From: From molecular to cellular form: modeling the first major transition during the arising of life
Descriptions | Magnitudes a | Default Values b | |
---|---|---|---|
Probabilities | |||
ᅟPAT | An RNA template attracting a substrate (by base-pairing) | [0.3, 0.5] | 0.4 |
ᅟPBB | A phosphodiester bond breaking within an RNA chain | [1 × 10− 6, 5 × 10− 6] | 2 × 10− 6 |
ᅟPFLR | The false ligation under the catalysis of a REP | [0.05, 0.2] | 0.1 |
ᅟPFP | The false base-pairing when a template attracts a substrate | [5 × 10−5, 0.0002] | 0.0001 |
ᅟPMV | The movement of nucleotides/amphiphiles or their precursors | [5 × 10−5, 0.0002] | 0.0001 |
ᅟPND | A nucleotide decaying into its precursor | [0.002, 0.01] | 0.005 |
ᅟPNDE | A nucleotide residue decaying at RNA’s chain end | [0.0001, 0.0005] | 0.0002 |
ᅟPNF | A nucleotide forming from its precursor (non-enzymatic) | [0.0001, 0.0005] | 0.0002 |
ᅟPNFR | A nucleotide forming from its precursor catalyzed by an NSR | [0.5, 0.9] | 0.9 |
ᅟPRBT | A REP binding onto the template containing a tag | [0.3, 0.5] | 0.4 |
ᅟPRD | A REP dropping from a template | [5 × 10−5, 0.0002] | 0.0001 |
ᅟPRL | The random ligation of two RNAs (including nucleotides) | [5 × 10−7, 2 × 10−6] | 1 × 10− 6 |
ᅟPRTT | An RNA turning to a template (for non-enzymatic synthesis) | [0.4, 0.6] | 0.5 |
ᅟPSP | The separation of a base pair | [0.3, 0.4] | 0.38 |
ᅟPTL | The template-directed ligation (non-enzymatic) | [5 × 10−5, 0.0002] | 0.0001 |
ᅟPTLR | The template-directed ligation catalyzed by a REP | [0.5, 0.9] | 0.9 |
ᅟPAD | An amphiphile decaying (out of membrane) | [0.0001, 0.0005] | 0.0002 |
ᅟPADM | An amphiphile decaying within membrane | [1 × 10−5, 5 × 10−5] | 2 × 10−5 |
ᅟPAF | An amphiphile forming from its precursor | [0.0005, 0.002] | 0.001 |
ᅟPAJM | An amphiphile joining the membrane | [0.7, 0.9] | 0.8 |
ᅟPALM | An amphiphile leaving the membrane | [0.0001, 0.0005] | 0.0002 |
ᅟPAPP | An amphiphile precursor permeating the membrane | [0.5, 1] | 1 |
ᅟPCB | A protocell breaking | [5 × 10−6, 2 × 10−5] | 1 × 10−5 |
ᅟPCC | A protocell engulfing molecules (cytophagy) | [1 × 10−7, 5 × 10−7] | 1 × 10−7 |
ᅟPCD | A protocell dividing | [5 × 10−5, 0.0002] | 0.0001 |
ᅟPCF | Two adjacent protocells fusing with each other | [0.002, 0.01] | 0.005 |
ᅟPMC | The movement of a protocell | [5 × 10−6, 2 × 10−5] | 1 × 10− 5 |
ᅟPMF | A membrane forming | [0.005, 0.02] | 0.01 |
ᅟPNPP | A nucleotide precursor permeating the membrane | [0.05, 0.2] | 0.1 |
Others | |||
ᅟN | The system is defined as an N × N grid | [20, 40] | 40 |
ᅟTNPB | Total nucleotide precursors introduced in the beginning | [80,000, 320,000] | 320,000 |
ᅟTAPB | Total amphiphile precursors introduced in the beginning | [60,000, 240,000] | 240,000 |
ᅟFOP | The factor for the effect of osmotic pressure | [5, 10] | 10 |
ᅟFDE | The factor for the effect of Donnan’s equilibrium | [5, 10] | 10 |
ᅟCT | Collision times in a step | [5, 10] | 8 |
ᅟLAM | The lower limit number of amphiphiles to form a membrane | [400, 600] | 500 |
ᅟCSREP | The characteristic (catalytic domain) sequence of REP | 8–10 nt long | CUCGACAGAU |
ᅟCSNSR | The characteristic (catalytic domain) sequence of NSR | 8–10 nt long | ACUGGCAUCU |
ᅟCSTag | The characteristic sequence of the tag | 3–5 nt long | ACGU |