matt_papers/SGI_Award_Application/application.tex

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\begin{document}


\title{A Mesoscale Model for Phospholipid Simulations}

\author{Matthew A. Meineke\\
Department of Chemistry and Biochemistry\\
University of Notre Dame\\
Notre Dame, Indiana 46556}

\date{\today}
\maketitle

\section{Research Summary}

Simulations of phospholipid bilayers are, by necessity, quite
complex. The lipid molecules are large, and contain many atoms. Also,
the head group of the lipid will typically contain charge separated
ions which set up a large dipole within the molecule. Adding to the
complexity are the number of water molecules needed to properly
solvate the lipid bilayer, typically 25 water molecules for every
lipid molecule. These factors make it dificult to study certain
biologically interesting phenomena that don't fit within a short time
or length scale. One such phenomenon is the existence of the ripple
phase ($P_{\beta'}$) of the bilayer between the gel phase
($L_{\beta'}$) and the fluid phase ($L_{\alpha}$). The $P_{\beta'}$
phase has been shown to have a ripple period of
100-200~$\mbox{\AA}$.\cite{katsaras00,sengupta00} A simulation of this
length scale would require approximately 1,300 lipid molecules in
addition to all the water needed to fully solvate the bilayer. Another
system of interest would be drug molecule diffusion through the
membrane. Due to the fluid-like properties of a lipid membrane, not
all diffusion takes place at membrane channels. It is of interest to
study certain molecules that may incorporate themselves directly into
the membrane. These molecules may then have an appreciable waiting
time (on the order of nanoseconds) within the bilayer.

\label{sec:ssdModel}

\begin{figure}
\centering
\includegraphics[width=50mm]{ssd.epsi}
\caption{The SSD model with the oxygen and hydrogen atoms drawn in for reference.}
\label{fig:ssdModel}
\end{figure} 


\label{sec:lipidModel}

\begin{figure}
\centering
\includegraphics[angle=-90,width=80mm]{lipidModel.epsi}
\caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ is the bend angle, $\mu$ is the dipole moment of the head group, and n is the chain length.}
\label{fig:lipidModel}
\end{figure}

The mesoscale model used in this research is designed to simplify the
number of calculations needed to properly simulate a phospholipid
bilayer. The water molecules in the simulation are replaced with the
Soft Sticky Dipole (SSD) model developed by Ichiye
et. al.\cite{liu96:new_model,liu96:monte_carlo,chandra99:ssd_md} This
model reduces water to a single point interaction, while still
maintaining the hydrogen-bonding behavior of water. The lipid molecule
itself is then modeled as a chain of ``tail'' atoms attached to a
large ``head'' atom. The head atom contains a freely rotating dipole
to eliminate the charge separation present in an actual phospholipid.

In the attached images, one can see that the model demonstrates very
promising initial results. In the images, the head atoms are colored
blue, the tail atoms are colored gray, and the water molecules reduced
in size for clarity. The actual simulation is enclosed within the
bounding box. In the simulation containing only 25 lipid models, the
system has demonstrated a spontaneous division into two leaflets, in
route toward a bilayer. In the 50 model system, the lipids show
spontaneous aggregation into micelles from a random initial
configuration. Future aspects of the research will focus on the
effects of tethering the orientation of the dipole, as well as
increasing the scale of the systems studied to gain insight into bulk
bilayer properties.

