--- trunk/xDissertation/md.tex	2008/03/24 21:32:11	3376
+++ trunk/xDissertation/md.tex	2008/04/16 21:56:34	3383
@@ -101,7 +101,8 @@ the ripple formation can be found in section
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdLipidModels.pdf} 
-\caption{Three different representations of DPPC lipid molecules,
+\caption[Three different representations of DPPC lipid
+molecules]{Three different representations of DPPC lipid molecules,
 including the chemical structure, an atomistic model, and the
 head-body ellipsoidal coarse-grained model used in this
 work.\label{mdfig:lipidModels}}
@@ -243,13 +244,14 @@ actual parameters used in our simulations are given in
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/md2LipidModel.pdf} 
-\caption{The parameters defining the behavior of the lipid
-models. $\sigma_h / d$ is the ratio of the head group to body diameter.
-Molecular bodies had a fixed aspect ratio of 3.0.  The solvent model
-was a simplified 4-water bead ($\sigma_w \approx d$) that has been
-used in other coarse-grained simulations.  The dipolar strength
-(and the temperature and pressure) were the only other parameters that
-were varied systematically.\label{mdfig:lipidModel}}
+\caption[The parameters defining the behavior of the lipid
+models]{The parameters defining the behavior of the lipid
+models. $\sigma_h / d$ is the ratio of the head group to body
+diameter.  Molecular bodies had a fixed aspect ratio of 3.0.  The
+solvent model was a simplified 4-water bead ($\sigma_w \approx d$)
+that has been used in other coarse-grained simulations.  The dipolar
+strength (and the temperature and pressure) were the only other
+parameters that were varied systematically.\label{mdfig:lipidModel}}
 \end{figure}
 
 To take into account the permanent dipolar interactions of the
@@ -321,8 +323,8 @@ water).
 \begin{table*}
 \begin{minipage}{\linewidth}
 \begin{center}
-\caption{Potential parameters used for molecular-scale coarse-grained
-lipid simulations}
+\caption{POTENTIAL PARAMETERS USED FOR MOLECULAR SCALE COARSE-GRAINED
+LIPID SIMULATIONS}
 \begin{tabular}{llccc}
 \hline 
   & &  Head & Chain & Solvent \\
@@ -343,8 +345,8 @@ $\mu$ (Debye) & & varied & 0 & 0 \\
 \end{minipage}
 \end{table*}
 
-\section{Experimental Methodology}
-\label{mdsec:experiment}
+\section{Simulation Methodology}
+\label{mdsec:simulation}
 
 The parameters that were systematically varied in this study were the
 size of the head group ($\sigma_h$), the strength of the dipole moment
@@ -439,18 +441,18 @@ phase observed when $\sigma_h = 1.35 d$.
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdPhaseCartoon.pdf} 
-\caption{The role of the ratio between the head group size and the
-width of the molecular bodies is to increase the local membrane
-curvature.  With strong attractive interactions between the head
-groups, this local curvature can be maintained in bilayer structures
-through surface corrugation.  Shown above are three phases observed in
-these simulations.  With $\sigma_h = 1.20 d$, the bilayer maintains a
-flat topology.  For larger heads ($\sigma_h = 1.35 d$) the local
-curvature resolves into a symmetrically rippled phase with little or
-no interdigitation between the upper and lower leaves of the membrane.
-The largest heads studied ($\sigma_h = 1.41 d$) resolve into an
-asymmetric rippled phases with interdigitation between the two
-leaves.\label{mdfig:phaseCartoon}} 
+\caption[ three phases observed in the simulations]{The role of the
+ratio between the head group size and the width of the molecular
+bodies is to increase the local membrane curvature.  With strong
+attractive interactions between the head groups, this local curvature
+can be maintained in bilayer structures through surface corrugation.
+Shown above are three phases observed in these simulations.  With
+$\sigma_h = 1.20 d$, the bilayer maintains a flat topology.  For
+larger heads ($\sigma_h = 1.35 d$) the local curvature resolves into a
+symmetrically rippled phase with little or no interdigitation between
+the upper and lower leaves of the membrane.  The largest heads studied
+($\sigma_h = 1.41 d$) resolve into an asymmetric rippled phases with
+interdigitation between the two leaves.\label{mdfig:phaseCartoon}}
 \end{figure}
 
