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# Line 101 | Line 101 | the ripple formation can be found in section
101   \begin{figure}
102   \centering
103   \includegraphics[width=\linewidth]{./figures/mdLipidModels.pdf}
104 < \caption{Three different representations of DPPC lipid molecules,
104 > \caption[Three different representations of DPPC lipid
105 > molecules]{Three different representations of DPPC lipid molecules,
106   including the chemical structure, an atomistic model, and the
107   head-body ellipsoidal coarse-grained model used in this
108   work.\label{mdfig:lipidModels}}
# Line 140 | Line 141 | $\sigma$ and $\epsilon$ parameters,
141   Pechukas.\cite{Berne72} The potential is constructed in the familiar
142   form of the Lennard-Jones function using orientation-dependent
143   $\sigma$ and $\epsilon$ parameters,
144 < \begin{equation}
144 < \begin{split}
144 > \begin{multline}
145   V_{ij}({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j}, {\mathbf{\hat
146 < r}_{ij}}) = & 4\epsilon ({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j},
146 > r}_{ij}}) = 4\epsilon ({\mathbf{\hat u}_i}, {\mathbf{\hat u}_j},
147   {\mathbf{\hat r}_{ij}})\left[ \left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i},
148 < {\mathbf{\hat u}_j}, {\mathbf{\hat r}_{ij}})+\sigma_0}\right)^{12} \right.\\
149 < &\left. -\left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i},
148 > {\mathbf{\hat u}_j}, {\mathbf{\hat r}_{ij}})+\sigma_0}\right)^{12}
149 > \right. \\
150 > \left. - \left(\frac{\sigma_0}{r_{ij}-\sigma({\mathbf{\hat u}_i},
151   {\mathbf{\hat u}_j}, {\mathbf{\hat
152   r}_{ij}})+\sigma_0}\right)^6\right]
152 \end{split}
153   \label{mdeq:gb}
154 < \end{equation}
154 > \end{multline}
155  
156   The range $(\sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf
157   \hat{r}}_{ij}))$, and strength $(\epsilon({\bf \hat{u}}_{i},{\bf
# Line 172 | Line 172 | calculate the range function,
172   where $l$ and $d$ describe the length and width of each uniaxial
173   ellipsoid.  These shape anisotropy parameters can then be used to
174   calculate the range function,
175 < \begin{equation}
176 < \begin{split}
177 < & \sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) =
178 < \sigma_{0} \times  \\
179 < & \left[ 1- \left\{ \frac{ \chi \alpha^2 ({\bf \hat{u}}_i \cdot {\bf
175 > \begin{multline}
176 > \sigma({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij}) = \\
177 > \sigma_0 \left[ 1 - \left\{ \frac{ \chi \alpha^2 ({\bf \hat{u}}_i \cdot {\bf
178   \hat{r}}_{ij} ) + \chi \alpha^{-2} ({\bf \hat{u}}_j \cdot {\bf
179   \hat{r}}_{ij} ) - 2 \chi^2 ({\bf \hat{u}}_i \cdot {\bf
180   \hat{r}}_{ij} )({\bf \hat{u}}_j \cdot {\bf
181   \hat{r}}_{ij} ) ({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j)}{1 - \chi^2
182   \left({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j\right)^2} \right\}
183 < \right]^{-1/2}
184 < \end{split}
187 < \end{equation}
183 > \right]^{-1/2}
184 > \end{multline}
185  
186   Gay-Berne ellipsoids also have an energy scaling parameter,
187   $\epsilon^s$, which describes the well depth for two identical
# Line 211 | Line 208 | The form of the strength function is somewhat complica
208   \left[1-\chi^{2}({\bf \hat{u}}_{i}.{\bf
209   \hat{u}}_{j})^{2}\right]^{-1/2}
210   \end{eqnarray*}
211 < \begin{equation*}
212 < \begin{split}
213 < & \epsilon_{2}({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij})
214 < = 1 - \\
218 < & \left\{ \frac{ \chi' \alpha'^2 ({\bf \hat{u}}_i \cdot {\bf
211 > \begin{multline*}
212 > \epsilon_{2}({\bf \hat{u}}_{i},{\bf \hat{u}}_{j},{\bf \hat{r}}_{ij})
213 > =  \\
