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Revision 549 by mmeineke, Thu Jun 5 19:37:58 2003 UTC vs.
Revision 553 by mmeineke, Tue Jun 10 16:04:33 2003 UTC

# Line 42 | Line 42
42   %%        2         = 2.00     (for A1)
43   %%  
44   %%
45 < %%\def\breite{452mm}     % Gives a 4.1 foot width
46 < \def\breite{390mm}       % Special Format.
45 > \def\breite{390mm}     % Special Format.
46   \def\hoehe{319.2mm}      % Scaled by 2.82 this gives 110cm x 90cm
47   \def\anzspalten{4}
48   %%
# Line 80 | Line 79
79   %%
80   %% Load the necessary packages
81   %%
83 %%\usepackage{berkeley}
82   \usepackage{palatino}
83   \usepackage[latin1]{inputenc}
84   \usepackage{epsf}
# Line 89 | Line 87
87   \usepackage{latexsym}
88   \usepackage{calc}
89   \usepackage{multicol}
90 <
93 < %% My Packages
94 < %%\usepackage{wrapfig}
95 <
90 > \usepackage{wrapfig}
91   %%
92   %% Define the required numbers, lengths and boxes
93   %%
# Line 166 | Line 161
161    \divide\kastenwidth by \anzspalten
162    \begin{minipage}[t]{\kastenwidth}}{\end{minipage}\hfill}
163  
169 %%\renewcommand{\emph}[1]{{\color{red}\textbf{#1}}}
164  
165  
166 +
167   \def\op#1{\hat{#1}}
168   \begin{document}
169 < \bibliographystyle{plain}
169 > \bibliographystyle{unsrt}
170   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
171   %%%               Background                     %%%            
172   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
173 <
179 < %%{\newrgbcolor{gradbegin}{0.87 0.82 0.59}%
180 < {\newrgbcolor{gradbegin}{0.0 0.1875 0.6992}%
173 > {\newrgbcolor{gradbegin}{0.0 0.01875 0.6992}%
174    \newrgbcolor{gradend}{1 1 1}%{1 1 0.5}%
175    \psframe[fillstyle=gradient,gradend=gradend,%
176    gradbegin=gradbegin,gradmidpoint=0.1](\bgwidth,-\bgheight)}
# Line 208 | Line 201
201   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
202   %%%                 first column                 %%%            
203   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
211
212
204      \begin{spalte}
205       \begin{kasten}
206   %
# Line 224 | Line 215 | A mesoscale model for phospholipids has been developed
215   {\color{ndblue}
216  
217   A mesoscale model for phospholipids has been developed for molecular
218 < dynamics simulations of lipid bilayers. The model makes several
218 > dynamics simulations of phospholipid phase transitions. The model makes several
219   simplifications to both the water and the phospholipids to reduce the
220   computational cost of each force evaluation. The water was represented
221   by the soft sticky dipole model of Ichiye \emph{et
# Line 233 | Line 224 | with a single point mass containing a centrally locate
224   in the tail groups to beads representing $\mbox{CH}_{2}$ and
225   $\mbox{CH}_{3}$ unified atoms, and the replacement of the head groups
226   with a single point mass containing a centrally located dipole. The
227 < model was then used to simulate micelle and bilayer formation from a
228 < configuration of randomly placed phospholipids which was simulated for
229 < times in excess of 30 nanoseconds.
227 > model was then used to simulate micelle formation from a configuration
228 > of randomly placed phospholipids which was simulated for times in
229 > excess of 20 nanoseconds.
230  
231   }
232        \end{kasten}
233  
234 +        
235 +  \begin{kasten}
236 +  \section{{\color{red}\underline{Introduction \& Background}}}
237 +  \label{sec:intro}
238  
239 + %%  \subsection{{\color{ndblue}Motivation}}
240 +  \label{sec:motivation}
241  
242 +
243 + Simulations of phospholipid phases are, by necessity, quite
244 + complex. The lipid molecules are large, and contain many
245 + atoms. Additionally, the head groups of the lipids are often
246 + zwitterions, and the large separation between charges results in a
247 + large dipole moment. Adding to the complexity are the number of water
248 + molecules needed to properly solvate the lipid bilayer, typically 25
249 + water molecules for every lipid molecule. These factors make it
250 + difficult to study certain biologically interesting phenomena that
251 + have large inherent length or time scale.
