X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kinetic_formalism_competition.Rnw;h=2ceb8116b3df87f6f9adfed6c26dccc4e0671654;hb=HEAD;hp=e2a375c65b64ebde0bae514aa9d912f9c965f49d;hpb=ac8372fb657e6caba5ce032b06ab55d89fbddac6;p=ool%2Flipid_simulation_formalism.git

diff --git a/kinetic_formalism_competition.Rnw b/kinetic_formalism_competition.Rnw
index e2a375c..2ceb811 100644
--- a/kinetic_formalism_competition.Rnw
+++ b/kinetic_formalism_competition.Rnw
@@ -22,11 +22,12 @@
 \usepackage{array}
 \usepackage{dcolumn}
 \usepackage{booktabs}
-\usepackage[noblocks]{authblk}
 \usepackage[backend=biber,natbib=true,hyperref=true,citestyle=numeric-comp,style=nature,autocite=inline]{biblatex}
 \addbibresource{references.bib}
 \usepackage[hyperfigures,bookmarks,colorlinks,citecolor=black,filecolor=black,linkcolor=black,urlcolor=black]{hyperref}
+\usepackage[noblocks,auth-sc]{authblk}
 \usepackage[capitalise]{cleveref}
+\usepackage[markifdraft,raisemark=0.01\paperheight,draft]{gitinfo2}
 %\usepackage[sectionbib,sort&compress,numbers]{natbib}
 % \usepackage[nomargin,inline,draft]{fixme}
 %\usepackage[x11names,svgnames]{xcolor}
@@ -51,11 +52,15 @@
 \clubpenalty = 10000
 \widowpenalty = 10000
 \pagestyle{fancy}
-\author{}
-\title{Supplemental Material}
-\date{}
-% rubber: module bibtex
-% rubber: module natbib
+\title{Kinetic formalism for R-GARD Simulations}
+\author[1,2]{Don Armstrong}
+%\ead{don@donarmstrong.com}
+\author[2]{Raphael Zidovetzki}
+%\ead{raphael.zidovetzki@ucr.edu}
+\affil[1]{Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA}
+\affil[2]{Cell Biology and Neuroscience, University of California at Riverside, Riverside, CA, USA}
+\affil[ ]{don@donarmstrong.com, raphael.zidovetzki@ucr.edu}
+%\date{}
 \onehalfspacing
 \begin{document}
 \maketitle
@@ -160,7 +165,7 @@ available, these were taken from literature (\cref{tab:kinetic_parameters_lipid_
     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 \\
+    & Area $\left(\mathrm{Å}^2\right)$ & Charge & $\mathrm{CF}1$ & Curvature \\
     \midrule
     PC   & $\Sexpr{kf[1]}$ & $3.7 \times 10^6$ & $2   \times 10^{-5}$ & 63 & 0  & 2  & 0.8  \\
     PS   & $\Sexpr{kf[2]}$ & $3.7 \times 10^6$ & $1.25\times 10^{-5}$ & 54 & -1 & 0  & 1    \\
@@ -213,7 +218,7 @@ exchange of the fluorescent label \ac{C6NBD} attached to different
 lipid species. Although the values of $k_\mathrm{b}$ are different for the labeled
 and unlabeled lipids, we assume that the ratios of the kinetics
 constants for the lipid types are the same. Furthermore we assume that
-PG behaves similarly to \ac{PS}. Thus, we can determine the $k_\mathrm{b}$ of \ac{PE} and
+\ac{PG} behaves similarly to \ac{PS}. Thus, we can determine the $k_\mathrm{b}$ of \ac{PE} and
 \ac{PS} from the already known $k_\mathrm{b}$ of \ac{PC}. For \ac{C6NBD} labeled \ac{PC},
 \citet{Nichols1982:ret_amphiphile_transfer} obtained a $k_\mathrm{b}$ of
 $0.89$~$\mathrm{min}^{-1}$, \ac{PE} of $0.45$~$\mathrm{min}^{-1}$ and PG of
@@ -254,16 +259,16 @@ 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
+measured the surface area of \ac{POPC} with a Langmuir film balance, and
 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
+\ac{DPPS}\citep{Cascales1996:mds_dpps_area,Pandit2002:mds_dpps}, which is
 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 \ac{SM} using a
 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 Å$^2$. \citet{Robinson1995:mds_chol_area}
+\ac{DPPE}-d$_{62}$ to be 55.4 Å$^2$. \citet{Robinson1995:mds_chol_area}
 found an area for \ac{CHOL} of 38~Å$^2$ using molecular dynamic
 simulations.
 
@@ -1094,11 +1099,11 @@ The most common $\left<\log cu_\mathrm{vesicle}\right>$ is around
 $-0.013$, which leads to a range of $\Delta \Delta G^\ddagger$ from
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(0.8))^2+1))))}
 \frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature 0.8 to
+to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$ for monomers with curvature
+near 1
 $\Sexpr{format(digits=3,to.kcal(7^(1-1/(20*(-0.013-log(1.3))^2+1))))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
-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
-\cref{fig:cub_graph}.
+for monomers with curvature 1.3. The full range of values possible for
+$cu_\mathrm{b}$ are shown in \cref{fig:cub_graph}.
 
 % \RZ{What about the opposite curvatures that actually do fit to each
 %   other?}
@@ -1188,7 +1193,7 @@ to $0\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length near 18 to
 $\Sexpr{format(digits=3,to.kcal(3.2^abs(24-17.75)))}\frac{\mathrm{kcal}}{\mathrm{mol}}$
 for monomers with length 24. The full range of possible values of
-$l_\mathrm{b}$ are shown in \cref{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
@@ -1569,6 +1574,11 @@ to produce later output.
 % silhouette~\citep{Rousseeuw1987:silhouettes} is chosen as the ideal
 % clustering~\citep{Shenhav2005:pgard}.
 
+\section*{Formalism}
+
+The most current revision of this formalism is available at
+\url{https://git.donarmstrong.com/ool/lipid_simulation_formalism.git}.
+This document is  \gitMarkPref • \gitMark.
 
 %\bibliographystyle{unsrtnat}
 %\bibliography{references.bib}