on the Ethical and Social Implications of the Nano-Bio-Info-Cogno Convergence, Avignon, France, 17-19 Dec 2006.

Bedau, M.A: The second creation of life. Systems Biology and Informatics Seminar, University of Rostock, Rostock, Germany, Feb 2007.

Bedau, M.A: The social and ethical implications of synthesizing living entities, BBSRC Synthetic Biology Workshop, Wiltshire, England, 7 February 2007.

Bedau, M.A: The second creation of life, Life Sciences Institute Lecture, University of Southampton, Southampton, England, 14 February 2007.

Bedau, M.A: Ethical and social aspects of systems biology research, Invited plenary lecture, ERASysBio Strategy Conference, St. Anne’s College, Oxford, United Kingdom, 28 March 2007.

Bedau, M.A: Living technology: scientific prospects, practical applications, and social implications, Invited Engineering, Technology and Culture lecture, University of Illinois, Urbana-Champaign, 11 April 2007.

Carletti, T.: Protocells under the Chemoton hypothesis may evolve: Emergence of species, Workshop WIVA3, 12–15 September 2006, Collegio, S. Chiara, Siena (Italy), 14 September 2006.

Carletti, T.: Evolution of a Population of Protocells: Emergence of Species, BIOMAT 2006, 25–30 November 2006, Manaus, Amazonia Brasil, 30 November 2006.

Carletti, T.: Surface–Reaction Models of Protocells, BIOMAT 2006, 25–30 November 2006, Manaus, Amazonia Brasil, 27 November 2006.

Carletti, T.: From chemical reactions to species, Workshop: Modelling Populations of Protocells, ECLT, Venezia, March 2007.

Eggenberger Hotz, P. and Füchslin, R.M. (Joint talk): Simulation of Assembling Vesicular Structures, ECLT workshop on simulation and self-assembly, Venice, Italy, March 20-21 2007.

Eriksson, A.: A framework for simulating combined lipid/template growth synchronisation and template evolution, PACE Workshop: Modelling populations of protocells. ECLT, 18-19 March 2007.

Fellermann, H., Rasmussen, S., Ziock, H., Solé, R.V.: Dissipative particle dynamics simulation of the Los Alamos Bug, Mesoscopic Simulation Workshop, European Center for LivingTechnology, Venice, Italy, October 3, 2006.

Fellermann, H., Rasmussen, S., Ziock, H., Solé, R.V.: Dissipative particle dynamics simulation of the Los Alamos Protocell, Protocell Simulation Workshop, European Center for Living Technology, Venice, Italy, March 18-19, 2007.

Fellermann, H., Rasmussen, S., Ziock, H., Solé, R.V.: A simple model of self-replicating protocells, 4th Annual Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO07), Snowbird, UT, USA, April 18-21, 2007.

Füchslin, R.M.: Dynamic compartmentalization using mprDPD, talk at the ECLT workshop on mesoscopic simulation, Venice Italy, October 2-14, 2006.

Füchslin, F., Maeke, T. and  McCaskill, J.S.: Studying dynamic compartmentalization using mpRDPD, Satellite Workshop at ECCS 06, Paris, November 2006

Füchslin, R.M.: Evolving Self-Assembling Digital Circuitry: Towards Realistic Models, Int. Conf. on Morphological Computation, Venice, Italy, March 26-28 2007.

Goranovic, G.: Artificial living systems in microfluidic computers, invited talk, Department of Micro and Nanotechnology (MIC), Technical University of Denmark, Oct 2006.

Goranovic, G., Rasmussen, S. and Nielsen, P.: Artificial life forms in microfluidic computers, É TAS2006, Tokyo, Japan, November 5-9, 2006.

Hellwig, N.: An experimental approach towards a protocell based on the chemoton idea, ECLT PACE-PA Workshop, Venice, March 2007.

Jiang, Y.: Protocell assembly, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China, June, 2006.

Jiang, Y.: Modeling self-assembly: Protocell and functional macromolecules, South China University of Technology, Guangzhou, China, July, 2006.

Jiang, Y.: Protocell assembly, APS March Meeting, Denver, CO, USA, March 5, 2007.

Lindgren, K.: Flows of information in chemical pattern formation, at workshop Morphogenesis from different viewpoints, Nov. 18-19, 2006, Göteborg.

McCaskill, J.S.: Bringing Complex Systems to Life: the PACE project in embedded IT, IST 06 Event – Strategies for Leadership, Helsinki, 21-23 November, 2006.

McCaskill, J.S.: Evolving amphiphiles and electronic membranes: a fast track to simple cells and complex chemistry, MPI Winterseminar on Biophysical Chemistry, Molecular Biology and Cybernetics of Cell Functions, 13-27 January, 2007.

McCaskill, J.S.: Evolving self-assembling molecular recognition systems, International Conference on Morphological Computation, ICMC07, Venice, March 26-28, 2007.

McCaskill, J.S.: Programmable Artificial Cell Evolution, Evry spring school, Paris, May 2-3, 2007.

McMullin, B.: Preliminary Steps toward Artificial Protocell Computation, PACE Workshop: Chemical Evolution and Self-Assembly. ECLT, 21-22 March 2007.

McMullin, B., Kelly, C., O'Brien, D., Mitchell, G. and Decraene, J.: Preliminary Steps toward Artificial Protocell Computation, International Conference on Morphological Computation (ICMC-07). Venice, Italy, March 27-28th, 2007.

Miyashita, S., Hadron, M. and Eggenberger Hotz, P.: Technical Proposal for an Active Floating Element, Proceedings of the 50th Anniversary summit of AI (ASAI50), July 2006.

Munteanu, A. and Solé, R.V.: Models of artificial protocells, Poster presented at Winter School: Systems Biology for Medical Applications 27th February - 2nd March 2007.

Nielsen, P.: Erice Meeting on Basic questions about the origin of life, Erice, Italy, Oct, 2006.

Nilsson Jacobi, M.: Quotient Manifold Projections and Hierarchical Dynamics, European Conference on Complex System – ECCS06. Oxford, September, 2006.

Nilsson Jacobi, M.: Error thresholds in multi-level replicator systems, PACE Workshop: Chemical Evolution and Self-Assembly. ECLT, 21-22 March 2007.

Nyström, J.: Presentation of Prototype Simulation Package for Physically Self-Assembling Units, PACE Workshop: Chemical Evolution and Self-Assembly. ECLT, 21-22 March 2007.

