| 1 |
% temporary preamble |
| 2 |
|
| 3 |
%\documentclass[ps,frames,final,nototal,slideColor,colorBG]{prosper} |
| 4 |
|
| 5 |
\documentclass[portrait]{seminar} |
| 6 |
\usepackage[usenames,dvips]{pstcol} |
| 7 |
\usepackage{semcolor} |
| 8 |
\usepackage[dvips]{color} |
| 9 |
%\usepackage[dvips]{graphicx} |
| 10 |
\usepackage{amsmath} |
| 11 |
\usepackage{amssymb} |
| 12 |
\usepackage{wrapfig} |
| 13 |
\usepackage{epsf} |
| 14 |
|
| 15 |
\usepackage[citefull=first, chicago, pages=always]{jurabib} |
| 16 |
|
| 17 |
|
| 18 |
\jurabibsetup{bibformat={tabular,ibidem,numbered}} |
| 19 |
\centerslidesfalse |
| 20 |
|
| 21 |
% ----------------------------- |
| 22 |
% | preamble + macros and crap | |
| 23 |
% ----------------------------- |
| 24 |
|
| 25 |
|
| 26 |
% Basic Color Defs used within this file |
| 27 |
\definecolor{lightblue}{rgb}{0.3296, 0.6648, 0.8644} % Sky Blue |
| 28 |
\definecolor{shadowcolor}{rgb}{0.0000, 0.0000, 0.6179} % Midnight Blue |
| 29 |
\definecolor{bulletcolor}{rgb}{ 0.8441, 0.1582, 0.0000} % Orange-Red |
| 30 |
\definecolor{bordercolor}{rgb}{0,0,.2380} % Midnight Blue |
| 31 |
|
| 32 |
%\psset{shadowcolor=shadowcolor} % Set all shadowdrops to same color |
| 33 |
|
| 34 |
% Change itemize environment to use funky color bullets |
| 35 |
\renewcommand\labelitemi{\textcolor{bulletcolor}{\textbullet}} |
| 36 |
\renewcommand\labelitemii{\textcolor{bulletcolor}{\textbullet}} |
| 37 |
\renewcommand\labelitemiii{\textcolor{bulletcolor}{\textbullet}} |
| 38 |
|
| 39 |
|
| 40 |
|
| 41 |
|
| 42 |
|
| 43 |
% Input corrections to 'seminar' |
| 44 |
|
| 45 |
\input{seminar.bug} |
| 46 |
\input{seminar.bg2} |
| 47 |
|
| 48 |
% Slides parameters: general setup |
| 49 |
|
| 50 |
\centerslidesfalse % Text not centered |
| 51 |
\slideframe{none} % No frame borders |
| 52 |
\raggedslides[2em] % Semi-ragged-right text |
| 53 |
\slidestyle{empty} % No labels |
| 54 |
\rotateheaderstrue % Header and slide orientation synchronized |
| 55 |
|
| 56 |
% Slides dimensions and header placement |
| 57 |
|
| 58 |
\addtolength{\slidewidth}{10mm} |
| 59 |
\addtolength{\slideheight}{10mm} |
| 60 |
\renewcommand{\slideleftmargin}{10mm} |
| 61 |
\renewcommand{\sliderightmargin}{10mm} |
| 62 |
\renewcommand{\slidetopmargin}{10mm} |
| 63 |
\renewcommand{\slidebottommargin}{15mm} |
| 64 |
|
| 65 |
% Landscape printing sequence (for dvips) |
| 66 |
|
| 67 |
\renewcommand{\printlandscape}{\special{landscape}} |
| 68 |
|
| 69 |
|
| 70 |
% My-itemize environment (3 levels): essentially not indented from |
| 71 |
% the left margin. New second- and third-level item markers. |
| 72 |
|
| 73 |
\newenvironment{myt} |
