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}

\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:	69
Committed:	Tue Aug 13 21:19:03 2002 UTC (22 years, 1 month ago) by mmeineke
Content type:	application/x-tex
File size:	14266 byte(s)
Log Message:	changed some of the figures, and put some more polish on the intro
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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			%-------------------------------------------------------------------
190			% Begin Document
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192			\begin{document}
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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	53	\textbf{Simulation Parameters:}
450	mmeineke	52
451	mmeineke	53	\begin{itemize}
452
453			\item Starting Configuration:
454	mmeineke	63	\begin{itemize}
455			\item 25 lipid molecules arranged in a 5 x 5 square
456			\item square was surrounded by a sea of 1386 waters
457			\begin{itemize}
458			\item final water to lipid ratio was 55.4:1
459			\end{itemize}
460			\end{itemize}
461	mmeineke	53
462			\item Lipid had only a single saturated chain of 16 carbons
463
464			\item Box Size: 34.5 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$
465
466			\item dt = 2.0 - 3.0 fs
467
468			\item T = 300 K
469
470			\item NVE ensemble
471
472			\item Periodic boundary conditions
473			\end{itemize}
474
475	mmeineke	52	\end{slide}
476
477
478	mmeineke	53	% Slide 13
479	mmeineke	52
480	mmeineke	54	\begin{slide}{5x5: Initial}
481	mmeineke	52
482	mmeineke	54	\begin{center}
483			\begin{figure}
484			\epsfxsize=50mm
485			\epsfbox{5x5-initial.eps}
486			\end{figure}
487			\end{center}
488	mmeineke	52
489	mmeineke	54	The initial configuration
490	mmeineke	52
491			\end{slide}
492
493	mmeineke	54	\begin{slide}{5x5: Final}
494	mmeineke	52
495	mmeineke	54	\begin{center}
496			\begin{figure}
497			\epsfxsize=60mm
498			\epsfbox{5x5-1.7ns.eps}
499			\end{figure}
500			\end{center}
501
502			The final configuration at 1.7 ns.
503
504			\end{slide}
505
506
507	mmeineke	53	% Slide 14
508	mmeineke	52
509			\begin{slide}{5x5: $g(r)$}
510
511	mmeineke	54	\begin{center}
512			\begin{figure}
513			\epsfxsize=60mm
514			\epsfbox{all5x5-HEAD-HEAD-gr.eps}
515			\end{figure}
516			\end{center}
517	mmeineke	52
518
519	mmeineke	54	\end{slide}
520	mmeineke	52
521	mmeineke	54	\begin{slide}{5x5: $g(r)$}
522
523			\begin{center}
524			\begin{figure}
525			\epsfxsize=60mm
526			\epsfbox{all5x5-HEAD-X-gr.eps}
527			\end{figure}
528			\end{center}
529
530
531	mmeineke	52	\end{slide}
532
533
534	mmeineke	53	% Slide 15
535	mmeineke	52
536			\begin{slide}{5x5: $\cos$ correlations}
537
538	mmeineke	54	\begin{center}
539			\begin{figure}
540			\epsfxsize=60mm
541			\epsfbox{all5x5-HEAD-HEAD-cr.eps}
542			\end{figure}
543			\end{center}
544	mmeineke	52
545			\end{slide}
546
547	mmeineke	54	\begin{slide}{5x5: $\cos$ correlations}
548	mmeineke	52
549	mmeineke	54	\begin{center}
550			\begin{figure}
551			\epsfxsize=60mm
552			\epsfbox{all5x5-HEAD-X-cr.eps}
553			\end{figure}
554			\end{center}
555
556			\end{slide}
557
558
559	mmeineke	53	% Slide 16
560	mmeineke	52
561	mmeineke	53	\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water}
562	mmeineke	52
563	mmeineke	53	\textbf{Simulation Parameters:}
564	mmeineke	52
565	mmeineke	53	\begin{itemize}
566
567			\item Starting Configuration:
568	mmeineke	63	\begin{itemize}
