matt_papers/canidacy_talk/canidacy_slides.tex

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

\title{A Mezzoscale 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


\nobibliography{canidacy_slides}
\bibliographystyle{jurabib}


% Slide 0 Title slide
\begin{slide}
  \begin{center}
    \bfseries
    \fontsize{24pt}{30pt}\selectfont \color{Black}
    A Mezzoscale Model for Phospholipid MD Simulations  \par
    \fontsize{16pt}{20pt}\selectfont \color{Green3}
     Matthew A. Meineke\par
    \fontsize{12pt}{15pt}\selectfont \color{Purple2}
    Department of Chemistry and Biochemisty \par
    University of Notre Dame \par
    Notre Dame, IN 46556 \par
    \fontsize{12pt}{15pt}\selectfont \color{Red} \date{today} \par
  \end{center}
 \end{slide}


% Slide 1
\begin{slide} {\LARGE 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}

\centerline{\LARGE Motivation A: Long Length Scales}

\begin{wrapfigure}{r}{60mm}

    \epsfxsize=45mm
    \epsfbox{ripple.epsi}

\end{wrapfigure}


%\epsfbox{ripple.epsi}
%\begin{floatingfigure}{0.45\linewidth}
%  \incffig{ripple.epsi}
%\end{floatingfigure}


\mbox{}
Ripple phase:
\begin{itemize}

\item
The ripple (~$P_{\beta'}$~) phase lies in the transition from the gel
to fluid phase.

\item
Periodicity of 100 - 200 $\mbox{\AA}$\footcite{Cevc87}

\item
Current simulations have box sizes ranging from 50 - 100 $\mbox{\AA}$
on a side.\footcite{Venable93}\footcite{Heller93}

\end{itemize}
\vspace{10mm}
\end{slide}


\begin{slide}{\LARGE Motivation B: Long Time Scales}

\begin{itemize}

\item
Drug Diffussion
        \begin{itemize}
        \item 
        Some drug molecules may spend appreciable amountsd of time in the
        membrane

        \item
        Long time scale dynamics are need to observe and charecterize their
        actions
        \end{itemize}

\item
Bilayer Formation Dynamics
        \begin{itemize}
        \item
        Current bilayer simulations indicate that lipids can take nearly
        20 ns to form completely.\footcite{Marrink01} 
        \end{itemize}
\end{itemize}
\end{slide}


% Slide 4

\begin{slide}{\LARGE Length Scale Simplification I}


Replace any charged interactions of the system with dipoles.

\begin{itemize}
\item Allows for computational scaling approximately by $N$ for
      dipole-dipole interactions.
        \begin{itemize}
        \item Relatively short range, $\frac{1}{r^3}$, interactions allow
        the application of computational simplification algorithms,
        ie. neighbor lists.
        \end{itemize}

\item In contrast, the Ewald sum, needed for calculating charge - charge 
        interactions, scales approximately by $N \log N$.
\end{itemize}
\end{slide}

\begin{slide}{\LARGE Length Scale Simplification II}

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 - water interactions alone reduced by $\frac{1}{9}$.

\end{itemize}

ADD FIGURE HERE


\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 hydrogens, bond vibrations are the fastest motion in
         a simulation
        \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 molecular
dynamics. 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
oxygens toward the hydrogens.

\end{itemize}

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 8b

\begin{slide}{SSD Diagram}

\begin{center}
\begin{figure}
\epsfxsize=50mm
\epsfbox{ssd.epsi}
\end{figure}
\end{center}

A Diagram of the SSD model.
\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 bonding network of water.


ICE SSD

ICE point Dipole


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


% Slide 10

\begin{slide}{The Lipid Model}

To eliminate the need for charge-charge interactions, our lipid model
replaces the phospholipid head group with a single large head group
atom containing a freely oriented dipole. The tail is a simple alkane chain.

