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 and interactions to simulate.

\end{itemize}


\begin{figure}
%\epsfxsize=30mm
%\leavevmode
\begin{center}
\includegraphics[width=50mm,angle=-90]{reduction.epsi}
\end{center}
\end{figure}


\end{slide}


% Slide 5

\begin{slide}{Time Scale Simplification}
\begin{itemize}
\item
Constrain all bonds to be of fixed length.

        \begin{itemize}
        \item bond vibrations are the fastest motion in
         a simulation
        \end{itemize}

\item
Allows time steps of up to 3 fs with the current integrator. In
contrast, a time step of 1 fs is usually required for resolving bond
vibration.

\end{itemize}
\end{slide}

% Slide 8

\begin{slide}{Soft Sticky Dipole Model\footcite{Liu96}}

\begin{figure}
\begin{center}
\includegraphics[width=40mm]{ssd.epsi}
\end{center}
\end{figure}


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}

The SSD model's $V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})$ recreates
the hydrogen bonding network of water.


\begin{figure}
\begin{center}
\mbox{%
        \subfigure[SSD relaxed on a diamond lattice]{%
                \mbox{\includegraphics[angle=-90,width=55mm]{ssd_ice.epsi}}}%
        \hspace{4mm}
        \subfigure[Stockmayer spheres relaxed on a diamond lattice]{%
                \mbox{\includegraphics[angle=-90,width=55mm]{dipole_ice.epsi}}}%
}

\end{center}
\end{figure}

\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}

\begin{wrapfigure}{r}{60mm}
        
        \includegraphics[width=55mm]{5x5-initial.eps}

\end{wrapfigure}

\textbf{Simulation Parameters:}

\begin{itemize}

\item $N_{\mbox{lipids}} = 25$

\item $N_{\mbox{H}_{2}\mbox{O}} = 1386$

\item Water to lipid ratio of 55.4:1

\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 T = 300 K

\item NVE ensemble

\item Periodic boundary conditions
\end{itemize}

\end{slide}

\begin{slide}{5x5: Final}


\begin{figure}
\begin{center}
\includegraphics[width=80mm]{5x5-1.7ns.eps}
\end{center}
\end{figure}

\begin{center}
The final configuration at 1.7 ns.
\end{center}

\end{slide}


% Slide 14

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

\begin{figure}
\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-HEAD-gr.eps}
\end{figure}


\end{slide}

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


\begin{figure}
\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-X-gr.eps}
\end{figure}

\end{slide}


% Slide 15

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

\begin{figure}
\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-HEAD-cr.eps}
\end{figure}

\end{slide}

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

\begin{figure}
\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-X-cr.eps}
\end{figure}

\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{figure}
\begin{center}
\includegraphics[width=100mm]{r50-initial.eps}
\end{center}
\end{figure}


The initial configuration

\end{slide}

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

\begin{center}
\begin{figure}
\includegraphics[width=100mm]{r50-521ps.eps}
\end{figure}
\end{center}

The fianl configuration at 521 ps

\end{slide}


% Slide 18

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


\begin{figure}
\includegraphics[width=60mm,angle=-90]{r50-HEAD-HEAD-gr.eps}
\end{figure}

\end{slide}


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


\begin{figure}
\includegraphics[width=60mm,angle=-90]{r50-HEAD-X-gr.eps}
\end{figure}

\end{slide}


% Slide 19

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


\begin{figure}
\includegraphics[width=60mm,angle=-90]{r50-HEAD-HEAD-cr.eps}
\end{figure}

\end{slide}

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

\begin{figure}
\includegraphics[width=60mm,angle=-90]{r50-HEAD-X-cr.eps}
\end{figure}

