Overview Topics

Status of Parameters

Parameters shown in green are based on detailed calculations, estimates, or values obtained from the literature. Those shown in red are somewhat arbitrary -- no values from the literature have been ascertained for these values at this time.

Click on parameter names to see sources of reference and derivations of values (where applicable).




Astrocyte Parameters

Name Description Value Units
initial astrocyte count Number of astrocyte agents in the simulation. 100  
activation level Concentration of IL-1B (at same site as astrocyte) that activates astrocytes to begin absorbing IL-1B. 0.1 nM
maximum density Maximum density of cells at site that prevent astrocytes from invading that site. 3  
number of cells per agent Number of astrocyte cells represented by an astrocyte agent. 10.0  
IL-1B threshold for motility Concentration of absorbed IL-1B that allows an astrocyte to move. 10.0 nM
maximum speed Maximum speed at which astrocytes can move. 1.0 micron/min
probability of moving towards stimulus Probability that an astrocyte will move towards fibrous amyloid when fibrous amyloid is sensed and the astrocyte is motile. 0.9  
probability of blocking The probability for each astrocyte represented by an agent to participate in blocking. 0.5  
reduction percentage for diffusivities The percent at which the diffusivity of chemicals is reduced due to every blocking astrocyte. 0.15  
IL-1B receptor equilibrium constant Ratio of the IL-1B receptor unbinding rate to binding rate. 1.0 nM
IL-1B receptor binding rate Rate at which IL-1B binds to an IL-1B receptor. 0.01 nM-1min-1
IL-1B receptors per astrocyte Number of IL-1B receptors per astrocyte. 2000.0  
IL-1B receptor conversion rate The rate at which a bound IL-1B receptor becomes internalized or triggers a corresponding signal. 60.0 min-1
fraction of bound IL-1B rec triggering IL-6 The fraction of IL-1B receptors that need to be bound in order to trigger the release of IL-16. 0.001  
fraction of bound IL-1B rec triggering TNF The fraction of IL-1B receptors that need to be bound in order to trigger the release of IL-16. 0.001  
typical cell duration The active life span of an astrocyte. (Not used in simulation.) 300.0 min


Microglia Parameters

Name Description Value Units
initial microglia count Number of microglia agents representing multiple microglial cells in region initially. 40  
maximum density Maximum number of microglial agents allowed to occupy one grid space in the simulation. 3  
number of cells per agent The number of microglia represented by one microglial agent. 10.0  
maximum speed The speed at which microglia move. Used in simulation to determine how many time steps to delay before moving. 1.5 micron/min
chemotactic sensitivity Probability that microglia will move up a gradient of soluble amyloid protein. 0.67  
half-sticking fiber level Concentration of fibrillar amyloid protein at which half the microglia would stick (i.e at which the probability of sticking is 50%). 50.0 nM
half-sticking sAB level Concentration of soluble amyloid that reduces fraction of adhering microglia by 50%. 20000.0 nM
maximum sAB microglia uptake rate Maximum rate of uptake of soluble amyloid protein by microglia. 0.1 nM/min
half max amyloid binding concentration Concentration of soluble amyloid protein at which half of the maximal binding rate occurs. 15.0 nM
chemical breakdown Rate of degradation of amyloid by microglia. 0.01 min-1
Cell Death Can be turned on to assume cells dying or stopping their activity. Off  
max sol-AB capacity Maximum amount of amyloid that a microglia cell can hold. 1.0 nM
typical cell duration Average time it takes for microglia to die or cease activity. 300.0 min
Cell Mitosis Can be turned on to assume birth of new microglia or recruitment of more microglia. Off  
legnth of cell cycle The time period between mitosis. 60.0 min
poison effects on mitosis The fraction of the maximum amyloid absorption that causes mitosis not to occur. 0.5  
chance of mitosis If all other mitosis conditions are satisfied, this gives the odds that mitosis actually occurs. 0.9  


