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Table 1 Parameters used in the computer simulation

From: From molecular to cellular form: modeling the first major transition during the arising of life

  Descriptions Magnitudes a Default Values b
Probabilities    
PAT An RNA template attracting a substrate (by base-pairing) [0.3, 0.5] 0.4
PBB A phosphodiester bond breaking within an RNA chain [1 × 10− 6, 5 × 10− 6] 2 × 10− 6
PFLR The false ligation under the catalysis of a REP [0.05, 0.2] 0.1
PFP The false base-pairing when a template attracts a substrate [5 × 10−5, 0.0002] 0.0001
PMV The movement of nucleotides/amphiphiles or their precursors [5 × 10−5, 0.0002] 0.0001
PND A nucleotide decaying into its precursor [0.002, 0.01] 0.005
PNDE A nucleotide residue decaying at RNA’s chain end [0.0001, 0.0005] 0.0002
PNF A nucleotide forming from its precursor (non-enzymatic) [0.0001, 0.0005] 0.0002
PNFR A nucleotide forming from its precursor catalyzed by an NSR [0.5, 0.9] 0.9
PRBT A REP binding onto the template containing a tag [0.3, 0.5] 0.4
PRD A REP dropping from a template [5 × 10−5, 0.0002] 0.0001
PRL The random ligation of two RNAs (including nucleotides) [5 × 10−7, 2 × 10−6] 1 × 10− 6
PRTT An RNA turning to a template (for non-enzymatic synthesis) [0.4, 0.6] 0.5
PSP The separation of a base pair [0.3, 0.4] 0.38
PTL The template-directed ligation (non-enzymatic) [5 × 10−5, 0.0002] 0.0001
PTLR The template-directed ligation catalyzed by a REP [0.5, 0.9] 0.9
PAD An amphiphile decaying (out of membrane) [0.0001, 0.0005] 0.0002
PADM An amphiphile decaying within membrane [1 × 10−5, 5 × 10−5] 2 × 10−5
PAF An amphiphile forming from its precursor [0.0005, 0.002] 0.001
PAJM An amphiphile joining the membrane [0.7, 0.9] 0.8
PALM An amphiphile leaving the membrane [0.0001, 0.0005] 0.0002
PAPP An amphiphile precursor permeating the membrane [0.5, 1] 1
PCB A protocell breaking [5 × 10−6, 2 × 10−5] 1 × 10−5
PCC A protocell engulfing molecules (cytophagy) [1 × 10−7, 5 × 10−7] 1 × 10−7
PCD A protocell dividing [5 × 10−5, 0.0002] 0.0001
PCF Two adjacent protocells fusing with each other [0.002, 0.01] 0.005
PMC The movement of a protocell [5 × 10−6, 2 × 10−5] 1 × 10− 5
PMF A membrane forming [0.005, 0.02] 0.01
PNPP A nucleotide precursor permeating the membrane [0.05, 0.2] 0.1
Others    
N The system is defined as an N × N grid [20, 40] 40
TNPB Total nucleotide precursors introduced in the beginning [80,000, 320,000] 320,000
TAPB Total amphiphile precursors introduced in the beginning [60,000, 240,000] 240,000
FOP The factor for the effect of osmotic pressure [5, 10] 10
FDE The factor for the effect of Donnan’s equilibrium [5, 10] 10
CT Collision times in a step [5, 10] 8
LAM The lower limit number of amphiphiles to form a membrane [400, 600] 500
CSREP The characteristic (catalytic domain) sequence of REP 8–10 nt long CUCGACAGAU
CSNSR The characteristic (catalytic domain) sequence of NSR 8–10 nt long ACUGGCAUCU
CSTag The characteristic sequence of the tag 3–5 nt long ACGU
  1. Note: The upper half of the probabilities include those for the naked scene (with names in alphabetical order), whereas the lower half are those introduced when the scene involving protocells is modeled (with names in alphabetical order). a. The magnitudes represent the general scopes of the values that were adopted in our study, but in the cases for investigating some parameters specially (see text), a broader range may be explored; and in some special cases, some key parameters may also adopt values beyond this scope (see text). b. The simulation cases shown in this paper adopt the default values listed here, unless being stated explicitly to be different