Lipid Properties:
\begin{itemize}
\item $|\vec{\mu}_{\text{HEAD}}| = 20.6\ \text{D}$
\item $m_{\text{HEAD}} = 196\ \text{amu}$
\item Tail atoms are unified CH, $\text{CH}_2$, and $\text{CH}_3$ atoms
        \begin{itemize}
        \item Alkane forcefield parameters taken from TraPPE
        \end{itemize}
\end{itemize}

\end{slide}


% Slide 11

\begin{slide}{Lipid Model}


\end{slide}


% Slide 12

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

\textbf{Simulation Parameters:}

\begin{itemize}

\item Starting Configuration:
        \begin{itemize}
        \item 25 lipid molecules arranged in a 5 x 5 square
        \item square was surrounded by a sea of 1386  waters
                \begin{itemize}
                \item final water to lipid ratio was 55.4:1
                \end{itemize}
        \end{itemize}

\item Lipid had only a single saturated chain of 16 carbons

\item Box Size: 34.5 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$

\item dt = 2.0 - 3.0 fs

\item T = 300 K

\item NVE ensemble

\item Periodic boundary conditions
\end{itemize}

\end{slide}


% Slide 13

\begin{slide}{5x5: Initial}

\begin{center}
\begin{figure}
\epsfxsize=50mm
\epsfbox{5x5-initial.eps}
\end{figure}
\end{center}

The initial configuration

\end{slide}

\begin{slide}{5x5: Final}

\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{5x5-1.7ns.eps}
\end{figure}
\end{center}

The final configuration at 1.7 ns.

\end{slide}


% Slide 14

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

\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{all5x5-HEAD-HEAD-gr.eps}
\end{figure}
\end{center}


\end{slide}

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

\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{all5x5-HEAD-X-gr.eps}
\end{figure}
\end{center}


\end{slide}


% Slide 15

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

\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{all5x5-HEAD-HEAD-cr.eps}
\end{figure}
\end{center}

\end{slide}

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

\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{all5x5-HEAD-X-cr.eps}
\end{figure}
\end{center}

\end{slide}


% Slide 16

\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water}

\textbf{Simulation Parameters:}

\begin{itemize}

\item Starting Configuration:
        \begin{itemize}
        \item 50 lipid molecules arranged randomly in a rectangular box
        \item The box was then filled with 1384 waters
                \begin{itemize}
                \item final water to lipid ratio was 27:1
                \end{itemize}
        \end{itemize}

\item Lipid had only a single saturated chain of 16 carbons

\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$

\item dt = 2.0 - 3.0 fs

\item T = 300 K

\item NVE ensemble

\item Periodic boundary conditions

\end{itemize}

\end{slide}


% Slide 17

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

\begin{center}
\begin{figure}
\epsfxsize=100mm
\epsfbox{r50-initial.eps}
\end{figure}
\end{center}

The initial configuration

\end{slide}

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

\begin{center}
\begin{figure}
\epsfxsize=100mm
\epsfbox{r50-521ps.eps}
\end{figure}
\end{center}

The fianl configuration at 521 ps

\end{slide}


% Slide 18

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


\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{r50-HEAD-HEAD-gr.eps}
\end{figure}
\end{center}

\end{slide}


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


\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{r50-HEAD-X-gr.eps}
\end{figure}
\end{center}

\end{slide}


% Slide 19

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


\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{r50-HEAD-HEAD-cr.eps}
\end{figure}
\end{center}

\end{slide}

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


\begin{center}
\begin{figure}
\epsfxsize=60mm
\epsfbox{r50-HEAD-X-cr.eps}
\end{figure}
\end{center}

\end{slide}


% Slide 20

\begin{slide}{Future Directions}

\begin{itemize}

\item
Simulation of a lipid with 2 chains, or perhaps expand the current
unified chain atoms to take up greater steric bulk.

\item
Incorporate constant pressure and constant temperature into the ensemble.

\item
Parrellize the code.

