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# Line 2 | Line 2 | Long range orientational order is one of the most fund
2  
3   \section{\label{liquidCrystalSection:introduction}Introduction}
4  
5 < Long range orientational order is one of the most fundamental
6 < properties of liquid crystal mesophases. This orientational
7 < anisotropy of the macroscopic phases originates in the shape
8 < anisotropy of the constituent molecules. Among these anisotropy
9 < mesogens, rod-like (calamitic) and disk-like molecules have been
10 < exploited in great detail in the last two decades\cite{Huh2004}.
11 < Typically, these mesogens consist of a rigid aromatic core and one
12 < or more attached aliphatic chains. For short chain molecules, only
13 < nematic phases, in which positional order is limited or absent, can
14 < be observed, because the entropy of mixing different parts of the
15 < mesogens is paramount to the dispersion interaction. In contrast,
16 < formation of the one dimension lamellar sematic phase in rod-like
17 < molecules with sufficiently long aliphatic chains has been reported,
18 < as well as the segregation phenomena in disk-like molecules.
5 > Rod-like (calamitic) and disk-like anisotropy liquid crystals have
6 > been investigated in great detail in the last two
7 > decades\cite{Huh2004}. Typically, these mesogens consist of a rigid
8 > aromatic core and one or more attached aliphatic chains. For short
9 > chain molecules, only nematic phases, in which positional order is
10 > limited or absent, can be observed, because the entropy of mixing
11 > different parts of the mesogens is larger than the dispersion
12 > interaction. In contrast, formation of one dimension lamellar
13 > smectic phase in rod-like molecules with sufficiently long aliphatic
14 > chains has been reported, as well as the segregation phenomena in
15 > disk-like molecules\cite{McMillan1971}. Recently, banana-shaped or
16 > bent-core liquid crystals have became one of the most active
17 > research areas in mesogenic materials and supramolecular
18 > chemistry\cite{Niori1996, Link1997, Pelzl1999}. Unlike rods and
19 > disks, the polarity and biaxiality of the banana-shaped molecules
20 > allow the molecules organize into a variety of novel liquid
21 > crystalline phases which show interesting material properties. Of
22 > particular interest is the spontaneous formation of macroscopic
23 > chiral layers from achiral banana-shaped molecules, where polar
24 > molecule orientational ordering exhibited layered plane as well as
25 > the tilted arrangement of the molecules relative to the polar axis.
26 > As a consequence of supramolecular chirality, the spontaneous
27 > polarization arises in ferroelectric (FE) and antiferroelectic (AF)
28 > switching of smectic liquid crystal phases, demonstrating some
29 > promising applications in second-order nonlinear optical devices.
30 > The most widely investigated mesophase formed by banana-shaped
31 > moleculed is the $\text{B}_2$ phase, which is also referred to as
32 > $\text{SmCP}$\cite{Link1997}. Of the most important discoveries in
33 > this tilt lamellar phase is the four distinct packing arrangements
34 > (two conglomerates and two macroscopic racemates), which depend on
35 > the tilt direction and the polar direction of the molecule in
36 > adjacent layer (see Fig.~\ref{LCFig:SMCP})\cite{Link1997}.
37  
20 Recently, the banana-shaped or bent-core liquid crystal have became
21 one of the most active research areas in mesogenic materials and
22 supramolecular chemistry\cite{Niori1996, Link1997, Pelzl1999}.
23 Unlike rods and disks, the polarity and biaxiality of the
24 banana-shaped molecules allow the molecules organize into a variety
25 of novel liquid crystalline phases which show interesting material
26 properties. Of particular interest is the spontaneous formation of
27 macroscopic chiral layers from achiral banana-shaped molecules,
28 where polar molecule orientational ordering is shown within the
29 layer plane as well as the tilted arrangement of the molecules
30 relative to the polar axis. As a consequence of supramolecular
31 chirality, the spontaneous polarization arises in ferroelectric (FE)
