Table 1 Parameters used in the Monte Carlo simulations
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 |