\end{itemize}
\end{slide}


% Slide 21

\begin{slide}{Acknowledgements}

\begin{itemize}

\item Dr. J. Daniel Gezelter
\item Christopher Fennel
\item Charles Vardeman
\item Teng Lin
\item Megan Sprauge
\item Patrick Conforti
\item Dan Combest

\end{itemize}

Funding by:
\begin{itemize}
\item Dreyfus New Faculty Award
\end{itemize}

\end{slide}


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

\end{document}
Revision:	64
Committed:	Fri Aug 9 21:23:42 2002 UTC (22 years, 1 month ago) by mmeineke
Content type:	application/x-tex
File size:	15698 byte(s)
Log Message:	fixed the citations. continueing to clean up the slides.
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168			\renewcommand{\bibapifont}[1]{} % gets rid of the article title in citation
169	mmeineke	63
170
171	mmeineke	64
172
173
174
175	mmeineke	49	% ----------------------
176			% \| Title \|
177			% ----------------------
178
179	mmeineke	62	\title{A Mezzoscale Model for Phospholipid MD Simulations}
180	mmeineke	49
181			\author{Matthew A. Meineke\\
182	mmeineke	63	Department of Chemistry and Biochemistry\\
183	mmeineke	49	University of Notre Dame\\
184			Notre Dame, Indiana 46556}
185
186			\date{\today}
187
188			%-------------------------------------------------------------------
189			% Begin Document
190
191			\begin{document}
192	mmeineke	62
193	mmeineke	63	%\maketitle
194	mmeineke	49
195
196
197	mmeineke	62
198
199	mmeineke	63	\nobibliography{canidacy_slides}
200			\bibliographystyle{jurabib}
201	mmeineke	62
202	mmeineke	63
203			% Slide 0 Title slide
204			\begin{slide}
205			\begin{center}
206			\bfseries
207			\fontsize{24pt}{30pt}\selectfont \color{Black}
208			A Mezzoscale Model for Phospholipid MD Simulations \par
209			\fontsize{16pt}{20pt}\selectfont \color{Green3}
210			Matthew A. Meineke\par
211			\fontsize{12pt}{15pt}\selectfont \color{Purple2}
212			Department of Chemistry and Biochemisty \par
213			University of Notre Dame \par
214			Notre Dame, IN 46556 \par
215			\fontsize{12pt}{15pt}\selectfont \color{Red} \date{today} \par
216			\end{center}
217			\end{slide}
218
219	mmeineke	64
220	mmeineke	49	% Slide 1
221	mmeineke	64	\begin{slide} {\LARGE Talk Outline}
222	mmeineke	49	\begin{itemize}
223
224			\item Discussion of the research motivation and goals
225
226			\item Methodology
227
228			\item Discussion of current research and preliminary results
229
230			\item Future research
231
232			\end{itemize}
233			\end{slide}
234
235
236			% Slide 2
237
238	mmeineke	63	\begin{slide}
239	mmeineke	62
240	mmeineke	64	\centerline{\LARGE Motivation A: Long Length Scales}
241
242	mmeineke	63	\begin{wrapfigure}{r}{60mm}
243	mmeineke	62
244	mmeineke	63	\epsfxsize=45mm
245			\epsfbox{ripple.epsi}
246	mmeineke	62
247	mmeineke	63	\end{wrapfigure}
248	mmeineke	62
249
250
251	mmeineke	63
252			%\epsfbox{ripple.epsi}
253			%\begin{floatingfigure}{0.45\linewidth}
254			% \incffig{ripple.epsi}
255			%\end{floatingfigure}
256
257
258
259			\mbox{}
260	mmeineke	62	Ripple phase:
261			\begin{itemize}
262
263	mmeineke	63	\item
264	mmeineke	62	The ripple (~$P_{\beta'}$~) phase lies in the transition from the gel
265			to fluid phase.
266
267	mmeineke	63	\item
268	mmeineke	64	Periodicity of 100 - 200 $\mbox{\AA}$\footcite{Cevc87}
269	mmeineke	62
270	mmeineke	64	\item