214 > 1 - \left\{ \frac{ \chi' \alpha'^2 ({\bf \hat{u}}_i \cdot {\bf
215   \hat{r}}_{ij} ) + \chi' \alpha'^{-2} ({\bf \hat{u}}_j \cdot {\bf
216   \hat{r}}_{ij} ) - 2 \chi'^2 ({\bf \hat{u}}_i \cdot {\bf
217   \hat{r}}_{ij} )({\bf \hat{u}}_j \cdot {\bf
218   \hat{r}}_{ij} ) ({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j)}{1 - \chi'^2
219   \left({\bf \hat{u}}_i \cdot {\bf \hat{u}}_j\right)^2} \right\},
220 < \end{split}
225 < \end{equation*}
220 > \end{multline*}
221   although many of the quantities and derivatives are identical with
222   those obtained for the range parameter. Ref. \citen{Luckhurst90}
223   has a particularly good explanation of the choice of the Gay-Berne
# Line 249 | Line 244 | actual parameters used in our simulations are given in
244   \begin{figure}
245   \centering
246   \includegraphics[width=\linewidth]{./figures/md2LipidModel.pdf}
247 < \caption{The parameters defining the behavior of the lipid
248 < models. $\sigma_h / d$ is the ratio of the head group to body diameter.
249 < Molecular bodies had a fixed aspect ratio of 3.0.  The solvent model
250 < was a simplified 4-water bead ($\sigma_w \approx d$) that has been
251 < used in other coarse-grained simulations.  The dipolar strength
252 < (and the temperature and pressure) were the only other parameters that
253 < were varied systematically.\label{mdfig:lipidModel}}
247 > \caption[The parameters defining the behavior of the lipid
248 > models]{The parameters defining the behavior of the lipid
249 > models. $\sigma_h / d$ is the ratio of the head group to body
250 > diameter.  Molecular bodies had a fixed aspect ratio of 3.0.  The
251 > solvent model was a simplified 4-water bead ($\sigma_w \approx d$)
252 > that has been used in other coarse-grained simulations.  The dipolar
253 > strength (and the temperature and pressure) were the only other
254 > parameters that were varied systematically.\label{mdfig:lipidModel}}
255   \end{figure}
256  
257   To take into account the permanent dipolar interactions of the
# Line 327 | Line 323 | water).
323   \begin{table*}
324   \begin{minipage}{\linewidth}
325   \begin{center}
326 < \caption{Potential parameters used for molecular-scale coarse-grained
327 < lipid simulations}
326 > \caption{POTENTIAL PARAMETERS USED FOR MOLECULAR SCALE COARSE-GRAINED
327 > LIPID SIMULATIONS}
328   \begin{tabular}{llccc}
329   \hline
330    & &  Head & Chain & Solvent \\
# Line 349 | Line 345 | $\mu$ (Debye) & & varied & 0 & 0 \\
345   \end{minipage}
346   \end{table*}
347  
348 < \section{Experimental Methodology}
349 < \label{mdsec:experiment}
348 > \section{Simulation Methodology}
349 > \label{mdsec:simulation}
350  
351   The parameters that were systematically varied in this study were the
352   size of the head group ($\sigma_h$), the strength of the dipole moment
# Line 445 | Line 441 | phase observed when $\sigma_h = 1.35 d$.
441   \begin{figure}
442   \centering
443   \includegraphics[width=\linewidth]{./figures/mdPhaseCartoon.pdf}
444 < \caption{The role of the ratio between the head group size and the
445 < width of the molecular bodies is to increase the local membrane
446 < curvature.  With strong attractive interactions between the head
447 < groups, this local curvature can be maintained in bilayer structures
448 < through surface corrugation.  Shown above are three phases observed in
449 < these simulations.  With $\sigma_h = 1.20 d$, the bilayer maintains a
450 < flat topology.  For larger heads ($\sigma_h = 1.35 d$) the local
451 < curvature resolves into a symmetrically rippled phase with little or
452 < no interdigitation between the upper and lower leaves of the membrane.
