update formalisms some more

[ool/lipid_simulation_formalism.git] / kinetic_formalism.Rnw

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index c3541f44b57fbf7cb75b290ae7213cb4387140ad..c7ae0ad9fbd677db74ac6e22f926fe95e38e1864 100644 (file)
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -750,7 +750,7 @@ many cases as possible, experimentally based)
 (see~\fref{sec:step_duration}), but for a given step is constant. This
 leads to the following:
 
-$n_i = k_{fi}k_{fi\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{ves}dt\mathrm{NA}$
+$n_i = k_{fi}k_{fi\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{ves}\mathrm{N_A}dt$
 
 In the cases where $n_i > 1$, the integer number of molecules is
 added. Fractional $n_i$ or the fractional remainder after the addition
@@ -761,7 +761,7 @@ fractional part of $n_i$, an additional molecule is added.
 
 Molecules leaving the vesicle are handled in a similar manner, with 
 
-$n_i = k_{bi}k_{bi\mathrm{adj}}C_{i_\mathrm{ves}}dt\mathrm{NA}$.
+$n_i = k_{bi}k_{bi\mathrm{adj}}C_{i_\mathrm{ves}}\mathrm{N_A}dt$.
 
 While programatically, the molecule removal happens after the
 addition, the properties that each operates on are the same, so they
@@ -807,8 +807,27 @@ to produce later output.
 
 \section{Analyzing output}
 
+Analyzing of output is handled by a separate perl program which shares
+many common modules with the simulation program. Current output
+includes simulation progress, summary tables, summary statistics, and
+various graphs.
+
 \subsection{PCA plots}
 
+Vesicles have many different axes which contribute to their variation
+between subsequent generations; two major groups of axes are the
+components and properties of vesicles. Each component in a vesicle is
+an axis on its own; it can be measured either as an absolute number of
+molecules in each component, or the fraction of molecules of that
+component over the total number of molecules; the second approach is
+often more convenient, as it allows vesicles of different number of
+molecules to be more directly compared (though it hides any affect of
+vesicle size).
+
+In order to visualize the transition of subsequent generations of
+vesicles from their initial state in the simulation, to their final
+state at the termination of 
+
 \subsection{Carpet plots}