271			Current simulations have box sizes ranging from 50 - 100 $\mbox{\AA}$
272			on a side.\footcite{Venable93}\footcite{Heller93}
273
274	mmeineke	62	\end{itemize}
275	mmeineke	64	\vspace{10mm}
276	mmeineke	62	\end{slide}
277
278
279	mmeineke	64	\begin{slide}{\LARGE Motivation B: Long Time Scales}
280	mmeineke	62
281	mmeineke	64	\begin{itemize}
282	mmeineke	62
283	mmeineke	64	\item
284			Drug Diffussion
285			\begin{itemize}
286			\item
287			Some drug molecules may spend appreciable amountsd of time in the
288			membrane
289	mmeineke	62
290	mmeineke	64	\item
291			Long time scale dynamics are need to observe and charecterize their
292			actions
293			\end{itemize}
294	mmeineke	62
295	mmeineke	64	\item
296			Bilayer Formation Dynamics
297			\begin{itemize}
298			\item
299			Current bilayer simulations indicate that lipids can take nearly
300			20 ns to form completely.\footcite{Marrink01}
301			\end{itemize}
302			\end{itemize}
303			\end{slide}
304	mmeineke	54
305
306	mmeineke	64	% Slide 4
307	mmeineke	49
308	mmeineke	64	\begin{slide}{\LARGE Length Scale Simplification I}
309	mmeineke	49
310
311	mmeineke	64	Replace any charged interactions of the system with dipoles.
312	mmeineke	49
313	mmeineke	64	\begin{itemize}
314			\item Allows for computational scaling approximately by $N$ for
315			dipole-dipole interactions.
316			\begin{itemize}
317			\item Relatively short range, $\frac{1}{r^3}$, interactions allow
318			the application of computational simplification algorithms,
319			ie. neighbor lists.
320			\end{itemize}
321
322			\item In contrast, the Ewald sum, needed for calculating charge - charge
323			interactions, scales approximately by $N \log N$.
324	mmeineke	49	\end{itemize}
325			\end{slide}
326
327	mmeineke	64	\begin{slide}{\LARGE Length Scale Simplification II}
328	mmeineke	49
329	mmeineke	64	Use unified models for the water and the lipid chain.
330	mmeineke	49
331			\begin{itemize}
332	mmeineke	64	\item
333			Drastically reduces the number of atoms to simulate.
334	mmeineke	49
335	mmeineke	64	\item
336			Number of water - water interactions alone reduced by $\frac{1}{9}$.
337	mmeineke	49
338	mmeineke	64	\end{itemize}
339	mmeineke	49
340	mmeineke	64	ADD FIGURE HERE
341	mmeineke	49
342	mmeineke	64
343	mmeineke	49	\end{slide}
344
345
346			% Slide 5
347
348			\begin{slide}{Time Scale Simplification}
349			\begin{itemize}
350
351			\item
352			No explicit hydrogens
353
354	mmeineke	63	\begin{itemize}
355			\item Hydrogen bond vibration is normally one of the fastest time
356			events in a simulation.
357			\end{itemize}
358	mmeineke	49
359			\item
360			Constrain all bonds to be of fixed length.
361
362	mmeineke	63	\begin{itemize}
363			\item As with the hydrogens, bond vibrations are the fastest motion in
364			a simulation
365			\end{itemize}
366	mmeineke	49
367			\item
368			Allows time steps of up to 3 fs with the current integrator.
369
370			\end{itemize}
371			\end{slide}
372
373
374			% Slide 6
375			\begin{slide}{Molecular Dynamics}
376
377	mmeineke	53	All of our simulations will be carried out using molecular
378			dynamics. This involves solving Newton's equations of motion using
379	mmeineke	49	the classical \emph{Hamiltonian} as follows:
380
381			\begin{equation}
382			H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q})
383			\end{equation}
384
