matt_papers/canidacy_talk/canidacy_slides.tex

% temporary preamble

\documentclass{seminar}
\usepackage{color}
\usepackage{amsmath}
\usepackage{amssymb}
\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 $V_{s\!p}$ are the
lenard-jones, dipole-dipole, and sticky potential interactions.

\end{slide}


% Slide 8

\begin{slide}{Soft Sticky Dipole Model}

The Soft-Sticky model for water is a reduced model.

\begin{itemize}

\item 
The model is represented by a single point mass at the water's center
of mass.

\item 
The point mass contains a fixed dipole of 2.35 D pointing from the
oxegens toward the hydrogens.

\end{itemize}

\color{red}
!!!!!!!!!!!!!SSD image goes here.!!!!!!!!!!!!!!!!
\color{black}


It's potential is as follows:

\begin{equation}
V_{s\!s\!d} = V_{l\!j}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
        + V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
\end{equation}
\end{slide}


% Slide 9
\begin{slide}{Hydrogen Bonding in SSD}

It is important to note that SSD has a potential specifically to
recreate the hydrogen bonfding network of water.

\color{red}
ICE SSD

ICE point Dipole
\color{black}

The importance of the hydrogen bond network is it's signifigant
contribution to the hydrophobic driving force of bilayer formation.
\end{slide}


% Slide 10

\begin{slide}{The Lipid Model}

\color{red}

Look at me, I'm a lipid.!!!!!!!!

