Table 1 Parameters of the model – ranges and defaults
From: In silico ribozyme evolution in a metabolically coupled RNA population
Parameter | Value (boldface: default) |
|---|---|
grid size (G×G) | 300x300 |
number of replicator diffusion steps (D) | ¼ … 4 (4) |
size of metabolic neighbourhood (h) | 3×3,5×5,7×7 (Moore-type) |
size of replication neighbourhood (r) | 5 (von Neumann type) |
number of different types of enzymes | 3 |
maximum length of replicators (L) | 70 |
claim of a site to remain empty, relative to the theoretical maximum of the sum of claims for an empty site (ε) | 0.1 |
constant in Boltzann-distribution (c) | 0.3 |
per base rate of substitution (p sub) | 0.01 |
per base rate of deletion (p del) | 0.001 |
per base rate of insertion (p ins) | 0.001 |
scaling factor of replicability (g) | 10 |
penalty factor of promiscuity (σ) | 1.1 |
prefactor of (1-p fold) in replicability (l) | 1 |
replication time (initiation) b 1 | 1 |
elongation “length penalty” per base b 2 | 0.001…0.5 (0.05) |