385			Here $T(\vec{p})$ is the kinetic energy of the system which is a
386	mmeineke	53	function of momentum. In Cartesian space, $T(\vec{p})$ can be
387	mmeineke	49	written as:
388
389			\begin{equation}
390			T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}}
391			\end{equation}
392
393			\end{slide}
394
395
396			% Slide 7
397			\begin{slide}{The Potential}
398
399			The main part of the simulation is then the calculation of forces from
400			the potential energy.
401
402			\begin{equation}
403			\vec{F}(\vec{q}) = - \nabla V(\vec{q})
404			\end{equation}
405
406			The potential itself is made of several parts.
407
408			\begin{equation}
409	mmeineke	63	V_{tot} =
410	mmeineke	49	\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} +
411			\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}}
412			\end{equation}
413
414			Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are
415			the bond, bend, and torsion potentials, and the non-bonded
416	mmeineke	51	interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!p}$ are the
417			lenard-jones, dipole-dipole, and sticky potential interactions.
418	mmeineke	49
419			\end{slide}
420
421
422	mmeineke	51	% Slide 8
423	mmeineke	49
424	mmeineke	51	\begin{slide}{Soft Sticky Dipole Model}
425	mmeineke	49
426	mmeineke	52	The Soft-Sticky model for water is a reduced model.
427	mmeineke	49
428	mmeineke	52	\begin{itemize}
429	mmeineke	49
430	mmeineke	63	\item
431	mmeineke	52	The model is represented by a single point mass at the water's center
432			of mass.
433	mmeineke	49
434	mmeineke	63	\item
435	mmeineke	52	The point mass contains a fixed dipole of 2.35 D pointing from the
436	mmeineke	53	oxygens toward the hydrogens.
437	mmeineke	51
438	mmeineke	52	\end{itemize}
439	mmeineke	51
440	mmeineke	52	It's potential is as follows:
441
442			\begin{equation}
443			V_{s\!s\!d} = V_{l\!j}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
444	mmeineke	63	+ V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
445	mmeineke	52	\end{equation}
446			\end{slide}
447
448	mmeineke	54	% Slide 8b
449	mmeineke	52
450	mmeineke	54	\begin{slide}{SSD Diagram}
451
452			\begin{center}
453			\begin{figure}
454			\epsfxsize=50mm
455			\epsfbox{ssd.epsi}
456			\end{figure}
457			\end{center}
458
459			A Diagram of the SSD model.
460			\end{slide}
461
462	mmeineke	52	% Slide 9
463			\begin{slide}{Hydrogen Bonding in SSD}
464
465			It is important to note that SSD has a potential specifically to
466	mmeineke	53	recreate the hydrogen bonding network of water.
467	mmeineke	52
468	mmeineke	54
469	mmeineke	52	ICE SSD
470
471			ICE point Dipole
472
473	mmeineke	54
474	mmeineke	53	The importance of the hydrogen bond network is it's significant
475	mmeineke	52	contribution to the hydrophobic driving force of bilayer formation.
476			\end{slide}
477
478
479			% Slide 10
480
481			\begin{slide}{The Lipid Model}
482
483	mmeineke	53	To eliminate the need for charge-charge interactions, our lipid model
484			replaces the phospholipid head group with a single large head group
485			atom containing a freely oriented dipole. The tail is a simple alkane chain.
486
487			Lipid Properties:
488			\begin{itemize}
489			\item $\|\vec{\mu}_{\text{HEAD}}\| = 20.6\ \text{D}$
490			\item $m_{\text{HEAD}} = 196\ \text{amu}$