Patzke, V.: Thiol disulfide exchange reactions in oligonucleotide replication, ECLT PACE-PA Workshop, Venice, March 2007.

Poli, I.: Model-based Design for combinatorially complex experiments, Workshop WIVA3, 12–15 September 2006, Collegio S.Chiara, Siena (Italy),16 September 2006.

Poli, I.: Modelling Genetic Algorithms (MGAs) for experimental design, workshop on chemical evolution and self-assembly, ECLT, Venezia, 21 March 2007.

Rasmussen, S., Bailey, J.A., Boncella, J.M., Chen, L., Collis, G., Colgate, S., DeClue, M.S., Fellermann, H., Goranovic, G., Jiang, Y., Knutson, C., Monnard, P.-A., Mouffouk, F., Nielsen, P., Sen, A., Shreve, A., Tamulis, A., Travis, B., Weronski, P., Woodruff, W.H., Zhang, J., Zhou, X. and Ziock, H.: Protocells: Minimal self-replicating nano-machines (Key note presentation), 3rd Annual Conference on Foundations of Nanoscience (FNANO06), April 23-27, 2006.

Rasmussen, S.: Assembly of minimal life, Santa Fe Institute, Santa Fe, NM, USA, September 6, 2006.

Rasmussen, S.: Summary of protocell modeling efforts in Pas, Protocell Simulation Workshop, European Center for Living Technology, Venice, Italy, March 18-19, 2007.

Rasmussen, S.: Self-replicating materials, information processing and the omega machine, CNLS/SFI Workshop on Unconventional Computing, Santa Fe, NM, USA, March 21-23, 2007.

Rasmussen, S.: Assembly of a minimal protocell, linking genetics, container and metabolism, IEEE Computational Intelligence Conference, Honolulu, Hawaii, USA, April 1-5, 2007.

Rasmussen, S.: Self-replicating materials and living technology, 1st International Conference on Living Technology, May 21-22, 2007, accepted.

Schroer, J. P. , and Lindgren, K.: Simulation of higher-order self-assembly, poster at European Conference on Complex System – ECCS06. Oxford, September 2006.

Serra, R.: Emergent synchronization in protocell models, Workshop WIVA3, 12–15 September 2006, Collegio S. Chiara, Siena (Italy), 14 September 2006.

Serra, R.: Is synchronization generic?, Workshop : Modelling, Populations of Protocells, ECLT, Venezia, 18 March 2007.

Solé, R.V.: Etude dâs un modelle de protocellule, Ecole Formation Doctorale 23-27 January 2006, Universita de Namur (Belgium), 24 January 2006.

Solé, R.V.: Stability, mutations and evolution of a population of Chemotons, Workshop Evolution and Self-Assembly, 16-18 March 2006, ECLT ,Venezia (Italy), 18 March 2006.

Solé, R.V.: Protocells under the Chemoton hypothesis may evolve: Emergence of species, Workshop WIVA3, 12-15 September 2006, Collegio S.Chiara, Siena (Italy), 14 September 2006.

Solé, R.V.: Surface Reaction Models of Protocells, BIOMAT 2006, 25-30 Novembre 2006, Manaus, Amazonia Brasil, 27 November 2006.

Solé, R.V.: Evolution of a Population of Protocells: Emergence of Species, BIOMAT 2006, 25-30 November 2006, Manaus, Amazonia Brasil, 30 November 2006.

Solé, R.V.: From chemical reactions to species, Workshop: Modelling Populations of Protocells, ECLT, Venezia (Italy) 19 March 2007.

Tangen, U.  From evolving software towards models of dynamically self-assembling processing systems, ECCS 2006, Oxford UK.

Tangen, U.: From evolving software towards models of dynamically assembled macro-molecules, Lecture at Zurich University, Dept. of Information Technology, Artificial Intelligence Laboratory, 24th January 2007.

v. Kiedrowski, G.: Nobel workshop in chemistry On the origin of life, Sanga Saby conf. center, Stockholm, 09.06.06.

v. Kiedrowski, G.: What-is-Life? series, Karolinska Inst., Stockholm, 26.10.06.

v. Kiedrowski, G.: Chembiogenesis 2006, 5th COST D27 annual meeting, Barcelona, 15.12.06.

v. Kiedrowski, G.: Coll. Theor. Chem., RUB, Bochum, 20.12.06.

v. Kiedrowski, G.: GDCh meeting on NMR problems, RUB, Bochum, 15.01.07.

v. Kiedrowski, G.: Coll. Org. Chem., Univ. Karlsruhe, Germany, 06.02.07.

v. Kiedrowski, G.: SymPOC 2007, Cardiff, UK, 19.04.07.

Wagler, P.F. and Tangen, U.: Microfluidic complementation and feedback, as part of ECLT PACE-PA Workshop, in Venice, March 15-16 2007.

Weronski, P., Jiang, Y. and Rasmussen, S.: Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine, 6thUnderstanding Complex Systems Symposium, Urbana-Champaign, IL, USA, May 15-18, 2006.

Weronski, P., Jiang, Y. and Rasmussen, S.: Molecular dynamics simulations of micellar dynamics and stability, Symposium 2006 Championing Scientific Careers, Los Alamos, NM, USA, August 2-3, 2006.

Weronski, P., Jiang, Y. and Rasmussen, S.: Molecular dynamics study of small PNA molecules in lipid-water system, Symposium 2006 Championing Scientific Careers, Los Alamos, NM, USA, August 2-3, 2006.

Weronski, P., Jiang, Y. and Rasmussen, S.: Molecular dynamics study of peptide nucleic acid affinity to lipid bilayer, 2006, Materials Research Society Fall Meeting, Boston, MA, USA, November 27 - December 1, 2006.

Weronski, P., Jiang, Y. and Rasmussen, S.: Molecular dynamics simulations of micellar dynamics and stability, 2006, Materials Research Society Fall Meeting, Boston, MA, USA, November 27 - December 1, 2006.

Weronski, P., Jiang, Y. and Rasmussen, S.: Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine, 4th Annual Conference on Fundations of Nanoscience: Self-Assembled Architectures and Devices (FNANO07), Snowbird, UT, USA, April 18-21, 2007.

