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.

\end{itemize}

\begin{center}

\begin{figure}
\epsfxsize=30mm
\epsfbox[angle=-90]{reduction.epsi}
\end{figure}
\end{center}

\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:	65
Committed:	Mon Aug 12 22:12:45 2002 UTC (22 years, 1 month ago) by mmeineke
Content type:	application/x-tex
File size:	15713 byte(s)
Log Message:	made a new figure. trying to add it to the slide
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167			\renewcommand{\bibjtfont}{\textit} % change journal title to italics
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	\end{itemize}
336	mmeineke	49
337	mmeineke	65	\begin{center}
338	mmeineke	49
339	mmeineke	65	\begin{figure}
340			\epsfxsize=30mm
341			\epsfbox[angle=-90]{reduction.epsi}
342			\end{figure}
343			\end{center}
344	mmeineke	64
345	mmeineke	49	\end{slide}
346
347
348			% Slide 5
349
350			\begin{slide}{Time Scale Simplification}
351			\begin{itemize}
352
353			\item
354			No explicit hydrogens
355
356	mmeineke	63	\begin{itemize}
357			\item Hydrogen bond vibration is normally one of the fastest time
358			events in a simulation.
359			\end{itemize}
360	mmeineke	49
361			\item
362			Constrain all bonds to be of fixed length.
363
364	mmeineke	63	\begin{itemize}
365			\item As with the hydrogens, bond vibrations are the fastest motion in
366			a simulation
367			\end{itemize}
368	mmeineke	49
369			\item
370			Allows time steps of up to 3 fs with the current integrator.
371
372			\end{itemize}
373			\end{slide}
374
375
376			% Slide 6
377			\begin{slide}{Molecular Dynamics}
378
379	mmeineke	53	All of our simulations will be carried out using molecular
380			dynamics. This involves solving Newton's equations of motion using
381	mmeineke	49	the classical \emph{Hamiltonian} as follows:
382
383			\begin{equation}
384			H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q})
385			\end{equation}
386
387			Here $T(\vec{p})$ is the kinetic energy of the system which is a
388	mmeineke	53	function of momentum. In Cartesian space, $T(\vec{p})$ can be
389	mmeineke	49	written as:
390
391			\begin{equation}
392			T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}}
393			\end{equation}
394
395			\end{slide}
396
397
398			% Slide 7
399			\begin{slide}{The Potential}
400
401			The main part of the simulation is then the calculation of forces from
402			the potential energy.
403
404			\begin{equation}
405			\vec{F}(\vec{q}) = - \nabla V(\vec{q})
406			\end{equation}
407
408			The potential itself is made of several parts.
409
410			\begin{equation}
411	mmeineke	63	V_{tot} =
412	mmeineke	49	\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} +
413			\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}}
414			\end{equation}
415
416			Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are
417			the bond, bend, and torsion potentials, and the non-bonded
418	mmeineke	51	interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!p}$ are the
419			lenard-jones, dipole-dipole, and sticky potential interactions.
420	mmeineke	49
421			\end{slide}
422
423
424	mmeineke	51	% Slide 8
425	mmeineke	49
426	mmeineke	51	\begin{slide}{Soft Sticky Dipole Model}
427	mmeineke	49
428	mmeineke	52	The Soft-Sticky model for water is a reduced model.
429	mmeineke	49
430	mmeineke	52	\begin{itemize}
431	mmeineke	49
432	mmeineke	63	\item
433	mmeineke	52	The model is represented by a single point mass at the water's center
434			of mass.
435	mmeineke	49
436	mmeineke	63	\item
437	mmeineke	52	The point mass contains a fixed dipole of 2.35 D pointing from the
438	mmeineke	53	oxygens toward the hydrogens.
439	mmeineke	51
440	mmeineke	52	\end{itemize}
441	mmeineke	51
442	mmeineke	52	It's potential is as follows:
443
444			\begin{equation}
445			V_{s\!s\!d} = V_{l\!j}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
446	mmeineke	63	+ V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
447	mmeineke	52	\end{equation}
448			\end{slide}
449
450	mmeineke	54	% Slide 8b
451	mmeineke	52
452	mmeineke	54	\begin{slide}{SSD Diagram}
453
454			\begin{center}
455			\begin{figure}
456			\epsfxsize=50mm
457			\epsfbox{ssd.epsi}
458			\end{figure}
459			\end{center}
460
461			A Diagram of the SSD model.
462			\end{slide}
463
464	mmeineke	52	% Slide 9
465			\begin{slide}{Hydrogen Bonding in SSD}
466
467			It is important to note that SSD has a potential specifically to
468	mmeineke	53	recreate the hydrogen bonding network of water.
