Table 1.
Nominal parameter values and initial conditions in VCell BioModelsa
| Parameter | Value | Units | Description |
|---|---|---|---|
| Biomodel FRAP_Membrane_Rel | |||
| BleachRadius | 2 | μm | radius of circular bleaching illumination |
| Duration | 1 | s | duration of bleaching flash |
| Kbleach | 10 | μm2 s−1 molecules−1 | bleaching rate (related to laser intensity) |
| Kr_Bleach | 0 | s−1 | reverse of the bleach reaction (always set to 0) |
| sigmaaxial | 1.5 | μm | axial Gaussian decay length |
| sigmalateral | 0.5 | μm | radial Gaussian decay length |
| Start | 1 | S | time before start of bleaching flash |
| Dark | 0 | molecules μm−2 | surface density of bleached Fluor |
| Dark diffusion coefficient | 0.1 | μm2 s−1 | |
| Fluor | 10 | molecules μm−2 | surface density of Fluor |
| Fluor diffusion coefficient | 0.1 | μm2 s−1 | |
| Laserb | distribution of bleaching light | ||
| Biomodel FRAP_cyt | |||
| BleachRadius | 2 | μm | radius of circular bleaching illumination |
| Duration | 1 | s | duration of bleaching flash |
| Kbleach | 1 | s−1μM−1 | bleaching rate (related to laser intensity) |
| Kf_BindF | 1 | s−1μM−1 | forward rate for binding of Fluor to Binder |
| Kf_BindD | 1 | s−1μM−1 | forward rate for binding of Dark to Binder (always = Kf_BindF) |
| Kr_BindF | 1 | s−1 | FluorB dissociation rate |
| Kr_BindD | 1 | s−1 | DarkB dissociation rate (=Kr_BindF) |
| sigmaaxial | 1.5 | μm | axial Gaussian decay length |
| sigmalateral | 0.5 | μm | radial Gaussian decay length |
| Start | 1 | s | time before start of bleaching flash |
| Binder | 2.702 | μM | initial concentration of Binderc |
| Binder diffusion coefficient | 0 | μm−2 s−1 | |
| Dark | 0 | μM | initial concentration of free bleached fluor |
| Dark diffusion coefficient | 10 | μm−2 s−1 | |
| DarkB | 0 | μM | initial concentration of bound bleached Fluor |
| DarkB diffusion coefficient | 0 | μm−2 s−1 | |
| Laserb | |||
| Fluor | 2.702 | μM | initial concentration of free Fluorc |
| Flour diffusion coefficient | 10 | μm−2 s−1 | |
| FluorB | 7.298 | μM | initial concentration of FluorB (bound form)c |
| FlourB diffusion coefficient | 0 | μm−2 s−1 | |
| BioModel FRAP Condensate Droplet | |||
| BleachRadius | 2 | μm | radius of circular bleaching illumination |
| Duration | 1 | s | duration of bleaching flash |
| Kbleach | 1 | s−1μM−1 | bleaching rate (related to laser intensity) |
| Kf_BindF | 0.025 | s−1μM−1 | forward rate for binding of Fluor to Binder |
| Kf_BindD | 0.025 | s−1μM−1 | forward rate for binding of Dark to Binder (always = Kf_BindF) |
| Kr_BindF | 2.5 | s−1 | FluorB dissociation rate |
| Kr_BindD | 2.5 | s−1 | DarkB dissociation rate (=Kr_BindF) |
| sigmaaxial | 1.5 | μm | axial Gaussian decay length |
| sigmalateral | 0.5 | μm | radial Gaussian decay length |
| Start | 1 | s | time before start of bleaching flash |
| Binder | 591.4 | μM | initial concentration of Binderc,d |
| Binder diffusion coefficient | 0.1 | μm−2 s−1 | diffusion is set to 0 outside the confines of the droplet |
| Dark | 0 | μM | initial concentration of free bleached fluor |
| Dark diffusion coefficient | 10 | μm−2 s−1 | diffusion is set to 10 outside the confines of the droplet and to 1 μm2 s−1 inside |
| DarkB | 0 | μM | concentration of bound bleached Fluord |
| DarkB diffusion coefficient | 0.1 | μm−2 s−1 | diffusion is set to 0 outside the confines of the droplet |
| Laserb | |||
| Fluor | 1.446 | μM | concentration of free Fluorc |
| Flour diffusion coefficient | 10 | μm−2 s−1 | diffusion is set to 10 outside the confines of the droplet and to 1 μm2 s−1 inside |
| FluorB | 8.554 | μM | concentration of FluorB (bound form)c,d |
| FlourB diffusion coefficient | 0.1 | μm−2 s−1 | diffusion is set to 0 outside the confines of the droplet |
| Biomodel FRAP_Cyt_Membrane_Binding | |||
| BleachRadius | 4 | μm | radius of circular bleaching illumination |
| duration | 1 | s | duration of bleaching flash |
| Kbleach | 1 | s−1μM−1 | bleaching rate (related to laser intensity) |
| Kf_BindF | 1 | s−1μM−1 | forward rate for binding of Fluor to Binder |
| Kf_BindD | 1 | s−1μM−1 | forward rate for binding of Dark to Binder (always = Kf_BindF) |
| Kr_BindF | 0.1 | s−1 | FluorB dissociation rate |
| Kr_BindD | 0.1 | s−1 | DarkB dissociation rate (=Kr_BindF) |
| sigmaaxial | 1.5 | μm | axial Gaussian decay length |
| sigmalateral | 0.5 | μm | radial Gaussian decay length |
| Start | 1 | s | time before start of bleaching flash |
| Binder | 2.111 | molecules μm−2 | initial surface density of Binderc |
| Binder diffusion coefficient | 0.1 | μm−2 s−1 | |
| Dark | 0 | μM | initial concentration of free bleached fluor |
| Dark diffusion coefficient | 25 | μm−2 s−1 | |
| DarkB | 0 | μM | initial surface density of bound bleached Fluor |
| DarkB diffusion coefficient | 0.1 | μm−2 s−1 | |
| Laserb | |||
| Fluor | 0.473 | μM | initial concentration of free Fluorc |
| Flour diffusion coefficient | 25 | μm−2 s−1 | |
| FluorB | 997.9 | molecules μm−2 | initial surface density of FluorB (bound form)c |
| FlourB diffusion coefficient | 0.1 | μm−2 s−1 | |
a
These default parameters in each BioModel are varied in the simulations to model different experimental scenarios. The actual parameter values used in the figures in this work are described in the text and figure captions.
b
The Laser variable defines the pattern of illumination in space and is presented in each Application as a function: Laser = f(x, y, z).
c
The prebleach concentrations are set to the steady-state values for the default KD.
d
In BioModel “FRAP Condensate Droplet” and the species Binder, FluorB, and DarkB are all confined to a spherical droplet by setting their initial concentrations and diffusion coefficients to be 0 outside the sphere. Shown here are their nominal diffusion coefficients and initial (prebleach) concentrations within the sphere. The KD and initial concentrations are set to correspond to a partition coefficient of 7, corresponding to the ratio of TotalF (free plus bound fluor) within the droplet to Fluor outside the droplet.