\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:	76
Committed:	Wed Aug 14 22:02:03 2002 UTC (22 years, 1 month ago) by mmeineke
Content type:	application/x-tex
File size:	13878 byte(s)
Log Message:	added figures fixed more of the graphs
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176	mmeineke	49	% ----------------------
177			% \| Title \|
178			% ----------------------
179
180	mmeineke	62	\title{A Mezzoscale Model for Phospholipid MD Simulations}
181	mmeineke	49
182			\author{Matthew A. Meineke\\
183	mmeineke	63	Department of Chemistry and Biochemistry\\
184	mmeineke	49	University of Notre Dame\\
185			Notre Dame, Indiana 46556}
186
187			\date{\today}
188
189			%-------------------------------------------------------------------
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192			\begin{document}
193	mmeineke	62
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204			% Slide 0 Title slide
205			\begin{slide}
206			\begin{center}
207			\bfseries
208			\fontsize{24pt}{30pt}\selectfont \color{Black}
209			A Mezzoscale Model for Phospholipid MD Simulations \par
210			\fontsize{16pt}{20pt}\selectfont \color{Green3}
211			Matthew A. Meineke\par
212			\fontsize{12pt}{15pt}\selectfont \color{Purple2}
213			Department of Chemistry and Biochemisty \par
214			University of Notre Dame \par
215			Notre Dame, IN 46556 \par
216			\fontsize{12pt}{15pt}\selectfont \color{Red} \date{today} \par
217			\end{center}
218			\end{slide}
219
220	mmeineke	64
221	mmeineke	49	% Slide 1
222	mmeineke	64	\begin{slide} {\LARGE Talk Outline}
223	mmeineke	49	\begin{itemize}
224
225			\item Discussion of the research motivation and goals
226
227			\item Methodology
228
229			\item Discussion of current research and preliminary results
230
231			\item Future research
232
233			\end{itemize}
234			\end{slide}
235
236
237			% Slide 2
238
239	mmeineke	63	\begin{slide}
240	mmeineke	62
241	mmeineke	64	\centerline{\LARGE Motivation A: Long Length Scales}
242
243	mmeineke	63	\begin{wrapfigure}{r}{60mm}
244	mmeineke	62
245	mmeineke	63	\epsfxsize=45mm
246			\epsfbox{ripple.epsi}
247	mmeineke	62
248	mmeineke	63	\end{wrapfigure}
249	mmeineke	62
250
251
252	mmeineke	63
253			%\epsfbox{ripple.epsi}
254			%\begin{floatingfigure}{0.45\linewidth}
255			% \incffig{ripple.epsi}
256			%\end{floatingfigure}
257
258
259
260			\mbox{}
261	mmeineke	62	Ripple phase:
262			\begin{itemize}
263
264	mmeineke	63	\item
265	mmeineke	62	The ripple (~$P_{\beta'}$~) phase lies in the transition from the gel
266			to fluid phase.
267
268	mmeineke	63	\item
269	mmeineke	64	Periodicity of 100 - 200 $\mbox{\AA}$\footcite{Cevc87}
270	mmeineke	62
271	mmeineke	64	\item
272			Current simulations have box sizes ranging from 50 - 100 $\mbox{\AA}$
273			on a side.\footcite{Venable93}\footcite{Heller93}
274
275	mmeineke	62	\end{itemize}
276	mmeineke	64	\vspace{10mm}
277	mmeineke	62	\end{slide}
278
279
280	mmeineke	64	\begin{slide}{\LARGE Motivation B: Long Time Scales}
281	mmeineke	62
282	mmeineke	64	\begin{itemize}
283	mmeineke	62
284	mmeineke	64	\item
285			Drug Diffussion
286			\begin{itemize}
287			\item
288			Some drug molecules may spend appreciable amountsd of time in the
289			membrane
290	mmeineke	62
291	mmeineke	64	\item
292			Long time scale dynamics are need to observe and charecterize their
293			actions
294			\end{itemize}
295	mmeineke	62
296	mmeineke	64	\item
297			Bilayer Formation Dynamics
298			\begin{itemize}
299			\item
