From: don <don@25fa0111-c432-4dab-af88-9f31a2f6ac42>
Date: Wed, 26 May 2010 00:51:49 +0000 (+0000)
Subject: fix kinetic formalism
X-Git-Url: https://git.donarmstrong.com/?p=ool%2Flipid_simulation_formalism.git;a=commitdiff_plain;h=fc6e2371729ed18c0084cdc62c96333a03b84eca

fix kinetic formalism

git-svn-id: svn+ssh://hemlock.ucr.edu/srv/svn/misc/trunk/origins_of_life@500 25fa0111-c432-4dab-af88-9f31a2f6ac42
---

diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw
index 683f29f..dfe266d 100644
--- a/kinetic_formalism.Rnw
+++ b/kinetic_formalism.Rnw
@@ -65,7 +65,7 @@ require(grid)
 # R in cal / mol K
 to.kcal <- function(k,temp=300) {
   gasconst <- 1.985
-  return(gasconst*temp*log(k)/1000)
+  return(-gasconst*temp*log(k)/1000)
 }
 @ 
 
@@ -121,7 +121,7 @@ curve(2^x,from=0,to=sd(c(0,4)),
 curve(to.kcal(2^x),from=0,to=sd(c(0,4)),
       main="Unsaturation forward",
       xlab="Standard Deviation of Unsaturation of Vesicle",
-      ylab="Unsaturation Forward (k cal)")
+      ylab="Unsaturation Forward (kcal/mol)")
 @ 
 
 
@@ -156,7 +156,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Average Vesicle Charge",rot=30),
           ylab=list("Component Charge",rot=-35),
-          zlab=list("Charge Forward (k cal)",rot=93)))
+          zlab=list("Charge Forward (kcal/mol)",rot=93)))
 rm(x,y,grid)
 @ 
 
@@ -183,7 +183,7 @@ curve(to.kcal(10^x),from=0,to=max(c(sd(abs(log(c(0.8,1.33)))),
                     sd(abs(log(c(0.8,1)))))),
       main="Curvature forward",
       xlab="Standard Deviation of Absolute value of the Log of the Curvature of Vesicle",
-      ylab="Curvature Forward Adjustment (kcal)")
+      ylab="Curvature Forward Adjustment (kcal/mol)")
 @ 
 
 
@@ -205,7 +205,7 @@ curve(3^x,from=0,to=sd(c(12,24)),
 curve(to.kcal(3^x),from=0,to=sd(c(12,24)),
       main="Length forward",
       xlab="Standard Deviation of Length of Vesicle",
-      ylab="Length Forward Adjustment (kcal)")
+      ylab="Length Forward Adjustment (kcal/mol)")
 @ 
 
 
@@ -251,7 +251,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Average Vesicle Unsaturation",rot=30),
           ylab=list("Monomer Unsaturation",rot=-35),
-          zlab=list("Unsaturation Backward (kcal)",rot=93)))
+          zlab=list("Unsaturation Backward (kcal/mol)",rot=93)))
 rm(grid)
 @ 
 
@@ -287,7 +287,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Average Vesicle Charge",rot=30),
           ylab=list("Component Charge",rot=-35),
-          zlab=list("Charge Backwards (kcal)",rot=93)))
+          zlab=list("Charge Backwards (kcal/mol)",rot=93)))
 rm(x,y,grid)
 @ 
 
@@ -320,7 +320,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Vesicle Curvature",rot=30),
           ylab=list("Monomer Curvature",rot=-35),
-          zlab=list("Curvature Backward (kcal)",rot=93)))
+          zlab=list("Curvature Backward (kcal/mol)",rot=93)))
 rm(grid)
 @ 
 
@@ -354,7 +354,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Average Vesicle Length",rot=30),
           ylab=list("Monomer Length",rot=-35),
-          zlab=list("Length Backward (kcal)",rot=93)))
+          zlab=list("Length Backward (kcal/mol)",rot=93)))
 rm(grid)
 @ 
 
@@ -388,7 +388,7 @@ print(wireframe(z~x*y,grid,cuts=50,
           scales=list(arrows=FALSE),
           xlab=list("Vesicle Complex Formation",rot=30),
           ylab=list("Monomer Complex Formation",rot=-35),
-          zlab=list("Complex Formation Backward (kcal)",rot=93)))
+          zlab=list("Complex Formation Backward (kcal/mol)",rot=93)))
 rm(grid)
 @