569			\item 50 lipid molecules arranged randomly in a rectangular box
570			\item The box was then filled with 1384 waters
571			\begin{itemize}
572			\item final water to lipid ratio was 27:1
573			\end{itemize}
574			\end{itemize}
575	mmeineke	53
576			\item Lipid had only a single saturated chain of 16 carbons
577
578			\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$
579
580			\item dt = 2.0 - 3.0 fs
581
582			\item T = 300 K
583
584			\item NVE ensemble
585
586	mmeineke	63	\item Periodic boundary conditions
587	mmeineke	53
588			\end{itemize}
589
590	mmeineke	52	\end{slide}
591
592
593	mmeineke	53	% Slide 17
594	mmeineke	52
595	mmeineke	54	\begin{slide}{R-50: Initial}
596	mmeineke	52
597	mmeineke	54	\begin{center}
598			\begin{figure}
599			\epsfxsize=100mm
600			\epsfbox{r50-initial.eps}
601			\end{figure}
602			\end{center}
603	mmeineke	52
604	mmeineke	54	The initial configuration
605	mmeineke	52
606			\end{slide}
607
608	mmeineke	54	\begin{slide}{R-50: Final}
609	mmeineke	52
610	mmeineke	54	\begin{center}
611			\begin{figure}
612			\epsfxsize=100mm
613			\epsfbox{r50-521ps.eps}
614			\end{figure}
615			\end{center}
616
617			The fianl configuration at 521 ps
618
619			\end{slide}
620
621
622	mmeineke	53	% Slide 18
623	mmeineke	52
624			\begin{slide}{R-50: $g(r)$}
625
626
627	mmeineke	54	\begin{center}
628			\begin{figure}
629			\epsfxsize=60mm
630			\epsfbox{r50-HEAD-HEAD-gr.eps}
631			\end{figure}
632			\end{center}
633	mmeineke	52
634	mmeineke	54	\end{slide}
635	mmeineke	52
636	mmeineke	54
637			\begin{slide}{R-50: $g(r)$}
638
639
640			\begin{center}
641			\begin{figure}
642			\epsfxsize=60mm
643			\epsfbox{r50-HEAD-X-gr.eps}
644			\end{figure}
645			\end{center}
646
647	mmeineke	52	\end{slide}
648
649
650	mmeineke	53	% Slide 19
651	mmeineke	52
652			\begin{slide}{R-50: $\cos$ correlations}
653
654
655	mmeineke	54	\begin{center}
656			\begin{figure}
657			\epsfxsize=60mm
658			\epsfbox{r50-HEAD-HEAD-cr.eps}
659			\end{figure}
660			\end{center}
661
662	mmeineke	52	\end{slide}
663
664	mmeineke	54	\begin{slide}{R-50: $\cos$ correlations}
665	mmeineke	52
666	mmeineke	54
667			\begin{center}
668			\begin{figure}
669			\epsfxsize=60mm
670			\epsfbox{r50-HEAD-X-cr.eps}
671			\end{figure}
672			\end{center}
673
674			\end{slide}
675
676
677	mmeineke	53	% Slide 20
678	mmeineke	52
679			\begin{slide}{Future Directions}
680
681	mmeineke	53	\begin{itemize}
682	mmeineke	52
683	mmeineke	63	\item
684	mmeineke	53	Simulation of a lipid with 2 chains, or perhaps expand the current
685			unified chain atoms to take up greater steric bulk.
686
687	mmeineke	63	\item
688	mmeineke	53	Incorporate constant pressure and constant temperature into the ensemble.
689
690			\item
691			Parrellize the code.
692
693			\end{itemize}
694	mmeineke	52	\end{slide}
695
696
697	mmeineke	53	% Slide 21
698	mmeineke	52
699			\begin{slide}{Acknowledgements}
700
701	mmeineke	53	\begin{itemize}
702	mmeineke	52
703	mmeineke	53	\item Dr. J. Daniel Gezelter
704			\item Christopher Fennel
705			\item Charles Vardeman
706			\item Teng Lin
707	mmeineke	64	\item Megan Sprauge
708			\item Patrick Conforti
709			\item Dan Combest
710	mmeineke	52
711	mmeineke	53	\end{itemize}
712
713			Funding by:
714			\begin{itemize}
715			\item Dreyfus New Faculty Award
716			\end{itemize}
717
718	mmeineke	52	\end{slide}
719
720
721
722
723
724
725
726
727	mmeineke	49	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
728
729			\end{document}