Zhou,X.: A General Method to Extend Molecular Dynamics Timescale in Atomistic Fluids: Time-Space Compression, Pair-Correlation Approximation and Applications, 6th understanding complex systems symposium, Champaign-Urbana, May 2006

Zhou,X.: A General Method to extend Molecular Dynamics Timescale In Atomistic Entropic Systems: Time-Space Compression, Pair-Correlation Approximation, High-Dimensional Density Proofreading and Application, 232nd American Chemical Society National Meeting, San Francisco, September 10-14, 2006.


Bedau, M., Craacc concept, goals overview, admin matters  (2006) paper presented at the The Critical Assessment of Artificial Chemical Cell (CRAACC), ECLT, 20/07/2006.

Bedau, M., Statistical models for evolutionary design of complex chemistry  (2007) paper presented at the Embodied Evolution of Complex Experimental Systems (EmboEvo), ECLT, 15/05/2007.

Bedau, M., The creative evolution of technology  (2007) paper presented at the Living Technology, Minich, 25/05/2007.

Bedau, M., A functional language for protocell schemes  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Bedau, M., The micelle effect  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Cawse, J., Genetic algorithms as screening designs  (2007) paper presented at the Embodied Evolution of Complex Experimental Systems (EmboEvo), ECLT, 15/05/2007.

Cawse, J., Genetic algorithms as screening designs  (2007) paper presented at the Optimization and Design of ExperimentS (ODES), ECLT, 15/06/2007.

Dieckmann, A., Kinetic and computational analysis of a fulvene replicator  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Fellerman, H., Dpd modelling of protocell life-cycle  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Forlin, M., Model-based genetic algorithms for designing      mixture experiments  (2007) paper presented at the Optimization and Design of ExperimentS (ODES), ECLT, 15/06/2007.

Füchslin, R., Evolutionary algorithms for self-assembling systems: Simulations as a tool for the development of novel optimization strategies  (2007) paper presented at the Optimization and Design of ExperimentS (ODES), ECLT, 15/06/2007.

Goranovic, G., Protocells in microfluidic environment  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Hayden, E., Toward the kinetic analysis of a self-replicating ribozyme  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Algorithms simfit  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Commands simfit  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Examples simfit  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Introduction to simfit  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Kinetic nmr titration of the tweezer-catalyzed pyridine alkylation  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Kiedrowski, G. v., Systems chemistry: From chemical self- to virus-shaped biomimetic artefacts  (2007) paper presented at the Living Technology, Minich, 25/05/2007.

McCaskill, J., Evolving amphiphilic systems  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Packard, N., Self-assembly and chemical reactions at the transition to life  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Plöger, T., Toward pna replication analysis via kinetic titrations using 19f nmr spectroscopy  (2007) paper presented at the Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, ECLT, 30/06/2007.

Poli, I., Modeling evolutionary designs of experiments  (2007) paper presented at the Optimization and Design of ExperimentS (ODES), ECLT, 15/06/2007.

Rasmussen, S., Living technology based on self-replicating materials  (2007) paper presented at the Living Technology, Minich, 25/05/2007.

Tamulis, A., Quantum processes of self assembly  (2007) paper presented at the PROTOCELL MODELLING, ECLT, 18/03/2007.

Tangen, U., Evolution of computer hardware  (2007) paper presented at the Embodied Evolution of Complex Experimental Systems (EmboEvo), ECLT, 15/05/2007.

Tangen, U., Microfluidics in an integrated system: Pros and cons of the pico-liter chemistry  (2007) paper presented at the Optimization and Design of ExperimentS (ODES), ECLT, 15/06/2007.


2005-6

Bedau, M.A.: Evolutionary design of self-assembling complex chemical systems. Workshop on Evolution and Self-assembly, ECLT, March 2006

Bedau, M.A.: Creating artificial cells, Invited keynote address, ACAL-05,  Australian Conference on Artificial Life, 7 December 2005, Sydney

Bedau, M.A.: Creating artificial cells, Invited seminar, Australian Defense Force Academy, 9 December 2005, Canberra

Bedau, M.A.: Living technology, Inaugural Distinguished Computer Science Seminar, University of Nottingham, Nottingham, England, 11 April 2005

Bedau, M.A.: Computational models of evolutionary creativity, Douglas Engelbart Keynote Address, North American Computers and Philosophy Conference, 6 August 2005

Bedau, M.A.: Adaptation and the edge of chaos. Invited presentation, Workshop on Evolution, Information, and Computation, European Center for Living Technology, 24 May 2005

Bedau, M.A.: Evolutionary design of complex chemical systems Invited seminar, Artificial Intelligence Laboratory, Department of Informatics, University of Zurich, 25 April 2006, Zurich, Switzerland

Bedau, M.A.: ECLT, PACE, and ProtoLife’s evolutionary design of complex chemical systems, Invited talk ChellNet meeting, University of Nottingham, 6 April 2006 Nottingham, England

Bedau, M.A.: Evolutionary design of complex chemical systems, Invited keynote lecture, Adaptation in Artificial and Biological Systems (AISB’06), 3 April 2006, University of Bristol, Bristol, England

Boncella, J., Bailey, J. and Collis, G.: Ruthenium Photocatalysis as an Integrated Approach to Coupling the Container Metabolism to the Information System of a Protocell, PACE-PAs Science Coordination Workshop, Los Alamos, July 19-22, 2005

Buchanan, A.: Software for evolving chemical reaction networks, ECLT workshop: Evolution and Self-Assembly, March 2006

Buchanan, A.: Evolutionary Design of a DDPD Model of Ligation, 7th International Conference on Artificial Evolution, Lille, France October 2005

Carletti, T.:Chemoton Model: the shape does matter, PACE-PA Coordination Workshop, Los Alamos, July 19-22, 2005

Carletti, T.:Chemoton Model: the geometry can affect the dynamics, System Chemistry, ECLT, Venice , October 3-4, 2005

Carletti, T.:Chemoton Model: stability, mutation and evolution of Chemoton families, PACE Workshop Evolution and Self Assembly, ECLT Venice, March 16-18, 2006

Eriksson, A.: Determining DPD parameters from Physical Properties, PACE-PAs science coordination workshop, LANL, July 19-23, 2005

Füchslin, R.M., Maeke, T., Tangen, U., McCaskill, J. S.: Genetic Self-Assembly: a novel route to complex design, poster at ECCS 05, Paris, France, 2005.

Görnerup, O.:Container growth and replicator dynamics in pre-biotic chemistry. European Conference on Complex Systems, Paris, France, November 2005.

