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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
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) 0.5
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
P 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
L 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
  1. 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