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+\usepackage[noblocks,auth-sc]{authblk}
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+\usepackage[markifdraft,raisemark=0.01\paperheight,draft]{gitinfo2}
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-\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
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 \\
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
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.
$-0.013$, 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?}
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
% 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.
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projects / ool / lipid_simulation_formalism.git / blobdiff