--- trunk/tengDissertation/Langevin.tex 2006/06/16 01:54:28 2865 +++ trunk/tengDissertation/Langevin.tex 2006/06/17 18:43:58 2867 @@ -98,7 +98,7 @@ sophisticated rigid body dynamics. estimation of friction tensor from hydrodynamics theory into the sophisticated rigid body dynamics. -\section{Computational methods{\label{methodSec}}} +\section{Computational Methods{\label{methodSec}}} \subsection{\label{introSection:frictionTensor}Friction Tensor} Theoretically, the friction kernel can be determined using velocity @@ -360,7 +360,7 @@ joining center of resistance $R$ and origin $O$. where $x_OR$, $y_OR$, $z_OR$ are the components of the vector joining center of resistance $R$ and origin $O$. -\subsection{Langevin dynamics for rigid particles of arbitrary shape\label{LDRB}} +\subsection{Langevin Dynamics for Rigid Particles of Arbitrary Shape\label{LDRB}} Consider a Langevin equation of motions in generalized coordinates \begin{equation} @@ -515,13 +515,13 @@ be advanced to the same time value. + \frac{h}{2} {\bf \tau}^b(t + h) . \end{align*} -\section{Results and discussion} +\section{Results and Discussion} The Langevin algorithm described in previous section has been implemented in {\sc oopse}\cite{Meineke2005} and applied to the studies of kinetics and thermodynamic properties in several systems. -\subsection{Temperature control} +\subsection{Temperature Control} As shown in Eq.~\ref{randomForce}, random collisions associated with the solvent's thermal motions is controlled by the external @@ -570,7 +570,6 @@ the temperature control ability. NVE (see green curve in Fig.~\ref{langevin:temperature}) which loses the temperature control ability. - \begin{figure} \centering \includegraphics[width=\linewidth]{temperature.eps} @@ -578,8 +577,10 @@ temperature fluctuation versus time.} \label{langevin: temperature fluctuation versus time.} \label{langevin:temperature} \end{figure} -\subsection{Langevin dynamics of banana-shaped molecule} +\subsection{Langevin Dynamics of Banana Shaped Molecule} + + \begin{figure} \centering \includegraphics[width=\linewidth]{one_banana.eps} @@ -589,14 +590,16 @@ temperature fluctuation versus time.} \label{langevin: \begin{figure} \centering \includegraphics[width=\linewidth]{roughShell.eps} -\caption[Rough Shell]{Rough Shell.} \label{langevin:roughShell} +\caption[Rough shell model for banana shaped molecule]{Rough shell +model for banana shaped molecule.} \label{langevin:roughShell} \end{figure} \begin{figure} \centering \includegraphics[width=\linewidth]{twoBanana.eps} -\caption[Two Banana Shaped Molecules]{Two Banana Shaped Molecules.} -\label{langevin:twoBanana} +\caption[Snapshot from Simulation of Two Banana Shaped Molecules and +256 Pentane Molecules]{Snapshot from simulation of two Banana shaped +molecules and 256 pentane molecules.} \label{langevin:twoBanana} \end{figure} \section{Conclusions}