Görnerup, O. and Nilsson Jacobi, M.J.:  Container Growth and Replicator Dynamics in Prebiotic Chemistry, Life Matters Conversations in Bionanotechnology, poster presentation at Chalmers, Göteborg, Sweden, October 2005.

Goranović, G.: A protocell's life cycle, PACE/PA coordination workshop, Los Alamos National Laboratory, USA, July 18-23, 2005 (invited talk)

Goranović, G.: Microfluidic approach to the onset of life, Seminars in Astrobiology, NORDITA Copenhagen, Nov 2005 (invited talk)

Jiang, Y.:  Vesicle in flow: Elasticity, phase separation and hydrodynamics, T-7 group seminar, Los Alamos, May 2005.

Jiang, Y.: News from Los Alamos. PACE-PAs Science Coordination Workshop, Los Alamos, July 19-22, 2005. 

v. Kiedrowski, G.: Self-replication and nanoconstruction from the eyes of a chemist, Colloquium of the German Chemical Society (GDCh), Bielefeld, 13.1.2005

v. Kiedrowski, G.: Systems Chemistry: Self-Replication Versus Self-Elongation, Seminar at the Center of Astrobiology (CAB), Madrid, 8.4.2005

v. Kiedrowski, G.: Self-replication and nanoconstruction using oligonucleotide building blocks, Colloquium of the German Chemical Society (GDCh), Kassel, 19.4.2005

v. Kiedrowski, G.: Self-replication and nanoconstruction of biomimetic systems, ESOR10, Plenary lecture, Rome, 25.-30.7.2005

v. Kiedrowski, G.: Self-replication and nanoconstruction of biomimetic systems, GBM Annual Fall Meeting, Invited lecture, Berlin/Potsdam, 18.-21.9.2005

v. Kiedrowski, G.: Systems Chemistry – A Perspective, Chembiogenesis 2005, COST D27 midterm evaluation conference, prepared contributed lecture with timeslot given to P. Strazewski, Venice, 30.9.2005

v. Kiedrowski, G.: Some ideas during final discussion, ECLT Systems Chemistry workshop, contributed lecture, Venice, 3.-4.10.2005

v. Kiedrowski, G.: Systems chemistry via examples, Colloquium of the institute of microbiology and molecular genetics, Göttingen, 1.11.2005

v. Kiedrowski, G.: Chemical replication and nanoconstruction using three-armed oligonucleotides, Colloquium of the German Chemical Society (GDCh), Darmstadt, 9.1.2006

v. Kiedrowski, G.: Chemical replication, Invited lecture, Nobel workshop on the origins of life, Stockholm, 9.-11.6.2006

Knutson, C.: Reaction kinetics of  the Boncella scheme, PACE-PAs Science Coordination Workshop. Los Alamos, July 19-22, 2005. 

Lindgren, K.: Flows of information as a driving force behind chemical pattern formation. Complex systems workshop organized by Cris Moore and Michel Morvain at Santa Fe Institute, July 2005.

Lindgren, K. and Eriksson, A.: Flows of information as a driving force behind chemical pattern formation. Life Matters Conversations in Bionanotechnology, poster presentation at Chalmers, Göteborg, Sweden, October 2005.

Lindgren, K.: Flows of information as a driving force behind chemical pattern formation. European Conference on Complex Systems, Paris, France, November 2005.

Lindgren, K.: Flows of information in spatially extended systems. Mini Symposium on Dynamical Systems, Norwegian University of Science and Technology, Trondheim, 12 January 2006.

Maeke, T., Füchslin, R.M., Tangen, U., McCaskill, J. S.: Reactive DPD multiscale simulations (preserving the hydrodynamic limit) for artificial cells with microfluidic support, poster Evolution, Information and Computation: From Living to Non-Living Matter, PACE Workshop, European Center for Living Technology, Venice, Italy, May 2005

McCaskill, J.S.: From self-replicating spots to self-replicating micelles: on the evolution of self-assembly in reaction-diffusion systems. ECLT workshop: Evolution and Self-Assembly, March 2006.

McCaskill, J.S.: Spatially resolved systems chemistry: Theory and experiment towards evolving artificial cells, Seminar given at the Max-Planck Institute of Molecular Physiology, Dortmund, September 2005

McCaskill, J.S.: Towards the evolution of artificial cells, Seminar at the Center of Astrobiology (CAB) Madrid, June 2005

McCaskill, J.S.: Microsystems Chemistry: Theory and Experiment towards Artificial Cells.’ Invited Lecture at the Tag der Chemie, Bochum University, July, 2005

McCaskill, J.S.: Physical Evolution of Amphiphile Self-assembly, PACE-PAs science coordination workshop, LANL, July 19-23, 2005.

McCaskill, J.S.: Microsystems Chemistry, Talk at Chalmers Technical University, Göteborg, August 2005

McCaskill, J.S.: Microsystem support for complex chemical system design, Satellite Workshop at ECCS 06, Paris, November 2006

McCaskill, J.S., Füchslin, R.F., Maeke, T. and Tangen, U.: From  Genetic Self-assembly to Organic Computing, Seminar on Organic Computing at Schloss Dagstuhl, January 2006.

McCaskill, J.S., Füchslin, R.F., Maeke, T.: On the evolution of dissipative and self-assembling structures, ECLT Workshop, March 2006.

McMullin, B.: Who Needs Genomes? Workshop on Evolution, Information, Computation (ECLT, May 2005).

McMullin, B.: Major Transitions in Artificial Chemistries? Workshop on Evolution and Self-Assembly (ECLT, March 2006).

Monnard, P.A.: Assembly of a simple self-replicating molecular aggregate, AbSciCon 2006, Astrobiology Science Conference, Washington DC, USA, March 26-30, 2006.

Munteanu, A.: Generic Darwinian selection in protocell assemblies. ECLT workshop: Evolution and Self-Assembly, March 2006.

Nilsson Jacobi, M.J.: Hierarchical dynamics. Complex systems workshop organized by Cris Moore and Michel Morvain at Santa Fe Institute, July 2005.

Nilsson Jacobi, M.J.: Hierarchical dynamics. European Conference on Complex Systems, Paris, France, November 2005.

Nilsson Jacobi, M.J.: Quasi-Species and Aggregate Dynamics. ECLT workshop: Evolution and Self-Assembly, March 2006.

Nilsson Jacobi, M.J.: Hierarchical dynamics. PACE-PAs science coordination workshop, LANL, July 19-23, 2005.