| 74 |
{\begin{list}{$\bullet$}% |
| 75 |
{\setlength{\labelwidth}{9pt}% |
| 76 |
\setlength{\labelsep}{4pt}% |
| 77 |
\setlength{\leftmargin}{13pt}% |
| 78 |
\setlength{\topsep}{\parskip}% |
| 79 |
\setlength{\partopsep}{\parskip}% |
| 80 |
\setlength{\itemsep}{0pt}}}% |
| 81 |
{\end{list}} |
| 82 |
|
| 83 |
|
| 84 |
\newenvironment{myt1} |
| 85 |
{\begin{list}{$\star$}% |
| 86 |
{\setlength{\labelwidth}{9pt}% |
| 87 |
\setlength{\labelsep}{4pt}% |
| 88 |
\setlength{\leftmargin}{13pt}% |
| 89 |
\setlength{\topsep}{0pt}% |
| 90 |
\setlength{\partopsep}{\parskip}% |
| 91 |
\setlength{\itemsep}{0pt}}}% |
| 92 |
{\end{list}} |
| 93 |
|
| 94 |
\newenvironment{myt2} |
| 95 |
{\begin{list}{$\rightsquigarrow$}% |
| 96 |
{\setlength{\labelwidth}{9pt}% |
| 97 |
\setlength{\labelsep}{4pt}% |
| 98 |
\setlength{\leftmargin}{13pt}% |
| 99 |
\setlength{\topsep}{0pt}% |
| 100 |
\setlength{\partopsep}{\parskip}% |
| 101 |
\setlength{\itemsep}{0pt}}}% |
| 102 |
{\end{list}} |
| 103 |
|
| 104 |
|
| 105 |
% Colors |
| 106 |
|
| 107 |
\definecolor{Red}{rgb}{1,0,0} % Text |
| 108 |
\definecolor{Green}{rgb}{0,1,0} |
| 109 |
\definecolor{Blue}{rgb}{0,0,1} |
| 110 |
\definecolor{SaddleBrown}{rgb}{0.55,0.27,0.07} % Page borders |
| 111 |
\definecolor{Blue2}{rgb}{0,0,0.93} |
| 112 |
\definecolor{Gold}{rgb}{1,0.84,0} |
| 113 |
%\definecolor{MintCream}{rgb}{0.96,1,0.98} % Page background |
| 114 |
\definecolor{NavyBlue}{rgb}{0,0,0.5} % Title page |
| 115 |
\definecolor{Green3}{rgb}{0,0.8,0} |
| 116 |
\definecolor{DarkSlateGray}{rgb}{0.18,0.31,0.31} |
| 117 |
\definecolor{Purple2}{rgb}{0.57,0.17,0.93} |
| 118 |
|
| 119 |
% Page and slides parameters |
| 120 |
|
| 121 |
\newpagestyle{slidot} |
| 122 |
{\color{Gold}\rule{10mm}{1.5pt}% |
| 123 |
\lower.22ex\hbox{% |
| 124 |
\textcolor{Blue2}{~~University of Notre Dame~~}}% |
| 125 |
\leavevmode\leaders\hrule height1.5pt\hfil} |
| 126 |
{\color{Gold}\rule{5mm}{1.5pt}% |
| 127 |
\lower.22ex\hbox{% |
| 128 |
\textcolor{SaddleBrown}{~~Matthew Meineke~~}}% |
| 129 |
\leavevmode\leaders\hrule height1.5pt\hfil% |
| 130 |
\lower.32ex\hbox{% |
| 131 |
\textcolor{Blue2}{~~\thepage~~}}% |
| 132 |
\rule{5mm}{1.5pt}} |
| 133 |
|
| 134 |
\pagestyle{slidot} |
| 135 |
|
| 136 |
|
| 137 |
|
| 138 |
|
| 139 |
% A couple of new counters for slide sequences |
| 140 |
|
| 141 |
\newcounter{sliq} |
| 142 |
\newcounter{slisup} |
| 143 |
\renewcommand{\thesliq}{\Roman{sliq}} |
| 144 |
\renewcommand{\theslisup}{\Roman{slisup}} |
| 145 |
|
| 146 |
% Set the background color of every slide |
| 147 |
|
| 148 |
\special{!userdict begin /bop-hook {gsave |
| 149 |
1.0 1.0 1.0 setrgbcolor clippath fill |