32 and antiferroelectic (AF) switching of smectic liquid crystal
33 phases, demonstrating some promising applications in second-order
34 nonlinear optical devices. The most widely investigated mesophase
35 formed by banana-shaped moleculed is the $\text{B}_2$ phase, which
36 is also referred to as $\text{SmCP}$\cite{Link1997}. Of the most
37 important discover in this tilt lamellar phase is the four distinct
38 packing arrangements (two conglomerates and two macroscopic
39 racemates), which depend on the tilt direction and the polar
40 direction of the molecule in adjacent layer (see
41 Fig.~\ref{LCFig:SMCP}).
42
38   \begin{figure}
39   \centering
40   \includegraphics[width=\linewidth]{smcp.eps}
41 < \caption[]
42 < {}
41 > \caption[SmCP Phase Packing] {Four possible SmCP phase packings that
42 > are characterized by the relative tilt direction(A and S refer an
43 > anticlinic tilt or a synclinic ) and the polarization orientation (A
44 > and F represent antiferroelectric or ferroelectric polar order).}
45   \label{LCFig:SMCP}
46   \end{figure}
47  
# Line 63 | Line 60 | limitation of time scale required for phase transition
60   smectic arrangements\cite{Cook2000, Lansac2001}, as well as other
61   bulk properties, such as rotational viscosity and flexoelectric
62   coefficients\cite{Cheung2002, Cheung2004}. However, due to the
63 < limitation of time scale required for phase transition and the
63 > limitation of time scales required for phase transition and the
64   length scale required for representing bulk behavior,
65   models\cite{Perram1985, Gay1981}, which are based on the observation
66   that liquid crystal order is exhibited by a range of non-molecular
67 < bodies with high shape anisotropies, became the dominant models in
68 < the field of liquid crystal phase behavior. Previous simulation
69 < studies using hard spherocylinder dimer model\cite{Camp1999} produce
70 < nematic phases, while hard rod simulation studies identified a
71 < Landau point\cite{Bates2005}, at which the isotropic phase undergoes
72 < a direct transition to the biaxial nematic, as well as some possible
73 < liquid crystal phases\cite{Lansac2003}. Other anisotropic models
74 < using Gay-Berne(GB) potential, which produce interactions that favor
75 < local alignment, give the evidence of the novel packing arrangements
79 < of bent-core molecules\cite{Memmer2002,Orlandi2006}.
67 > bodies with high shape anisotropies, have become the dominant models
68 > in the field of liquid crystal phase behavior. Previous simulation
69 > studies using a hard spherocylinder dimer model\cite{Camp1999}
70 > produced nematic phases, while hard rod simulation studies
71 > identified a direct transition to the biaxial nematic and other
72 > possible liquid crystal phases\cite{Lansac2003}. Other anisotropic
73 > models using the Gay-Berne(GB) potential, which produces
74 > interactions that favor local alignment, give evidence of the novel
75 > packing arrangements of bent-core molecules\cite{Memmer2002}.
76  
77   Experimental studies by Levelut {\it et al.}~\cite{Levelut1981}
78   revealed that terminal cyano or nitro groups usually induce
79   permanent longitudinal dipole moments, which affect the phase
80 < behavior considerably. A series of theoretical studies also drawn
81 < equivalent conclusions. Monte Carlo studies of the GB potential with
82 < fixed longitudinal dipoles (i.e. pointed along the principal axis of
83 < rotation) were shown to enhance smectic phase
80 > behavior considerably. Equivalent conclusions have also been drawn
81 > from a series of theoretical studies. Monte Carlo studies of the GB
82 > potential with fixed longitudinal dipoles (i.e. pointed along the
83 > principal axis of rotation) were shown to enhance smectic phase
84   stability~\cite{Berardi1996,Satoh1996}. Molecular simulation of GB
85   ellipsoids with transverse dipoles at the terminus of the molecule
86   also demonstrated that partial striped bilayer structures were
# Line 97 | Line 93 | In this chapter, we consider system consisting of bana
93   bent-core molecules, could be modeled more accurately by
94   incorporating electrostatic interaction.
95  
96 < In this chapter, we consider system consisting of banana-shaped
97 < molecule represented by three rigid GB particles with one or two
98 < point dipoles at different location. Performing a series of
99 < molecular dynamics simulations, we explore the structural properties
100 < of tilted smectic phases as well as the effect of electrostatic
105 < interactions.
96 > In this chapter, we consider a system consisting of banana-shaped
97 > molecule represented by three rigid GB particles with two point
98 > dipoles. Performing a series of molecular dynamics simulations, we
99 > explore the structural properties of tilted smectic phases as well
100 > as the effect of electrostatic interactions.