Poli, I.: Evolutionary probabilistic design for protocell, PACE Workshop on Evolution and Self Assembly, ECLT, Venice March,16-18 2006.

Poli, I.:  Evolutionary Designs and Modelling, Fondazione di Venezia, April 6, 2006.

Poli, I.:  Evolutionary wavelet network, University of Rome Tor Vergata, April 19, 2006.

Packard, N.: Evolution of self-assembly and chemical reactions Synthetic Biology: Constructing and Deconstructing Life, Castilla, Spain, October 2005.

Packard, N.: Self-assembly with chemical reactions European Conference on Complex Systems, Paris, France, November 2005.

Packard, N.: Coevolution of structure and dynamics. Santa Fe Institute, Santa Fe, USA, May 2005.

Packard, N.: Interaction, simulation, and chemistry, Simulation, Visualization, Interaction, Mixed Reality, Workshop, European Commision, Brussels,  June 2005.

Packard, N.: Embodied physics, computation, and chemistry, Workshop on: Evolution, Information and Computation: From living to nonliving matter ECLT, May 23-25, 2005.

Packard, N.: Sistemi Complessi e Tecnologia Vivente, Public Lecture at ISI, Torino May, 2005

Packard, N.: Coevolution of chemistry and self-assembly, at Synthetic Biology: Constructing and Deconstructing Life, workshop, Castillo de Magalia (Avila, Spain), October 2005.

Packard, N.:  Artificial cells as living technology, PopTech, public lecture, Camden, Maine, Oct 2005.

Rasmussen, S.: Minimal self-replicators, invited seminar at the University of Southern Denmark, Odense, Denmark, May 25, 2005.

Rasmussen, S.:  Assembling minimal self-replicating nano-machines, invited presentation at the TTI Vanguard Conference, Miami FL, USA, July 12-13, 2005.

Rasmussen, S.: Update on evolutionary issues from the Los Alamos project. ECLT workshop: Evolution and Self-Assembly, March 2006.

Rasmussen, S.: Assembly of minimal self-replicating nanomachines, USAF-WPARB, Dayton OH, USA, September 2005.

Rasmussen, S.: Assembling minimal self-replicating nanomachines, Public Lecture, sponsored by AAAS, Washington DC, USA, December 1, 2005.

Rasmussen, S.: How close are we from making life from scratch, Public Lecture, sponsored by University of Alaska, Anchorage, USA, April 2006, 2006.

Rasmussen, S.: Assembling minimal self-replicating nanomachines, University of Alaska, Anchorage, USA, April 2006.

Rasmussen, S.: The thermodynamics-kinetics connection for protocells, ECLT Workshop, March 13-17, 2006,Venice, Italy.

Rasmussen, S.: Protocells: Minimal self-replicating nanomachines, Key Note Presentation, 3rd Annual Conference on Foundations of Nanoscience (FNANO), Snowbird, Utah, USA, April 23-26, 2006.

Rasmussen, S.: The Science of Living Technology, University of Southern Denmark, April 27, 2006.

Rasmussen, S.: Summary of the PACE-PAs Science Coordination Workshop, Los Alamos, July 19-22, 2005.

Rasmussen, S.: Assembling minimal self-replicating nano-machines, invited presentation at the Cell-Life Entities (CLT) Workshop, WPAFB, USAF, Dayton OH, USA, September 13-14, 2005.

 Schroer, J.: Higher-order self-assembly. ECLT workshop: Evolution and Self-Assembly, March 2006

Roberto, R.: A model for the study of the dynamics of a population of protocells, PACE Workshop on Evolution and Self Assembly, ECLT Venice 16-18 March 2006. 

Roberto, R.: Population dynamics of los alamos bugs. ECLT workshop: Evolution and Self-Assembly, March 2006.

Shreve, A. and Doshi, D.: Manipulations of fatty acid containers, PACE-PAs Science Coordination Workshop, Los Alamos, July 19-22, 2005.

Tamulis, A., Tamuliene, J.  and Tamulis, V.: Quantum mechanical modelling of elements of artificial minimal living organisms, „Protocell Assembly workshop at LANL Centre for Nonlinear Studies (CNLS) Monday 11 am (February 14,  2005), Los Alamos, New Mexico, USA. Electronically delivered abstract, 

Tamulis, A., Tamulis, V. and Tamuliene, J.: Self-Assembly of Protocell and Metabolism Modelled by Quantum Mechanical Molecular Dynamics (QMMD) and Classical Molecular Dynamical (MD) Methods, „Protocell Assembly and PACE joint workshop at LANL, July 18-23, 2005, Los Alamos, New Mexico, USA.

Tamulis, A., Tamulis, V: Quantum Mechanical Modeling of Self-Reproducible Living PNA Chip Immersed in the Lipid Bilayer Vesicle Controlled by Quantum Computing Logic Gates, Workshop in „Biological Physics, Physics of Life: From Single Molecules to Networks, Krogerup Hojskole, Humlebaek, Denmark, 21-27 August, 2005.

Tamulis, A., Tamulis,V.:Creation of Variety of Self-Replicating Complex Living Systems Based on Quantum Information, Brainstorming meeting of ONCE-CS European Complex Systems Society, University of Paris, France, September 19-23, 2005. 

Tangen, U.: Electronic complementation principle towards artificial cells, PACE-PAs science coordination workshop, LANL, July 19-23, 2005.

Tangen, U.: Aspects of information technology with feedback-controlled BioPRO-setup  at Workshop Protocells: Experiments, Ethics, and Technological Potential in Venice, ECLT, 2005

Tangen, U., Wagler, P.F., Chemnitz, S.,  Goranovic, G., Maeke, T., McCaskill, J.S.: An electronically controlled microfluidics approach towards artifical cells. ECCS 2005, Paris 2005.

Tangen, U.: From evolving software towards models of dynamically assembled macro-molecules. ECLT workshop: Evolution and Self-Assembly, March 2006.

Weronski., P., Y. Jiang, and Rasmussen, S.: Molecular dynamics (MD) study of a small PNA molecule in a lipid-water system, PACE-PAs Science Coordination Workshop, Los Alamos, July 19-22, 2005.

Weronski., P., Yi Jiang and Rasmussen, S.: Molecular Dynamics Study of a Small PNA Molecule in a Lipid-Water System, Symposium 2005 Championing Scientific Careers, Los Alamos, August 2005.  (Pawel won the Award for Outstanding Oral Presentation in Biosciences).