YAY!!!!!!!!!!!!!!!!!!!!!
\color{black}

\end{slide}


% Slide 11

\begin{slide}{Initial Runs: 25 Lipids in water}

\color{red}
5x5 parameters
\color{black}

\end{slide}


% Slide 12

\begin{slide}{5x5: Initial and Final}

\color{red}
picture of initial

picture of final
\color{black}

\end{slide}


% Slide 13

\begin{slide}{5x5: $g(r)$}

\color{red}

GofR's baby

\color{black}

\end{slide}


% Slide 14

\begin{slide}{5x5: $\cos$ correlations}

\color{red}
Cosine correlation functions
\color{black}

\end{slide}


% Slide 15

\begin{slide}{Initial Runs: 50 Lipids radomly arrangend in water}

\color{red}
R-50 parameters
\color{black}

\end{slide}


% Slide 16

\begin{slide}{R-50: Initial and Final}

\color{red}
picture of initial

picture of final
\color{black}

\end{slide}


% Slide 17

\begin{slide}{R-50: $g(r)$}

\color{red}

GofR's baby

\color{black}

\end{slide}


% Slide 18

\begin{slide}{R-50: $\cos$ correlations}

\color{red}
Cosine correlation functions
\color{black}

\end{slide}


% Slide 19

\begin{slide}{Future Directions}

\color{red}
THe future is wide open
\color{black}

\end{slide}


% Slide 20

\begin{slide}{Acknowledgements}

\color{red}
Mad Props to all my homies

I'll mourn ya till I join Ya.
\color{black}

\end{slide}


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

\end{document}
Revision:	52
Committed:	Sat Jul 27 18:12:14 2002 UTC (23 years, 3 months ago) by mmeineke
Content type:	application/x-tex
File size:	6290 byte(s)
Log Message:	Skeletons of most every slide
#	User	Rev	Content
1	mmeineke	49	% temporary preamble
2
3			\documentclass{seminar}
4	mmeineke	52	\usepackage{color}
5	mmeineke	49	\usepackage{amsmath}
6	mmeineke	52	\usepackage{amssymb}
7	mmeineke	49	\usepackage{epsf}
8
9			% ----------------------
10			% \| Title \|
11			% ----------------------
12
13			\title{A Coarse Grain Model for Phospholipid MD Simulations}
14
15			\author{Matthew A. Meineke\\
16			Department of Chemistry and Biochemistry\\
17			University of Notre Dame\\
18			Notre Dame, Indiana 46556}
19
20			\date{\today}
21
22			%-------------------------------------------------------------------
23			% Begin Document
24
25			\begin{document}
26			\maketitle
27
28
29
30			% Slide 1
31			\begin{slide} {Talk Outline}
32			\begin{itemize}
33
34			\item Discussion of the research motivation and goals
35
36			\item Methodology
37
38			\item Discussion of current research and preliminary results
39
40			\item Future research
41
42			\end{itemize}
43			\end{slide}
44
45
46			% Slide 2
47
48			\begin{slide}{Motivation}
49			\begin{itemize}
50
51			% make sure to come back and talk about the need for long time and length
52			% scales
53
54			\item Drug diffusion
55
56			\item ripple phase
57
58			\item bilayer formation dynamics
59
60			\end{itemize}
61			\end{slide}
62
63
64			% Slide 3
65
66			\begin{slide}{Research Goals}
67			\begin{itemize}
68
69			\item
70			To develop a coarse-grain simulation model with which to simulate
71			phospholipid bilayers.
72
73			\item To use the model to observe:
74
75			\begin{itemize}
76
77			\item Phospholipid properties with long length scales
78
79			\begin{itemize}
80			\item The ripple phase.
81			\end{itemize}
82
83			\item Long time scale dynamics of biological relevance
84
85			\begin{itemize}
86			\item Trans-membrane diffusion of drug molecules
87			\end{itemize}
88			\end{itemize}
89			\end{itemize}
90			\end{slide}
91
92
93			% Slide 4
94
95			\begin{slide}{Length Scale Simplification}
96			\begin{itemize}
97
98			\item
99			Replace any charged interactions of the system with dipoles.
100
101			\begin{itemize}
102			\item Allows for computational scaling aproximately by $N$ for
103			dipole-dipole interactions.
104			\item In contrast, the Ewald sum scales aproximately by $N \log N$.
105			\end{itemize}
106
107			\item
108			Use unified models for the water and the lipid chain.
109
110			\begin{itemize}
111			\item Drastically reduces the number of atoms to simulate.
112			\item Number of water interactions alone reduced by $\frac{1}{3}$.
113			\end{itemize}
114			\end{itemize}
115			\end{slide}
116
117
118			% Slide 5
119
120			\begin{slide}{Time Scale Simplification}
121			\begin{itemize}
122
123			\item
124			No explicit hydrogens
125
126			\begin{itemize}
127			\item Hydrogen bond vibration is normally one of the fastest time
128			events in a simulation.
129			\end{itemize}
130
131			\item
132			Constrain all bonds to be of fixed length.
133
134			\begin{itemize}
135			\item As with the hydrgoens, bond vibrations are the fastest motion in
136			asimulation
137			\end{itemize}
138
139			\item
140			Allows time steps of up to 3 fs with the current integrator.
141
142			\end{itemize}
143			\end{slide}
144
145
146			% Slide 6
147			\begin{slide}{Molecular Dynamics}
148
149			All of our simulations will be carried out using molcular