| 150 |
grestore} def end |
| 151 |
} |
| 152 |
|
| 153 |
% And here we are... |
| 154 |
|
| 155 |
\setcounter{slide}{-1} |
| 156 |
%\includeonly{slide10} |
| 157 |
|
| 158 |
|
| 159 |
% setup the jurabib style |
| 160 |
|
| 161 |
\renewcommand{\jbbtasep}{; } % bta = between two authors sep |
| 162 |
\renewcommand{\jbbfsasep}{; } % bfsa = between first and second author sep |
| 163 |
\renewcommand{\jbbstasep}{; } % bsta = between second and third author sep |
| 164 |
%\renewcommand{\bibansep}{. } % seperator after name |
| 165 |
|
| 166 |
\renewcommand{\bibtfont}{\textit} % change book title to italics |
| 167 |
\renewcommand{\bibjtfont}{\textit} % change journal title to italics |
| 168 |
\renewcommand{\bibapifont}[1]{} % gets rid of the article title in citation |
| 169 |
|
| 170 |
|
| 171 |
|
| 172 |
|
| 173 |
|
| 174 |
|
| 175 |
% ---------------------- |
| 176 |
% | Title | |
| 177 |
% ---------------------- |
| 178 |
|
| 179 |
\title{A Mezzoscale Model for Phospholipid MD Simulations} |
| 180 |
|
| 181 |
\author{Matthew A. Meineke\\ |
| 182 |
Department of Chemistry and Biochemistry\\ |
| 183 |
University of Notre Dame\\ |
| 184 |
Notre Dame, Indiana 46556} |
| 185 |
|
| 186 |
\date{\today} |
| 187 |
|
| 188 |
%------------------------------------------------------------------- |
| 189 |
% Begin Document |
| 190 |
|
| 191 |
\begin{document} |
| 192 |
|
| 193 |
%\maketitle |
| 194 |
|
| 195 |
|
| 196 |
|
| 197 |
|
| 198 |
|
| 199 |
\nobibliography{canidacy_slides} |
| 200 |
\bibliographystyle{jurabib} |
| 201 |
|
| 202 |
|
| 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 |
|
| 220 |
% Slide 1 |
| 221 |
\begin{slide} {\LARGE Talk Outline} |
| 222 |
\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 |
\begin{slide} |
| 239 |
|
| 240 |
\centerline{\LARGE Motivation A: Long Length Scales} |
| 241 |
|
| 242 |
\begin{wrapfigure}{r}{60mm} |
| 243 |
|
| 244 |
\epsfxsize=45mm |
| 245 |
\epsfbox{ripple.epsi} |
| 246 |
|
| 247 |
\end{wrapfigure} |
| 248 |
|
| 249 |
|
| 250 |
|
| 251 |
|
| 252 |
%\epsfbox{ripple.epsi} |
| 253 |
%\begin{floatingfigure}{0.45\linewidth} |
| 254 |
% \incffig{ripple.epsi} |
| 255 |
%\end{floatingfigure} |
| 256 |
|
| 257 |
|
| 258 |
|
| 259 |
\mbox{} |
| 260 |
Ripple phase: |
| 261 |
\begin{itemize} |
| 262 |
|
| 263 |
\item |
| 264 |
The ripple (~$P_{\beta'}$~) phase lies in the transition from the gel |
| 265 |
to fluid phase. |
| 266 |
|
| 267 |
\item |
| 268 |
Periodicity of 100 - 200 $\mbox{\AA}$\footcite{Cevc87} |
| 269 |
|
| 270 |
\item |
| 271 |
Current simulations have box sizes ranging from 50 - 100 $\mbox{\AA}$ |
| 272 |