453 < The largest heads studied ($\sigma_h = 1.41 d$) resolve into an
454 < asymmetric rippled phases with interdigitation between the two
455 < leaves.\label{mdfig:phaseCartoon}}
444 > \caption[ three phases observed in the simulations]{The role of the
445 > ratio between the head group size and the width of the molecular
446 > bodies is to increase the local membrane curvature.  With strong
447 > attractive interactions between the head groups, this local curvature
448 > can be maintained in bilayer structures through surface corrugation.
449 > Shown above are three phases observed in these simulations.  With
450 > $\sigma_h = 1.20 d$, the bilayer maintains a flat topology.  For
451 > larger heads ($\sigma_h = 1.35 d$) the local curvature resolves into a
452 > symmetrically rippled phase with little or no interdigitation between
453 > the upper and lower leaves of the membrane.  The largest heads studied
454 > ($\sigma_h = 1.41 d$) resolve into an asymmetric rippled phases with
455 > interdigitation between the two leaves.\label{mdfig:phaseCartoon}}
456   \end{figure}
457  
458   Sample structures for the flat ($\sigma_h = 1.20 d$), symmetric
# Line 482 | Line 478 | for PE head groups.
478   for PE head groups.
479  
480   \begin{table*}
485 \begin{minipage}{\linewidth}
481   \begin{center}
482 < \caption{Phase, bilayer spacing, area per lipid, ripple wavelength
483 < and amplitude observed as a function of the ratio between the head
484 < beads and the diameters of the tails.  Ripple wavelengths and
490 < amplitudes are normalized to the diameter of the tail ellipsoids.}
482 > \caption{PHASE, BILAYER SPACING, AREA PER LIPID, RIPPLE WAVELENGTH AND
483 > AMPLITUDE OBSERVED AS A FUNCTION OF THE RATIO BETWEEN THE HEAD BEADS
484 > AND THE DIAMETERS OF THE TAILS}
485   \begin{tabular}{lccccc}
486   \hline
487   $\sigma_h / d$ & type of phase & bilayer spacing (\AA) & area per
# Line 498 | Line 492 | lipid (\AA$^2$) & $\lambda / d$ & $A / d$\\
492   1.35 & symmetric ripple & 42.9 & 51.7 & 17.2 & 2.2 \\
493   1.41 & asymmetric ripple & 37.1 & 63.1 & 15.4 & 1.5 \\
494   \end{tabular}
495 + \begin{minipage}{\linewidth}
496 + %\centering
497 + \vspace{2mm}    
498 + Ripple wavelengths and amplitudes are normalized to the diameter of
499 + the tail ellipsoids.