 Sample structures for the flat ($\sigma_h = 1.20 d$), symmetric
@@ -476,12 +478,10 @@ for PE head groups.
 for PE head groups.
 
 \begin{table*}
-\begin{minipage}{\linewidth}
 \begin{center}
-\caption{Phase, bilayer spacing, area per lipid, ripple wavelength
-and amplitude observed as a function of the ratio between the head
-beads and the diameters of the tails.  Ripple wavelengths and
-amplitudes are normalized to the diameter of the tail ellipsoids.}
+\caption{PHASE, BILAYER SPACING, AREA PER LIPID, RIPPLE WAVELENGTH AND
+AMPLITUDE OBSERVED AS A FUNCTION OF THE RATIO BETWEEN THE HEAD BEADS
+AND THE DIAMETERS OF THE TAILS}
 \begin{tabular}{lccccc}
 \hline 
 $\sigma_h / d$ & type of phase & bilayer spacing (\AA) & area per
@@ -492,9 +492,14 @@ lipid (\AA$^2$) & $\lambda / d$ & $A / d$\\
 1.35 & symmetric ripple & 42.9 & 51.7 & 17.2 & 2.2 \\
 1.41 & asymmetric ripple & 37.1 & 63.1 & 15.4 & 1.5 \\
 \end{tabular}
+\begin{minipage}{\linewidth}
+%\centering
+\vspace{2mm}    
+ Ripple wavelengths and amplitudes are normalized to the diameter of
+ the tail ellipsoids.
 \label{mdtab:property}
-\end{center}
 \end{minipage}
+\end{center}
 \end{table*}
 
 The membrane structures and the reduced wavelength $\lambda / d$,
@@ -510,14 +515,16 @@ likely to underestimate of the true amplitudes.
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdTopDown.pdf} 
-\caption{Top views of the flat (upper), symmetric ripple (middle),
-and asymmetric ripple (lower) phases.  Note that the head-group
-dipoles have formed head-to-tail chains in all three of these phases,
-but in the two rippled phases, the dipolar chains are all aligned {\it
-perpendicular} to the direction of the ripple.  Note that the flat
-membrane has multiple vortex defects in the dipolar ordering, and the
-ordering on the lower leaf of the bilayer can be in an entirely
-different direction from the upper leaf.\label{mdfig:topView}}
+\caption[Top views of the flat, symmetric ripple, and asymmetric
+ripple phases]{Top views of the flat (upper), symmetric ripple
+(middle), and asymmetric ripple (lower) phases.  Note that the
+head-group dipoles have formed head-to-tail chains in all three of
+these phases, but in the two rippled phases, the dipolar chains are
+all aligned {\it perpendicular} to the direction of the ripple.  Note
+that the flat membrane has multiple vortex defects in the dipolar
+ordering, and the ordering on the lower leaf of the bilayer can be in
+an entirely different direction from the upper
+leaf.\label{mdfig:topView}}
 \end{figure}
 
 The orientational ordering in the system is observed by $P_2$ order
@@ -582,9 +589,11 @@ rapidly decreasing $P_2$ ordering for the molecular bo
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdRP2.pdf} 
-\caption{The $P_2$ order parameters for head groups (circles) and
-molecular bodies (squares) as a function of the ratio of head group
-size ($\sigma_h$) to the width of the molecular bodies ($d$). \label{mdfig:rP2}}
+\caption[The $P_2$ order parameters as a function of the ratio of head group
+size to the width of the molecular bodies]{The $P_2$ order parameters
+for head groups (circles) and molecular bodies (squares) as a function
+of the ratio of head group size ($\sigma_h$) to the width of the
+molecular bodies ($d$). \label{mdfig:rP2}}
 \end{figure}
 