101  
102   \section{\label{liquidCrystalSection:model}Model}
103  
# Line 129 | Line 124 | orientation of two molecules $i$ and $j$ separated by
124   } \right] \label{LCEquation:gb}
125   \end{equation}
126   where $\hat u_i,\hat u_j$ are unit vectors specifying the
127 < orientation of two molecules $i$ and $j$ separated by intermolecular
128 < vector $r_{ij}$. $\hat r_{ij}$ is the unit vector along the
129 < intermolecular vector. A schematic diagram of the orientation
130 < vectors is shown in Fig.\ref{LCFigure:GBScheme}. The functional form
131 < for $\sigma$ is given by
127 > orientation of two ellipsoids $i$ and $j$ separated by
128 > intermolecular vector $r_{ij}$. $\hat r_{ij}$ is the unit vector
129 > along the inter-ellipsoid vector. A schematic diagram of the
130 > orientation vectors is shown in Fig.\ref{LCFigure:GBScheme}. The
131 > functional form for $\sigma$ is given by
132   \begin{equation}
133   \sigma (\hat u_i ,\hat u_i ,\hat r_{ij} ) = \sigma _0 \left[ {1 -
134   \frac{\chi }{2}\left( {\frac{{(\hat r_{ij}  \cdot \hat u_i  + \hat
# Line 181 | Line 176 | ratio between \textit{end-to-end} well depth $\epsilon
176   \begin{figure}
177   \centering
178   \includegraphics[width=\linewidth]{banana.eps}
179 < \caption[]{} \label{LCFig:BananaMolecule}
179 > \caption[Schematic representation of a typical banana shaped
180 > molecule]{Schematic representation of a typical banana shaped
181 > molecule.} \label{LCFig:BananaMolecule}
182   \end{figure}
186
187 %\begin{figure}
188 %\centering
189 %\includegraphics[width=\linewidth]{bananGB.eps}
190 %\caption[]{} \label{LCFigure:BananaGB}
191 %\end{figure}
192
183   \begin{figure}
184   \centering
185   \includegraphics[width=\linewidth]{gb_scheme.eps}
186 < \caption[]{Schematic diagram showing definitions of the orientation
187 < vectors for a pair of Gay-Berne molecules}
188 < \label{LCFigure:GBScheme}
186 > \caption[Schematic diagram showing definitions of the orientation
187 > vectors for a pair of Gay-Berne molecules]{Schematic diagram showing
188 > definitions of the orientation vectors for a pair of Gay-Berne
189 > ellipsoids} \label{LCFigure:GBScheme}
190   \end{figure}
200
191   To account for the permanent dipolar interactions, there should be
192   an electrostatic interaction term of the form
193   \begin{equation}
# Line 208 | Line 198 | where $\epsilon _{fs}$ is the permittivity of free spa
198   \end{equation}
199   where $\epsilon _{fs}$ is the permittivity of free space.
200  
201 < \section{Computational Methodology}
201 > \section{Results and Discussion}
202  
203   A series of molecular dynamics simulations were perform to study the
204   phase behavior of banana shaped liquid crystals. In each simulation,
# Line 220 | Line 210 | temperature and pressure.
210   a $160\times 160 \times 120$ box. After the dipolar interactions are
211   switched on, 2~ns NPTi cooling run with themostat of 2~ps and
212   barostat of 50~ps were used to equilibrate the system to desired
213 < temperature and pressure.
213 > temperature and pressure. NPTi Production runs last for 40~ns with
214 > time step of 20~fs.
215  
216   \subsection{Order Parameters}
217  
# Line 228 | Line 219 | the largest eigen value obtained by diagonalizing the
219   calculated various order parameters and correlation functions.
220   Particulary, the $P_2$ order parameter allows us to estimate average
221   alignment along the director axis $Z$ which can be identified from
222 < the largest eigen value obtained by diagonalizing the order
223 < parameter tensor
222 > the largest eigenvalue obtained by diagonalizing the order parameter
223 > tensor
224   \begin{equation}
225   \overleftrightarrow{\mathsf{Q}} = \frac{1}{N}\sum_i^N %
226      \begin{pmatrix} %
# Line 237 | Line 228 | parameter tensor
228      u_{iy}u_{ix} & u_{iy}u_{iy}-\frac{1}{3} & u_{iy}u_{iz} \\
229      u_{iz}u_{ix} & u_{iz}u_{iy} & u_{iz}u_{iz}-\frac{1}{3} %
230      \end{pmatrix},
231 < \label{lipidEq:po1}
231 > \label{lipidEq:p2}
232   \end{equation}
233   where the $u_{i\alpha}$ is the $\alpha$ element of the unit vector
234   $\mathbf{\hat{u}}_i$, and the sum over $i$ averages over the whole
# Line 247 | Line 238 | In addition to the $P_2$ order parameter, $ R_{2,2}^2$
238   \langle P_2 \rangle = \frac{3}{2}\lambda_{\text{max}}.
