Analyzing interactions in a multi-agent simulation of cross replicating RNA enzymes
Author: 
David AllenAuthors Info & Claims
Article No.: 4, Pages 1 - 7
Abstract
Evolutionary adaptation and synchronization with an environment is a key component of many real-world systems. In this work we seek to further understand the first nonbiological system that undergoes self-sustained replication using a multi-agent simulation of the system's evolutionary dynamics. [Lincoln & Joyce, 2009] demonstrated two RNA enzymes that catalyze each other's synthesis and undergo self-sustained exponential amplification. Due to the cost and difficulty of real-world experiments we leverage agent simulation to better explore and analyze the experiments and suggest possible extensions.
We leverage tools from the emerging field of Network Science to generate a recombination network of the agent-agent interactions and demonstrate that under resource limitations the system is driven to generate more variation, thereby enabling adaptation to environmental pressures. We measure this variation using recombination network properties such as the average degree, network diameter, and clustering coefficient. Additionally, we show agent-environment synchronization by measuring the population growth of agents while adjusting the temporal influence of environmental pressures and analyzing the system's ability to adapt and compensate.
By developing a simulation of the real-world experiments we were able to quickly and cost effectively test out various experiment extensions to determine which would be interesting and feasible to further explore.
References
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J. Ackermann, T. Kirner, and S. H. L. Klapp. "Complex pattern formation of simple biochemical amplification reactions in micro-structured flow reactors." Zeitschrift fur Naturforschung A, 61, 60--68, 2006.
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A. Clauset, C. Moore, and M. Newman. "Hierarchical structure and the prediction of missing links in networks." Nature 453, 98--101, 2008.
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T. Lincoln and G. Joyce. "Self-Sustained Replication of an RNA Enzyme." Science 323, 1229--1232, 2009.
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- Analyzing interactions in a multi-agent simulation of cross replicating RNA enzymes
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Published: 26 March 2012
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