include references.bib

[ool/lipid_simulation_formalism.git] / kinetic_formalism_competition.Rnw

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index 54e7fa8c02f5a022c0ffb1447bf0495cf14970f1..4044fc743e6f020bea34d08d56843438872ee18b 100644 (file)
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -1406,6 +1406,12 @@ $10^{-10}\mathrm{M}$. The base concentration ($10^{-10}\mathrm{M}$)
 can also be altered at the initialization of the experiment to
 specific values for specific lipid types or components.
 
+The environment is a volume which is the maximum number of vesicles
+from a single simulation (4096) times the maximum size of the vesicle
+(usually 10000) divided by Avagadro's number divided by the total
+environmental lipid concentration, or usually
+\Sexpr{4096*10000/6.022E23/141E-10}~L.
+
 \subsection{Initial Vesicle Creation}
 
 Initial vesicles are seeded by selecting lipid molecules from the
@@ -1434,8 +1440,10 @@ lipid types, weighted by their concentration in the environment.)
 Once the environment has been created and the initial vesicle has been
 formed, molecules join and leave the vesicle based on the kinetic
 parameters and state equation discussed above until the vesicle splits
-forming two progeny vesicles, one of which the program continues to
-follow.
+forming two progeny vesicles. The program then follows both vesicles
+and their progeny until the simulation reaches either the maximum
+number of vesicles (usually 4096), or the maximum simulation time
+(usually 100~s).
 
 \subsubsection{Calculation of Vesicle Properties}