252 +
253 +  \end{kasten}
254 +
255 +  \begin{kasten}
256 +  \subsection{{\color{ndblue}Ripple Phase}}
257 +
258 + \begin{wrapfigure}{o}{60mm}
259 + \centering
260 + \includegraphics[width=40mm]{ripple.epsi}
261 + \end{wrapfigure}
262 +
263 + \mbox{}
264 + \begin{itemize}
265 + \item The ripple (~$P_{\beta'}$~) phase lies in the transition from the gel to fluid phase.
266 + \item Periodicity of 100 - 200 $\mbox{\AA}$\cite{Cevc87}
267 + \item Current simulations have box sizes ranging from 50 - 100 $\mbox{\AA}$ on a side.\cite{saiz02,lindahl00,venable00}
268 + \end{itemize}
269 +
270 +  \label{sec:ripplePhase}
271 +
272 +   \end{kasten}
273 +
274 +
275 +  \begin{kasten}
276 + \subsection{{\color{ndblue}Diffusion \& Formation Dynamics}}
277 + \begin{itemize}
278 +
279 + \item
280 + Drug Diffusion
281 +        \begin{itemize}
282 +        \item
283 +        Some drug molecules may spend appreciable amounts of time in the
284 +        membrane
285 +
286 +        \item
287 +        Long time scale dynamics are need to observe and characterize their
288 +        actions
289 +        \end{itemize}
290 +
291 + \item
292 + Bilayer Formation Dynamics
293 +        \begin{itemize}
294 +        \item
295 +        Current lipid simulations indicate\cite{Marrink01}:
296 +                \begin{itemize}
297 +                \item Aggregation can happen as quickly as 200 ps
298 +
299 +                \item Bilayers can take up to 20 ns to form completely
300 +                \end{itemize}
301 +
302 +        \end{itemize}
303 + \end{itemize}
304 +  \end{kasten}
305 +
306 +  \begin{kasten}
307 + \subsection{{\color{ndblue}Our Simplifications}}
308 + \begin{itemize}
309 + \item Unified atoms with fixed bond lengths replace groups of atoms.
310 + \item Charge distributions are replaced with dipoles.
311 + \begin{itemize}
312 +        \item Relatively short range, $\frac{1}{r^3}$, interactions allow
313 +        the application of neighbor lists.
314 + \end{itemize}
315 + \end{itemize}
316 + \begin{equation}
317 + V^{\text{dp}}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},
318 +        \boldsymbol{\Omega}_{j}) = \frac{1}{4\pi\epsilon_{0}} \biggl[
319 +        \frac{\boldsymbol{\mu}_{i} \cdot \boldsymbol{\mu}_{j}}{r^{3}_{ij}}
320 +        -
321 +        \frac{3(\boldsymbol{\mu}_i \cdot \mathbf{r}_{ij}) %
322 +                (\boldsymbol{\mu}_j \cdot \mathbf{r}_{ij}) }
323 +                {r^{5}_{ij}} \biggr]
324 + \label{eq:dipole}
325 + \end{equation}
326 +  \end{kasten}
327 +
328 +
329 +
330       \end{spalte}
331   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
332   %%%               second column                  %%%            
333   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
334      \begin{spalte}
250    
251     \begin{kasten}
252     \section{{\color{ndblue}Ima second column holder}}
335  
254        hello
336  
337 +  \begin{kasten}
338 + \subsection{{\color{ndblue}Reduction in calculations}}
339 + Unified water and lipid models and decrease the number of interactions
340 + needed between two molecules.
