Figure 1.
The models of reversible dimer formation in the compartmentalized plasma membrane.
a. Schematic illustration of the compartmentalized view of the plasma membrane according to the membrane skeleton fence model [13], and the kinetics of reversible dimer formation as described in the text. The thin lines correspond to the random paths traced by the molecules while diffusing in the membrane. b. illustration of the lattice-based model of diffusion and reaction in two-dimensions (2D) (see the Methods section for details, and Video S1 for an animation based on this model).
Figure 2.
Total number of reactions, and local reaction rate as a function of time.
a. Total number of reactions involving the tracer molecule as a function of time, obtained by Monte Carlo simulations. In all plots, black data points correspond to no activity and colored data points indicate reaction events. Different colors correspond to different confinement strengths such that (red),
(cyan),
(green), and 0.25(blue) which represents the case of no confinement. The values of other parameters are:
, i.e. reactions are diffusion limited,
,
,
, and there are 10 molecules in the lattice such that
. The main figure shows short samples of the simulation data, covering
reaction events for each case, and is plotted with an arbitrary offset for visual clarity. The inset shows full data sets for single runs on logarithmic axes. b. local reaction rate as a function of time for strong confinement
(red), and for no confinement
0.25(blue). All parameter values are the same as in a. When confinement is strong, the local reaction rate exhibits bursts during which its amplitude is abruptly increased, that are followed by silent periods, or gaps. See the text for the details of how local rate is calculated. In b,
simulation steps.
Figure 3.
Behavior of the ratio of the mean and standard deviation of the time between reactions in the presence of confining domains to that in the absence of confining domains, denoted by
and
, respectively (see text). Data obtained by Monte Carlo simulations. a. the dependence of
and
on confinement strength characterized by
.
takes on values between
and
. Other parameter values are:
,
,
,
,
. b.
and
as a function of reaction probability
, with other parameters fixed at:
,
,
,
,
. c. density dependence of
and
. In this case
,
,
,
, and the density
varies between 0.05 and 2 molecules per compartment. Error bars in all plots are smaller than the data points.
Figure 4.
The mean gap duration, or the time between subsequent bursts, as a function of model parameters, obtained by Monte Carlo simulations.
a. the effect of confinement strength on .
varies between
and
. Other parameter values are:
,
,
,
,
. In order to identify bursts, we considered
, for
, respectively. b.
plotted against
, with other parameters fixed at:
,
,
,
,
. c.
as a function of density. Parameters were fixed at:
,
,
,
, and
varies between 0.05 and 2 molecules per compartment. Error bars in all plots are smaller than the data points. In b and c,
simulation steps.
Figure 5.
The mean burst amplitude versus model parameters, obtained by Monte Carlo simulations.
a. the effect of confinement strength on .
varies between
and
. Other parameter values are:
,
,
,
,
. In order to identify bursts, we considered
, for
, respectively. b.
as a function of
, with other parameters fixed at:
,
,
,
,
. c.
as a function of density. Parameters were fixed at:
,
,
,
, and
varies between 0.05 and 2 molecules per compartment. Error bars in all plots are smaller than the data points. In b and c,
simulation steps.