Weronski., P., Jiang, Y. and S. Rasmussen, Molecular Dynamics Study of a Small PNA Molecule in a Lipid-Water System, CNLS seminar. August 18, 2005.

Woodruff, W.: Protocell and bio-energetics, Joint PACE and PAs Protocell Chemistry Workshop at ECLT, Venice, Italy, February 21-26, 2005.

Zhang, J., and Jiang, Y.: Dissipative Particle Dynamics Studies of Complex Structures of Lipids in Water, American Physical Society Annual Meeting, Los Angeles, March 2005.

Ziock, H.: Life and information, PACE-PAs Science Coordination Workshop, Los Alamos NM, USA, July 19-22, 2005.

Ziock, H. and Rasmussen, S.: The Los Alamos Protocell, invited presentation at the Chemobiogenesis COST 2005 Conference, Venice, Italy, September 27-October 2, 2005.


Bedau, M., Computation at the edge of chaos  (2005) paper presented at the EVOLUTION,  INFORMATION AND COMPUTATION from  living to nonliving matter, ECLT, 23/05/2005.

Bedau, M., Social responsibility and protocell technology  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.

Hanczyk, M., Container chemistry  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.

Kiedrowski, G. v., Information chemistry  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.

McCaskill, J., Replicator chemistry in channels and fan reactor  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.

Müller, S., Allosteric regulation of ribozyme activity in response to surrounding conditions: A redox-sensitive riboswitch  (2005) paper presented at the Prebiotic Chemistry and Early Evolution, ECLT, 28/10/2005.

Nielsen, P. E., Peptide nucleic acid (pna). A psedopeptide with sequence information relevance for the discussion of origin of life?  (2005) paper presented at the Prebiotic Chemistry and Early Evolution, ECLT, 28/10/2005.

Packard, N., Morphological computation  (2005) paper presented at the EVOLUTION,  INFORMATION AND COMPUTATION from  living to nonliving matter, ECLT, 23/05/2005.

Sole, R. V., The computation landscape, from rna to feedforward networks  (2005) paper presented at the EVOLUTION,  INFORMATION AND COMPUTATION from  living to nonliving matter, ECLT, 23/05/2005.

Sole, R. V., Information and computation at the edge of life  (2005) paper presented at the EVOLUTION,  INFORMATION AND COMPUTATION from  living to nonliving matter, ECLT, 23/05/2005.

Tamulis, A., Variety of self-replicating complex living systems based on quantum information  (2005) paper presented at the Prebiotic Chemistry and Early Evolution, ECLT, 28/10/2005.

Tangen, U., Electronic control of protocell chemistry  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.

Valverde, S., Noise and reliable computation, von neumann revisited  (2005) paper presented at the EVOLUTION,  INFORMATION AND COMPUTATION from  living to nonliving matter, ECLT, 23/05/2005.

Wagler, P., Container chemistry in 2d gradient reactor and flow systems  (2005) paper presented at the Protocells: experiments, ethics, and technological potential, Bonn, 21/02/2005.


2004-5

Bedau, M.A.: Living technology, Inaugural Distinguished Computer Science Seminar, University of Nottingham, Nottingham, England, 11 April 2005

Bedau, M.A.: The problem of life, Invited symposium (with Carol Cleland and Michael Ruse) on Life. American Philosophical Association Pacific Division Meetings, San Francisco, March 2005.

Füchslin, R.M.: Evolving Logical Circuits via Genetic Self-Assembly, Evolution and Statistics, international workshop in Erice, June 2004.

Hanczyc, M.: Experimental models of primitive cellular organization: the role of clays and the dynamics of membranes. Research Center for integrated Sciences. Life as a Complex System: Constructive and Dynamic Approach to Cell and Developmental Biology. March 5-6, 2005, University of Tokyo at Komaba.

Lichtensteiger, L.: Self-assembling submersible robots, NeuroIT Workshop, Munich, December 2004  

McCaskill, J.S.: Evolution of inductive principles via genetic self-assembly.  Evolution and statistics, international workshop in Erice, June 2004.

McCaskill, J.S.: The PACE project ‘Programmable Artificial Cell Evolution’. Invited lecture on the 3rd COST D27 workshop, Heraklion, Kreta, 30.09-03.10.2004. 

McCaskill, J.S.: Intelligent non-equilibrium microenvironments: an enabling technology for bringing chemistry to life. European Conference On Complex Systems, Torino, Villa Gualino, December 5-7, 2004.

McMullin, B. : 30 Years of Computational Autopoiesis: A Review, From Autopoiesis to Neurophenomenology. Paris, June 2004.

McMullin, B.:  What is Artificial Life? Artificial Life IX, Boston, September 2004.

Packard, N. and R. Shaw: Presentation of Morphological computation at the University of Zurich, Feb, 3, 2005 

Tangen, U., Füchslin, R.M., Maeke, T., Wagler, P.F., McCaskill, J. S.: Closing the loop: wet in silico bioprocessing. Poster presentation at 39th MPI Winter Seminar, Klosters, CH, 2004.

Tangen, U.: Electronic control of micro-reactors, ECLT, 2004 

Tangen, U.: Experiments in microflow-reactors of type BioModul, ECLT, 2004 

v. Kiedrowski, G.: Selbstreplication and the origin of life. – Seminar in the planetological colloquium, University of Münster, 26.05.2004.

v. Kiedrowski, G.: Self-Replication in Synthetic Molecular Systems. – Plenary lecture on the 5th International Conference in Biological Physics (ICBP 2004), Göteborg, Sweden, 23.-27.8.2004. Due to temporary health issues lecture was given by Eors Szathmary. 27.08.2004 

v. Kiedrowski, G.: Self-Replication Versus Self-Elongation. Or: How to make long oligonucleotides without templates, enzymes, primers, surfaces, or stepwise feeding? – Invited lecture on the 3rd COST D27 workshop, Heraklion, Kreta, 30.09-03.10.2004. 

v. Kiedrowski, G.: Self-replication and nanoconstruction from the eyes of a chemist. – Plenary lecture on the International symposium on nano-organization and function, Tokyo Institute of Technology, 11.-12.11.2004.

v. Kiedrowski, G.: Minimal Life. – Invited contribution to a round table discussion during the „1st Course: Towards the Minimal Cell of the „Erice International School on Complexity, Erice, Sicily, 7.-10.12.2004.

v. Kiedrowski, G.: Self-replication between origin-of-life research and nanoscience. – Colloquium in organic chemistry, University of Zürich. 14.12.2004 

v. Kiedrowski, G.: Self-replication and nanoconstruction from the eyes of a chemist. – Invited lecture on the symposium Bio Nano Engineering for Nanodevices, Institut Curie, Paris, 15.12.2004.


