\begin{document}
%\maketitle
-<<results=hide,echo=FALSE>>=
+<<results="hide",echo=FALSE>>=
require(lattice)
require(grid)
require(Hmisc)
not include a term for it in this formalism.
-\setkeys{Gin}{width=3.2in}
-<<fig=TRUE,echo=FALSE,results=hide,width=5,height=5>>=
+<<echo=FALSE,results="hide",fig.width=5,fig.height=5,out.width="3.2in">>=
curve(2^x,from=0,to=sd(c(0,4)),
main="Unsaturation Forward",
xlab="Standard Deviation of Unsaturation of Vesicle",
ylab="Unsaturation Forward Adjustment")
@
-<<fig=TRUE,echo=FALSE,results=hide,width=5,height=5>>=
+<<echo=FALSE,results="hide",fig.width=5,fig.height=5,out.width="3.2in">>=
curve(to.kcal(2^x),from=0,to=sd(c(0,4)),
main="Unsaturation forward",
xlab="Standard Deviation of Unsaturation of Vesicle",
$\Sexpr{format(digits=3,to.kcal(60^(-.165*-1)))}
\frac{\mathrm{kcal}}{\mathrm{mol}}$ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
x <- seq(-1,0,length.out=20)
y <- seq(-1,0,length.out=20)
grid <- expand.grid(x=x,y=y)
zlab=list("Charge Forward",rot=93)))
rm(x,y,grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
x <- seq(-1,0,length.out=20)
y <- seq(-1,0,length.out=20)
grid <- expand.grid(x=x,y=y)
relatively matched curvatures in our environment.
% 1.5 to 0.75 3 to 0.33
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0,max(c(sd(abs(log(c(1,3)))),
-y sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
+ sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
y=seq(0,max(c(mean(log(c(1,3)),
mean(log(c(1,0.33))),
mean(log(c(0.33,3)))))),length.out=20))
zlab=list("Vesicle Curvature Forward",rot=93)))
rm(grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0,max(c(sd(abs(log(c(1,3)))),
sd(abs(log(c(1,0.33)))),sd(abs(log(c(0.33,3)))))),length.out=20),
y=seq(0,max(c(mean(log(c(1,3)),
chain length. {take into account for the formula; rz 8/17/2010}.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=5>>=
curve(2^x,from=0,to=sd(c(12,24)),
main="Length forward",
xlab="Standard Deviation of Length of Vesicle",
ylab="Length Forward Adjustment")
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=5>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=5>>=
curve(to.kcal(2^x),from=0,to=sd(c(12,24)),
main="Length forward",
xlab="Standard Deviation of Length of Vesicle",
for monomers with 4 unsaturations.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0,4,length.out=20),
y=seq(0,4,length.out=20))
grid$z <- (7^(1-1/(5*(2^-grid$x-2^-grid$y)^2+1)))
zlab=list("Unsaturation Backward",rot=93)))
rm(grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0,4,length.out=20),
y=seq(0,4,length.out=20))
grid$z <- to.kcal((7^(1-1/(5*(2^-grid$x-2^-grid$y)^2+1))))
for monomers with charge $0$.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
x <- seq(-1,0,length.out=20)
y <- seq(-1,0,length.out=20)
grid <- expand.grid(x=x,y=y)
zlab=list("Charge Backwards",rot=93)))
rm(x,y,grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
x <- seq(-1,0,length.out=20)
y <- seq(-1,0,length.out=20)
grid <- expand.grid(x=x,y=y)
for monomers with curvature 1.3 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near 1.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0.8,1.33,length.out=20),
y=seq(0.8,1.33,length.out=20))
grid$z <- 7^(1-1/(20*(log(grid$x)-log(grid$y))^2+1))
zlab=list("Curvature Backward",rot=93)))
rm(grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(0.8,1.33,length.out=20),
y=seq(0.8,1.33,length.out=20))
grid$z <- to.kcal(7^(1-1/(20*(log(grid$x)-log(grid$y))^2+1)))
for monomers with length 24 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near 18.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(12,24,length.out=20),
y=seq(12,24,length.out=20))
grid$z <- 3.2^(abs(grid$x-grid$y))
zlab=list("Length Backward",rot=93)))
rm(grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(12,24,length.out=20),
y=seq(12,24,length.out=20))
grid$z <- to.kcal(3.2^(abs(grid$x-grid$y)))
formation $0$.
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(-1,3,length.out=20),
y=seq(-1,3,length.out=20))
grid$z <- 1.5^(grid$x*grid$y-abs(grid$x*grid$y))
zlab=list("Complex Formation Backward",rot=93)))
rm(grid)
@
-<<fig=TRUE,echo=FALSE,results=hide,width=7,height=7>>=
+<<echo=FALSE,results="hide",fig.width=7,fig.height=7>>=
grid <- expand.grid(x=seq(-1,3,length.out=20),
y=seq(-1,3,length.out=20))
grid$z <- to.kcal(1.5^(grid$x*grid$y-abs(grid$x*grid$y)))
\begin{document}
\maketitle
-<<results=hide,echo=FALSE>>=
+<<results='hide',echo=FALSE>>=
require(lattice)
require(grid)
require(Hmisc)
\subsection{Per-Lipid Kinetic Parameters}
-<<echo=FALSE,results=hide>>=
+<<echo=FALSE,results='hide'>>=
kf.prime <- c(3.7e6,3.7e6,5.1e7,3.7e6,2.3e6)
kf <- (as.numeric(kf.prime)*10^-3)/(63e-20*6.022e23)
@
\setkeys{Gin}{width=6.4in}
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=10,height=5>>=
+<<echo=FALSE,results='hide',fig.width=10,fig.height=5>>=
layout(matrix(1:2,nrow=1,ncol=2))
curve(2^x,from=0,to=sd(c(0,4)),
xlab=expression(paste(stdev,group("(",italic(un[vesicle]),")"))),
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
% 1.5 to 0.75 3 to 0.33
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=5>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=5>>=
layout(matrix(1:2,nrow=1,ncol=2))
curve(2^x,from=0,to=sd(c(12,24)),
xlab=expression(paste(stdev,group("(",italic(l[vesicle]),")"))),
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))
\begin{figure}
-<<fig=TRUE,echo=FALSE,results=hide,width=14,height=7>>=
+<<echo=FALSE,results='hide',fig.width=14,fig.height=7>>=
trellis.device(new=F,color=TRUE)
trellis.par.set(list(axis.line =list(col="transparent")))
pushViewport(viewport(layout=grid.layout(nrow=1,ncol=2),clip="off"))