Neuron Parameters

Name Description Value Units
IL-1B receptor equilibrium constant Ratio of the neuron IL-1B receptor-ligand unbinding rate to binding rate. 1.0 nM
IL1B receptor binding rate Rate at which IL-1B binds to receptors. 0.01 nM-1 min-1
IL-1B receptors per neuron Number of IL-1B receptors per neuron. 2000.0  
IL-1B receptor conversion rate The rate at which bound IL-1B receptors get internalized and signal activity within the neuron. 60.0 min-1
source triggering level Level of IL-1B in neurons that cause neuron to become a new source of soluble amyloid. 100.0 nM
maximum proportion of sources The probability that a neuron will become an amyloid source once the triggering level is reached. 0.01  
maximum IL-1B absorbed The maximum amount of IL-1B that a neuron will absorb (also determines the level at which neurons secrete the maximum amount of amyloid). 200.0 nM
IL-6 receptor equilibrium constant Ratio of the neuron IL-6 receptor-ligand unbinding rate to binding rate. 4.32 nM
IL-6 receptor binding rate Rate at which IL-6 binds to receptors on neuron. 0.01 nM-1 min-1
IL-6 receptors per neuron Number of IL-6 receptors per neuron. 500.0  
IL-6 receptor conversion rate The rate at which bound IL-6 receptors get internalized and signal activity within the neuron. 60.0 min-1
maximum IL-6 absorbed Maximum amount of IL-6 absorbed by a neuron. 50.0 nM
TNF receptor equilibrium constant Ratio of the neuron TNF receptor-ligand unbinding rate to binding rate. 1.3 nM
TNF receptor binding rate Rate at which TNF binds to receptors on neuron. 0.01 nM-1 min-1
TNF receptors per neuron Number of TNF receptors on a neuron. 1100.0  
TNF receptor conversion rate The rate at which bound TNF receptors get internalized and signal activity within the neuron. 60.0 min-1
maximum TNF absorbed Maximum concentration of TNF in neuron. 100.0 nM
amyloid conc affecting health A scaling factor for determining how soluble amyloid affects health. 200.0 nM
fiber conc affecting health A scaling factor for determing how fibrous amyloid affects health. 50.0 nM
IL-1B effects on health A factor used to determine how IL-1B affects the health of a neuron (negative values mean that IL-1B is detrimental to neuron health, positive values mean that IL-1B is beneficial to neuron health and a value equal to zero means that IL-1B has no effect). 0.0  
IL-6 effects on health A factor used to determine how IL-6 affects the health of a neuron (negative values mean that IL-6 is detrimental to neuron health, positive values mean that IL-6 is beneficial to neuron health and a value equal to zero means that IL-6 has no effect). -10.0  
TNF effects on health A factor used to determine how TNF affects the health of a neuron (negative values mean that TNF is detrimental to neuron health, positive values mean that TNF is beneficial to neuron health and a value equal to zero means that TNF has no effect). 1.0  
amyloid effects on health A factor used to determine how soluble amyloid affects the health of a neuron (negative values mean that amyloid is detrimental to neuron health, positive values mean that amyloid is beneficial to neuron health and a value equal to zero means that amyloid has no effect). 0.0  
fiber effects on health A factor used to determine how fibers affect the health of a neuron (negative values mean that fibers are detrimental to neuron health, positive values mean that fibers are beneficial to neuron health and a value equal to zero means that fibers have no effect). -0.1  
health recovery rate Rate at which a neuron recovers from detrimental effects. 0.1 min-1
threshold of no recovery The health value below which simple neuron recovery is ineffective. 0.05  


Chemical Parameters (for amyloid)

Name Description Value Units
diffusivity Diffusion coefficient of soluble beta-amyloid protein. 1500.0 micron2/min
source concentration Maximum magnitude of source of soluble amyloid protein. 200.0 nM
initial fiber occupancy Percent of region initially seeded with fibrillar amyloid deposits. 0.01  
critical sol-AB for fibers Concentration of soluble amyloid necessary for fibers to grow. 50.0 nM
new fiber nucleation effectiveness Factor controlling the probability of new fiber nucleation (A value of 1 means no influence. Lower values decrease probability while greater values increase probability of nucleation). 1.0  
sol to fiber transition rate (times 10^(-6)) Rate at which soluble amyloid protein gets incorporated into fiberous deposits. 10.0 nM/min


IL-1B Parameters

Name Description Value Units
IL-1B diffusivity Diffusion coefficient of IL-1B. 900 micron2/min
triggering concentration Concentration of amyloid in microglia at which the microglia is activated to secrete IL-1B. 0.5 nM
IL-1B secretion rate Rate of secretion of IL-1B by microglia. 7.0 nM/min


IL-6 Parameters

Name Description Value Units
IL-6 diffusivity Diffusion coefficient of IL-6. 810 micron2/min
secretion rate Rate of secretion of IL-6 by astrocytes. 1.4 nM/min


TNF-alpha Parameters

Name Description Value Units
TNF diffusivity Diffusion coefficient of TNF. 900.0 micron2/min
TNF secretion rate Rate of secretion of TNF. 0.5 nM/min