341 +
342 + \begin{center}
343 + \includegraphics[width=50mm,angle=-90]{reduction.epsi}
344 + \end{center}
345       \end{kasten}
346          
347 +
348 +  \begin{kasten}
349 + \section{{\color{red}\underline{Models}}}
350 + \label{sec:model}
351 + \subsection{{\color{ndblue}The Water Model}}
352 + \label{sec:waterModel}
353 +
354 + The waters in the simulation were modeled after the Soft Sticky Dipole
355 + (SSD) model of Ichiye.\cite{liu96:new_model} Where:
356 +
357 + \begin{wrapfigure}[10]{o}{60mm}
358 + \begin{center}
359 + \includegraphics[width=40mm]{ssd.epsi}
360 + \end{center}
361 + \end{wrapfigure}
362 + \mbox{}
363 + \begin{itemize}
364 + \item $\sigma$ is the Lennard-Jones length parameter
365 + \item $\boldsymbol{\mu}_i$ is the dipole vector of molecule $i$
366 + \item $\mathbf{r}_{ij}$ is the vector between molecules $i$ and $j$
367 + \item $\boldsymbol{\Omega}_i$ and $\boldsymbol{\Omega}_j$ are the Euler angles of molecule $i$ or $j$ respectively
368 + \end{itemize}
369 +
370 + It's potential is as follows:
371 + \begin{equation}
372 + V_{s\!s\!d} = V_{L\!J}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
373 +        + V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})
374 + \label{eq:ssdPot}
375 + \end{equation}
376 + Where $V_{d\!p}(r_{i\!j})$ is given in Eq.~\ref{eq:dipole}, and $V_{L\!J}(r_{i\!j})$ is the Lennard-Jones potential.
377 +  \end{kasten}
378 +
379 +  \begin{kasten}
380 +        \subsection{{\color{ndblue}Soft Sticky Potential}}
381 +        \label{sec:SSeq}
382 +
383 +        Hydrogen bonding in the SSD model is described by the
384 +        $V_{\text{sp}}$ term in Eq.~\ref{eq:ssdPot}. Its form is as follows:
385 + \begin{equation}
386 + V_{\text{sp}}(\mathbf{r}_{i\!j},\boldsymbol{\Omega}_{i},
387 +        \boldsymbol{\Omega}_{j}) =
388 +        v^{\circ}[s(r_{ij})w_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},
389 +                \boldsymbol{\Omega}_{j})
390 +        +
391 +        s'(r_{ij})w^{x}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},
392 +                \boldsymbol{\Omega}_{j})]
393 + \label{eq:spPot}
394 + \end{equation}
395 + Where $v^\circ$ scales the strength of the interaction.
396 + $w_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j})$
397 + and
398 + $w^{x}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j})$
399 + are responsible for the tetrahedral potential and a correction to the
400 + tetrahedral potential respectively. They are,
401 + \begin{equation}
402 + w_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j}) =
403 +        \sin\theta_{ij} \sin 2\theta_{ij} \cos 2\phi_{ij}
404 +        + \sin \theta_{ji} \sin 2\theta_{ji} \cos 2\phi_{ji}
405 + \label{eq:spPot2}
406 + \end{equation}
407 + and
408 + \begin{equation}
409 + \begin{split}
410 + w^{x}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j}) =
411 +        &(\cos\theta_{ij}-0.6)^2(\cos\theta_{ij} + 0.8)^2 \\
412 +        &+ (\cos\theta_{ji}-0.6)^2(\cos\theta_{ji} + 0.8)^2 - 2w^{\circ}
413 + \end{split}
414 + \label{eq:spCorrection}
415 + \end{equation}
416 + The angles $\theta_{ij}$ and $\phi_{ij}$ are defined by the spherical
417 + coordinates of the position of molecule $j$ in the reference frame
418 + fixed on molecule $i$ with the z-axis aligned with the dipole moment.
419 + The correction
420 + $w^{x}_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j})$
421 + is needed because
422 + $w_{ij}(\mathbf{r}_{ij},\boldsymbol{\Omega}_{i},\boldsymbol{\Omega}_{j})$
423 + vanishes when $\theta_{ij}$ is $0^\circ$ or $180^\circ$. Finally, the
424 + potential is scaled by the switching function $s(r_{ij})$,
425 + which scales smoothly from 0 to 1.