239   \label{lipidEq:po3}
240   \end{equation}
241 < In addition to the $P_2$ order parameter, $ R_{2,2}^2$ order
242 < parameter for biaxial phase is introduced to describe the ordering
243 < in the plane orthogonal to the director by
244 < \begin{equation}
245 < R_{2,2}^2  = \frac{1}{4}\left\langle {(x_i  \cdot X)^2  - (x_i \cdot
246 < Y)^2  - (y_i  \cdot X)^2  + (y_i  \cdot Y)^2 } \right\rangle
247 < \end{equation}
248 < where $X$, $Y$ and $Z$ are axis of the director frame.
241 > %In addition to the $P_2$ order parameter, $ R_{2,2}^2$ order
242 > %parameter for biaxial phase is introduced to describe the ordering
243 > %in the plane orthogonal to the director by
244 > %\begin{equation}
245 > %R_{2,2}^2  = \frac{1}{4}\left\langle {(x_i  \cdot X)^2  - (x_i \cdot
246 > %Y)^2  - (y_i  \cdot X)^2  + (y_i  \cdot Y)^2 } \right\rangle
247 > %\end{equation}
248 > %where $X$, $Y$ and $Z$ are axis of the director frame.
249 > The unit vector for the banana shaped molecule was defined by the
250 > principle aixs of its middle GB particle. The $P_2$ order parameters
251 > for the bent-core liquid crystal at different temperature is
252 > summarized in Table~\ref{liquidCrystal:p2} which identifies a phase
253 > transition temperature range.
254  
255 < \subsection{Structure Properties}
255 > \begin{table}
256 > \caption{LIQUID CRYSTAL STRUCTURAL PROPERTIES AS A FUNCTION OF
257 > TEMPERATURE} \label{liquidCrystal:p2}
258 > \begin{center}
259 > \begin{tabular}{cccccc}
260 > \hline
261 > Temperature (K) & 420 & 440 & 460 & 480 & 600\\
262 > \hline
263 > $\langle P_2\rangle$ & 0.984 & 0.982 & 0.975 & 0.967 & 0.067\\
264 > \hline
265 > \end{tabular}
266 > \end{center}
267 > \end{table}
268  
269 < It is more important to show the density correlation along the
270 < director
269 > \subsection{Structural Properties}
270 >
271 > The molecular organization obtained at temperature $T = 460K$ (below
272 > transition temperature) is shown in Figure~\ref{LCFigure:snapshot}.
273 > The diagonal view in Fig~\ref{LCFigure:snapshot}(a) shows the
274 > stacking of the banana shaped molecules while the side view in n
275 > Figure~\ref{LCFigure:snapshot}(b) demonstrates formation of a
276 > chevron structure. The first peak of the radial distribution
277 > function $g(r)$ in Fig.~\ref{LCFigure:gofrz}(a) shows that the
278 > minimum distance for two in plane banana shaped molecules is 4.9
279 > \AA, while the second split peak implies the biaxial packing. It is
280 > also important to show the density correlation along the director
281 > which is given by :
282   \begin{equation}
283 < g(z) =< \delta (z-z_{ij})>_{ij} / \pi R^{2} \rho
283 > g(z) =\frac{1}{\pi R^{2} \rho}< \delta (z-z_{ij})>_{ij}
284   \end{equation},
285 < where $z_{ij} = r_{ij} \dot Z$ was measured in the director frame
286 < and $R$ is the radius of the cylindrical sampling region.
285 > where $ z_{ij}  = r_{ij}  \cdot \hat Z $ was measured in the
286 > director frame and $R$ is the radius of the cylindrical sampling
287 > region. The oscillation in density plot along the director in
288 > Fig.~\ref{LCFigure:gofrz}(b) implies the existence of the layered
289 > structure, and the peak at 27 \AA is attributed to a defect in the
290 > system.
291  
292   \subsection{Rotational Invariants}
293  
294   As a useful set of correlation functions to describe
295   position-orientation correlation, rotation invariants were first
296   applied in a spherical symmetric system to study x-ray and light
297 < scatting\cite{Blum1971}. Latterly, expansion of the orientation pair
297 > scatting\cite{Blum1972}. Latterly, expansion of the orientation pair
298   correlation in terms of rotation invariant for molecules of
299 < arbitrary shape was introduce by Stone\cite{Stone1978} and adopted
300 < by other researchers in liquid crystal studies\cite{Berardi2000}.
