From: don <don@25fa0111-c432-4dab-af88-9f31a2f6ac42>
Date: Thu, 17 Jun 2010 21:51:02 +0000 (+0000)
Subject: add the length adjustment concerns
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=cdfa80877ac6e29ad4a2534fe996d52c1ebcd5fb;p=ool%2Flipid_simulation_formalism.git

add the length adjustment concerns

git-svn-id: svn+ssh://hemlock.ucr.edu/srv/svn/misc/trunk/origins_of_life@537 25fa0111-c432-4dab-af88-9f31a2f6ac42
---

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index 4acbbf0..e52b838 100644
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -148,6 +148,11 @@ $1.5$, which leads to a $\Delta \Delta G^\ddagger$ of
 $\Sexpr{format(digits=3,to.kcal(2^1.5))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$.
 
+It is not clear that the unsaturation of the inserted monomer will
+affect the rate of the insertion positively or negatively, so we do
+not include a term for it in this formalism.
+
+
 \setkeys{Gin}{width=3.2in}
 <<fig=TRUE,echo=FALSE,results=hide,width=5,height=5>>=
 curve(2^x,from=0,to=sd(c(0,4)),
@@ -316,6 +321,13 @@ a range of $\Delta \Delta G^\ddagger$ of
 $\Sexpr{format(digits=3,to.kcal(2^(3.4)))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$.
 
+While it could be argued that increased length of the monomer could
+affect the rate of insertion into the membrane, it's not clear whether
+it would increase (by decreasing the number of available hydrogen
+bonds, for example) or decrease (by increasing the time taken to fully
+insert the acyl chain, for example) the rate of insertion or to what
+degree, so we do not take it into account in this formalism.
+
 
 <<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
 curve(2^x,from=0,to=sd(c(12,24)),