426 + \begin{equation}
427 + s(r_{ij}) =
428 +        \begin{cases}
429 +        1&      \text{if $r_{ij} < r_{L}$}, \\
430 +        \frac{(r_{U} - r_{ij})^2 (r_{U} + 2r_{ij}
431 +                - 3r_{L})}{(r_{U}-r_{L})^3}&
432 +                \text{if $r_{L} \leq r_{ij} \leq r_{U}$},\\
433 +        0&      \text{if $r_{ij} \geq r_{U}$}.
434 +        \end{cases}
435 + \label{eq:spCutoff}
436 + \end{equation}
437  
438 +  \end{kasten}
439  
440  
441      \end{spalte}
# Line 264 | Line 444 | times in excess of 30 nanoseconds.
444   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
445      \begin{spalte}
446  
447 <     \begin{kasten}
448 <    
449 <     \section{{\color{ndblue}Ima third column holder}}
270 <    
271 <        hello
447 > \begin{kasten}
448 >        \subsection{{\color{ndblue}Hydrogen Bonding in SSD}}
449 >        \label{sec:hbonding}
450  
451 <     \end{kasten}
451 >        The SSD model's $V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j})$
452 >        recreates the hydrogen bonding network of water.
453 >        \begin{center}
454 >        \begin{minipage}{100mm}
455 >          \begin{minipage}[t]{48mm}
456 >                \begin{center}
457 >                \includegraphics[width=48mm]{iced_final.eps}\\
458 >                SSD Relaxed on a diamond lattice
459 >                \end{center}
460 >          \end{minipage}
461 >          \hspace{4mm}%
462 >          \begin{minipage}[t]{48mm}
463 >                \begin{center}
464 >                \includegraphics[width=48mm]{dipoled_final.eps}\\
465 >                Stockmayer Spheres relaxed on a diamond lattice
466 >                \end{center}
467 >          \end{minipage}
468 >        \end{minipage}
469  
470 +        \end{center}
471 +        
472  
473 +  \end{kasten}
474 +
475 +
476 +  \begin{kasten}
477 +
478 +        \subsection{{\color{ndblue}The Lipid Model}}
479 +        \label{sec:lipidModel}
480 +
481 +        \begin{center}
482 +        \includegraphics[width=25mm,angle=-90]{lipidModel.epsi}
483 +        \end{center}
484 +
485 +        \begin{itemize}
486 +        \item PC \& PE head groups are replaced by a Lennard-Jones sphere containing a dipole at its center
487 +        \item Atoms in the tail chains modeled as unified groups of atoms
488 +        \item Tail group interaction parameters based on those of TraPPE\cite{Siepmann1998}
489 +        \end{itemize}
490 +
491 +        The total potential is given by:
492 +        \begin{equation}
493 + V_{\text{lipid}} =
494 +        \sum_{i}V_{i}^{\text{internal}}
495 +        + \sum_i \sum_{j>i} \sum_{\text{$\alpha$ in $i$}}
496 +        \sum_{\text{$\beta$ in $j$}}
497 +        V_{\text{LJ}}(r_{\alpha_{i}\beta_{j}})
498 +        +\sum_i\sum_{j>i}V_{\text{dp}}(r_{1_i,1_j},\Omega_{1_i},\Omega_{1_j})
499 + \end{equation}
500 + Where
501 + \begin{equation}
502 + V_{i}^{\text{internal}} =
503 +        \sum_{\text{bends}}V_{\text{bend}}(\theta_{\alpha\beta\gamma})
504 +        + \sum_{\text{torsions}}V_{\text{tors.}}(\phi_{\alpha\beta\gamma\zeta})
505 +        + \sum_{\alpha} \sum_{\beta>\alpha}V_{\text{LJ}}(r_{\alpha \beta})
506 + \end{equation}
507 + The bend and torsion potentials were of the form:
508 + \begin{equation}
509 + V_{\text{bend}}(\theta_{\alpha\beta\gamma})
510 +        = k_{\theta}\frac{(\theta_{\alpha\beta\gamma} - \theta_0)^2}{2}
511 + \label{eq:bendPot}
512 + \end{equation}
513 + \begin{equation}
514 + V_{\text{tors.}}(\phi_{\alpha\beta\gamma\zeta})
515 +        = c_1 [1+\cos\phi_{\alpha\beta\gamma\zeta}]
516 +        + c_2 [1 - \cos(2\phi_{\alpha\beta\gamma\zeta})]
517 +        + c_3 [1 + \cos(3\phi_{\alpha\beta\gamma\zeta})]
518 + \label{eq:torsPot}
519 + \end{equation}
520 +        
521 +