Agostinelli, C., Simulator approaches  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Bedau, M., Buchanan, A., Lipid structures and simple chemistry in dpd  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Eriksson, A., Molecular gaming  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Füchslin, R., Toward chemistry in dpd  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Goranovic, G., Microfluidic fluid dynamic phenomenology  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Lindgren, K., Information flow in spatial chemical systems  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Nilsson, M., Lipid assembly in md lattice gases  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Poli, I., Serra, R., Minerva, T., Evolutionary statistical methods  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Poli, I., Serra, R., Romanazzi, M., Statistics for experimental design: Questions for the chemistry  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Shaw, R., Asymmetric diffusion  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Speroni, P., Organizations in chemical reaction networks  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Tamulis, A., Tamuliene, J., Quantum mechanical md modelling of sensitizers of artificial living organisms  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Tangen, U., Maeke, T., Framework for interactions between simulator and experiment  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Walker, R., Cancedda, S., Stillo, G., Simulation presentations  (2004) paper presented at the Multiscale Molecular Simulations and Stochastic Feedback, ECLT, 22/11/2004.

Organization of workshops and conferences, tutorials and teaching, summer schools and project presentations


2004-5


Chalmers University

PACE integration in the Complex Adaptive Systems masters programme of Chalmers University: Presentation of PACE to attract students for MSc thesis projects. Current thesis projects of relevance for PACE include: 

(i) development of MDLG simulation method, 

(ii) evolution in the Gray-Scott model, 

(iii) investigation of transition between molecular and concentration based description of reaction-diffusion dynamics.


Zürich University

Isha Geigenfeind. Evolution of Adaptive Agents in a 2D Fluid Simulation. Term project of the AILab, 2004.


Reed College

M. Bedau “Computational Insights into The Creativity of Evolution” PSA 2004, Austin TX, 19 November 2004.


Ruhr University Bochum

P.F. Wagler “Microfluidics and programmable Biochips - filling the gap between biomolecules and nano-tools”. International Master courses in Nanotechnologies (IMN) Coordinamento Interuniversitario Veneto per le Nanotechnologie (CIVEN), May 2004, http://www.civen.org/IMN/faculty.php


ECLT


Protocells: experiments, ethics, and technological potential, PACE Workshop

ECLT, Palazzo Giovannelli, 21 Feb-5 March 2005

Thread 1: Microfluidic technology for protocell experiments  

Organizers: John McCaskill, Patrick Wagler 

 Thread 2: Protocell chemistry  

Organizers: Peter Nielsen, Steen Rasmussen, Günter von Kiedrowski 

 Thread 3: Social and ethical implications of protocell technology  

Organizer: Mark Bedau  

Thread 4: IT potential of programmable artificial cells  

Organizers: Lukas Lichtensteiger, Peter Eggenberger, Rolf Pfeifer 


Workshop on “Multiscale Molecular Simulations and Stochastic Feedback”, PACE –ECLT Integrated Twin-Workshop

ECLT, Palazzo Giovannelli, 22 Nov-5 Dec 2004

Organizers: S. Rasmussen, N. Packard

PACE Kickoff Meeting and Workshop

ECLT, Palazzo Giovannelli, 22 Nov-5 Dec 2004

Organizer: J.S.McCaskill



2005-6


Chalmers University

The International masters programme in Complex Adaptive Systems at Chalmers includes several lectures dealing with theory, models and examples from the PACE project.


At Chalmers, there are several students each year who do their MSc thesis project in connection with the PACE project. For example, at the March workshop at ECLT on Evolution and Self-Assembly, Jens Schroer gave a presentation based on work in his MSc thesis.


Ruhr University Bochum

P.F. Wagler “Microfluidics and programmable Biochips - filling the gap between biomolecules and nano-tools”, International Master courses in Nanotechnologies (IMN) Coordinamento Interuniversitario Veneto per le Nanotecnologie (CIVEN) July 2005, http://www.civen.org/IMN/


ECLT

Conference on Prebiotic Chemistry and Early Evolution

ECLT, Venice International University, September 28-October 1, 2005

COST Action D27

Organizer: Günter von Kiedrowski


Evolution and Self-Assembly, ECLT Workshop
Palazzo Cavalli Franchetti, Venice, Italy, March 16-18, 2006
Organizers: Kristian Lindgren, Martin Jacobi, Norman Packard

Social and Ethical Issues Concerning Protocells: Key Questions and Answers
ECLT Workshop
Palazzo Cavalli Franchetti, Venice, Italy, 16-17 March 2006
Organizers: Mark Bedau and Emily Parke

Programmable Microenvironments for Artificial Cells, ECLT Workshop
Protolife Srl Labs, Parco Vega, Venice, 13-14 March 2006
Organizers: Patrick Wagler and John McCaskill

Social and Ethical Issues in Protocell Research: Assessing Risk and Responsibilities in an Uncertain World, PACE Workshop
ECLT, Venice International University, October 2, 2005
Organizers: Mark Bedau and  Emily Parke 

Systems Chemistry, PACE Workshop
ECLT, Venice International University, October 3-4, 2005 
Organizer:  Günter von Kiedrowski 

PACE-PAs Science Coordination - Protocell components interactions
Los Alamos National Laboratory, NM – USA, July 19-23, 2005
Organizer: Steen Rasmussen

EVOLUTION, INFORMATION, AND COMPUTATION: from living to nonliving matter,
PACE Workshop
ECLT, Palazzo Giovanelli, Venice, 23-25 May 2005
Organizer: Ricard Solé


2006-7


Chalmers University

K. Lindgren: Presentation of the PACE project for Gentekniknämnden (The Swedish Gene Technology Advisory Board) on Oct. 25, 2006.


Nilsson Jacobi, M.: Presentation of the PACE project for Nordita (Nordic Institute for Theoretical Physics) on Febr. 9, 2007.


MSc theses related to PACE finished at Chalmers: Schroer, J. P.: Simulation of higher-order self-assembly. Chalmers, 2006.


