--- trunk/tengDissertation/Langevin.tex 2006/06/23 21:33:52 2882 +++ trunk/tengDissertation/Langevin.tex 2006/06/26 13:42:53 2889 @@ -28,24 +28,23 @@ systems\cite{Garcia-Palacios1998,Berkov2002,Denisov200 between the native and denatured states. Because of its stability against noise, Langevin dynamics is very suitable for studying remagnetization processes in various -systems\cite{Garcia-Palacios1998,Berkov2002,Denisov2003}. For -instance, the oscillation power spectrum of nanoparticles from -Langevin dynamics simulation has the same peak frequencies for -different wave vectors,which recovers the property of magnetic -excitations in small finite structures\cite{Berkov2005a}. In an -attempt to reduce the computational cost of simulation, multiple -time stepping (MTS) methods have been introduced and have been of -great interest to macromolecule and protein -community\cite{Tuckerman1992}. Relying on the observation that -forces between distant atoms generally demonstrate slower -fluctuations than forces between close atoms, MTS method are -generally implemented by evaluating the slowly fluctuating forces -less frequently than the fast ones. Unfortunately, nonlinear -instability resulting from increasing timestep in MTS simulation -have became a critical obstruction preventing the long time -simulation. Due to the coupling to the heat bath, Langevin dynamics -has been shown to be able to damp out the resonance artifact more -efficiently\cite{Sandu1999}. +systems\cite{Palacios1998,Berkov2002,Denisov2003}. For instance, the +oscillation power spectrum of nanoparticles from Langevin dynamics +simulation has the same peak frequencies for different wave +vectors,which recovers the property of magnetic excitations in small +finite structures\cite{Berkov2005a}. In an attempt to reduce the +computational cost of simulation, multiple time stepping (MTS) +methods have been introduced and have been of great interest to +macromolecule and protein community\cite{Tuckerman1992}. Relying on +the observation that forces between distant atoms generally +demonstrate slower fluctuations than forces between close atoms, MTS +method are generally implemented by evaluating the slowly +fluctuating forces less frequently than the fast ones. +Unfortunately, nonlinear instability resulting from increasing +timestep in MTS simulation have became a critical obstruction +preventing the long time simulation. Due to the coupling to the heat +bath, Langevin dynamics has been shown to be able to damp out the +resonance artifact more efficiently\cite{Sandu1999}. %review langevin/browninan dynamics for arbitrarily shaped rigid body Combining Langevin or Brownian dynamics with rigid body dynamics, @@ -79,11 +78,11 @@ term\cite{Beard2001}. As a complement to IBD which has average acceleration is not always true for cooperative motion which is common in protein motion. An inertial Brownian dynamics (IBD) was proposed to address this issue by adding an inertial correction -term\cite{Beard2001}. As a complement to IBD which has a lower bound +term\cite{Beard2000}. As a complement to IBD which has a lower bound in time step because of the inertial relaxation time, long-time-step inertial dynamics (LTID) can be used to investigate the inertial behavior of the polymer segments in low friction -regime\cite{Beard2001}. LTID can also deal with the rotational +regime\cite{Beard2000}. LTID can also deal with the rotational dynamics for nonskew bodies without translation-rotation coupling by separating the translation and rotation motion and taking advantage of the analytical solution of hydrodynamics properties. However, @@ -172,12 +171,13 @@ exactly. Introducing an elliptic integral parameter $S due to the complexity of the elliptic integral, only the ellipsoid with the restriction of two axes having to be equal, \textit{i.e.