491			\item Tail atoms are unified CH, $\text{CH}_2$, and $\text{CH}_3$ atoms
492	mmeineke	63	\begin{itemize}
493			\item Alkane forcefield parameters taken from TraPPE
494			\end{itemize}
495	mmeineke	53	\end{itemize}
496
497			\end{slide}
498
499
500			% Slide 11
501
502			\begin{slide}{Lipid Model}
503
504	mmeineke	52
505	mmeineke	63
506	mmeineke	52	\end{slide}
507
508
509	mmeineke	53	% Slide 12
510	mmeineke	52
511			\begin{slide}{Initial Runs: 25 Lipids in water}
512
513	mmeineke	53	\textbf{Simulation Parameters:}
514	mmeineke	52
515	mmeineke	53	\begin{itemize}
516
517			\item Starting Configuration:
518	mmeineke	63	\begin{itemize}
519			\item 25 lipid molecules arranged in a 5 x 5 square
520			\item square was surrounded by a sea of 1386 waters
521			\begin{itemize}
522			\item final water to lipid ratio was 55.4:1
523			\end{itemize}
524			\end{itemize}
525	mmeineke	53
526			\item Lipid had only a single saturated chain of 16 carbons
527
528			\item Box Size: 34.5 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$
529
530			\item dt = 2.0 - 3.0 fs
531
532			\item T = 300 K
533
534			\item NVE ensemble
535
536			\item Periodic boundary conditions
537			\end{itemize}
538
539	mmeineke	52	\end{slide}
540
541
542	mmeineke	53	% Slide 13
543	mmeineke	52
544	mmeineke	54	\begin{slide}{5x5: Initial}
545	mmeineke	52
546	mmeineke	54	\begin{center}
547			\begin{figure}
548			\epsfxsize=50mm
549			\epsfbox{5x5-initial.eps}
550			\end{figure}
551			\end{center}
552	mmeineke	52
553	mmeineke	54	The initial configuration
554	mmeineke	52
555			\end{slide}
556
557	mmeineke	54	\begin{slide}{5x5: Final}
558	mmeineke	52
559	mmeineke	54	\begin{center}
560			\begin{figure}
561			\epsfxsize=60mm
562			\epsfbox{5x5-1.7ns.eps}
563			\end{figure}
564			\end{center}
565
566			The final configuration at 1.7 ns.
567
568			\end{slide}
569
570
571	mmeineke	53	% Slide 14
572	mmeineke	52
573			\begin{slide}{5x5: $g(r)$}
574
575	mmeineke	54	\begin{center}
576			\begin{figure}
577			\epsfxsize=60mm
578			\epsfbox{all5x5-HEAD-HEAD-gr.eps}
579			\end{figure}
580			\end{center}
581	mmeineke	52
582
583	mmeineke	54	\end{slide}
584	mmeineke	52
585	mmeineke	54	\begin{slide}{5x5: $g(r)$}
586
587			\begin{center}
588			\begin{figure}
589			\epsfxsize=60mm
590			\epsfbox{all5x5-HEAD-X-gr.eps}
591			\end{figure}
592			\end{center}
593
594
595	mmeineke	52	\end{slide}
596
597
598	mmeineke	53	% Slide 15
599	mmeineke	52
600			\begin{slide}{5x5: $\cos$ correlations}
601
602	mmeineke	54	\begin{center}
603			\begin{figure}
604			\epsfxsize=60mm
605			\epsfbox{all5x5-HEAD-HEAD-cr.eps}
606			\end{figure}
607			\end{center}
608	mmeineke	52
609			\end{slide}
610
611	mmeineke	54	\begin{slide}{5x5: $\cos$ correlations}
612	mmeineke	52
613	mmeineke	54	\begin{center}
614			\begin{figure}
615			\epsfxsize=60mm
616			\epsfbox{all5x5-HEAD-X-cr.eps}
617			\end{figure}
618			\end{center}
619
620			\end{slide}
621
622
623	mmeineke	53	% Slide 16
624	mmeineke	52
625	mmeineke	53	\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water}
626	mmeineke	52
627	mmeineke	53	\textbf{Simulation Parameters:}
628	mmeineke	52
629	mmeineke	53	\begin{itemize}
630
631			\item Starting Configuration:
632	mmeineke	63	\begin{itemize}
633			\item 50 lipid molecules arranged randomly in a rectangular box
634			\item The box was then filled with 1384 waters
635			\begin{itemize}
