add changes raphael suggested; fix PG and POPC acronym

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index a744afe8e649a813196a97b68faffba07d6fdfa6..2ceb8116b3df87f6f9adfed6c26dccc4e0671654 100644 (file)
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -218,7 +218,7 @@ exchange of the fluorescent label \ac{C6NBD} attached to different
 lipid species. Although the values of $k_\mathrm{b}$ are different for the labeled
 and unlabeled lipids, we assume that the ratios of the kinetics
 constants for the lipid types are the same. Furthermore we assume that
 lipid species. Although the values of $k_\mathrm{b}$ are different for the labeled
 and unlabeled lipids, we assume that the ratios of the kinetics
 constants for the lipid types are the same. Furthermore we assume that

-PG behaves similarly to \ac{PS}. Thus, we can determine the $k_\mathrm{b}$ of \ac{PE} and
+\ac{PG} behaves similarly to \ac{PS}. Thus, we can determine the $k_\mathrm{b}$ of \ac{PE} and

 \ac{PS} from the already known $k_\mathrm{b}$ of \ac{PC}. For \ac{C6NBD} labeled \ac{PC},
 \citet{Nichols1982:ret_amphiphile_transfer} obtained a $k_\mathrm{b}$ of
 $0.89$~$\mathrm{min}^{-1}$, \ac{PE} of $0.45$~$\mathrm{min}^{-1}$ and PG of
 \ac{PS} from the already known $k_\mathrm{b}$ of \ac{PC}. For \ac{C6NBD} labeled \ac{PC},
 \citet{Nichols1982:ret_amphiphile_transfer} obtained a $k_\mathrm{b}$ of
 $0.89$~$\mathrm{min}^{-1}$, \ac{PE} of $0.45$~$\mathrm{min}^{-1}$ and PG of


@@ -259,16 +259,16 @@ minutes, leading to a $k_{\mathrm{b}_\mathrm{CHOL}} = \frac{\log 2}{41\times
 
 Different lipids have different headgroup surface areas, which contributes to
 $\left[S_\mathrm{vesicle}\right]$. \citet{Smaby1997:pc_area_with_chol}
 
 Different lipids have different headgroup surface areas, which contributes to
 $\left[S_\mathrm{vesicle}\right]$. \citet{Smaby1997:pc_area_with_chol}

-measured the surface area of POPC with a Langmuir film balance, and
+measured the surface area of \ac{POPC} with a Langmuir film balance, and

 found it to be 63~Å$^2$ at $30$~$\frac{\mathrm{mN}}{\mathrm{m}}$.
 Molecular dynamic simulations found an area of 54 Å$^2$ for
 found it to be 63~Å$^2$ at $30$~$\frac{\mathrm{mN}}{\mathrm{m}}$.
 Molecular dynamic simulations found an area of 54 Å$^2$ for

-DPPS\citep{Cascales1996:mds_dpps_area,Pandit2002:mds_dpps}, which is
+\ac{DPPS}\citep{Cascales1996:mds_dpps_area,Pandit2002:mds_dpps}, which is

 in agreement with the experimental value of 56~Å$^2$ found using a
 Langmuir balance by \citet{Demel1987:ps_area}.
 \citet{Shaikh2002:pe_phase_sm_area} measured the area of \ac{SM} using a
 Langmuir film balance, and found it to be 61~Å$^2$. Using $^2$H NMR,
 \citet{Thurmond1991:area_of_pc_pe_2hnmr} found the area of
 in agreement with the experimental value of 56~Å$^2$ found using a
 Langmuir balance by \citet{Demel1987:ps_area}.
 \citet{Shaikh2002:pe_phase_sm_area} measured the area of \ac{SM} using a
 Langmuir film balance, and found it to be 61~Å$^2$. Using $^2$H NMR,
 \citet{Thurmond1991:area_of_pc_pe_2hnmr} found the area of

-DPPE-d$_{62}$ to be 55.4 Å$^2$. \citet{Robinson1995:mds_chol_area}
+\ac{DPPE}-d$_{62}$ to be 55.4 Å$^2$. \citet{Robinson1995:mds_chol_area}

 found an area for \ac{CHOL} of 38~Å$^2$ using molecular dynamic
 simulations.
 
 found an area for \ac{CHOL} of 38~Å$^2$ using molecular dynamic
 simulations.
 


@@ -1099,11 +1099,11 @@ The most common $\left<\log cu_\mathrm{vesicle}\right>$ is around
 $-0.013$, which leads to a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(0.8))^2+1))))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature 0.8 to
 $-0.013$, which leads to a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(0.8))^2+1))))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature 0.8 to

+to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature
+near 1

 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$

-for monomers with curvature 1.3 to
-$0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near
-1. The full range of values possible for $cu_\mathrm{b}$ are shown in
-\cref{fig:cub_graph}.
+for monomers with curvature 1.3. The full range of values possible for
+$cu_\mathrm{b}$ are shown in \cref{fig:cub_graph}.

 
 % \RZ{What about the opposite curvatures that actually do fit to each
 %   other?}
 
 % \RZ{What about the opposite curvatures that actually do fit to each
 %   other?}


@@ -1193,7 +1193,7 @@ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length near 18 to
 $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length 24. The full range of possible values of
 for monomers with length near 18 to
 $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length 24. The full range of possible values of

-$l_\mathrm{b}$ are shown in \cref{fig:lb_graph}
+$l_\mathrm{b}$ are shown in \cref{fig:lb_graph}.

 
 % (for methods? From McLean84LIB: The activation free energies and free
 % energies of transfer from self-micelles to water increase by 2.2 and
 
 % (for methods? From McLean84LIB: The activation free energies and free
 % energies of transfer from self-micelles to water increase by 2.2 and