} prolate($ a \ge b = c$) and oblate ($ a < b = c $), can be solved -exactly. Introducing an elliptic integral parameter $S$ for prolate, +exactly. Introducing an elliptic integral parameter $S$ for prolate +: \[ S = \frac{2}{{\sqrt {a^2 - b^2 } }}\ln \frac{{a + \sqrt {a^2 - b^2 } }}{b}, \] -and oblate, +and oblate : \[ S = \frac{2}{{\sqrt {b^2 - a^2 } }}arctg\frac{{\sqrt {b^2 - a^2 } }}{a} @@ -186,14 +186,15 @@ tensors tensors \[ \begin{array}{l} - \Xi _a^{tt} = 16\pi \eta \frac{{a^2 - b^2 }}{{(2a^2 - b^2 )S - 2a}} \\ - \Xi _b^{tt} = \Xi _c^{tt} = 32\pi \eta \frac{{a^2 - b^2 }}{{(2a^2 - 3b^2 )S + 2a}} \\ - \end{array}, + \Xi _a^{tt} = 16\pi \eta \frac{{a^2 - b^2 }}{{(2a^2 - b^2 )S - 2a}}. \\ + \Xi _b^{tt} = \Xi _c^{tt} = 32\pi \eta \frac{{a^2 - b^2 }}{{(2a^2 - 3b^2 )S + + 2a}}, + \end{array} \] and \[ \begin{array}{l} - \Xi _a^{rr} = \frac{{32\pi }}{3}\eta \frac{{(a^2 - b^2 )b^2 }}{{2a - b^2 S}} \\ + \Xi _a^{rr} = \frac{{32\pi }}{3}\eta \frac{{(a^2 - b^2 )b^2 }}{{2a - b^2 S}}, \\ \Xi _b^{rr} = \Xi _c^{rr} = \frac{{32\pi }}{3}\eta \frac{{(a^4 - b^4 )}}{{(2a^2 - b^2 )S - 2a}} \\ \end{array}. \] @@ -541,8 +542,8 @@ rate at lower viscosity regime. explained by the finite size effect and relative slow relaxation rate at lower viscosity regime. \begin{table} -\caption{Average temperatures from Langevin dynamics simulations of -SSD water molecules with reference temperature at 300~K.} +\caption{AVERAGE TEMPERATURES FROM LANGEVIN DYNAMICS SIMULATIONS OF +SSD WATER MOLECULES WITH REFERENCE TEMPERATURE AT 300~K.} \label{langevin:viscosity} \begin{center} \begin{tabular}{|l|l|l|} @@ -584,12 +585,10 @@ simulations and compare their dynamic properties. the systems absent of explicit solvents, we carried out two sets of simulations and compare their dynamic properties. -\subsubsection{Simulations Contain One Banana Shaped Molecule} - -Fig.~\ref{langevin:oneBanana} shows a snapshot of the simulation -made of 256 pentane molecules and one banana shaped molecule at +Fig.~\ref{langevin:twoBanana} shows a snapshot of the simulation +made of 256 pentane molecules and two banana shaped molecules at 273~K. It has an equivalent implicit solvent system containing only -one banana shaped molecule with viscosity of 0.289 center poise. To +two banana shaped molecules with viscosity of 0.289 center poise. To calculate the hydrodynamic properties of the banana shaped molecule, we create a rough shell model (see Fig.~\ref{langevin:roughShell}), in which the banana shaped molecule is represented as a ``shell'' @@ -609,6 +608,8 @@ -6.561e-16&-0.007063&0.7494&0.2057&4.846e-14&1.5036e-1 \end{array}} \right). \] + + \begin{figure} \centering \includegraphics[width=\linewidth]{roughShell.eps} @@ -616,19 +617,25 @@ model for banana shaped molecule.} \label{langevin:rou model for banana shaped molecule.} \label{langevin:roughShell} \end{figure} -%\begin{figure} -%\centering -%\includegraphics[width=\linewidth]{oneBanana.eps} -%\caption[Snapshot from Simulation of One Banana Shaped Molecules and -%256 Pentane Molecules]{Snapshot from simulation of one Banana shaped -%molecules and 256 pentane molecules.} \label{langevin:oneBanana} -%\end{figure} +\begin{figure} +\centering +\includegraphics[width=\linewidth]{twoBanana.eps} +\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} -\subsubsection{Simulations Contain Two Banana Shaped Molecules} +\begin{figure} +\centering +\includegraphics[width=\linewidth]{vacf.eps} +\caption[Plots of Velocity Auto-correlation functions]{Velocity +Auto-correlation function of NVE (blue) and Langevin dynamics +(red).} \label{langevin:twoBanana} +\end{figure} \begin{figure} \centering -\includegraphics[width=\linewidth]{twoBanana.eps} +\includegraphics[width=\linewidth]{uacf.eps} \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}