636			\item final water to lipid ratio was 27:1
637			\end{itemize}
638			\end{itemize}
639	mmeineke	53
640			\item Lipid had only a single saturated chain of 16 carbons
641
642			\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$
643
644			\item dt = 2.0 - 3.0 fs
645
646			\item T = 300 K
647
648			\item NVE ensemble
649
650	mmeineke	63	\item Periodic boundary conditions
651	mmeineke	53
652			\end{itemize}
653
654	mmeineke	52	\end{slide}
655
656
657	mmeineke	53	% Slide 17
658	mmeineke	52
659	mmeineke	54	\begin{slide}{R-50: Initial}
660	mmeineke	52
661	mmeineke	54	\begin{center}
662			\begin{figure}
663			\epsfxsize=100mm
664			\epsfbox{r50-initial.eps}
665			\end{figure}
666			\end{center}
667	mmeineke	52
668	mmeineke	54	The initial configuration
669	mmeineke	52
670			\end{slide}
671
672	mmeineke	54	\begin{slide}{R-50: Final}
673	mmeineke	52
674	mmeineke	54	\begin{center}
675			\begin{figure}
676			\epsfxsize=100mm
677			\epsfbox{r50-521ps.eps}
678			\end{figure}
679			\end{center}
680
681			The fianl configuration at 521 ps
682
683			\end{slide}
684
685
686	mmeineke	53	% Slide 18
687	mmeineke	52
688			\begin{slide}{R-50: $g(r)$}
689
690
691	mmeineke	54	\begin{center}
692			\begin{figure}
693			\epsfxsize=60mm
694			\epsfbox{r50-HEAD-HEAD-gr.eps}
695			\end{figure}
696			\end{center}
697	mmeineke	52
698	mmeineke	54	\end{slide}
699	mmeineke	52
700	mmeineke	54
701			\begin{slide}{R-50: $g(r)$}
702
703
704			\begin{center}
705			\begin{figure}
706			\epsfxsize=60mm
707			\epsfbox{r50-HEAD-X-gr.eps}
708			\end{figure}
709			\end{center}
710
711	mmeineke	52	\end{slide}
712
713
714	mmeineke	53	% Slide 19
715	mmeineke	52
716			\begin{slide}{R-50: $\cos$ correlations}
717
718
719	mmeineke	54	\begin{center}
720			\begin{figure}
721			\epsfxsize=60mm
722			\epsfbox{r50-HEAD-HEAD-cr.eps}
723			\end{figure}
724			\end{center}
725
726	mmeineke	52	\end{slide}
727
728	mmeineke	54	\begin{slide}{R-50: $\cos$ correlations}
729	mmeineke	52
730	mmeineke	54
731			\begin{center}
732			\begin{figure}
733			\epsfxsize=60mm
734			\epsfbox{r50-HEAD-X-cr.eps}
735			\end{figure}
736			\end{center}
737
738			\end{slide}
739
740
741	mmeineke	53	% Slide 20
742	mmeineke	52
743			\begin{slide}{Future Directions}
744
745	mmeineke	53	\begin{itemize}
746	mmeineke	52
747	mmeineke	63	\item
748	mmeineke	53	Simulation of a lipid with 2 chains, or perhaps expand the current
749			unified chain atoms to take up greater steric bulk.
750
751	mmeineke	63	\item
752	mmeineke	53	Incorporate constant pressure and constant temperature into the ensemble.
753
754			\item
755			Parrellize the code.
756
757			\end{itemize}
758	mmeineke	52	\end{slide}
759
760
761	mmeineke	53	% Slide 21
762	mmeineke	52
763			\begin{slide}{Acknowledgements}
764
765	mmeineke	53	\begin{itemize}
766	mmeineke	52
767	mmeineke	53	\item Dr. J. Daniel Gezelter
768			\item Christopher Fennel
769			\item Charles Vardeman
770			\item Teng Lin
771	mmeineke	64	\item Megan Sprauge
772			\item Patrick Conforti
773			\item Dan Combest
774	mmeineke	52
775	mmeineke	53	\end{itemize}
776
777			Funding by:
778			\begin{itemize}
779			\item Dreyfus New Faculty Award
780			\end{itemize}
781
782	mmeineke	52	\end{slide}
783
784
785
786
787
788
789
790
791	mmeineke	49	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
792
793			\end{document}