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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