From: Don Armstrong Date: Fri, 3 Feb 2017 01:10:35 +0000 (-0800) Subject: switch to cleveref X-Git-Url: https://git.donarmstrong.com/?p=ool%2Flipid_simulation_formalism.git;a=commitdiff_plain;h=22e0b2cf36d4fd09674626bb920bd8c4ff4a5ee2 switch to cleveref --- diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw index 505fb00..9db4183 100644 --- a/kinetic_formalism_competition.Rnw +++ b/kinetic_formalism_competition.Rnw @@ -18,6 +18,7 @@ \usepackage{booktabs} \usepackage[noblocks]{authblk} \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref} +\usepackage[capitalise]{cleveref} \usepackage[sectionbib,sort&compress,numbers]{natbib} \usepackage[nomargin,inline,draft]{fixme} \usepackage[x11names,svgnames]{xcolor} @@ -99,35 +100,35 @@ to.kcal <- function(k,temp=300) { \renewcommand{\thetable}{S\@arabic\c@table} \makeatother -\section{Competition Implementation} -\subsection{Implementation changes} - -\begin{itemize} -\item settable maximum number of vesicles to track (default $10^4$) -\item start with 1~L ($10^{-3}$~m$^3$) cube -\item if at any point the number of vesicles exceeds the maximum - number, chop the volume and environment molecule number into tenths, - randomly select one tenth of the vesicles, and continue tracking. -\item generations will be counted per vesicle, and each progeny - vesicle will have a generation number one greater than the parental - vesicle. -\item 100 generations can result in as many as $2^{100}$ - ($\Sexpr{to.latex(format(digits=3,2^100))}$) vesicles or as few as - 101 vesicles. -\item Environment will use a specific number of each component instead - of a constant concentration; as the number may be larger than - \texttt{long long} ($2^{64}$), we use libgmp to handle an arbitrary - precision number of components -\end{itemize} - -\subsection{Infrastructure changes} -\begin{itemize} -\item Rewrite core bits in C -\item Use libgmp for handling large ints -\item Use openmpi to split the calculations out over multiple - machines/processors and allow deploying to larger - clusters/supercomputers -\end{itemize} +% \section{Competition Implementation} +% \subsection{Implementation changes} +% +% \begin{itemize} +% \item settable maximum number of vesicles to track (default $10^4$) +% \item start with 1~L ($10^{-3}$~m$^3$) cube +% \item if at any point the number of vesicles exceeds the maximum +% number, chop the volume and environment molecule number into tenths, +% randomly select one tenth of the vesicles, and continue tracking. +% \item generations will be counted per vesicle, and each progeny +% vesicle will have a generation number one greater than the parental +% vesicle. +% \item 100 generations can result in as many as $2^{100}$ +% ($\Sexpr{2^100}$) vesicles or as few as +% 101 vesicles. +% \item Environment will use a specific number of each component instead +% of a constant concentration; as the number may be larger than +% \texttt{long long} ($2^{64}$), we use libgmp to handle an arbitrary +% precision number of components +% \end{itemize} +% +% \subsection{Infrastructure changes} +% \begin{itemize} +% \item Rewrite core bits in C +% \item Use libgmp for handling large ints +% \item Use openmpi to split the calculations out over multiple +% machines/processors and allow deploying to larger +% clusters/supercomputers +% \end{itemize} @@ -149,20 +150,18 @@ The base forward kinetic parameter for the $i$th component is $k_{\mathrm{f}i}$ and is dependent on the particular lipid type (PC, PS, SM, etc.). The forward adjustment