Artificial Life VI


Evolving Reaction-Diffusion Ecosystems with Self-Assembling Structures in Thin Films.

Jens Breyer
Institute for Molecular Biotechnology (IMB) Jena
http://www.imb-jena.de/~breyer

Joerg Ackermann
Institute for Molecular Biotechnology (IMB) Jena
http://www.imb-jena.de/~jack

John S. McCaskill
Institute for Molecular Biotechnology (IMB) Jena
http://www.imb-jena.de/mip


Abstract

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of {\em in vitro } evolution have been established that are based on the multi-enzyme 3SR. Micro-structured thin-film open bioreactors have been constructed in our laboratory to run these systems spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the {\em in vitro } biochemistry of these systems have been developed which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules each with a defined sequence and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures --- allowing the additional stabilization of cooperation through semi-permeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular {\em in vitro } evolution can be extended to include the influence of self-assembling flexible membranes.


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