on a side.\footcite{Venable93}\footcite{Heller93} |
| 273 |
|
| 274 |
\end{itemize} |
| 275 |
\vspace{10mm} |
| 276 |
\end{slide} |
| 277 |
|
| 278 |
|
| 279 |
\begin{slide}{\LARGE Motivation B: Long Time Scales} |
| 280 |
|
| 281 |
\begin{itemize} |
| 282 |
|
| 283 |
\item |
| 284 |
Drug Diffussion |
| 285 |
\begin{itemize} |
| 286 |
\item |
| 287 |
Some drug molecules may spend appreciable amountsd of time in the |
| 288 |
membrane |
| 289 |
|
| 290 |
\item |
| 291 |
Long time scale dynamics are need to observe and charecterize their |
| 292 |
actions |
| 293 |
\end{itemize} |
| 294 |
|
| 295 |
\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 |
|
| 305 |
|
| 306 |
% Slide 4 |
| 307 |
|
| 308 |
\begin{slide}{\LARGE Length Scale Simplification I} |
| 309 |
|
| 310 |
|
| 311 |
Replace any charged interactions of the system with dipoles. |
| 312 |
|
| 313 |
\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 |
\end{itemize} |
| 325 |
\end{slide} |
| 326 |
|
| 327 |
\begin{slide}{\LARGE Length Scale Simplification II} |
| 328 |
|
| 329 |
Use unified models for the water and the lipid chain. |
| 330 |
|
| 331 |
\begin{itemize} |
| 332 |
\item |
| 333 |
Drastically reduces the number of atoms to simulate. |
| 334 |
|
| 335 |
\item |
| 336 |
Number of water - water interactions alone reduced by $\frac{1}{9}$. |
| 337 |
|
| 338 |
\end{itemize} |
| 339 |
|
| 340 |
ADD FIGURE HERE |
| 341 |
|
| 342 |
|
| 343 |
\end{slide} |
| 344 |
|
| 345 |
|
| 346 |
% Slide 5 |
| 347 |
|
| 348 |
\begin{slide}{Time Scale Simplification} |
| 349 |
\begin{itemize} |
| 350 |
|
| 351 |
\item |
| 352 |
No explicit hydrogens |
| 353 |
|
| 354 |
\begin{itemize} |
| 355 |
\item Hydrogen bond vibration is normally one of the fastest time |
| 356 |
events in a simulation. |
| 357 |
\end{itemize} |
| 358 |
|
| 359 |
\item |
| 360 |
Constrain all bonds to be of fixed length. |
| 361 |
|
| 362 |
\begin{itemize} |
| 363 |
\item As with the hydrogens, bond vibrations are the fastest motion in |
| 364 |
a simulation |
| 365 |
\end{itemize} |
| 366 |
|
| 367 |
\item |
| 368 |
Allows time steps of up to 3 fs with the current integrator. |
| 369 |
|
| 370 |
\end{itemize} |
| 371 |
\end{slide} |
| 372 |
|
| 373 |
|
| 374 |
% Slide 6 |
| 375 |
\begin{slide}{Molecular Dynamics} |
| 376 |
|
| 377 |
All of our simulations will be carried out using molecular |
| 378 |
dynamics. This involves solving Newton's equations of motion using |
| 379 |
the classical \emph{Hamiltonian} as follows: |
| 380 |
|
| 381 |
\begin{equation} |
| 382 |
H(\vec{q},\vec{p}) = T(\vec{p}) + V(\vec{q}) |
| 383 |
\end{equation} |
| 384 |
|
| 385 |