Ruhr University Bochum 

N. Hellwig: Presentation of the PACE project to the Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, May 1, 2006.

Doctoral Thesis: Chemnitz, S.: Hybrid microfludic systems as a programmable environment to study biochemical model reactions, (2006) Univ. Saarland (Advis. McCaskill, J.S. and Seidel, H.), Recent developments in MEMS Vol. 3 Editors Schütze, A. and Seidel, H. (Shaker Verlag, 2007) ISBN 978-3-8322-5865-8.


P.F. Wagler “Microfluidics and programmable Biochips - filling the gap between biomolecules and nano-tools”, International Master courses in International Master in Nanotechnologies (IMN) Coordinamento Interuniversitario Veneto per le Nanotechnologie (CIVEN) 4.-7. April 2006.


Venice University

Several project presentation to an academic audience by UVen


ECLT

International Conference on Morphological Computation ICMC07 

ECLT, Ca’ Minich, March 26-28, 2007

Organizers: Norman Packard, Rolf Pfeifer, Mark Bedau, Fumiya Iida


PACE-PA Coordination Meeting
March 15-17 Venice 2007
Organizers: John S. McCaskill and Steen Rasmussen

Chemical Evolution and Self-Assembly
Venice, March 21-22, 2007
Organizers: K. Lindgren, O. Görnerup

Protocell Modelling Workshop
Venice, March 18-19, 2007
Organizers: Steen Rasmussen, Roberto Serra

The Critical Assessment of Artificial Chemical Cell (CRAACC), PACE Workshop
ECLT, Isle of San Servolo, 20-22 July 2006
Organizers: N. Krasnogor, L. Cronin, B. Davis, M. Bedau

2007-8


ECLT

Conference on Living Technology

ECLT, Ca’ Minich, 25-26 May 2007

Organizers: I. Poli, N. Packard, K. Lindgren, S. Nolfi


Reed College

M. Bedau taught course on “Foundations of the life sciences.” European School of Molecular Medicine, Milan, Italy. 21-30 April 2008. 

M. Bedau will teach course on “Artificial life.” European School of Molecular Medicine, Milan, Italy. 22-26 September 2008.

M. Bedau will teach course on “Foundations of the life sciences.” European School of Molecular Medicine, Milan, Italy. 25 May – 5 June 2008.

M. Bedau, Organizing Committee, the First Workshop on Philosophy & Engineering, Delft University of Technology, The Netherlands, 29-31 October 2007.

M. Bedau, Organizing Committee, Artificial Life XI, The Eleventh International Conference, England, August 2008.


Ruhr University Bochum 

P.F. Wagler “Microfluidics and programmable Biochips - filling the gap between biomolecules and nano-tools”, International Master courses in International Master in Nanotechnologies (IMN) Coordinamento Interuniversitario Veneto per le Nanotecnologie (CIVEN) 4.-6. June 2007.

P.F. Wagler “Microfluidics and programmable Biochips - filling the gap between biomolecules and nano-tools”, International Master courses in International Master in Nanotechnologies (IMN) Coordinamento Interuniversitario Veneto per le Nanotecnologie (CIVEN) 4.-7. July 2008.


Vilnius University

A. Tamulis, “Scientists meet new challenges in nanoecology and nanomedicine (PACE project)” (in Lithuanian language), in the book: “Participation of Lithuania in the FP6 of European Union, examples of successes”, issued by Agency for International Science and Development Programs in Lithuania, pages 32-33, 2007  http://www.tpa.lt/publikacijos.htm


A. Tamulis proposed idea of Molecular Quantum Computing Life is published on the Lithuanian WEBsite: 

http://mokslasplius.lt/mokslo-naujienos/2007/04/04/kvantine-gyvybe and in the The Encyclopedia of Science http://www.daviddarling.info/encyclopedia/M/molecular_quantum_computing_cloud.html 


Protolife Srl

N. Packard co-organized the workshop  „Optimization and Design of Experiments“ (ODES)  at ECLT with the participation of academic and industrial experts in the area of the design of experiments in high dimensional settings (June 15-16, 2007).


Chalmers University

K. Lindgren: Parts of the Chalmers course “Information theory for complex systems” overlaps with theoretical development within PACE. In 2008 the lecture notes for the course was expanded, partly as a result of PACE-related research. The plan is to revise and expand this further into a book.


K. Lindgren: Lecture on Artificial Life for graduate students at Chalmers, Oct. 25, 2007.


M. Nilsson Jacobi: The Chalmers course “Simulation of complex systems” include examples from simulation development in PACE.


An MSc thesis project at Chalmers related to PACE was finished in June 2007 by Chris Foley: “Investigation of the effects of structural information in the inflow of a chemical system.”


ECLT


Final PACE Ethics Workshop 

ECLT, Ca’ Minich, 13-14 March 2008

Organizers: M. Bedau, E. Parke, U. Tangen, B. Hantsche-Tangen

 

Protocell Modelling Workshop 

ECLT, Ca’ Minich, 10 -12 March 2008

Organizers: R. Serra, K. Lindgren, T. Carletti


Mathematics In The Science OF Complex Systems

MITSOCS Workshop, The Open University

Ca’ Minich, 24-26 October 2007

Organizers: J. Johnson, I. Poli


Dynamic Modelling and Kinetic Data Fitting Using Sim-Fit – A practical approach, PACE Workshop

ECLT, Isle of San Servolo,Venice, 30 June-1 July 2007

Organizer: G. von Kiedrowski


Optimization and Design of ExperimentS (ODES), PACE Workshop

ECLT, Ca’ Minich, 15/16 June 2007

Organizers: I. Poli, M. Forlin


Embodied Evolution of Complex Experimental Systems (EmboEvo), PACE Workshop

ECLT, Ca’ Minich, 15/16 May 2007

Organizers: N. Krasgonor, M. Bedau


Blueprint for an Artifical Cell

ECLT Summer School

Venice May 4-17, 2008

Awards

Rasmussen, S., Danish National Science Foundation, with matching funding from the University of Southern Denmark (~$7.2M) for Fundamental Living Technology Center (FLinT), start November 1, 2007, focussing on the basic science underpinning self-replicating materials. The initial project life-time is 5 years.  The Center Director is Steen Rasmussen.


Tangen, U. Best Paper Award at ECCS 2006, Oxford, UK:

From evolving software towards models of dynamically self-assembling processing systems.


Rasmussen, S., Top Five Innovator 2005. Biotechnology Category (for Los Alamos protocell design), World Technology Network, San Francisco CA, November 2005.


Rasmussen, S., Los Alamos Achievement Award, 2004, Los Alamos Protocell design.

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