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Table 1 Parameters used in the model (part 1a)

From: The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover

Probabilities Descriptions Valuesb
ᅟP DND Deoxynucleotide decaying into its precursor 5 × 10−4
ᅟP DNDE Deoxynucleotide decaying into its precursor at DNA’s chain end 1 × 10−5
ᅟP DNF Deoxynucleotide forming from its precursor 5 × 10−4
ᅟP DNO Deoxynucleotide being oxidizedc 1 × 10−4
ᅟP DNPD Deoxynucleotide precursor decaying into its precursor 5 × 10−4
ᅟP DNPF Deoxynucleotide precursor forming from its precursor 5 × 10−4
ᅟP DNPO Deoxynucleotide precursor being oxidizedc 1 × 10−4
ᅟP DNPPO Deoxynucleotide precursor’s precursor being oxidizedc 1 × 10−4
ᅟP FPDD False base-pairing when DNA attracting deoxynucleotides/DNA 0.001
ᅟP FPDR False base-pairing when DNA attracting nucleotides/RNA 0.02
ᅟP FPRD False base-pairing when RNA attracting deoxynucleotides/DNA 0.01
ᅟP NPPR Nucleotide precursor’s precursor being reducedc 1 × 10−4
ᅟP NPR Nucleotide precursor being reducedc 1 × 10−4
ᅟP NR Nucleotide being reducedc (not catalyzed) 1 × 10−4
ᅟP NRR Nucleotide being reducedc (catalyzed by Nrr) ---
Others Descriptions Valuesb
ᅟF BBD Factor for phosphodiester-bond-breaking in DNA (vs RNA) 0.01
ᅟF SFD Factor for single DNA chain folding 1
ᅟF SFR Factor for single RNA chain folding 2
  1. aThis part contains parameters newly introduced here. See Table 2 for the others, which were also used in the previous model [15]
  2. bThese parameter values, as well as those shown in Table 2, are for the cases shown in Figs. 1, 2, 3 (about the adjustment of some key parameters during simulation in these cases, see the figures’ legend for details). There are only a few differences for the cases shown in Fig. 4, which have been elucidated in the text. As explained previously [14, 15], such values are adopted according to logic, knowledge (see also “Methods” of this paper) and experience, and though they are listed here with an “accurate appearance”, the dynamics of the model system is generally not sensitive to their moderate changes
  3. cHere the oxidation and reduction mean the mutual transformation between deoxynucleotides and nucleotides, between their precursors, or between their precursors’ precursors