Here $T(\vec{p})$ is the kinetic energy of the system which is a |
| 386 |
function of momentum. In Cartesian space, $T(\vec{p})$ can be |
| 387 |
written as: |
| 388 |
|
| 389 |
\begin{equation} |
| 390 |
T(\vec{p}) = \sum_{i=1}^{N} \sum_{\alpha = x,y,z} \frac{p^{2}_{i\alpha}}{2m_{i}} |
| 391 |
\end{equation} |
| 392 |
|
| 393 |
\end{slide} |
| 394 |
|
| 395 |
|
| 396 |
% Slide 7 |
| 397 |
\begin{slide}{The Potential} |
| 398 |
|
| 399 |
The main part of the simulation is then the calculation of forces from |
| 400 |
the potential energy. |
| 401 |
|
| 402 |
\begin{equation} |
| 403 |
\vec{F}(\vec{q}) = - \nabla V(\vec{q}) |
| 404 |
\end{equation} |
| 405 |
|
| 406 |
The potential itself is made of several parts. |
| 407 |
|
| 408 |
\begin{equation} |
| 409 |
V_{tot} = |
| 410 |
\overbrace{V_{l} + V_{\theta} + V_{\omega}}^{\mbox{bonded}} + |
| 411 |
\overbrace{V_{l\!j} + V_{d\!p} + V_{s\!s\!d}}^{\mbox{non-bonded}} |
| 412 |
\end{equation} |
| 413 |
|
| 414 |
Where the bond interactions $V_{l}$, $V_{\theta}$, and $V_{\omega}$ are |
| 415 |
the bond, bend, and torsion potentials, and the non-bonded |
| 416 |
interactions $V_{l\!j}$, $V_{d\!p}$, and $V_{s\!p}$ are the |
| 417 |
lenard-jones, dipole-dipole, and sticky potential interactions. |
| 418 |
|
| 419 |
\end{slide} |
| 420 |
|
| 421 |
|
| 422 |
% Slide 8 |
| 423 |
|
| 424 |
\begin{slide}{Soft Sticky Dipole Model} |
| 425 |
|
| 426 |
The Soft-Sticky model for water is a reduced model. |
| 427 |
|
| 428 |
\begin{itemize} |
| 429 |
|
| 430 |
\item |
| 431 |
The model is represented by a single point mass at the water's center |
| 432 |
of mass. |
| 433 |
|
| 434 |
\item |
| 435 |
The point mass contains a fixed dipole of 2.35 D pointing from the |
| 436 |
oxygens toward the hydrogens. |
| 437 |
|
| 438 |
\end{itemize} |
| 439 |
|
| 440 |
It's potential is as follows: |
| 441 |
|
| 442 |
\begin{equation} |
| 443 |
V_{s\!s\!d} = V_{l\!j}(r_{i\!j}) + V_{d\!p}(r_{i\!j},\Omega_{i},\Omega_{j}) |
| 444 |
+ V_{s\!p}(r_{i\!j},\Omega_{i},\Omega_{j}) |
| 445 |
\end{equation} |
| 446 |
\end{slide} |
| 447 |
|
| 448 |
% Slide 8b |
| 449 |
|
| 450 |
\begin{slide}{SSD Diagram} |
| 451 |
|
| 452 |
\begin{center} |
| 453 |
\begin{figure} |
| 454 |
\epsfxsize=50mm |
| 455 |
\epsfbox{ssd.epsi} |
| 456 |
\end{figure} |
| 457 |
\end{center} |
| 458 |
|
| 459 |
A Diagram of the SSD model. |
| 460 |
\end{slide} |
| 461 |
|
| 462 |
% Slide 9 |
| 463 |
\begin{slide}{Hydrogen Bonding in SSD} |
| 464 |
|
| 465 |
It is important to note that SSD has a potential specifically to |
| 466 |
recreate the hydrogen bonding network of water. |
| 467 |
|
| 468 |
|
| 469 |
ICE SSD |
| 470 |
|
