Table 2 Parameters used in the model (part 2a)
From: The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover
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 |