301 <
299 > arbitrary shape has been introduced by Stone\cite{Stone1978} and
300 > adopted by other researchers in liquid crystal
301 > studies\cite{Berardi2003}. In order to study the correlation between
302 > biaxiality and molecular separation distance $r$, we calculate a
303 > rotational invariant function $S_{22}^{220} (r)$, which is given by
304 > :
305   \begin{eqnarray}
306 < S_{22}^{220} (r) & = & \frac{1}{{4\sqrt 5 }}\left\langle {\delta (r
307 < - r_{ij} )((\hat x_i  \cdot \hat x_j )^2  - (\hat x_i  \cdot \hat
308 < y_j )^2  - (\hat y_i  \cdot \hat x_j )^2  + (\hat y_i  \cdot \hat
309 < y_j
310 < )^2 ) \right.\\
311 < & & \left.- 2(\hat x_i  \cdot \hat y_j )(\hat y_i \cdot \hat x_j ) -
286 < 2(\hat x_i  \cdot \hat x_j )(\hat y_i  \cdot \hat y_j ))}
287 < \right\rangle
306 > S_{22}^{220} (r) & = & \frac{1}{{4\sqrt 5 }} \left< \delta (r -
307 > r_{ij} )((\hat x_i  \cdot \hat x_j )^2  - (\hat x_i  \cdot \hat y_j
308 > )^2  - (\hat y_i  \cdot \hat x_j )^2  + (\hat y_i  \cdot \hat y_j
309 > )^2 ) \right. \notag \\
310 > & & \left. - 2(\hat x_i  \cdot \hat y_j )(\hat y_i \cdot \hat x_j ) -
311 > 2(\hat x_i  \cdot \hat x_j )(\hat y_i  \cdot \hat y_j )) \right>.
312   \end{eqnarray}
313 + The long range behavior of second rank orientational correlation
314 + $S_{22}^{220} (r)$ in Fig~\ref{LCFigure:S22220} also confirm the
315 + biaxiality of the system.
316  
317 < \begin{equation}
318 < S_{00}^{221} (r) =  - \frac{{\sqrt 3 }}{{\sqrt {10} }}\left\langle
319 < {\delta (r - r_{ij} )((\hat z_i  \cdot \hat z_j )(\hat z_i  \cdot
320 < \hat z_j  \times \hat r_{ij} ))} \right\rangle
321 < \end{equation}
317 > \begin{figure}
318 > \centering
319 > \includegraphics[width=4.5in]{snapshot.eps}
320 > \caption[Snapshot of the molecular organization in the layered phase
321 > formed at temperature T = 460K and pressure P = 1 atm]{Snapshot of
322 > the molecular organization in the layered phase formed at
323 > temperature T = 460K and pressure P = 1 atm. (a) diagonal view; (b)
324 > side view.} \label{LCFigure:snapshot}
325 > \end{figure}
326  
327 < \section{Results and Conclusion}
328 < \label{sec:results and conclusion}
327 > \begin{figure}
328 > \centering
329 > \includegraphics[width=\linewidth]{gofr_gofz.eps}
330 > \caption[Correlation Functions of a Bent-core Liquid Crystal System
331 > at Temperature T = 460K and Pressure P = 10 atm]{Correlation
332 > Functions of a Bent-core Liquid Crystal System at Temperature T =
333 > 460K and Pressure P = 10 atm. (a) radial correlation function
334 > $g(r)$; and (b) density along the director $g(z)$.}
335 > \label{LCFigure:gofrz}
336 > \end{figure}
337  
338 < To investigate the molecular organization behavior due to different
339 < dipolar orientation and position with respect to the center of the
340 < molecule,
338 > \begin{figure}
339 > \centering
340 > \includegraphics[width=\linewidth]{s22_220.eps}
341 > \caption[Average orientational correlation Correlation Functions of
342 > a Bent-core Liquid Crystal System at Temperature T = 460K and
343 > Pressure P = 10 atm]{Average orientational correlation Correlation
344 > Functions of a Bent-core Liquid Crystal System at Temperature T =
345 > 460K and Pressure P = 10 atm.} \label{LCFigure:S22220}
346 > \end{figure}
347 >
348 > \section{Conclusion}
349 >
350 > We have presented a simple dipolar three-site GB model for banana
351 > shaped molecules which are capable of forming smectic phases from
352 > isotropic configuration. Various order parameters and correlation
353 > functions were used to characterized the structural properties of
354 > these smectic phase. However, the forming layered structure still
355 > had some defects because of the mismatching between the layer
356 > structure spacing and the shape of simulation box. This mismatching
357 > can be broken by using NPTf integrator in further simulations. The
358 > role of terminal chain in controlling transition temperatures and
359 > the type of mesophase formed have been studied
360 > extensively\cite{Pelzl1999}. The lack of flexibility in our model
361 > due to the missing terminal chains could explain the fact that we
362 > did not find evidence of chirality.

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