469	mmeineke	52
470	mmeineke	54
471	mmeineke	52	ICE SSD
472
473			ICE point Dipole
474
475	mmeineke	54
476	mmeineke	53	The importance of the hydrogen bond network is it's significant
477	mmeineke	52	contribution to the hydrophobic driving force of bilayer formation.
478			\end{slide}
479
480
481			% Slide 10
482
483			\begin{slide}{The Lipid Model}
484
485	mmeineke	53	To eliminate the need for charge-charge interactions, our lipid model
486			replaces the phospholipid head group with a single large head group
487			atom containing a freely oriented dipole. The tail is a simple alkane chain.
488
489			Lipid Properties:
490			\begin{itemize}
491			\item $\|\vec{\mu}_{\text{HEAD}}\| = 20.6\ \text{D}$
492			\item $m_{\text{HEAD}} = 196\ \text{amu}$
493			\item Tail atoms are unified CH, $\text{CH}_2$, and $\text{CH}_3$ atoms
494	mmeineke	63	\begin{itemize}
495			\item Alkane forcefield parameters taken from TraPPE
496			\end{itemize}
497	mmeineke	53	\end{itemize}
498
499			\end{slide}
500
501
502			% Slide 11
503
504			\begin{slide}{Lipid Model}
505
506	mmeineke	52
507	mmeineke	63
508	mmeineke	52	\end{slide}
509
510
511	mmeineke	53	% Slide 12
512	mmeineke	52
513			\begin{slide}{Initial Runs: 25 Lipids in water}
514
515	mmeineke	53	\textbf{Simulation Parameters:}
516	mmeineke	52
517	mmeineke	53	\begin{itemize}
518
519			\item Starting Configuration:
520	mmeineke	63	\begin{itemize}
521			\item 25 lipid molecules arranged in a 5 x 5 square
522			\item square was surrounded by a sea of 1386 waters
523			\begin{itemize}
524			\item final water to lipid ratio was 55.4:1
525			\end{itemize}
526			\end{itemize}
527	mmeineke	53
528			\item Lipid had only a single saturated chain of 16 carbons
529
530			\item Box Size: 34.5 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$
531
532			\item dt = 2.0 - 3.0 fs
533
534			\item T = 300 K
535
536			\item NVE ensemble
537
538			\item Periodic boundary conditions
539			\end{itemize}
540
541	mmeineke	52	\end{slide}
542
543
544	mmeineke	53	% Slide 13
545	mmeineke	52
546	mmeineke	54	\begin{slide}{5x5: Initial}
547	mmeineke	52
548	mmeineke	54	\begin{center}
549			\begin{figure}
550			\epsfxsize=50mm
551			\epsfbox{5x5-initial.eps}
552			\end{figure}
553			\end{center}
554	mmeineke	52
555	mmeineke	54	The initial configuration
556	mmeineke	52
557			\end{slide}
558
559	mmeineke	54	\begin{slide}{5x5: Final}
560	mmeineke	52
561	mmeineke	54	\begin{center}
562			\begin{figure}
563			\epsfxsize=60mm
564			\epsfbox{5x5-1.7ns.eps}
565			\end{figure}
566			\end{center}
567
568			The final configuration at 1.7 ns.
569
570			\end{slide}
571
572
573	mmeineke	53	% Slide 14
574	mmeineke	52
575			\begin{slide}{5x5: $g(r)$}
576
577	mmeineke	54	\begin{center}
578			\begin{figure}
579			\epsfxsize=60mm
580			\epsfbox{all5x5-HEAD-HEAD-gr.eps}
581			\end{figure}
582			\end{center}
583	mmeineke	52
584
585	mmeineke	54	\end{slide}
586	mmeineke	52
587	mmeineke	54	\begin{slide}{5x5: $g(r)$}
588
589			\begin{center}
590			\begin{figure}
591			\epsfxsize=60mm
592			\epsfbox{all5x5-HEAD-X-gr.eps}
593			\end{figure}
594			\end{center}
595
596
597	mmeineke	52	\end{slide}
598
599
600	mmeineke	53	% Slide 15
601	mmeineke	52
602			\begin{slide}{5x5: $\cos$ correlations}
603
604	mmeineke	54	\begin{center}
605			\begin{figure}
606			\epsfxsize=60mm
607			\epsfbox{all5x5-HEAD-HEAD-cr.eps}
608			\end{figure}
609			\end{center}
610	mmeineke	52
611			\end{slide}
612
613	mmeineke	54	\begin{slide}{5x5: $\cos$ correlations}
614	mmeineke	52
615	mmeineke	54	\begin{center}
616			\begin{figure}
617			\epsfxsize=60mm
618			\epsfbox{all5x5-HEAD-X-cr.eps}
619			\end{figure}
620			\end{center}
621
622			\end{slide}
623
624
625	mmeineke	53	% Slide 16
626	mmeineke	52
