From 921403fd57dc9b98fe85f161cc6976b1363e0060 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 21 Mar 2017 18:41:36 -0700
Subject: [PATCH] add changes raphael suggested; fix PG and POPC acronym

---
 kinetic_formalism_competition.Rnw | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index a744afe..2ceb811 100644
--- 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
-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
@@ -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}
-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
-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
-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.
 
@@ -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
+to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature
+near 1
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
-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?}
@@ -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
-$l_\mathrm{b}$ 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
-- 
2.39.2