update notes, start competition work

[ool/lipid_simulation_formalism.git] / kinetic_formalism.Rnw

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index b653d8173c7b4a91789171b0be02ebcddf974461..8c4fe20aa35bfef2f0d1c0f6c29065e9e450d675 100644 (file)
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -62,6 +62,11 @@
 <<results=hide,echo=FALSE>>=
 require(lattice)
 require(grid)
+require(Hmisc)
+require(gridBase)
+to.latex <- function(x){
+  gsub("\\\\","\\\\\\\\",latexSN(x))
+}
 # R in cal / mol K
 to.kcal <- function(k,temp=300) {
   gasconst <- 1.985
@@ -72,19 +77,21 @@ to.kcal <- function(k,temp=300) {
 \section{State Equation}
 % double check this with the bits in the paper
 
-Given a base forward kinetic parameter for the $i$th specie $k_{fi}$
-(which is dependent on lipid type, that is PC, PE, PS, etc.), an
-adjustment parameter $k_{fi\mathrm{adj}}$ based on the vesicle and the
-specific specie (length, unsaturation, etc.) (see~\fref{eq:kf_adj}),
-the molar concentration of monomer of the $i$th specie
-$\left[C_{i_\mathrm{monomer}}\right]$, the surface area of the vesicle
-$S_\mathrm{ves}$, the base backwards kinetic parameter for the $i$th
-specie $k_{bi}$ which is also dependent on lipid type, its adjustment
-parameter $k_{bi\mathrm{adj}}$ (see~\fref{eq:kb_adj}), and the molar
-concentration of the $i$th specie in the vesicle
-$\left[C_{i_\mathrm{ves}}\right]$, the change in concentration of the
-$i$th specie in the vesicle per change in time $\frac{d
-  C_{i_\mathrm{ves}}}{dt}$ can be calculated:
+The base forward kinetic parameter for the $i$th component is
+$k_{\mathrm{f}i}$ and is dependent on the particular lipid type (PC,
+PS, SM, etc.). The forward adjustment parameter,
+$k_{\mathrm{f}i\mathrm{adj}}$, is based on the properties of the
+vesicle and the specific component (type, length, unsaturation, etc.)
+(see Equation~\ref{eq:kf_adj}, and
+Section~\ref{sec:kinetic_adjustments}).
+$\left[C_{i_\mathrm{monomer}}\right]$ is the molar concentration of
+monomer of the $i$th component. $\left[S_\mathrm{vesicle}\right]$ is
+the surface area of the vesicle per volume. The base backwards kinetic
+parameter for the $i$th component is $k_{\mathrm{b}i}$ and its
+adjustment parameter $k_{\mathrm{b}i\mathrm{adj}}$ (see
+Equation~\ref{eq:kb_adj}, and Section~\ref{sec:kinetic_adjustments}).
+$\left[C_{i_\mathrm{vesicle}}\right]$ is the molar concentration of
+the $i$th component in the vesicle.
 
 \begin{equation}
   \frac{d C_{i_\mathrm{ves}}}{dt} = k_{fi}k_{fi\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{ves} -