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Table 6 Overview of parameters used for the integrative 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 0.07 μm2
Creation rate of phagophores 0.44 min-1
Linear nutrient factor creation phagophores 0.206
Exponential nutrient factor creation phagophores 1.179
Mean maturation time of phagophores 7.5 min
Growth rate of phagophores 5e-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 0.1 μm2
Creation rate of lysosomes 1.23 min-1
Linear nutrient factor creation lysosomes 0.112
Exponential nutrient factor creation lysosomes 1.124
Mean life time of lysosomes 18 min
Growth rate of lysosomes 0.0021 μm2 min-1
Initial number of autolysosomes 28
Initial size of autolysosomes 0.225 μm2
Degradation rate autolysosomes 0.15 min-1
Linear nutrient factor degradation autolysosomes 0.0069
Exponential nutrient factor degradation autolysosomes 3.14
Growth rate of autolysosomes 0.00065 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 basis 55%
Chance of lysosomal movement towards nucleus via nutrient status +0.5% DifferenceNutrition-1
Chance of fusion of a non-autolysosome and an autolysosome 45%
Chance of fusion of two autolysosomes 30%
Mean free nutrients for initialization of the model 20
Mean bound nutrients for initialization of the model 20
Diffusion of free nutrients 70%
Diffusion of bound nutrients 50%
Local increase of free nutrients 1.1 min-1 borderpatch-1
Global decrease of free nutrients 0.05 min-1 patch-1
Global conversion of free nutrients to bound nutrients 0.045 min-1 patch-1
Lysosomal conversion of bound nutrients to free nutrients 1.5 min-1 lysosome-1
Autophagosomal uptake of bound nutrients 2.25 min-1 autophagosome-1
Autolysosomal release of free nutrients 2.25 min-1 autolysosome-1
Effect BAF on the degradation rate of autolysosomes Degradation rate AL × 0.05
  1. Initial number of autophagosomes, lysosomes and autolysosomes were chosen according to our biological data, all other parameters were chosen according to the parameter fitting.