| 471 |
ICE point Dipole |
| 472 |
|
| 473 |
|
| 474 |
The importance of the hydrogen bond network is it's significant |
| 475 |
contribution to the hydrophobic driving force of bilayer formation. |
| 476 |
\end{slide} |
| 477 |
|
| 478 |
|
| 479 |
% Slide 10 |
| 480 |
|
| 481 |
\begin{slide}{The Lipid Model} |
| 482 |
|
| 483 |
To eliminate the need for charge-charge interactions, our lipid model |
| 484 |
replaces the phospholipid head group with a single large head group |
| 485 |
atom containing a freely oriented dipole. The tail is a simple alkane chain. |
| 486 |
|
| 487 |
Lipid Properties: |
| 488 |
\begin{itemize} |
| 489 |
\item $|\vec{\mu}_{\text{HEAD}}| = 20.6\ \text{D}$ |
| 490 |
\item $m_{\text{HEAD}} = 196\ \text{amu}$ |
| 491 |
\item Tail atoms are unified CH, $\text{CH}_2$, and $\text{CH}_3$ atoms |
| 492 |
\begin{itemize} |
| 493 |
\item Alkane forcefield parameters taken from TraPPE |
| 494 |
\end{itemize} |
| 495 |
\end{itemize} |
| 496 |
|
| 497 |
\end{slide} |
| 498 |
|
| 499 |
|
| 500 |
% Slide 11 |
| 501 |
|
| 502 |
\begin{slide}{Lipid Model} |
| 503 |
|
| 504 |
|
| 505 |
|
| 506 |
\end{slide} |
| 507 |
|
| 508 |
|
| 509 |
% Slide 12 |
| 510 |
|
| 511 |
\begin{slide}{Initial Runs: 25 Lipids in water} |
| 512 |
|
| 513 |
\textbf{Simulation Parameters:} |
| 514 |
|
| 515 |
\begin{itemize} |
| 516 |
|
| 517 |
\item Starting Configuration: |
| 518 |
\begin{itemize} |
| 519 |
\item 25 lipid molecules arranged in a 5 x 5 square |
| 520 |
\item square was surrounded by a sea of 1386 waters |
| 521 |
\begin{itemize} |
| 522 |
\item final water to lipid ratio was 55.4:1 |
| 523 |
\end{itemize} |
| 524 |
\end{itemize} |
| 525 |
|
| 526 |
\item Lipid had only a single saturated chain of 16 carbons |
| 527 |
|
| 528 |
\item Box Size: 34.5 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ x 39.4 $\mbox{\AA}$ |
| 529 |
|
| 530 |
\item dt = 2.0 - 3.0 fs |
| 531 |
|
| 532 |
\item T = 300 K |
| 533 |
|
| 534 |
\item NVE ensemble |
| 535 |
|
| 536 |
\item Periodic boundary conditions |
| 537 |
\end{itemize} |
| 538 |
|
| 539 |
\end{slide} |
| 540 |
|
| 541 |
|
| 542 |
% Slide 13 |
| 543 |
|
| 544 |
\begin{slide}{5x5: Initial} |
| 545 |
|
| 546 |
\begin{center} |
| 547 |
\begin{figure} |
| 548 |
\epsfxsize=50mm |
| 549 |
\epsfbox{5x5-initial.eps} |
| 550 |
\end{figure} |
| 551 |
\end{center} |
| 552 |
|
| 553 |
The initial configuration |
| 554 |
|
| 555 |
\end{slide} |
| 556 |
|
| 557 |
\begin{slide}{5x5: Final} |
| 558 |
|
| 559 |
\begin{center} |
| 560 |
\begin{figure} |
| 561 |
\epsfxsize=60mm |
| 562 |
\epsfbox{5x5-1.7ns.eps} |
| 563 |
\end{figure} |
| 564 |
\end{center} |
