matt_papers/canidacy_talk/canidacy_slides.tex

% temporary preamble

\documentclass{seminar}

\usepackage{amsmath}
\usepackage{epsf}

% ----------------------
% |      Title         |
% ----------------------

\title{A Coarse Grain Model for Phospholipid MD Simulations}

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

\date{\today}

%-------------------------------------------------------------------
%                       Begin Document

\begin{document}
\maketitle


% Slide 1
\begin{slide} {Talk Outline}
\begin{itemize}

\item Discussion of the research motivation and goals

\item Methodology

\item Discussion of current research and preliminary results

\item Future research

\end{itemize}
\end{slide}


% Slide 2

\begin{slide}{Motivation}
\begin{itemize}

% make sure to come back and talk about the need for long time and length 
% scales

\item Drug diffusion

\item ripple phase

\item bilayer formation dynamics

\end{itemize}
\end{slide}


% Slide 3

\begin{slide}{Research Goals}
\begin{itemize}

\item 
To develop a coarse-grain simulation model with which to simulate
phospholipid bilayers.

\item To use the model to observe:

        \begin{itemize}
        
        \item Phospholipid properties with long length scales

                \begin{itemize}
                \item The ripple phase.
                \end{itemize}

        \item Long time scale dynamics of biological relevance
                
                \begin{itemize}
                \item Trans-membrane diffusion of drug molecules
                \end{itemize}
        \end{itemize}
\end{itemize}
\end{slide}


% Slide 4

\begin{slide}{Length Scale Simplification}
\begin{itemize}

\item 
Replace any charged interactions of the system with dipoles.

        \begin{itemize}
        \item Allows for computational scaling aproximately by $N$ for 
              dipole-dipole interactions.
        \item In contrast, the Ewald sum scales aproximately by $N \log N$.
        \end{itemize}

\item
Use unified models for the water and the lipid chain.

        \begin{itemize}
        \item Drastically reduces the number of atoms to simulate.
        \item Number of water interactions alone reduced by $\frac{1}{3}$.
        \end{itemize}
\end{itemize}
\end{slide}


% Slide 5

\begin{slide}{Time Scale Simplification}
\begin{itemize}

\item
No explicit hydrogens

        \begin{itemize}
        \item Hydrogen bond vibration is normally one of the fastest time 
                events in a simulation.
        \end{itemize}

\item
Constrain all bonds to be of fixed length.

        \begin{itemize}
        \item As with the hydrgoens, bond vibrations are the fastest motion in
         asimulation
        \end{itemize}

\item
Allows time steps of up to 3 fs with the current integrator.

\end{itemize}
\end{slide}


% Slide 6
\begin{slide}{Molecular Dynamics}

All of our simulations will be carried out using molcular
dymnamics. This involves solving Newton's equations of motion using
the classical \emph{Hamiltonian} as follows:

\begin{equation}
H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q})
\end{equation}

Here $T(\vec{p})$ is the kinetic energy of the system which is a
function of momentum. In cartesian space, $T(\vec{p})$ can be
written as:

\begin{equation}
T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}}
\end{equation}

\end{slide}


% Slide 7
\begin{slide}{The Potential}

The main part of the simulation is then the calculation of forces from
the potential energy.

\begin{equation}
\vec{F}(\vec{q}) = - \nabla V(\vec{q})
\end{equation}

The potential itself is made of several parts.

\begin{equation}
V_{tot} = 
\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} +
\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}}
\end{equation}

Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are
the bond, bend, and torsion potentials, and the non-bonded
interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!s\!d}$ are the
lenard-jones, dipole-dipole, and soft sticky dipole interactions.