 In addition to varying the size of the head groups, we studied the
@@ -633,8 +642,9 @@ vector. 
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdSP2.pdf} 
-\caption{The $P_2$ order parameters for head group dipoles (a) and
-molecular bodies (b) as a function of the strength of the dipoles.
+\caption[The $P_2$ order parameters as a function of the strength of
+the dipoles.]{The $P_2$ order parameters for head group dipoles (a)
+and molecular bodies (b) as a function of the strength of the dipoles.
 These order parameters are shown for four values of the head group /
 molecular width ratio ($\sigma_h / d$). \label{mdfig:sP2}}
 \end{figure}
@@ -665,10 +675,11 @@ the ripple to gel ($L_{\beta'}$) phase transition.
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdTP2.pdf} 
-\caption{The $P_2$ order parameters for head group dipoles (a) and
-molecular bodies (b) as a function of temperature.
-These order parameters are shown for four values of the head group /
-molecular width ratio ($\sigma_h / d$).\label{mdfig:tP2}}
+\caption[The $P_2$ order parameters as a function of temperature]{The
+$P_2$ order parameters for head group dipoles (a) and molecular bodies
+(b) as a function of temperature.  These order parameters are shown
+for four values of the head group / molecular width ratio ($\sigma_h /
+d$).\label{mdfig:tP2}}
 \end{figure}
 
 Fig. \ref{mdfig:phaseDiagram} shows a phase diagram for the model as a
@@ -687,10 +698,10 @@ dipole region of this diagram.
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{./figures/mdPhaseDiagram.pdf} 
-\caption{Phase diagram for the simple molecular model as a function
-of the head group / molecular width ratio ($\sigma_h / d$) and the
-strength of the head group dipole moment
-($\mu$).\label{mdfig:phaseDiagram}}
+\caption[Phase diagram for the simple molecular model]{Phase diagram
+for the simple molecular model as a function of the head group /
+molecular width ratio ($\sigma_h / d$) and the strength of the head
+group dipole moment ($\mu$).\label{mdfig:phaseDiagram}}
 \end{figure}
 
 We have computed translational diffusion constants for lipid molecules
@@ -739,20 +750,11 @@ times that are too fast when compared with experimenta
 times that are too fast when compared with experimental measurements.
 
 \begin{table*}
-\begin{minipage}{\linewidth}
 \begin{center}
-\caption{Fit values for the rotational correlation times for the head
-groups ($\tau^h$) and molecular bodies ($\tau^b$) as well as the
-translational diffusion constants for the molecule as a function of
-the head-to-body width ratio.  All correlation functions and transport
-coefficients were computed from microcanonical simulations with an
-average temperture of 300 K.  In all of the phases, the head group
-correlation functions decay with an fast librational contribution ($12
-\pm 1$ ps).  There are additional moderate ($\tau^h_{\rm mid}$) and
-slow $\tau^h_{\rm slow}$ contributions to orientational decay that
-depend strongly on the phase exhibited by the lipids.  The symmetric
-ripple phase ($\sigma_h / d = 1.35$) appears to exhibit the slowest
-molecular reorientation.}
+\caption{FIT VALUES FOR THE ROTATIONAL CORRELATION TIMES FOR THE HEAD
+GROUPS ($\tau^h$) AND MOLECULAR BODIES ($\tau^b$) AS WELL AS THE
+TRANSLATIONAL DIFFUSION CONSTANTS FOR THE MOL\-E\-CULE AS A FUNCTION
+OF THE HEAD-TO-BODY WIDTH RATIO}
 \begin{tabular}{lcccc}
 \hline 
 $\sigma_h / d$ & $\tau^h_{\rm mid} (ns)$ & $\tau^h_{\rm
@@ -763,9 +765,20 @@ slow} (\mu s)$ & $\tau^b (\mu s)$ & $D (\times 10^{-11
 1.35 & $3.2$ &  $4.0$ & $0.9$ & $3.42(1)$ \\
 1.41 & $0.3$ & $23.8$ & $6.9$ & $7.16(1)$ \\
 \end{tabular}
+\begin{minipage}{\linewidth}
+%\centering
+\vspace{2mm}
+All correlation functions and transport coefficients were computed
+from microcanonical simulations with an average temperture of 300 K.
+In all of the phases, the head group correlation functions decay with
+an fast librational contribution ($12 \pm 1$ ps).  There are
+additional moderate ($\tau^h_{\rm mid}$) and slow $\tau^h_{\rm slow}$
+contributions to orientational decay that depend strongly on the phase
+exhibited by the lipids.  The symmetric ripple phase ($\sigma_h / d =
+1.35$) appears to exhibit the slowest molecular reorientation.
 \label{mdtab:relaxation}
-\end{center}
 \end{minipage}
+\end{center}
 \end{table*}
 
 \section{Discussion}