Table 2.
Parameters used in the model (part 2a)
| Probabilities | Descriptions | Values |
| ᅟP AD | Amphiphile decaying into its precursor (out of membrane) | 5 × 10−4 |
| ᅟP ADM | Amphiphile decaying into its precursor within membrane | 5 × 10−5 |
| ᅟP AF | Amphiphile forming from its precursor (not catalyzed) | 5 × 10−4 |
| ᅟP AFR | Amphiphile forming from its precursor (catalyzed by Asr) | 0.5 |
| ᅟP AJM | Amphiphile joining membrane | 0.9 |
| ᅟP ALM | Amphiphile leaving membrane | 5 × 10−5 |
| ᅟP APP | Amphiphile precursor permeating membrane | 0.05 |
| ᅟP AT | Nucleic acid template attracting momomers/oligomers by base-pairing | 0.2 |
| ᅟP BBR | Phosphodiester bond breaking in an RNA chain | 2 × 10−6 |
| ᅟP CB | Protocell breaking | 1 × 10−5 |
| ᅟP CD | Protocell dividing | 0.005 |
| ᅟP CF | Protocell fusing | 5 × 10−4 |
| ᅟP CTT | A circular nucleic acid chain turning to a template | 0.9 |
| ᅟP EL | End-to-end ligation of a nucleic acid chain (cyclization) | 1 × 10−7 |
| ᅟP FLR | Ligating with false base-pairing on template (by Rep) | 0.1 |
| ᅟP FPRR | False base-pairing when RNA attracting nucleotides/RNA | 0.01 |
| ᅟP LTT | A linear nucleic acid chain turning to a template | 0.01 |
| ᅟP MC | Movement of a protocell | 0.05 |
| ᅟP MF | Membrane forming | 0.1 |
| ᅟP MV | Movement of a (deoxy/)nucleotide, amphiphile or 2their precursors | 0.5 |
| ᅟP ND | Nucleotide decaying into its precursor | 5 × 10−4 |
| ᅟP NDE | Nucleotide decaying into its precursor at RNA’s chain end | 1 × 10−5 |
| ᅟP NF | Nucleotide forming from its precursor (not catalyzed) | 5 × 10−4 |
| ᅟP NFR | Nucleotide forming from its precursor (catalyzed by Nsr) | 0.5 |
| ᅟP NPD | Nucleotide precursor decaying into its precursor | 5 × 10−4 |
| ᅟP NPF | Nucleotide precursor forming from its precursor (not catalyzed) | 5 × 10−4 |
| ᅟP NPFR | Nucleotide precursor forming from its precursor (catalyzed by Npsr) | 0.5 |
| ᅟP NPP | (Deoxy/)nucleotide precursor permeating membrane | 0.01 |
| ᅟP NPPP | (Deoxy/)nucleotide precursor’s precursor permeating membrane | 0.2 |
| ᅟP RB | Rep binding onto a nucleic acid template | 0.9 |
| ᅟP RD | Rep dropping from a nucleic acid template | 0.9 |
| ᅟP RL | Random ligation of RNA with RNA or that of DNA with DNA | 1 × 10−7 |
| ᅟP SP | Separation of a base pair | 0.5 |
| ᅟP TL | Template-directed ligation (not catalyzed) | 5 × 10−4 |
| ᅟP TLR | Template-directed ligation (catalyzed by Rep) | 0.5 |
| Others | Descriptions | Values |
| ᅟF DE | Factor for the effect of Donnan’s equilibrium | 5 |
| ᅟF DO | Factor for the degradation/decay of molecules out of protocells | 100 |
| ᅟF IB | Factor for intermediate RNA breaking (at sites between genes) | 1000 |
| ᅟF OP | Factor for the effect of osmotic pressure | 5 |
| ᅟL AM | Lower limit of amphiphiles to form protocell membrane | 600 |
| ᅟN | The system surface is defined as an N × N grid. | 60 |
| ᅟT APB | Total amphiphile precursors introduced in the beginning | 1.2 × 105 |
| ᅟT NPPB | Total nucleotide precursors’ precursors introduced in the beginning | 1.8 × 105 |
aThis part of parameter list is derived directly from the parameter list of the previous model [15]. P BBR was originally named P BB, P FPRR originally P FP, P CTT originally P CRTT, and P LTT originally P LRTT. To suit the aim of the present model, into which DNA is introduced,the roles of P AT, P CTT, P EL, P LTT, P MV, P NPP, P NPPP, and P RL have been modified (see “Descriptions”), and the “working values” of P AFR, P CD, P FLR, P NDE, P NFR, P NPFR, P TLR, F DO and F IB are adjusted to some extent. The values of N, T NPPB and T APB are enlarged to increase the scale of the model system, and thus the dynamics of the present model system is more robust against casual events and bears a better statistical property