| 565 |
|
| 566 |
The final configuration at 1.7 ns. |
| 567 |
|
| 568 |
\end{slide} |
| 569 |
|
| 570 |
|
| 571 |
% Slide 14 |
| 572 |
|
| 573 |
\begin{slide}{5x5: $g(r)$} |
| 574 |
|
| 575 |
\begin{center} |
| 576 |
\begin{figure} |
| 577 |
\epsfxsize=60mm |
| 578 |
\epsfbox{all5x5-HEAD-HEAD-gr.eps} |
| 579 |
\end{figure} |
| 580 |
\end{center} |
| 581 |
|
| 582 |
|
| 583 |
\end{slide} |
| 584 |
|
| 585 |
\begin{slide}{5x5: $g(r)$} |
| 586 |
|
| 587 |
\begin{center} |
| 588 |
\begin{figure} |
| 589 |
\epsfxsize=60mm |
| 590 |
\epsfbox{all5x5-HEAD-X-gr.eps} |
| 591 |
\end{figure} |
| 592 |
\end{center} |
| 593 |
|
| 594 |
|
| 595 |
\end{slide} |
| 596 |
|
| 597 |
|
| 598 |
% Slide 15 |
| 599 |
|
| 600 |
\begin{slide}{5x5: $\cos$ correlations} |
| 601 |
|
| 602 |
\begin{center} |
| 603 |
\begin{figure} |
| 604 |
\epsfxsize=60mm |
| 605 |
\epsfbox{all5x5-HEAD-HEAD-cr.eps} |
| 606 |
\end{figure} |
| 607 |
\end{center} |
| 608 |
|
| 609 |
\end{slide} |
| 610 |
|
| 611 |
\begin{slide}{5x5: $\cos$ correlations} |
| 612 |
|
| 613 |
\begin{center} |
| 614 |
\begin{figure} |
| 615 |
\epsfxsize=60mm |
| 616 |
\epsfbox{all5x5-HEAD-X-cr.eps} |
| 617 |
\end{figure} |
| 618 |
\end{center} |
| 619 |
|
| 620 |
\end{slide} |
| 621 |
|
| 622 |
|
| 623 |
% Slide 16 |
| 624 |
|
| 625 |
\begin{slide}{Initial Runs: 50 Lipids randomly arranged in water} |
| 626 |
|
| 627 |
\textbf{Simulation Parameters:} |
| 628 |
|
| 629 |
\begin{itemize} |
| 630 |
|
| 631 |
\item Starting Configuration: |
| 632 |
\begin{itemize} |
| 633 |
\item 50 lipid molecules arranged randomly in a rectangular box |
| 634 |
\item The box was then filled with 1384 waters |
| 635 |
\begin{itemize} |
| 636 |
\item final water to lipid ratio was 27:1 |
| 637 |
\end{itemize} |
| 638 |
\end{itemize} |
| 639 |
|
| 640 |
\item Lipid had only a single saturated chain of 16 carbons |
| 641 |
|
| 642 |
\item Box Size: 26.6 $\mbox{\AA}$ x 26.6 $\mbox{\AA}$ x 108.4 $\mbox{\AA}$ |
| 643 |
|
| 644 |
\item dt = 2.0 - 3.0 fs |
| 645 |
|
| 646 |
\item T = 300 K |
| 647 |
|
| 648 |
\item NVE ensemble |
| 649 |
|
| 650 |
\item Periodic boundary conditions |
| 651 |
|
| 652 |
\end{itemize} |
| 653 |
|
| 654 |
\end{slide} |
| 655 |
|
| 656 |
|
| 657 |
% Slide 17 |
| 658 |
|
| 659 |
\begin{slide}{R-50: Initial} |
| 660 |
|
| 661 |
\begin{center} |
| 662 |
\begin{figure} |
| 663 |
\epsfxsize=100mm |
| 664 |
\epsfbox{r50-initial.eps} |
| 665 |
\end{figure} |
| 666 |
\end{center} |
| 667 |
|
| 668 |
The initial configuration |
| 669 |
|
| 670 |
\end{slide} |
| 671 |
|
| 672 |
\begin{slide}{R-50: Final} |
| 673 |
|
| 674 |
\begin{center} |
| 675 |
\begin{figure} |
