High-Performance Simulation of Evolutionary Aspects of Epidemics
PARA '98 Proceedings of the 4th International Workshop on Applied Parallel Computing, Large Scale Scientific and Industrial Problems
High-Performance Computing Tools for Modeling Evolution in Epidemics
HICSS '99 Proceedings of the Thirty-second Annual Hawaii International Conference on System Sciences-Volume 8 - Volume 8
Emergency preparation and mobile notification through cluster computing
International Journal of Mobile Communications
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Prevailing hypotheses concerning origins of life assume that rare configurations of prebiotic polymers allowed their accurate replication, the precursor of biological reproduction. In particular, the "RNA world" hypothesis equates the linear sequence of an RNA's nucleotides with its genotype. Individual RNA molecules may fold into different 3- dimensional structures, or conformers. Each such folding of a given genotype specifies a different phenotype. These phenotypes exhibit chemical properties that may result in replication of the genotype. Each phenotype has a fitness depending on replication rate, and so the phenotype distribution would be subject to natural selection. To model replication and extinction of prebiotic polymers, we combine computational and biological approaches. We consider a single genotype that can fold into two different phenotypes. Each phenotype's capacity to replicate its genotype depends on abiotic and biotic factors in the physical environment, which may change as time advances. We begin with a spatially detailed, individual based model, required for accurate modelingof small populations where the variability caused by random events among individual replicators dominates population dynamics. For efficient modelingof large populations where mean behavior tends to dominate, we derive a corresponding mean-field model that aggregates large, well mixed populations of common phenotypes to compare its behavior to the individual based version.