Skip to main content

Table 2 Deterministic rates against propensity density probability for reacting and transport events.

From: Stochastic simulations of minimal cells: the Ribocell model

Event Deterministic Rate
Propensity Density Probability
s -1
Internal Chemical reactions (a)
a 1 , ρ X 1 + a N , ρ X N r ρ b 1 , ρ X 1 + b N , ρ X N
k ρ j N n j C V C N A a j , ρ k ρ V C N A M ρ - 1 j N n j C a j , p
Solute Xn membrane transport (b) P n S μ V C C n E - C n C D n S μ C n E - C n C λ μ ( c )
Membrane Lipid Release k o u t n L μ N A V C k o u t n L μ
Membrane Lipid Uptake k i n S μ [ X L C ] N A V C k i n S μ [ X L C ]
Water Flux (d) v a q P a q S μ C T E - C T C V C = i = 1 N n i C / N A C T E
  1. a)a and b stoichiometric matrixes, NA Avogadro's number, kρ kinetic constant, Mρmolecularity [22]
  2. (b) The relationship between the macroscopic permeability Pn and the molecular diffusion coefficient Dn is: Dn = PnλμNA, λμ being the membrane thickness.
  3. (c) The absolute value guarantees that the propensity density probability is positive and the molecules move in the opposite direction from the concentration gradient.
  4. (d)vaq is the water molar volume, while CTE and CTC are the total osmotic concentration in the external and internal aqueous solutions, respectively.