300			Current bilayer simulations indicate that lipids can take nearly
301			20 ns to form completely.\footcite{Marrink01}
302			\end{itemize}
303			\end{itemize}
304			\end{slide}
305	mmeineke	54
306
307	mmeineke	64	% Slide 4
308	mmeineke	49
309	mmeineke	64	\begin{slide}{\LARGE Length Scale Simplification I}
310	mmeineke	49
311
312	mmeineke	64	Replace any charged interactions of the system with dipoles.
313	mmeineke	49
314	mmeineke	64	\begin{itemize}
315			\item Allows for computational scaling approximately by $N$ for
316			dipole-dipole interactions.
317			\begin{itemize}
318			\item Relatively short range, $\frac{1}{r^3}$, interactions allow
319			the application of computational simplification algorithms,
320			ie. neighbor lists.
321			\end{itemize}
322
323			\item In contrast, the Ewald sum, needed for calculating charge - charge
324			interactions, scales approximately by $N \log N$.
325	mmeineke	49	\end{itemize}
326			\end{slide}
327
328	mmeineke	64	\begin{slide}{\LARGE Length Scale Simplification II}
329	mmeineke	49
330	mmeineke	64	Use unified models for the water and the lipid chain.
331	mmeineke	49
332			\begin{itemize}
333	mmeineke	64	\item
334	mmeineke	69	Drastically reduces the number of atoms and interactions to simulate.
335	mmeineke	49
336	mmeineke	64	\end{itemize}
337	mmeineke	49
338
339	mmeineke	69
340	mmeineke	65	\begin{figure}
341	mmeineke	69	%\epsfxsize=30mm
342			%\leavevmode
343			\begin{center}
344			\includegraphics[width=50mm,angle=-90]{reduction.epsi}
345			\end{center}
346	mmeineke	65	\end{figure}
347	mmeineke	64
348	mmeineke	69
349	mmeineke	49	\end{slide}
350
351
352			% Slide 5
353
354			\begin{slide}{Time Scale Simplification}
355			\begin{itemize}
356			\item
357			Constrain all bonds to be of fixed length.
358
359	mmeineke	63	\begin{itemize}
360	mmeineke	69	\item bond vibrations are the fastest motion in
361	mmeineke	63	a simulation
362			\end{itemize}
363	mmeineke	49
364			\item
365	mmeineke	69	Allows time steps of up to 3 fs with the current integrator. In
366			contrast, a time step of 1 fs is usually required for resolving bond
367			vibration.
368	mmeineke	49
369			\end{itemize}
370			\end{slide}
371
372	mmeineke	51	% Slide 8
373	mmeineke	49
374	mmeineke	69	\begin{slide}{Soft Sticky Dipole Model\footcite{Liu96}}
375	mmeineke	49
376	mmeineke	69	\begin{figure}
377			\begin{center}
378			\includegraphics[width=40mm]{ssd.epsi}
379			\end{center}
380			\end{figure}
381	mmeineke	49
382
383	mmeineke	52	It's potential is as follows:
384
385			\begin{equation}
386	mmeineke	69	V_{s\!s\!d} = V_{L\!J}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
387	mmeineke	63	+ V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
388	mmeineke	52	\end{equation}
389			\end{slide}
390
391
392			% Slide 9
393			\begin{slide}{Hydrogen Bonding in SSD}
394
395	mmeineke	69	The SSD model's $V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})$ recreates
396			the hydrogen bonding network of water.
397	mmeineke	52
398	mmeineke	54
399	mmeineke	69	\begin{figure}
400			\begin{center}
401			\mbox{%
402			\subfigure[SSD relaxed on a diamond lattice]{%
403			\mbox{\includegraphics[angle=-90,width=55mm]{ssd_ice.epsi}}}%
404			\hspace{4mm}
405			\subfigure[Stockmayer spheres relaxed on a diamond lattice]{%
406			\mbox{\includegraphics[angle=-90,width=55mm]{dipole_ice.epsi}}}%
407			}
408	mmeineke	52
409	mmeineke	69	\end{center}
410			\end{figure}
411	mmeineke	52
412			\end{slide}
413
