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|
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\subsection{\label{methodSection:otherSpecialEnsembles}Other Special Ensembles} |
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|
614 |
< |
\subsubsection{\label{methodSection:NPAT}Constant Normal Pressure, Constant Lateral Surface Area and Constant Temperature (NPAT) Ensemble} |
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> |
\subsubsection{\label{methodSection:NPAT}NPAT Ensemble} |
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|
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A comprehensive understanding of structure¨Cfunction relations of |
617 |
|
biological membrane system ultimately relies on structure and |
633 |
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Note that the iterative schemes for NPAT are identical to those |
634 |
|
described for the NPTi integrator. |
635 |
|
|
636 |
< |
\subsubsection{\label{methodSection:NPrT}Constant Normal Pressure, Constant Lateral Surface Tension and Constant Temperature (NP\gamma T) Ensemble } |
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> |
\subsubsection{\label{methodSection:NPrT}NP$\gamma$T Ensemble} |
637 |
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|
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Theoretically, the surface tension $\gamma$ of a stress free |
639 |
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membrane system should be zero since its surface free energy $G$ is |
643 |
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\] |
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However, a surface tension of zero is not appropriate for relatively |
645 |
|
small patches of membrane. In order to eliminate the edge effect of |
646 |
< |
the membrane simulation, a special ensemble, NP\gamma T, is proposed |
647 |
< |
to maintain the lateral surface tension and normal pressure. The |
648 |
< |
equation of motion for cell size control tensor, $\eta$, in NP\gamma |
649 |
< |
T is |
646 |
> |
the membrane simulation, a special ensemble, NP$\gamma$T, is |
647 |
> |
proposed to maintain the lateral surface tension and normal |
648 |
> |
pressure. The equation of motion for cell size control tensor, |
649 |
> |
$\eta$, in NP\gamma T is |
650 |
|
\begin{equation} |
651 |
|
\dot |
652 |
|
\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\leftrightarrow$}} |
674 |
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integrator is a special case of $NP\gamma T$ if the surface tension |
675 |
|
$\gamma$ is set to zero. |
676 |
|
|
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+ |
%\section{\label{methodSection:constraintMethod}Constraint Method} |
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+ |
|
679 |
+ |
%\subsection{\label{methodSection:bondConstraint}Bond Constraint for Rigid Body} |
680 |
+ |
|
681 |
+ |
%\subsection{\label{methodSection:zcons}Z-constraint Method} |
682 |
+ |
|
683 |
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\section{\label{methodSection:langevin}Integrators for Langevin Dynamics of Rigid Bodies} |
684 |
|
|
685 |
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\subsection{\label{methodSection:temperature}Temperature Control} |