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Table 2 Overview of the main used parameters for the core model

From: Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics

Parameter name Value
Initial number of phagophores 3
Initial size of phagophores 0.06 μm2
Creation rate of phagophores 0.42 min-1
Mean maturation time of phagophores 7.5 min
Growth rate of phagophores 6e-04 μm2 min-1
Initial number of autophagosomes 31
Growth rate of autophagosomes 8e-05 μm2 min-1
Initial number of lysosomes 19
Initial size of lysosomes 0.095 μm2
Creation rate of lysosomes 1.26 min-1
Mean life time of lysosomes 18 min
Growth rate of lysosomes 0.002 μm2 min-1
Initial number of autolysosomes 28
Initial size of autolysosomes 0.225 μm2
Mean life time of autolysosomes 95 min
Growth rate of autolysosomes 0.0012 μm2 min-1
Chance of reformation autolysosome to lysosome 50%
Rate of movement 2 μm min-1
Chance of autophagosomal movement towards nucleus 85%
Chance of lysosomal movement towards nucleus 55%
Chance of fusion between a non-autolysosome and an autolysosome 45%
Chance of fusion between two autolysosomes 15%
  1. Initial number of autophagosomes, lysosomes and autolysosomes were chosen according to biological data (Figure 2), all other parameters were chosen according to the parameter fitting.