522 +  \end{kasten}
523 +
524 +  \begin{kasten}
525 +
526 +        \section{{\color{red}\underline{Initial Results}}}
527 +        \label{sec:results}    
528 +        \subsection{{\color{ndblue}Simulation Snapshots:50 lipids in a sea of 1384 waters}}
529 +        \label{sec:r50snapshots}
530 +        
531 +        \begin{center}
532 +        \includegraphics[width=105mm]{r50-montage.eps}
533 +        \end{center}
534 +
535 +  \end{kasten}
536 +
537 +
538      \end{spalte}
539   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
540   %%%               fourth column                  %%%            
541   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
542      \begin{spalte}
543  
544 +  \begin{kasten}
545 +        
546 +        \subsection{{\color{ndblue}Position and Angular Correlations}}
547 +        \label{sec:r50corr}
548  
549 +        \begin{center}
550 +        \begin{minipage}{110mm}
551 +                \begin{minipage}[t]{55mm}
552 +                \begin{center}
553 +                \includegraphics[width=36mm,angle=-90]{r50-HEAD-HEAD.epsi}\\
554 +                The self correlation of the head groups
555 +                \end{center}
556 +                \end{minipage}
557 +                \begin{minipage}[t]{55mm}
558 +                \begin{center}
559 +                \includegraphics[width=36mm,angle=-90]{r50-CH2-CH2.epsi}\\
560 +                The self correlation of the tail beads.
561 +                \end{center}
562 +                \end{minipage}
563 +        \end{minipage}
564 +        \end{center}
565 + \begin{equation}
566 + g(r) = \frac{V}{N_{\text{pairs}}}\langle \sum_{i} \sum_{j > i}
567 +        \delta(|\mathbf{r} - \mathbf{r}_{ij}|) \rangle
568 + \label{eq:gofr}
569 + \end{equation}
570 + \begin{equation}
571 + g_{\gamma}(r) = \langle \sum_i \sum_{j>i}
572 +        (\cos \gamma_{ij}) \delta(| \mathbf{r} - \mathbf{r}_{ij}|) \rangle
573 + \label{eq:gammaofr}
574 + \end{equation}
575  
576 +  \end{kasten}
577  
578  
579 +  \begin{kasten}
580 +
581 +        \subsection{{\color{red}\underline{Discussion}}}
582 +        \label{sec:discussion}
583 +        
584 +        The initial results show much promise for the model. The
585 +        system of 50 lipids was able to form micelles quickly, however
586 +        bilayer formation was not seen on the time scale of the
587 +        current simulation. Current simulations are exploring the
588 +        parameter space of the model when the tail beads are larger than
589 +        the head group. This should help to drive the system toward a
590 +        bilayer rather than a micelle. Work is also being done on the
591 +        simulation engine to allow for the box size of the system to
592 +        be adjustable in all three dimensions to allow for constant
593 +        pressure.
594 +
595 +  \end{kasten}
596 +
597 +
598       \begin{kasten}
599          \begin{center}  
600          {\large{\color{red} \underline{Acknowledgments}}}
# Line 291 | Line 603 | engine. MAM would also like to extend a special thank
603   The authors would like to acknowledge Charles Vardeman, Christopher
604   Fennell, and Teng lin for their contributions to the simulation
605   engine. MAM would also like to extend a special thank you to Charles
606 < Vardeman for his help with the TeX formatting of this
607 < poster. Computaion time was provided on the Bunch-of-Boxes (B.o.B.)
606 > Vardeman for his help with the \TeX formatting of this
607 > poster. Computation time was provided on the Notre Dame Bunch-of-Boxes (B.o.B.)
608   cluster under NSF grant DMR 00 79647. The authors acknowledge support
609   under NSF grant CHE-0134881.
610  

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