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Table 1 Parameters used in the Monte Carlo simulations

From: Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell

Probabilities Descriptions Values *
P AD Amphiphile decaying into its precursor (out of membrane) 5 × 10-4
P ADM Amphiphile decaying into its precursor within membrane 5 × 10-5
P AF Amphiphile forming from its precursor (not catalyzed) 5 × 10-4
P AFR Amphiphile forming from its precursor (catalyzed by Asr) 0.9
P AJM Amphiphile joining membrane 0.9
P ALM Amphiphile leaving membrane 5 × 10-5
P APP Amphiphile precursor permeating membrane 0.05
P AT RNA attracting nucleotides/oligomers by base-pairing 0.2
P BB Phosphodiester bond breaking in an RNA chain 2 × 10-6
P CB Protocell breaking 1 × 10-5
P CD Protocell dividing 0.02
P CF Protocell fusing 5 × 10-4
P CRTT A circular RNA turning to a template 0.9
P EL End-to-end ligation of an RNA chain (cyclization) 1 × 10-7
P FLR Ligating with false base-pairing on template (by Rep) 0.01
P FP False base-pairing in RNA attracting nucleotides/oligomers 0.01
P LRTT A linear RNA turning to a template (i.e., unfolding) 0.01
P MC Movement of a protocell 0.05
P MF Membrane forming 0.1
P MV Movement of a nucleotide, amphiphile or their precursors 0.5
P ND Nucleotide decaying into its precursor 5 × 10-4
P NDE Nucleotide decaying into its precursor at RNA’s chain end 2 × 10-5
P NF Nucleotide forming from its precursor (not catalyzed) 5 × 10-4
P NFR Nucleotide forming from its precursor (catalyzed by Nsr) 0.9
P NPD Nucleotide precursor decaying into its precursor 5 × 10-4
P NPF Nucleotide precursor forming from its precursor (not catalyzed) 5 × 10-4
P NPFR Nucleotide precursor forming from its precursor (catalyzed by Npsr) 0.9
P NPP Nucleotide precursor permeating membrane 0.01
P NPPP Nucleotide precursor’s precursor permeating membrane 0.2
P RB Rep binding onto an RNA template 0.9
P RD Rep dropping from an RNA template 0.9
P RL Random ligation of nucleotides and RNA 1 × 10-7
P SP Separation of a base pair 0.5
P TL Template-directed ligation (not catalyzed) 5 × 10-4
P TLR Template-directed ligation (catalyzed by Rep) 0.9
Others Descriptions Values *
F DE Factor for the effect of Donnan’s equilibrium [28] 5
F DO Factor for the degradation/decay of molecules out of protocells 20
F IB Factor for intermediate RNA breaking (at sites between genes) 100
F OP Factor for the effect of osmotic pressure [27] 5
L AM Lower limit of amphiphiles to form protocell membrane 600
N The system surface is defined as an N × N grid. 40
T APB Total amphiphile precursors introduced in the beginning 6 × 104
T NPPB Total nucleotide precursors’ precursors introduced in the beginning 8 × 104
  1. * This set of parameter values is for the case shown in Figure 2, and also represents the common parameter list that was used for the parameter analysis in Figure 4 and in the Additional file 1: Figures S2-S5.