414
415			% Slide 10
416
417			\begin{slide}{The Lipid Model}
418
419	mmeineke	53	To eliminate the need for charge-charge interactions, our lipid model
420			replaces the phospholipid head group with a single large head group
421			atom containing a freely oriented dipole. The tail is a simple alkane chain.
422
423			Lipid Properties:
424			\begin{itemize}
425			\item $\|\vec{\mu}_{\text{HEAD}}\| = 20.6\ \text{D}$
426			\item $m_{\text{HEAD}} = 196\ \text{amu}$
427			\item Tail atoms are unified CH, $\text{CH}_2$, and $\text{CH}_3$ atoms
428	mmeineke	63	\begin{itemize}
429			\item Alkane forcefield parameters taken from TraPPE
430			\end{itemize}
431	mmeineke	53	\end{itemize}
432
433			\end{slide}
434
435
436			% Slide 11
437
438			\begin{slide}{Lipid Model}
439
440	mmeineke	52
441	mmeineke	63
442	mmeineke	52	\end{slide}
443
444
445	mmeineke	53	% Slide 12
446	mmeineke	52
447			\begin{slide}{Initial Runs: 25 Lipids in water}
448
449	mmeineke	76	\begin{wrapfigure}{r}{60mm}
450
451			\includegraphics[width=55mm]{5x5-initial.eps}
452
453			\end{wrapfigure}
454
455	mmeineke	53	\textbf{Simulation Parameters:}
456	mmeineke	52
457	mmeineke	53	\begin{itemize}
458
459	mmeineke	76	\item $N_{\mbox{lipids}} = 25$
460	mmeineke	53
461	mmeineke	76	\item $N_{\mbox{H}_{2}\mbox{O}} = 1386$
462
463			\item Water to lipid ratio of 55.4:1
464
465	mmeineke	53	\item Lipid had only a single saturated chain of 16 carbons
466
467	mmeineke	76	\item Box Size: 34.5~$\mbox{\AA}$~x~39.4~$\mbox{\AA}$~x~39.4~$\mbox{\AA}$
468	mmeineke	53
469			\item T = 300 K
470
471			\item NVE ensemble
472
473			\item Periodic boundary conditions
474			\end{itemize}
475
476	mmeineke	52	\end{slide}
477
478	mmeineke	76	\begin{slide}{5x5: Final}
479	mmeineke	52
480
481	mmeineke	76	\begin{figure}
482	mmeineke	54	\begin{center}
483	mmeineke	76	\includegraphics[width=80mm]{5x5-1.7ns.eps}
484			\end{center}
485	mmeineke	54	\end{figure}
486	mmeineke	52
487	mmeineke	54	\begin{center}
488	mmeineke	76	The final configuration at 1.7 ns.
489	mmeineke	54	\end{center}
490
491			\end{slide}
492
493
494	mmeineke	53	% Slide 14
495	mmeineke	52
496			\begin{slide}{5x5: $g(r)$}
497
498	mmeineke	54	\begin{figure}
499	mmeineke	76	\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-HEAD-gr.eps}
500	mmeineke	54	\end{figure}
501	mmeineke	52
502
503	mmeineke	76
504	mmeineke	54	\end{slide}
505	mmeineke	52
506	mmeineke	54	\begin{slide}{5x5: $g(r)$}
507
508	mmeineke	76
509	mmeineke	54	\begin{figure}
510	mmeineke	76	\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-X-gr.eps}
511	mmeineke	54	\end{figure}
512
513	mmeineke	52	\end{slide}
514
515
516	mmeineke	53	% Slide 15
517	mmeineke	52
518			\begin{slide}{5x5: $\cos$ correlations}
519
520	mmeineke	54	\begin{figure}
521	mmeineke	76	\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-HEAD-cr.eps}
522	mmeineke	54	\end{figure}
523	mmeineke	52
524			\end{slide}
525
526	mmeineke	54	\begin{slide}{5x5: $\cos$ correlations}
527	mmeineke	52
528	mmeineke	54	\begin{figure}
529	mmeineke	76	\includegraphics[width=60mm,angle=-90]{all5x5-HEAD-X-cr.eps}
530	mmeineke	54	\end{figure}
531
532			\end{slide}
533
534
535	mmeineke	53	% Slide 16
536	mmeineke	52
537	mmeineke	53	\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water}
538	mmeineke	52
539	mmeineke	53	\textbf{Simulation Parameters:}
540	mmeineke	52
541	mmeineke	53	\begin{itemize}
542
543			\item Starting Configuration:
544	mmeineke	63	\begin{itemize}