150			dymnamics. This involves solving Newton's equations of motion using
151			the classical \emph{Hamiltonian} as follows:
152
153			\begin{equation}
154			H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q})
155			\end{equation}
156
157			Here $T(\vec{p})$ is the kinetic energy of the system which is a
158			function of momentum. In cartesian space, $T(\vec{p})$ can be
159			written as:
160
161			\begin{equation}
162			T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}}
163			\end{equation}
164
165			\end{slide}
166
167
168			% Slide 7
169			\begin{slide}{The Potential}
170
171			The main part of the simulation is then the calculation of forces from
172			the potential energy.
173
174			\begin{equation}
175			\vec{F}(\vec{q}) = - \nabla V(\vec{q})
176			\end{equation}
177
178			The potential itself is made of several parts.
179
180			\begin{equation}
181			V_{tot} =
182			\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} +
183			\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}}
184			\end{equation}
185
186			Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are
187			the bond, bend, and torsion potentials, and the non-bonded
188	mmeineke	51	interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!p}$ are the
189			lenard-jones, dipole-dipole, and sticky potential interactions.
190	mmeineke	49
191			\end{slide}
192
193
194	mmeineke	51	% Slide 8
195	mmeineke	49
196	mmeineke	51	\begin{slide}{Soft Sticky Dipole Model}
197	mmeineke	49
198	mmeineke	52	The Soft-Sticky model for water is a reduced model.
199	mmeineke	49
200	mmeineke	52	\begin{itemize}
201	mmeineke	49
202	mmeineke	52	\item
203			The model is represented by a single point mass at the water's center
204			of mass.
205	mmeineke	49
206	mmeineke	52	\item
207			The point mass contains a fixed dipole of 2.35 D pointing from the
208			oxegens toward the hydrogens.
209	mmeineke	51
210	mmeineke	52	\end{itemize}
211	mmeineke	51
212	mmeineke	52	\color{red}
213			!!!!!!!!!!!!!SSD image goes here.!!!!!!!!!!!!!!!!
214			\color{black}
215	mmeineke	51
216
217	mmeineke	52	It's potential is as follows:
218
219			\begin{equation}
220			V_{s\!s\!d} = V_{l\!j}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
221			+ V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
222			\end{equation}
223			\end{slide}
224
225
226			% Slide 9
227			\begin{slide}{Hydrogen Bonding in SSD}
228
229			It is important to note that SSD has a potential specifically to
230			recreate the hydrogen bonfding network of water.
231
232			\color{red}
233			ICE SSD
234
235			ICE point Dipole
236			\color{black}
237
238			The importance of the hydrogen bond network is it's signifigant
239			contribution to the hydrophobic driving force of bilayer formation.
240			\end{slide}
241
242
243			% Slide 10
244
245			\begin{slide}{The Lipid Model}
246
247			\color{red}
248
249			Look at me, I'm a lipid.!!!!!!!!
250
251			YAY!!!!!!!!!!!!!!!!!!!!!
252			\color{black}
253
254			\end{slide}
255
256
257			% Slide 11
258
259			\begin{slide}{Initial Runs: 25 Lipids in water}
260
261			\color{red}
262			5x5 parameters
263			\color{black}
264
265			\end{slide}
266
267
268			% Slide 12
269
270			\begin{slide}{5x5: Initial and Final}
271
272			\color{red}
273			picture of initial
274
275			picture of final
276			\color{black}
277
278			\end{slide}
279
280
281			% Slide 13
282
283			\begin{slide}{5x5: $g(r)$}
284
285			\color{red}
286
287			GofR's baby
288
289			\color{black}
290
291			\end{slide}
292
293
294			% Slide 14
295
296			\begin{slide}{5x5: $\cos$ correlations}
297
298			\color{red}
299			Cosine correlation functions
300			\color{black}
301
302			\end{slide}
303
304
305			% Slide 15
306
307			\begin{slide}{Initial Runs: 50 Lipids radomly arrangend in water}
308
309			\color{red}
310			R-50 parameters
311			\color{black}
312
313			\end{slide}
314
315
316			% Slide 16
317
318			\begin{slide}{R-50: Initial and Final}
319
320			\color{red}
321			picture of initial
322
323			picture of final
324			\color{black}
325
326			\end{slide}
327
328
329			% Slide 17
330
331			\begin{slide}{R-50: $g(r)$}
332
333			\color{red}
334
335			GofR's baby
336
337			\color{black}
338
339			\end{slide}
340
341
342			% Slide 18
343
344			\begin{slide}{R-50: $\cos$ correlations}
345
346			\color{red}
347			Cosine correlation functions
348			\color{black}
349
350			\end{slide}
351
352
353			% Slide 19
354
355			\begin{slide}{Future Directions}
356
357			\color{red}
358			THe future is wide open
359			\color{black}
360
361			\end{slide}
362
363
364			% Slide 20
365
366			\begin{slide}{Acknowledgements}
367
368			\color{red}
369			Mad Props to all my homies
370
371			I'll mourn ya till I join Ya.
372			\color{black}
373
374			\end{slide}
375
376
377
378
379
380
381
382
383	mmeineke	49	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
384
385			\end{document}