\end{slide}


%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\end{document}
Revision:	50
Committed:	Fri Jul 26 20:51:52 2002 UTC (21 years, 11 months ago) by mmeineke
Content type:	application/x-tex
File size:	3937 byte(s)
Log Message:	This commit was generated by cvs2svn to compensate for changes in r49, which included commits to RCS files with non-trunk default branches.
#	User	Rev	Content
1	mmeineke	49	% temporary preamble
2
3			\documentclass{seminar}
4
5			\usepackage{amsmath}
6			\usepackage{epsf}
7
8			% ----------------------
9			% \| Title \|
10			% ----------------------
11
12			\title{A Coarse Grain Model for Phospholipid MD Simulations}
13
14			\author{Matthew A. Meineke\\
15			Department of Chemistry and Biochemistry\\
16			University of Notre Dame\\
17			Notre Dame, Indiana 46556}
18
19			\date{\today}
20
21			%-------------------------------------------------------------------
22			% Begin Document
23
24			\begin{document}
25			\maketitle
26
27
28
29			% Slide 1
30			\begin{slide} {Talk Outline}
31			\begin{itemize}
32
33			\item Discussion of the research motivation and goals
34
35			\item Methodology
36
37			\item Discussion of current research and preliminary results
38
39			\item Future research
40
41			\end{itemize}
42			\end{slide}
43
44
45			% Slide 2
46
47			\begin{slide}{Motivation}
48			\begin{itemize}
49
50			% make sure to come back and talk about the need for long time and length
51			% scales
52
53			\item Drug diffusion
54
55			\item ripple phase
56
57			\item bilayer formation dynamics
58
59			\end{itemize}
60			\end{slide}
61
62
63			% Slide 3
64
65			\begin{slide}{Research Goals}
66			\begin{itemize}
67
68			\item
69			To develop a coarse-grain simulation model with which to simulate
70			phospholipid bilayers.
71
72			\item To use the model to observe:
73
74			\begin{itemize}
75
76			\item Phospholipid properties with long length scales
77
78			\begin{itemize}
79			\item The ripple phase.
80			\end{itemize}
81
82			\item Long time scale dynamics of biological relevance
83
84			\begin{itemize}
85			\item Trans-membrane diffusion of drug molecules
86			\end{itemize}
87			\end{itemize}
88			\end{itemize}
89			\end{slide}
90
91
92			% Slide 4
93
94			\begin{slide}{Length Scale Simplification}
95			\begin{itemize}
96
97			\item
98			Replace any charged interactions of the system with dipoles.
99
100			\begin{itemize}
101			\item Allows for computational scaling aproximately by $N$ for
102			dipole-dipole interactions.
103			\item In contrast, the Ewald sum scales aproximately by $N \log N$.
104			\end{itemize}
105
106			\item
107			Use unified models for the water and the lipid chain.
108
109			\begin{itemize}
110			\item Drastically reduces the number of atoms to simulate.
111			\item Number of water interactions alone reduced by $\frac{1}{3}$.
112			\end{itemize}
113			\end{itemize}
114			\end{slide}
115
116
117			% Slide 5
118
119			\begin{slide}{Time Scale Simplification}
120			\begin{itemize}
121
122			\item
123			No explicit hydrogens
124
125			\begin{itemize}
126			\item Hydrogen bond vibration is normally one of the fastest time
127			events in a simulation.
128			\end{itemize}
129
130			\item
131			Constrain all bonds to be of fixed length.
132
133			\begin{itemize}
134			\item As with the hydrgoens, bond vibrations are the fastest motion in
135			asimulation
136			\end{itemize}
137
138			\item
139			Allows time steps of up to 3 fs with the current integrator.
140
141			\end{itemize}
142			\end{slide}
143
144
145			% Slide 6
146			\begin{slide}{Molecular Dynamics}
147
148			All of our simulations will be carried out using molcular
149			dymnamics. This involves solving Newton's equations of motion using
150			the classical \emph{Hamiltonian} as follows:
151
152			\begin{equation}
153			H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q})
154			\end{equation}
155
156			Here $T(\vec{p})$ is the kinetic energy of the system which is a
157			function of momentum. In cartesian space, $T(\vec{p})$ can be
158			written as:
159
160			\begin{equation}
161			T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}}
162			\end{equation}
163
164			\end{slide}
165
166
167			% Slide 7
168			\begin{slide}{The Potential}
169
170			The main part of the simulation is then the calculation of forces from
171			the potential energy.
172
173			\begin{equation}
174			\vec{F}(\vec{q}) = - \nabla V(\vec{q})
175			\end{equation}
176
177			The potential itself is made of several parts.
178
179			\begin{equation}
180			V_{tot} =
181			\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} +
182			\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}}
183			\end{equation}
184
185			Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are
186			the bond, bend, and torsion potentials, and the non-bonded
187			interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!s\!d}$ are the
188			lenard-jones, dipole-dipole, and soft sticky dipole interactions.
189
190			\end{slide}
191
192
193
194
195
196
197
198			%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
199
200			\end{document}