Fig 1.
Schematic diagram of the virus-DIPs system.
Fig 2.
An illustration of the domain division and interface of the j-th reaction.
Here we show an example with two reactants. The domain is modeled by PDE and the domain
is modeled by compartment-based SSA. The amount of each species in a compartment in
is
. If any reactant amount is below the threshold Θ, then that compartment is part of
. Individuals can move between the boundary compartment of
and the pseudo-compartment in
. In the two-dimensional case, diffusion takes four directions: up, down, left and right.
Table 1.
Parameters used in the simulations.
Fig 3.
A representative example of interpreting the preprocessing of experimental figures.
A: An original experiment figure. B: The red single channel is extracted (virus expression) and denoised. C: Morphological transformations (dilation followed by erosion).
Fig 4.
Spatial distributions of virus and DIP in cells in PDE simulations and experiments.
A: Spatial distributions of virus in cells () and DIP in cells (
) in PDE simulations and representative experiment with initial DIP equal to 0. B: Spatial distributions of virus in cells (
) and DIP in cells (
) in PDE simulations and representative experiment with initial DIP equal to 84.
Fig 5.
Dynamics of virus and DIP in cells in 2 scenarios simulations and representative experiment with initial DIP equal to 0.
A: spatial distribution of virus in cells () and DIP in cells (
) in Scenario 1 (infected cells produce virus and DIPs through cell bursting) at time t = 17h and t = 25h; B: spatial distribution of those in Scenario 2 (infected cells keep producing viruses and DIPs); C: the representative experimental results.
Fig 6.
Dynamics of virus and DIP in cells in 2 scenarios simulations with CVD22,22(0) = 4 and representative experiment with initial DIP equal to 1.
A: spatial distribution of virus in cells () and DIP in cells (
) in Scenario 1 (infected cells produce virus and DIPs through cell bursting) at time t = 17h and t = 25h; B: spatial distribution of those in Scenario 2 (infected cells keep producing viruses and DIPs); C: the representative experimental results.
Fig 7.
Dynamics of virus and DIP in cells in 2 scenarios simulations with CVD22,22(0) = 40 and representative experiment with initial DIP equal to 10.
A: spatial distribution of virus in cells () and DIP in cells (
) in Scenario 1 (infected cells produce virus and DIPs through cell bursting) at time t = 17h and t = 25h; B: spatial distribution of those in Scenario 2 (infected cells keep producing viruses and DIPs); C: the representative experimental results.
Fig 8.
Radius of virus against time with different initial DIP inputs in 2 scenarios simulations and experiments.
In each subfigure, curves in different colors are different simulations (or experiments) with the same initial conditions. The initial conditions for the same row are the same.
Fig 9.
The growth rate of virus radius against initial DIP inputs in 2 scenarios simulations and experiments.
The x-axis is a logarithmic scale and the errors are described by the 95% confidence intervals.
Fig 10.
The average q-statistics of against initial DIP inputs at time t = 25h in 2 scenarios simulations and experiments.
A: the blue (red) line is the q-statistic of Scenario 1 (Scenario 2), and the bands show the 95% confidence intervals; B: the q-statistic for each experimental image.