From 5837d5afaa96f6e151a0f1d25cc9c74310faf201 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Thu, 2 Feb 2017 16:56:29 -0800 Subject: [PATCH] switch to knitr and add chunk names --- kinetic_formalism_competition.Rnw | 59 ++++++++++++++++--------------- 1 file changed, 30 insertions(+), 29 deletions(-) diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw index 88cebad..505fb00 100644 --- a/kinetic_formalism_competition.Rnw +++ b/kinetic_formalism_competition.Rnw @@ -60,7 +60,6 @@ \newcommand{\OM}[1]{\textcolor{red}{\fxnote{OM: #1}}} -%\SweaveOpts{prefix.string=pub_318_phys_bio_submission_figures_suppl/pub_318_phys_bio_sub_suppl_fig,pdf=TRUE,eps=TRUE} \oddsidemargin 0.0in \textwidth 6.5in \raggedbottom @@ -76,11 +75,14 @@ \begin{document} \maketitle -<>= -require(lattice) -require(grid) -require(Hmisc) -require(gridBase) +<>= +opts_chunk$set(dev="CairoPDF",out.width="\\columnwidth",out.height="0.7\\textheight",out.extra="keepaspectratio") +opts_chunk$set(cache=TRUE, autodep=TRUE) +options(scipen = -2, digits = 1) +library("lattice") +library("grid") +library("Hmisc") +library("gridBase") to.latex <- function(x){ gsub("\\\\","\\\\\\\\",latexSN(x)) } @@ -217,7 +219,7 @@ exchange of [$^3$H]DMPC between LUV at 30\textdegree C, and found it to be 9.6 hr. As this is a first order reaction, and the primary limiting step in exchange is lipid desorption, $k_\mathrm{b}$ for DMPC is $k_{\mathrm{b}_\mathrm{PC}}=\frac{\log 2}{9.6 \times 60 \times 60} \approx -\Sexpr{to.latex(format(log(2)/(9.6*60*60),digits=2))} +\Sexpr{log(2)/(9.6*60*60)} \mathrm{s}^{-1}$. We assume that $k_\mathrm{b}$ for SM is the same as for PC. To estimate the $k_\mathrm{b}$ of PE and PS, we used the data from \citet{Nichols1982:ret_amphiphile_transfer} who measured the rate of @@ -237,9 +239,9 @@ us to $k_{\mathrm{b}_\mathrm{PE}} = \frac{k_{\mathrm{b}_\mathrm{PC}}\times\mathrm{PE}}{\mathrm{PC}} \approx \frac{2\times 10^{-5}\,\mathrm{s}^{-1} \times 0.45\,\mathrm{min}^{-1}}{0.89\,\mathrm{min}^{-1}} \approx -\Sexpr{to.latex(format(log(2)/(9.6*60*60)*0.45/0.89,digits=2))}$~$\mathrm{s}^{-1}$ +\Sexpr{log(2)/(9.6*60*60)*0.45/0.89}$~$\mathrm{s}^{-1}$ and likewise, $k_{\mathrm{b}_\mathrm{PS}}\approx -\Sexpr{to.latex(format(log(2)/(9.6*60*60)*0.55/0.89,digits=3))}$~$\mathrm{s}^{-1}$. +\Sexpr{log(2)/(9.6*60*60)*0.55/0.89}$~$\mathrm{s}^{-1}$. The $k_\mathrm{b}$ of SM was determined using the work of \citet{Bai1997:lipid_movementbodipy}, who measured spontaneous transfer of C$_5$-DMB-SM and C$_5$-DMB-PC from donor and acceptor @@ -247,15 +249,15 @@ vesicles, finding $3.4\times10^{-2}$~$\mathrm{s}^{-1}$ and $2.2\times10^{-3}$~$\mathrm{s}^{-1}$ respectively; using the ratio of $k_\mathrm{b}$ of C$_5$-DMB-SM to the $k_\mathrm{b}$ of C$_5$-DMB-PC times the $k_\mathrm{b}$ of PC ($\frac{3.4 \times 10^{-2}\mathrm{s}^{-1}}{2.2 \times - 10^{-3}\mathrm{s}^{-1}} -\Sexpr{to.latex(format(log(2)/(9.6*60*60),digits=2))}\mathrm{s}^{-1}$, + 10^{-3}\mathrm{s}^{-1}}\approx +\Sexpr{log(2)/(9.6*60*60)}\mathrm{s}^{-1}$), we obtain $k_{\mathrm{b}_\mathrm{SM}} \approx -\Sexpr{to.latex(format(log(2)/(9.6*60*60)*3.4e-2/2.2e-3,digits=2,scientific=TRUE))}$. +\Sexpr{log(2)/(9.6*60*60)*3.4e-2/2.2e-3}$. In the case of CHOL, \citet{Jones1990:lipid_transfer} measured the $t_{1/2}$ of [$^3$H] transfer from POPC vesicles and found it to be 41 minutes, leading to a $k_{\mathrm{b}_\mathrm{CHOL}} = \frac{\log 2}{41\times 60} \approx -\Sexpr{to.latex(format(log(2)/(41*60),digits=2,scientific=TRUE))}$~$\mathrm{s}^{-1}$. +\Sexpr{log(2)/(41*60)}$~$\mathrm{s}^{-1}$. \subsubsection{Headgroup Surface Area for lipid types} @@ -267,16 +269,16 @@ 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 -found it to be 63~$\AA^2$ at $30$~$\frac{\mathrm{mN}}{\mathrm{m}}$. -Molecular dynamic simulations found an area of 54 $\AA^2$ 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 -in agreement with the experimental value of 56~$\AA^2$ found using a +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 SM using a -Langmuir film balance, and found it to be 61~$\AA^2$. Using $^2$H NMR, +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 $\AA^2$. \citet{Robinson1995:mds_chol_area} -found an area for CHOL of 38~$\AA^2$ using molecular dynamic +DPPE-d$_{62}$ to be 55.4 Å$^2$. \citet{Robinson1995:mds_chol_area} +found an area for CHOL of 38~Å$^2$ using molecular dynamic simulations. % robinson's chol area is kind of crappy; they did it using MDS, but @@ -585,9 +587,8 @@ values depicted in Figure~\ref{fig:unf_graph}. % not include a term for it in this formalism. -\setkeys{Gin}{width=6.4in} \begin{figure} -<>= +<>= 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]),")"))), @@ -653,7 +654,7 @@ values seen in Figure~\ref{fig:chf_graph}. \begin{figure} -<>= +<>= 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")) @@ -748,7 +749,7 @@ $cu_\mathrm{f}$ values possible are shown in Figure~\ref{fig:cuf_graph}. % 1.5 to 0.75 3 to 0.33 \begin{figure} -<>= +<>= 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")) @@ -862,7 +863,7 @@ $\Sexpr{format(digits=3,to.kcal(2^(3.4)))} \begin{figure} -<>= +<>= 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]),")"))), @@ -960,7 +961,7 @@ the full range of possible values. \begin{figure} -<>= +<>= 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")) @@ -1028,7 +1029,7 @@ of $ch_\mathrm{b}$. \begin{figure} -<>= +<>= 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")) @@ -1125,7 +1126,7 @@ Figure~\ref{fig:cub_graph} \begin{figure} -<>= +<>= 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")) @@ -1209,7 +1210,7 @@ $l_\mathrm{b}$ are shown in Figure~\ref{fig:lb_graph} \begin{figure} -<>= +<>= 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")) @@ -1298,7 +1299,7 @@ depicted in Figure~\ref{fig:cf1b_graph}. \begin{figure} -<>= +<>= 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")) -- 2.39.2