From 71fe9a449493874b80afa86025743dec8dd4051b Mon Sep 17 00:00:00 2001 From: don Date: Wed, 12 May 2010 05:33:04 +0000 Subject: [PATCH] add kinetic formalisms git-svn-id: svn+ssh://hemlock.ucr.edu/srv/svn/misc/trunk/origins_of_life@492 25fa0111-c432-4dab-af88-9f31a2f6ac42 --- Makefile | 30 +++++ kinetic_formalism.Rnw | 266 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 296 insertions(+) create mode 100644 Makefile create mode 100644 kinetic_formalism.Rnw diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..7ca3bee --- /dev/null +++ b/Makefile @@ -0,0 +1,30 @@ +#!/bin/make + +all: kinetic_formalism.pdf + +R=R + +%.pdf: %.svg + inkscape -A $@ $< + pdfcrop $@ + mv $(dir $@)*-crop.pdf $@ + +%.png: %.svg + inkscape -e $@ -d 300 $< + +%.pdf: %.png + bmeps -lpdf -olevel=1.4 $< $@ + +%.tex: %.Rnw + $(R) CMD Sweave $< + +%.pdf: %.tex $(wildcard *.bib) $(wildcard *.tex) + rubber -fd $< + +clean: + rubber -d --clean *.tex + rm -f *.tmp + +.PHONY: clean all + +.DELETE_ON_ERROR: %.tex \ No newline at end of file diff --git a/kinetic_formalism.Rnw b/kinetic_formalism.Rnw new file mode 100644 index 0000000..d7d8bfe --- /dev/null +++ b/kinetic_formalism.Rnw @@ -0,0 +1,266 @@ +\documentclass[english,12pt]{article} +\usepackage{fancyhdr} +%\usepackage[pdftex]{graphicx} +\usepackage{graphicx} +\usepackage[bf]{caption2} +\usepackage{rotating} +\usepackage{multirow} +\usepackage{textcomp} +\usepackage{mathrsfs} +\usepackage{amssymb} +\usepackage{setspace} +\usepackage{txfonts} +\usepackage[light,all]{draftcopy} +\usepackage{fancyref} +\usepackage[hyperfigures,backref,bookmarks,colorlinks]{hyperref} +\usepackage[sectionbib,sort&compress,square,numbers]{natbib} +\usepackage[margin,inline,draft]{fixme} +\usepackage[x11names,svgnames]{xcolor} +\usepackage{texshade} +\newenvironment{narrow}[2]{% + \begin{list}{}{% + \setlength{\topsep}{0pt}% + \setlength{\leftmargin}{#1}% + \setlength{\rightmargin}{#2}% + \setlength{\listparindent}{\parindent}% + \setlength{\itemindent}{\parindent}% + \setlength{\parsep}{\parskip}}% + \item[]}{\end{list}} +\newenvironment{paperquote}{% + \begin{quote}% + \it + }% + {\end{quote}} +\renewcommand{\textfraction}{0.15} +\renewcommand{\topfraction}{0.85} +\renewcommand{\bottomfraction}{0.65} +\renewcommand{\floatpagefraction}{0.60} +%\renewcommand{\baselinestretch}{1.8} +\newenvironment{enumerate*}% + {\begin{enumerate}% + \setlength{\itemsep}{0pt}% + \setlength{\parskip}{0pt}}% + {\end{enumerate}} +\newenvironment{itemize*}% + {\begin{itemize}% + \setlength{\itemsep}{0pt}% + \setlength{\parskip}{0pt}}% + {\end{itemize}} +\oddsidemargin 0.0in +\textwidth 6.5in +\raggedbottom +\clubpenalty = 10000 +\widowpenalty = 10000 +\pagestyle{fancy} +\author{Don Armstrong} +\title{OOL Kinetic Formalisms} +%\date{} +\onehalfspacing +\begin{document} +%\maketitle + +<>= +require(lattice) +require(grid) +@ + +\section{State Equation} +% double check this with the bits in the paper +\begin{equation} + \frac{d C^{j}_{i_\mathrm{ves}}}{dt} = k_{fi}k_{fi\mathrm{adj}}\left[C^j_{i_\mathrm{monomer}}\right] - + k_{bi}k_{bi\mathrm{adj}}C^j_{i_\mathrm{ves}} + \label{eq:state} +\end{equation} + +\subsection{Forward adjustments ($k_{fi\mathrm{adj}}$)} + +\begin{equation} + k_{fi\mathrm{adj}} = un_f \cdot ch_f \cdot cu_f \cdot l_f \cdot CF1_f + \label{eq:kf_adj} +\end{equation} + +\newpage +\subsubsection{Unsaturation Forward} +\begin{equation} + un_f = 2^{\mathrm{stdev}\left(un_\mathrm{ves}\right)} + \label{eq:unsaturation_forward} +\end{equation} + +<>= +curve(2^x,from=0,to=sd(c(0,4)), + main="Unsaturation forward", + xlab="Standard Deviation of Unsaturation of Vesicle", + ylab="Unsaturation Forward Adjustment") +@ + +\newpage +\subsubsection{Charge Forward} +\begin{equation} + ch_f = 60^{-\left<{ch}_v\right> {ch}_m} + \label{eq:charge_forward} +\end{equation} + +<>= +x <- seq(-1,0,length.out=20) +y <- seq(-1,0,length.out=20) +grid <- expand.grid(x=x,y=y) +grid$z <- as.vector(60^(-outer(x,y))) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Average Vesicle Charge", + ylab="Component Charge", + zlab="Charge Forward")) +rm(x,y,grid) +@ + +\newpage +\subsubsection{Curvature Forward} +\begin{equation} + cu_f = 10^{\mathrm{stdev}\left|\log cu_\mathrm{vesicle}\right|} + \label{eq:curvature_forward} +\end{equation} + +<>= +curve(10^x,from=0,to=sd(c(0.8,1.33)), + main="Curvature forward", + xlab="Standard Deviation of Curvature of Vesicle", + ylab="Curvature Forward Adjustment") +@ + +\newpage +\subsubsection{Length Forward} +\begin{equation} + l_f = 3^{\mathrm{stdev}\left|\log l_\mathrm{ves}\right|} + \label{eq:length_forward} +\end{equation} + +<>= +curve(3^x,from=0,to=sd(c(12,24)), + main="Length forward", + xlab="Standard Deviation of Length of Vesicle", + ylab="Length Forward Adjustment") +@ + +\subsubsection{Complex Formation} +\begin{equation} + CF1_f=1 + \label{eq:complex_formation_forward} +\end{equation} + +\subsection{Backward adjustments ($k_{bi\mathrm{adj}}$)} + +\begin{equation} + k_{bi\mathrm{adj}} = un_b \cdot ch_b \cdot cu_b \cdot l_b \cdot CF1_b + \label{eq:kf_adj} +\end{equation} + +\newpage +\subsubsection{Unsaturation Backward} +\begin{equation} + un_b = 10^{\left|3.5^{-\left}-3.5^{-\left}\right|} + \label{eq:unsaturation_backward} +\end{equation} + +<>= +grid <- expand.grid(x=seq(0,4,length.out=20), + y=seq(0,4,length.out=20)) +grid$z <- 10^(abs(3.5^-grid$x-3.5^-grid$y)) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Average Vesicle Unsaturation", + ylab="Monomer Unsaturation", + zlab="Unsaturation Backward")) +rm(grid) +@ + +\newpage +\subsubsection{Charge Backwards} +\begin{equation} + ch_b = 60^{-\left<{ch}_v\right> {ch}_m} + \label{eq:charge_backwards} +\end{equation} + +<>= +x <- seq(-1,0,length.out=20) +y <- seq(-1,0,length.out=20) +grid <- expand.grid(x=x,y=y) +grid$z <- as.vector(60^(-outer(x,y))) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Average Vesicle Charge", + ylab="Component Charge", + zlab="Charge Backwards")) +rm(x,y,grid) +@ + +\newpage +\subsubsection{Curvature Backwards} +\begin{equation} + cu_f = 4^{\left|\left|\log cu_\mathrm{vesicle}\right|-\left|\log cu_\mathrm{monomer}\right|\right|} + \label{eq:curvature_backwards} +\end{equation} + +<>= +grid <- expand.grid(x=seq(0.8,1.33,length.out=20), + y=seq(0.8,1.33,length.out=20)) +grid$z <- 10^(abs(3.5^-grid$x-3.5^-grid$y)) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Vesicle Curvature", + ylab="Monomer Curvature", + zlab="Curvature Backward")) +rm(grid) +@ + +\newpage +\subsubsection{Length Backwards} +\begin{equation} + l_b = 3.2^{\left|l_\mathrm{ves}-l_\mathrm{monomer}\right|} + \label{eq:length_backward} +\end{equation} + +<>= +grid <- expand.grid(x=seq(12,24,length.out=20), + y=seq(12,24,length.out=20)) +grid$z <- 3.2^(abs(grid$x-grid$y)) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Average Vesicle Length", + ylab="Monomer Length", + zlab="Length Backward")) +rm(grid) +@ + +\newpage +\subsubsection{Complex Formation Backward} +\begin{equation} + CF1_b=1.5^{CF1_\mathrm{ves} CF1_\mathrm{monomer}-\left|CF1_\mathrm{ves} CF1_\mathrm{monomer}\right|} + \label{eq:complex_formation_backward} +\end{equation} + +<>= +grid <- expand.grid(x=seq(-1,3,length.out=20), + y=seq(-1,3,length.out=20)) +grid$z <- 3.2^(grid$x*grid$y-abs(grid$x*grid$y)) +print(wireframe(z~x*y,grid,cuts=50, + drape=TRUE, + scales=list(arrows=FALSE), + xlab="Vesicle Complex Formation", + ylab="Monomer Complex Formation", + zlab="Complex Formation Backward")) +rm(grid) +@ + + + + +% \bibliographystyle{plainnat} +% \bibliography{references.bib} + + +\end{document} -- 2.39.2