| 676 |
\epsfxsize=100mm |
| 677 |
\epsfbox{r50-521ps.eps} |
| 678 |
\end{figure} |
| 679 |
\end{center} |
| 680 |
|
| 681 |
The fianl configuration at 521 ps |
| 682 |
|
| 683 |
\end{slide} |
| 684 |
|
| 685 |
|
| 686 |
% Slide 18 |
| 687 |
|
| 688 |
\begin{slide}{R-50: $g(r)$} |
| 689 |
|
| 690 |
|
| 691 |
\begin{center} |
| 692 |
\begin{figure} |
| 693 |
\epsfxsize=60mm |
| 694 |
\epsfbox{r50-HEAD-HEAD-gr.eps} |
| 695 |
\end{figure} |
| 696 |
\end{center} |
| 697 |
|
| 698 |
\end{slide} |
| 699 |
|
| 700 |
|
| 701 |
\begin{slide}{R-50: $g(r)$} |
| 702 |
|
| 703 |
|
| 704 |
\begin{center} |
| 705 |
\begin{figure} |
| 706 |
\epsfxsize=60mm |
| 707 |
\epsfbox{r50-HEAD-X-gr.eps} |
| 708 |
\end{figure} |
| 709 |
\end{center} |
| 710 |
|
| 711 |
\end{slide} |
| 712 |
|
| 713 |
|
| 714 |
% Slide 19 |
| 715 |
|
| 716 |
\begin{slide}{R-50: $\cos$ correlations} |
| 717 |
|
| 718 |
|
| 719 |
\begin{center} |
| 720 |
\begin{figure} |
| 721 |
\epsfxsize=60mm |
| 722 |
\epsfbox{r50-HEAD-HEAD-cr.eps} |
| 723 |
\end{figure} |
| 724 |
\end{center} |
| 725 |
|
| 726 |
\end{slide} |
| 727 |
|
| 728 |
\begin{slide}{R-50: $\cos$ correlations} |
| 729 |
|
| 730 |
|
| 731 |
\begin{center} |
| 732 |
\begin{figure} |
| 733 |
\epsfxsize=60mm |
| 734 |
\epsfbox{r50-HEAD-X-cr.eps} |
| 735 |
\end{figure} |
| 736 |
\end{center} |
| 737 |
|
| 738 |
\end{slide} |
| 739 |
|
| 740 |
|
| 741 |
% Slide 20 |
| 742 |
|
| 743 |
\begin{slide}{Future Directions} |
| 744 |
|
| 745 |
\begin{itemize} |
| 746 |
|
| 747 |
\item |
| 748 |
Simulation of a lipid with 2 chains, or perhaps expand the current |
| 749 |
unified chain atoms to take up greater steric bulk. |
| 750 |
|
| 751 |
\item |
| 752 |
Incorporate constant pressure and constant temperature into the ensemble. |
| 753 |
|
| 754 |
\item |
| 755 |
Parrellize the code. |
| 756 |
|
| 757 |
\end{itemize} |
| 758 |
\end{slide} |
| 759 |
|
| 760 |
|
| 761 |
% Slide 21 |
| 762 |
|
| 763 |
\begin{slide}{Acknowledgements} |
| 764 |
|
| 765 |
\begin{itemize} |
| 766 |
|
| 767 |
\item Dr. J. Daniel Gezelter |
| 768 |
\item Christopher Fennel |
| 769 |
\item Charles Vardeman |
| 770 |
\item Teng Lin |
| 771 |
\item Megan Sprauge |
| 772 |
\item Patrick Conforti |
| 773 |
\item Dan Combest |
| 774 |
|
| 775 |
\end{itemize} |
| 776 |
|
| 777 |
Funding by: |
| 778 |
\begin{itemize} |
| 779 |
\item Dreyfus New Faculty Award |
| 780 |
\end{itemize} |
| 781 |
|
| 782 |
\end{slide} |
| 783 |
|
| 784 |
|
| 785 |
|
| 786 |
|
| 787 |
|
| 788 |
|
| 789 |
|
| 790 |
|
| 791 |
%%%%%%%%%%%%%%%%%%%%%%%%%% END %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| 792 |
|
| 793 |
\end{document} |
