TABLE 1.
Parameters and initial conditions used in the simulations
| Parameter | Description | Value | Notes |
|---|---|---|---|
| rs (r1) | Spine radius | 0.29 μm | (49) |
| rn | Spine neck radius | 0.1 μm | (49) |
| r2 | Dendrite radius | 1 μm | (30) |
| ln (l12) | Spine neck length | 0.66 μm | (49) |
| s | Linear spine density | 14 μm−1 | (49) |
| l2 | Length of adjacent dendrite compartment (compartmental model) | 27.98 μm | Calculated |
| l23 | Distance between adjacent and distal dendrite compartments | 5.63 μm | Calculated |
| DCa | Ca2+ diffusion coefficient | 223 μm2 s−1 | (51) |
| DIP3 | IP3 diffusion coefficient | 283 μm2 s−1 | (51) |
| DPV | PV diffusion coefficient | 43 μm2 s−1 | (30) |
| DCD28k | CD28k diffusion coefficient | 28 μm2 s−1 | (30) |
| DCG | CG diffusion coefficient | 15 μm2 s−1 | (52) |
| kon,CD28k,high | Forward rate coefficient | 5.5 μM−1 s−1 | (29) |
| kon,CD28k,med | Forward rate coefficient | 43.5 μM−1 s−1 | (29) |
| koff,CD28k,high | Reverse rate coefficient | 2.6 s−1 | (29) |
| koff,CD28k,med | Reverse rate coefficient | 35.8 s−1 | (29) |
| kon,PV,Ca | Forward rate coefficient | 107.0 μM−1 s−1 | (30) |
| kon,PV,Mg | Forward rate coefficient | 0.8 μM−1 s−1 | (30) |
| koff,PV,Ca | Reverse rate coefficient | 0.95 s−1 | (53) |
| koff,PV,Mg | Reverse rate coefficient | 25.0 s−1 | (53) |
| kon,CG | Forward rate coefficient | 430.0 μM−1 s−1 | (30) |
| koff,CG | Reverse rate coefficient | 140.0 s−1 | (54) |
| a | IP3R Ca2+ release amplitude (abundance) | 21,000.0 μM s−1 | 10× the value in (41) |
| [Ca2+]er | ER [Ca2+] | 400 μM (constant) | (55) |
| dCa | IP3R Ca2+ binding constant | 0.3 μM | (41) |
| dIP3 | IP3R IP3 binding constant | 20.0 μM | 10× the value in (41) |
| Vmax | Amplitude of SERCA pump intake | 3.75 μM s−1 | (41) |
| ker | Pump binding constant | 0.27 μM | (56) |
| L | Leak constant | 0.12 μM s−1 | (41) |
| K1 | Dissociation constant for IP3R | 0.2 μM | (41) |
| K2 | Forward rate coefficient, Ca2+ binding to inactivating IP3R site | 2.7 μM−1 s−1 | (41) |
| τ1 | Start time of CF Ca2+ influx | 0.1 s | (30) |
| τ2 | End time of CF Ca2+ influx | 0.105 s | (30) |
| Jch,1 | Magnitude of CF Ca2+ entry signal in the spine | 13.25 s−1 | (30) |
| Jch,2 | Magnitude of CF Ca2+ entry signal in the adjacent dendrite compartment | 6.25 s−1 | (30) |
| [Ca2+]ex | Extracellular [Ca2+] | 1.0 mM (constant) | (57) |
| Jp | IP3 pulse magnitude | 80.0 μM s−1 | Calculated |
| τ3 | Time between IP3 pulses | 0.012 s | (10) |
| K3 | IP3 pulse decay factor | 1.188 s−1 | (41) |
| Kdeg | IP3 degradation rate | 0.14 s−1 | (41) |
| P | Ca2+ pumping rate | 8.0 μm s−1 | (46) |
| [Ca2+]T | Threshold [Ca2+] | 0.2 μM | (46) |
| [Ca2+]o | Initial [Ca2+] | 0.045 μM | (58) |
| [IP3]o | Initial [IP3] | 0.16 μM | (41) |
| [PV]o | Total [PV] | 40 μM | (30) |
| [CD28k]o | Total [CD28k] | 40 μM | (30) |
| [CG]o | Total [CG] | 160 μM | (30) |
| [Mg2+] | [Mg2+] | 590 μM (constant) | (30) |