<<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
\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} -