627	mmeineke	53	\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water}
628	mmeineke	52
629	mmeineke	53	\textbf{Simulation Parameters:}
630	mmeineke	52
631	mmeineke	53	\begin{itemize}
632
633			\item Starting Configuration:
634	mmeineke	63	\begin{itemize}
635			\item 50 lipid molecules arranged randomly in a rectangular box
636			\item The box was then filled with 1384 waters
637			\begin{itemize}
638			\item final water to lipid ratio was 27:1
639			\end{itemize}
640			\end{itemize}
641	mmeineke	53
642			\item Lipid had only a single saturated chain of 16 carbons
643
644			\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$
645
646			\item dt = 2.0 - 3.0 fs
647
648			\item T = 300 K
649
650			\item NVE ensemble
651
652	mmeineke	63	\item Periodic boundary conditions
653	mmeineke	53
654			\end{itemize}
655
656	mmeineke	52	\end{slide}
657
658
659	mmeineke	53	% Slide 17
660	mmeineke	52
661	mmeineke	54	\begin{slide}{R-50: Initial}
662	mmeineke	52
663	mmeineke	54	\begin{center}
664			\begin{figure}
665			\epsfxsize=100mm
666			\epsfbox{r50-initial.eps}
667			\end{figure}
668			\end{center}
669	mmeineke	52
670	mmeineke	54	The initial configuration
671	mmeineke	52
672			\end{slide}
673
674	mmeineke	54	\begin{slide}{R-50: Final}
675	mmeineke	52
676	mmeineke	54	\begin{center}
677			\begin{figure}
678			\epsfxsize=100mm
679			\epsfbox{r50-521ps.eps}
680			\end{figure}
681			\end{center}
682
683			The fianl configuration at 521 ps
684
685			\end{slide}
686
687
688	mmeineke	53	% Slide 18
689	mmeineke	52
690			\begin{slide}{R-50: $g(r)$}
691
692
693	mmeineke	54	\begin{center}
694			\begin{figure}
695			\epsfxsize=60mm
696			\epsfbox{r50-HEAD-HEAD-gr.eps}
697			\end{figure}
698			\end{center}
699	mmeineke	52
700	mmeineke	54	\end{slide}
701	mmeineke	52
702	mmeineke	54
703			\begin{slide}{R-50: $g(r)$}
704
705
706			\begin{center}
707			\begin{figure}
708			\epsfxsize=60mm
709			\epsfbox{r50-HEAD-X-gr.eps}
710			\end{figure}
711			\end{center}
712
713	mmeineke	52	\end{slide}
714
715
716	mmeineke	53	% Slide 19
717	mmeineke	52
718			\begin{slide}{R-50: $\cos$ correlations}
719
720
721	mmeineke	54	\begin{center}
722			\begin{figure}
723			\epsfxsize=60mm
724			\epsfbox{r50-HEAD-HEAD-cr.eps}
725			\end{figure}
726			\end{center}
727
728	mmeineke	52	\end{slide}
729
730	mmeineke	54	\begin{slide}{R-50: $\cos$ correlations}
731	mmeineke	52
732	mmeineke	54
733			\begin{center}
734			\begin{figure}
735			\epsfxsize=60mm
736			\epsfbox{r50-HEAD-X-cr.eps}
737			\end{figure}
738			\end{center}
739
740			\end{slide}
741
742
743	mmeineke	53	% Slide 20
744	mmeineke	52
745			\begin{slide}{Future Directions}
746
747	mmeineke	53	\begin{itemize}
748	mmeineke	52
749	mmeineke	63	\item
750	mmeineke	53	Simulation of a lipid with 2 chains, or perhaps expand the current
751			unified chain atoms to take up greater steric bulk.
752
753	mmeineke	63	\item
754	mmeineke	53	Incorporate constant pressure and constant temperature into the ensemble.
755
756			\item
757			Parrellize the code.
758
759			\end{itemize}
760	mmeineke	52	\end{slide}
761
762
763	mmeineke	53	% Slide 21
764	mmeineke	52
765			\begin{slide}{Acknowledgements}
766
767	mmeineke	53	\begin{itemize}
768	mmeineke	52
769	mmeineke	53	\item Dr. J. Daniel Gezelter
770			\item Christopher Fennel
771			\item Charles Vardeman
772			\item Teng Lin
773	mmeineke	64	\item Megan Sprauge
774			\item Patrick Conforti
775			\item Dan Combest
776	mmeineke	52
777	mmeineke	53	\end{itemize}
778
779			Funding by:
780			\begin{itemize}
781			\item Dreyfus New Faculty Award
782			\end{itemize}
783
784	mmeineke	52	\end{slide}
785
786
787
788
789
790
791
792
793	mmeineke	49	%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
794
795			\end{document}