parameter, $k_{\mathrm{f}i\mathrm{adj}}$, is based on the properties of the vesicle and the specific component (type, length, -unsaturation, etc.) (see Equation~\ref{eq:kf_adj}, and -Section~\ref{sec:kinetic_adjustments}). +unsaturation, etc.) (see \cref{eq:kf_adj,sec:kinetic_adjustments}). $\left[C_{i_\mathrm{monomer}}\right]$ is the molar concentration of monomer of the $i$th component. $\left[S_\mathrm{vesicle}\right]$ is the surface area of the vesicle per volume. The base backwards kinetic parameter for the $i$th component is $k_{\mathrm{b}i}$ and its adjustment parameter -$k_{\mathrm{b}i\mathrm{adj}}$ (see Equation~\ref{eq:kb_adj}, and -Section~\ref{sec:kinetic_adjustments}). +$k_{\mathrm{b}i\mathrm{adj}}$ (see \cref{eq:kb_adj,sec:kinetic_adjustments}). $\left[C_{i_\mathrm{vesicle}}\right]$ is the molar concentration of the $i$th component in the vesicle. \subsection{Per-Lipid Kinetic Parameters} -<>= +<>= kf.prime <- c(3.7e6,3.7e6,5.1e7,3.7e6,2.3e6) kf <- (as.numeric(kf.prime)*10^-3)/(63e-20*6.022e23) @ @@ -174,7 +173,7 @@ available, these were taken from literature. % \centering % \begin{tabular}{c c c c c c c c} % \toprule -% Type & $k_\mathrm{f}$ $\left(\frac{\mathrm{m}}{\mathrm{s}}\right)$ & $k'_\mathrm{f}$ $\left(\frac{1}{\mathrm{M} \mathrm{s}}\right)$ & $k_\mathrm{b}$ $\left(\mathrm{s}^{-1}\right)$ & Area $\left({\AA}^2\right)$ & Charge & $\mathrm{CF}1$ & Curvature \\ +% Type & $k_\mathrm{f}$ $\left(\frac{\mathrm{m}}{\mathrm{s}}\right)$ & $k'_\mathrm{f}$ $\left(\frac{1}{\mathrm{M} \mathrm{s}}\right)$ & $k_\mathrm{b}$ $\left(\mathrm{s}^{-1}\right)$ & Area $\left({Å}^2\right)$ & Charge & $\mathrm{CF}1$ & Curvature \\ % \midrule % PC & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[1]))}$ & $3.7 \times 10^6$ & $2 \times 10^{-5}$ & 63 & 0 & 2 & 0.8 \\ % PS & $\Sexpr{to.latex(format(digits=3,scientific=TRUE,kf[2]))}$ & $3.7 \times 10^6$ & $1.25\times 10^{-5}$ & 54 & -1 & 0 & 1 \\ @@ -188,7 +187,7 @@ available, these were taken from literature. % \end{table} %%% \DLA{I think we may just reduce these three sections; area, $k_\mathrm{f}$ -%%% and $k_\mathrm{b}$ to Table~\ref{tab:kinetic_parameters_lipid_types} with +%%% and $k_\mathrm{b}$ to \cref{tab:kinetic_parameters_lipid_types} with %%% references.} %%% %%% \RZ{Yes, but we also have to have then as comments the numbers that @@ -576,7 +575,7 @@ The mean $\mathrm{stdev}\left(un_\mathrm{vesicle}\right)$ in our simulations is around $1.5$, which leads to a $\Delta \Delta G^\ddagger$ of $\Sexpr{to.latex(format(digits=3,to.kcal(2^1.5)))} \frac{\mathrm{kcal}}{\mathrm{mol}}$, and a total range of possible -values depicted in Figure~\ref{fig:unf_graph}. +values depicted in \cref{fig:unf_graph}. % \RZ{Explain here, or even earlier that the formulas were ad hoc % adjusted to correspond to ``reasonable'' changes in the Eyring @@ -650,7 +649,7 @@ to a range of $\Delta \Delta G^\ddagger$ from $\Sexpr{format(digits=3,to.kcal(60^(-.165*-1)))} \frac{\mathrm{kcal}}{\mathrm{mol}}$ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$, and the total range of possible -values seen in Figure~\ref{fig:chf_graph}. +values seen in \cref{fig:chf_graph}. \begin{figure} @@ -745,7 +744,7 @@ cu_\mathrm{vesicle}$ of $0.213$ leads to a $\Delta \Delta G^\ddagger$ of $\Sexpr{format(digits=3,to.kcal(10^(0.13*0.213)))} \frac{\mathrm{kcal}}{\mathrm{mol}}$. This is a consequence of the relatively matched curvatures in our environment. The full range of -$cu_\mathrm{f}$ values possible are shown in Figure~\ref{fig:cuf_graph}. +$cu_\mathrm{f}$ values possible are shown in \cref{fig:cuf_graph}. % 1.5 to 0.75 3 to 0.33 \begin{figure} @@ -956,7 +955,7 @@ $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-0)^2+1))))} \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with 0 unsaturation to $\Sexpr{format(digits=3,to.kcal(7^(1-1/(5*(2^-1.7-2^-4)^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$ -for monomers with 4 unsaturations. See Figure~\ref{fig:unb_graph} for +for monomers with 4 unsaturations. See \cref{fig:unb_graph} for the full range of possible values. @@ -1024,7 +1023,7 @@ a range of $\Delta \Delta G^\ddagger$ from $\Sexpr{format(digits=3,to.kcal(20^(-.164*-1)))} \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $-1$ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with charge $0$. -See Figure~\ref{fig:chb_graph} for the full range of possible values +See \cref{fig:chb_graph} for the full range of possible values of $ch_\mathrm{b}$. @@ -1111,7 +1110,7 @@ $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\math for monomers with curvature 1.3 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature near 1. The full range of values possible for $cu_\mathrm{b}$ are shown in -Figure~\ref{fig:cub_graph} +\cref{fig:cub_graph} % \RZ{What about the opposite curvatures that actually do fit to each % other?} @@ -1200,7 +1199,7 @@ $\Sexpr{format(digits=3,to.kcal(3.2^abs(12-17.75)))} $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with length 24 to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with length near 18. The full range of possible values of -$l_\mathrm{b}$ are shown in Figure~\ref{fig:lb_graph} +$l_\mathrm{b}$ are shown in \cref{fig:lb_graph} % (for methods? From McLean84LIB: The activation free energies and free % energies of transfer from self-micelles to water increase by 2.2 and @@ -1294,7 +1293,7 @@ $\Sexpr{format(digits=3,to.kcal(1.5^(0.925*2-abs(0.925*2))))}\frac{\mathrm{kcal} for monomers with complex formation $2$ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with complex formation $0$. The full range of possible values for $CF1_\mathrm{b}$ are -depicted in Figure~\ref{fig:cf1b_graph}. +depicted in \cref{fig:cf1b_graph}. @@ -1458,15 +1457,15 @@ vesicle properties, we only plot the mean of the property. Determining the number of molecules to add to the lipid membrane ($n_i$) requires knowing $k_{\mathrm{f}i_\mathrm{adj}}$, the surface area of the -vesicle $S_\mathrm{vesicle}$ (see Section \ref{sec:ves_prop}), the time interval +vesicle $S_\mathrm{vesicle}$ (see \cref{sec:ves_prop}), the time interval $dt$ during which lipids are added, the base $k_{\mathrm{f}i}$, and the concentration of the monomer in the environment -$\left[C_{i\mathrm{vesicle}}\right]$ (see Equation~\ref{eq:state}). -$k_{\mathrm{f}i\mathrm{adj}}$ is calculated (see Equation~\ref{eq:kf_adj}) based on the +$\left[C_{i\mathrm{vesicle}}\right]$ (see \cref{eq:state}). +$k_{\mathrm{f}i\mathrm{adj}}$ is calculated (see \cref{eq:kf_adj}) based on the vesicle properties and their hypothesized effect on the rate (in as many cases as possible, experimentally based) -(see Section~\ref{sec:kinetic_adjustments} for details). $dt$ can be varied -(see Section~\ref{sec:step_duration}), but for a given step is constant. This +(see \cref{sec:kinetic_adjustments} for details). $dt$ can be varied +(see \cref{sec:step_duration}), but for a given step is constant. This leads to the following: $n_i = k_{\mathrm{f}i}k_{\mathrm{f}i_\mathrm{adj}}\left[C_{i_\mathrm{monomer}}\right]S_\mathrm{vesicle}\mathrm{N_A}dt$