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Revision 4013 by jmarr, Thu Jan 30 23:00:02 2014 UTC vs.
Revision 4017 by jmarr, Mon Feb 3 16:27:55 2014 UTC

# Line 199 | Line 199 | $\frac{V}{\text{\AA}}$. The three field environments w
199   $\frac{V}{\text{\AA}}$. The three field environments were, 1) no field
200    applied, 2) 0.01 $\frac{V}{\text{\AA}}$ (0.5 V) and 3) 0.024
201      $\frac{V}{\text{\AA}}$ (1.2 V). Each field was applied in the
202 <    Z-axis of the simulation box.
202 >    Z-axis of the simulation box. For the simplicity of this paper,
203 >    each field will be called zero, partial and full, respectively.
204  
205   For quantum calculation of the nitrile bond frequency, Gaussian 09 was
206   used. A single 5CB molecule was selected for the center of the
# Line 256 | Line 257 | $S$ takes on values close to 1 in highly ordered phase
257   $S$ is the largest eigenvalue of $Q_{\alpha \beta}$, and the
258   corresponding eigenvector defines the director axis for the phase.
259   $S$ takes on values close to 1 in highly ordered phases, but falls to
260 < zero for isotropic fluids.
260 > zero for isotropic fluids. In the context of 5CB, this value would be
261 > close to zero for its isotropic phase and raise closer to one as it
262 > moved to the nematic and crystalline phases.
263 >
264 > This value indicates phases changes at temperature boundaries but also
265 > when a phase changes occurs due to external field applications. In
266 > Figure 1, this phase change can be clearly seen over the course of 60
267 > ns. Each system starts with an ordering paramter near 0.1 to 0.2,
268 > which is an isotropic phase. Over the course 10 ns, the full external field
269 > causes a shift in the ordering of the system to 0.5, the nematic phase
270 > of the liquid crystal. This change is consistent over the full 50 ns
271 > with no drop back into the isotropic phase. This change is clearly
272 > field induced and stable over a long period of simulation time.
273 >
274 > Interestingly, the field that is needed to switch the phase of 5CB
275 > macroscopically is larger than 1 V. However, in this case, only a
276 > voltage of 1.2 V was need to induce a phase change. This is impart due
277 > to the distance the field is being applied across. At such a small
278 > distance, the field is much larger than the macroscopic and thus
279 > easily induces a field dependent phase change.
280  
281 + This change in phase was followed by two courses of further
282 + simulation. First, was replacement of the static nitrile bond with a
283 + morse oscillator bond. This was then simulated for a period of time
284 + and a classical spetrum was calculated. Second, ab intio calcualtions were performe to investigate
285 + if the phase change caused any change spectrum from quantum
286 + effects.
287 +
288 + In respect to the classical calculations, it was first seen if previous
289 + studies of nitriles within water and neat simulation done by Cho
290 + et. al. could be used for the spectrum.
291 +
292 + After Gaussian calculations were performed on a set of snapshots, any
293 +
294   \begin{figure}
295    \includegraphics[trim = 5mm 10mm 3mm 10mm, clip, width=3.25in]{P2}
296 <  \caption{Order Parameter}
296 >  \caption{Ordering of each external field application over the course
297 >    of 60 ns with a sampling every 100 ps. Each trajectory was started
298 >  after equilibration with zero field applied.}
299    \label{fig:orderParameter}
300   \end{figure}
301  
302   \begin{figure}
303    \includegraphics[width=3.25in]{2Spectra}
304 <  \caption{The classically calculated nitrile bond spetrum from }
304 >  \caption{The classically calculated nitrile bond spetrum for no
305 >    external field application (black) and full external field
306 >    application (red)}
307    \label{fig:twoSpectra}
308   \end{figure}
309  
273
310   \begin{figure}
311          \centering
312          \begin{subfigure}[b]{0.3\textwidth}

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