500   \label{mdtab:property}
502 \end{center}
501   \end{minipage}
502 + \end{center}
503   \end{table*}
504  
505   The membrane structures and the reduced wavelength $\lambda / d$,
# Line 516 | Line 515 | likely to underestimate of the true amplitudes.
515   \begin{figure}
516   \centering
517   \includegraphics[width=\linewidth]{./figures/mdTopDown.pdf}
518 < \caption{Top views of the flat (upper), symmetric ripple (middle),
519 < and asymmetric ripple (lower) phases.  Note that the head-group
520 < dipoles have formed head-to-tail chains in all three of these phases,
521 < but in the two rippled phases, the dipolar chains are all aligned {\it
522 < perpendicular} to the direction of the ripple.  Note that the flat
523 < membrane has multiple vortex defects in the dipolar ordering, and the
524 < ordering on the lower leaf of the bilayer can be in an entirely
525 < different direction from the upper leaf.\label{mdfig:topView}}
518 > \caption[Top views of the flat, symmetric ripple, and asymmetric
519 > ripple phases]{Top views of the flat (upper), symmetric ripple
520 > (middle), and asymmetric ripple (lower) phases.  Note that the
521 > head-group dipoles have formed head-to-tail chains in all three of
522 > these phases, but in the two rippled phases, the dipolar chains are
523 > all aligned {\it perpendicular} to the direction of the ripple.  Note
524 > that the flat membrane has multiple vortex defects in the dipolar
525 > ordering, and the ordering on the lower leaf of the bilayer can be in
526 > an entirely different direction from the upper
527 > leaf.\label{mdfig:topView}}
528   \end{figure}
529  
530   The orientational ordering in the system is observed by $P_2$ order
# Line 588 | Line 589 | rapidly decreasing $P_2$ ordering for the molecular bo
589   \begin{figure}
590   \centering
591   \includegraphics[width=\linewidth]{./figures/mdRP2.pdf}
592 < \caption{The $P_2$ order parameters for head groups (circles) and
593 < molecular bodies (squares) as a function of the ratio of head group
594 < size ($\sigma_h$) to the width of the molecular bodies ($d$). \label{mdfig:rP2}}
592 > \caption[The $P_2$ order parameters as a function of the ratio of head group
593 > size to the width of the molecular bodies]{The $P_2$ order parameters
594 > for head groups (circles) and molecular bodies (squares) as a function
595 > of the ratio of head group size ($\sigma_h$) to the width of the
596 > molecular bodies ($d$). \label{mdfig:rP2}}
597   \end{figure}
598  
599   In addition to varying the size of the head groups, we studied the
# Line 639 | Line 642 | vector.
642   \begin{figure}
643   \centering
644   \includegraphics[width=\linewidth]{./figures/mdSP2.pdf}
645 < \caption{The $P_2$ order parameters for head group dipoles (a) and
646 < molecular bodies (b) as a function of the strength of the dipoles.
645 > \caption[The $P_2$ order parameters as a function of the strength of
646 > the dipoles.]{The $P_2$ order parameters for head group dipoles (a)
647 > and molecular bodies (b) as a function of the strength of the dipoles.
648   These order parameters are shown for four values of the head group /
649   molecular width ratio ($\sigma_h / d$). \label{mdfig:sP2}}
650   \end{figure}
# Line 671 | Line 675 | the ripple to gel ($L_{\beta'}$) phase transition.
675   \begin{figure}
676   \centering
677   \includegraphics[width=\linewidth]{./figures/mdTP2.pdf}
678 < \caption{The $P_2$ order parameters for head group dipoles (a) and
679 < molecular bodies (b) as a function of temperature.
680 < These order parameters are shown for four values of the head group /
681 < molecular width ratio ($\sigma_h / d$).\label{mdfig:tP2}}
678 > \caption[The $P_2$ order parameters as a function of temperature]{The
679 > $P_2$ order parameters for head group dipoles (a) and molecular bodies
680 > (b) as a function of temperature.  These order parameters are shown
681 > for four values of the head group / molecular width ratio ($\sigma_h /
682 > d$).\label{mdfig:tP2}}
683   \end{figure}
684  
685   Fig. \ref{mdfig:phaseDiagram} shows a phase diagram for the model as a
# Line 693 | Line 698 | dipole region of this diagram.
698   \begin{figure}
699   \centering
700   \includegraphics[width=\linewidth]{./figures/mdPhaseDiagram.pdf}
701 < \caption{Phase diagram for the simple molecular model as a function
702 < of the head group / molecular width ratio ($\sigma_h / d$) and the
703 < strength of the head group dipole moment
704 < ($\mu$).\label{mdfig:phaseDiagram}}
701 > \caption[Phase diagram for the simple molecular model]{Phase diagram
702 > for the simple molecular model as a function of the head group /
703 > molecular width ratio ($\sigma_h / d$) and the strength of the head
704 > group dipole moment ($\mu$).\label{mdfig:phaseDiagram}}
705   \end{figure}
706  
707   We have computed translational diffusion constants for lipid molecules
708   from the mean-square displacement,
709   \begin{equation}
710 < D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle {|\left({\bf r}_{i}(t) - {\bf r}_{i}(0) \right)|}^2 \rangle,
710 > D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle {|\left({\bf
711 > r}_{i}(t) - {\bf r}_{i}(0) \right)|}^2 \rangle,
712 > \label{mdeq:msdisplacement}
713   \end{equation}
714   of the lipid bodies. Translational diffusion constants for the
715   different head-to-tail size ratios (all at 300 K) are shown in table
# Line 743 | Line 750 | times that are too fast when compared with experimenta
750   times that are too fast when compared with experimental measurements.