545			\item 50 lipid molecules arranged randomly in a rectangular box
546			\item The box was then filled with 1384 waters
547			\begin{itemize}
548			\item final water to lipid ratio was 27:1
549			\end{itemize}
550			\end{itemize}
551	mmeineke	53
552			\item Lipid had only a single saturated chain of 16 carbons
553
554			\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$
555
556			\item dt = 2.0 - 3.0 fs
557
558			\item T = 300 K
559
560			\item NVE ensemble
561
562	mmeineke	63	\item Periodic boundary conditions
563	mmeineke	53
564			\end{itemize}
565
566	mmeineke	52	\end{slide}
567
568
569	mmeineke	53	% Slide 17
570	mmeineke	52
571	mmeineke	54	\begin{slide}{R-50: Initial}
572	mmeineke	52
573	mmeineke	76
574			\begin{figure}
575	mmeineke	54	\begin{center}
576	mmeineke	76	\includegraphics[width=100mm]{r50-initial.eps}
577			\end{center}
578	mmeineke	54	\end{figure}
579	mmeineke	52
580	mmeineke	76
581	mmeineke	54	The initial configuration
582	mmeineke	52
583			\end{slide}
584
585	mmeineke	54	\begin{slide}{R-50: Final}
586	mmeineke	52
587	mmeineke	54	\begin{center}
588			\begin{figure}
589	mmeineke	76	\includegraphics[width=100mm]{r50-521ps.eps}
590	mmeineke	54	\end{figure}
591			\end{center}
592
593			The fianl configuration at 521 ps
594
595			\end{slide}
596
597
598	mmeineke	53	% Slide 18
599	mmeineke	52
600			\begin{slide}{R-50: $g(r)$}
601
602
603	mmeineke	54	\begin{figure}
604	mmeineke	76	\includegraphics[width=60mm,angle=-90]{r50-HEAD-HEAD-gr.eps}
605	mmeineke	54	\end{figure}
606	mmeineke	52
607	mmeineke	54	\end{slide}
608	mmeineke	52
609	mmeineke	54
610			\begin{slide}{R-50: $g(r)$}
611
612
613			\begin{figure}
614	mmeineke	76	\includegraphics[width=60mm,angle=-90]{r50-HEAD-X-gr.eps}
615	mmeineke	54	\end{figure}
616
617	mmeineke	52	\end{slide}
618
619
620	mmeineke	53	% Slide 19
621	mmeineke	52
622			\begin{slide}{R-50: $\cos$ correlations}
623
624
625	mmeineke	54	\begin{figure}
626	mmeineke	76	\includegraphics[width=60mm,angle=-90]{r50-HEAD-HEAD-cr.eps}
627	mmeineke	54	\end{figure}
628
629	mmeineke	52	\end{slide}
630
631	mmeineke	54	\begin{slide}{R-50: $\cos$ correlations}
632	mmeineke	52
633	mmeineke	54	\begin{figure}
634	mmeineke	76	\includegraphics[width=60mm,angle=-90]{r50-HEAD-X-cr.eps}
635	mmeineke	54	\end{figure}
636
637			\end{slide}
638
639
640	mmeineke	53	% Slide 20
641	mmeineke	52
642			\begin{slide}{Future Directions}
643
644	mmeineke	53	\begin{itemize}
645	mmeineke	52
646	mmeineke	63	\item
647	mmeineke	53	Simulation of a lipid with 2 chains, or perhaps expand the current
648			unified chain atoms to take up greater steric bulk.
649
650	mmeineke	63	\item
651	mmeineke	53	Incorporate constant pressure and constant temperature into the ensemble.
652
653			\item
654			Parrellize the code.
655
656			\end{itemize}
657	mmeineke	52	\end{slide}
658
659
660	mmeineke	53	% Slide 21
661	mmeineke	52
662			\begin{slide}{Acknowledgements}
663
664	mmeineke	53	\begin{itemize}
665	mmeineke	52
666	mmeineke	53	\item Dr. J. Daniel Gezelter
667			\item Christopher Fennel
668			\item Charles Vardeman
669			\item Teng Lin
670	mmeineke	64	\item Megan Sprauge
671			\item Patrick Conforti
672			\item Dan Combest
673	mmeineke	52
674	mmeineke	53	\end{itemize}
675
676			Funding by:
677			\begin{itemize}
678			\item Dreyfus New Faculty Award
679			\end{itemize}
680
681	mmeineke	52	\end{slide}
682
683
684
685
686
687
688
689
690	mmeineke	49	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
691
692			\end{document}