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 (22 years, 9 months ago) by mmeineke
Content type:	application/x-tex
File size:	6290 byte(s)
Log Message:	Skeletons of most every slide
#	Content
1	% temporary preamble
2
3	\documentclass{seminar}
4	\usepackage{color}
5	\usepackage{amsmath}
6	\usepackage{amssymb}
7	\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	interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!p}$ are the
189	lenard-jones, dipole-dipole, and sticky potential interactions.
190
191	\end{slide}
192
193
194	% Slide 8
195
196	\begin{slide}{Soft Sticky Dipole Model}
197
198	The Soft-Sticky model for water is a reduced model.
199
200	\begin{itemize}
201
202	\item
203	The model is represented by a single point mass at the water's center
204	of mass.
205
206	\item
207	The point mass contains a fixed dipole of 2.35 D pointing from the
208	oxegens toward the hydrogens.
209
210	\end{itemize}
211
212	\color{red}
213	!!!!!!!!!!!!!SSD image goes here.!!!!!!!!!!!!!!!!
214	\color{black}
215
216
217	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	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
384
385	\end{document}