751  
752   \begin{table*}
746 \begin{minipage}{\linewidth}
753   \begin{center}
754 < \caption{Fit values for the rotational correlation times for the head
755 < groups ($\tau^h$) and molecular bodies ($\tau^b$) as well as the
756 < translational diffusion constants for the molecule as a function of
757 < the head-to-body width ratio.  All correlation functions and transport
752 < coefficients were computed from microcanonical simulations with an
753 < average temperture of 300 K.  In all of the phases, the head group
754 < correlation functions decay with an fast librational contribution ($12
755 < \pm 1$ ps).  There are additional moderate ($\tau^h_{\rm mid}$) and
756 < slow $\tau^h_{\rm slow}$ contributions to orientational decay that
757 < depend strongly on the phase exhibited by the lipids.  The symmetric
758 < ripple phase ($\sigma_h / d = 1.35$) appears to exhibit the slowest
759 < molecular reorientation.}
754 > \caption{FIT VALUES FOR THE ROTATIONAL CORRELATION TIMES FOR THE HEAD
755 > GROUPS ($\tau^h$) AND MOLECULAR BODIES ($\tau^b$) AS WELL AS THE
756 > TRANSLATIONAL DIFFUSION CONSTANTS FOR THE MOL\-E\-CULE AS A FUNCTION
757 > OF THE HEAD-TO-BODY WIDTH RATIO}
758   \begin{tabular}{lcccc}
759   \hline
760   $\sigma_h / d$ & $\tau^h_{\rm mid} (ns)$ & $\tau^h_{\rm
# Line 767 | Line 765 | slow} (\mu s)$ & $\tau^b (\mu s)$ & $D (\times 10^{-11
765   1.35 & $3.2$ &  $4.0$ & $0.9$ & $3.42(1)$ \\
766   1.41 & $0.3$ & $23.8$ & $6.9$ & $7.16(1)$ \\
767   \end{tabular}
768 + \begin{minipage}{\linewidth}
769 + %\centering
770 + \vspace{2mm}
771 + All correlation functions and transport coefficients were computed
772 + from microcanonical simulations with an average temperture of 300 K.
773 + In all of the phases, the head group correlation functions decay with
774 + an fast librational contribution ($12 \pm 1$ ps).  There are
775 + additional moderate ($\tau^h_{\rm mid}$) and slow $\tau^h_{\rm slow}$
776 + contributions to orientational decay that depend strongly on the phase
777 + exhibited by the lipids.  The symmetric ripple phase ($\sigma_h / d =
778 + 1.35$) appears to exhibit the slowest molecular reorientation.
779   \label{mdtab:relaxation}
771 \end{center}
780   \end{minipage}
781 + \end{center}
782   \end{table*}
783  
784   \section{Discussion}
# Line 843 | Line 852 | have recently used axially-specific chromophores
852   orientations of the membrane dipoles may be available from
853   fluorescence detected linear dichroism (LD).  Benninger {\it et al.}
854   have recently used axially-specific chromophores
855 < 2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3-phospocholine
856 < ($\beta$-BODIPY FL C5-HPC or BODIPY-PC) and 3,3'
855 > 2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3-\\
856 > phospocholine ($\beta$-BODIPY FL C5-HPC or BODIPY-PC) and 3,3'
857   dioctadecyloxacarbocyanine perchlorate (DiO) in their
858   fluorescence-detected linear dichroism (LD) studies of plasma
859   membranes of living cells.\cite{Benninger:2005qy} The DiO dye aligns

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