\bibliographystyle{achemso} 
\bibliography{application}
\end{document}
Revision:	333
Committed:	Thu Mar 13 15:57:43 2003 UTC (22 years, 7 months ago) by mmeineke
Content type:	application/x-tex
File size:	4136 byte(s)
Log Message:	just working on some changes to the application.
#	User	Rev	Content
1	mmeineke	333	\documentclass[11pt]{article}
2
3			\usepackage{graphicx}
4			\usepackage{color}
5			\usepackage{floatflt}
6			\usepackage{amsmath}
7			\usepackage{amssymb}
8			\usepackage{subfigure}
9			\usepackage{palatino}
10			\usepackage[ref]{overcite}
11
12
13
14			\pagestyle{plain}
15			\pagenumbering{arabic}
16			\oddsidemargin 0.0cm \evensidemargin 0.0cm
17			\topmargin -21pt \headsep 10pt
18			\textheight 9.0in \textwidth 6.5in
19			\brokenpenalty=10000
20			\renewcommand{\baselinestretch}{1.2}
21			\renewcommand\citemid{\ } % no comma in optional reference note
22
23
24			\begin{document}
25
26
27			\title{A Mesoscale Model for Phospholipid Simulations}
28
29			\author{Matthew A. Meineke\\
30			Department of Chemistry and Biochemistry\\
31			University of Notre Dame\\
32			Notre Dame, Indiana 46556}
33
34			\date{\today}
35			\maketitle
36
37			\section{Research Summary}
38
39			Simulations of phospholipid bilayers are, by necessity, quite
40			complex. The lipid molecules are large, and contain many atoms. Also,
41			the head group of the lipid will typically contain charge separated
42			ions which set up a large dipole within the molecule. Adding to the
43			complexity are the number of water molecules needed to properly
44			solvate the lipid bilayer, typically 25 water molecules for every
45			lipid molecule. These factors make it dificult to study certain
46			biologically interesting phenomena that don't fit within a short time
47			or length scale. One such phenomenon is the existence of the ripple
48			phase ($P_{\beta'}$) of the bilayer between the gel phase
49			($L_{\beta'}$) and the fluid phase ($L_{\alpha}$). The $P_{\beta'}$
50			phase has been shown to have a ripple period of
51			100-200~$\mbox{\AA}$.\cite{katsaras00,sengupta00} A simulation of this
52			length scale would require approximately 1,300 lipid molecules in
53			addition to all the water needed to fully solvate the bilayer. Another
54			system of interest would be drug molecule diffusion through the
55			membrane. Due to the fluid-like properties of a lipid membrane, not
56			all diffusion takes place at membrane channels. It is of interest to
57			study certain molecules that may incorporate themselves directly into
58			the membrane. These molecules may then have an appreciable waiting
59			time (on the order of nanoseconds) within the bilayer.
60
61			\label{sec:ssdModel}
62
63			\begin{figure}
64			\centering
65			\includegraphics[width=50mm]{ssd.epsi}
66			\caption{The SSD model with the oxygen and hydrogen atoms drawn in for reference.}
67			\label{fig:ssdModel}
68			\end{figure}
69
70
71			\label{sec:lipidModel}
72
73			\begin{figure}
74			\centering
75			\includegraphics[angle=-90,width=80mm]{lipidModel.epsi}
76			\caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ is the bend angle, $\mu$ is the dipole moment of the head group, and n is the chain length.}
77			\label{fig:lipidModel}
78			\end{figure}
79
80			The mesoscale model used in this research is designed to simplify the
81			number of calculations needed to properly simulate a phospholipid
82			bilayer. The water molecules in the simulation are replaced with the
83			Soft Sticky Dipole (SSD) model developed by Ichiye
84			et. al.\cite{liu96:new_model,liu96:monte_carlo,chandra99:ssd_md} This
85			model reduces water to a single point interaction, while still
86			maintaining the hydrogen-bonding behavior of water. The lipid molecule
87			itself is then modeled as a chain of ``tail'' atoms attached to a
88			large ``head'' atom. The head atom contains a freely rotating dipole
89			to eliminate the charge separation present in an actual phospholipid.
90
91			In the attached images, one can see that the model demonstrates very
92			promising initial results. In the images, the head atoms are colored
93			blue, the tail atoms are colored gray, and the water molecules reduced
94			in size for clarity. The actual simulation is enclosed within the
95			bounding box. In the simulation containing only 25 lipid models, the
96			system has demonstrated a spontaneous division into two leaflets, in
97			route toward a bilayer. In the 50 model system, the lipids show
98			spontaneous aggregation into micelles from a random initial
99			configuration. Future aspects of the research will focus on the
100			effects of tethering the orientation of the dipole, as well as
101			increasing the scale of the systems studied to gain insight into bulk
102			bilayer properties.
103
104			\bibliographystyle{achemso}
105			\bibliography{application}
106			\end{document}