98 |
|
estimation of friction tensor from hydrodynamics theory into the |
99 |
|
sophisticated rigid body dynamics. |
100 |
|
|
101 |
< |
\section{Computational methods{\label{methodSec}}} |
101 |
> |
\section{Computational Methods{\label{methodSec}}} |
102 |
|
|
103 |
|
\subsection{\label{introSection:frictionTensor}Friction Tensor} |
104 |
< |
Theoretically, the friction kernel can be determined using velocity |
105 |
< |
autocorrelation function. However, this approach become impractical |
106 |
< |
when the system become more and more complicate. Instead, various |
107 |
< |
approaches based on hydrodynamics have been developed to calculate |
108 |
< |
the friction coefficients. The friction effect is isotropic in |
109 |
< |
Equation, $\zeta$ can be taken as a scalar. In general, friction |
110 |
< |
tensor $\Xi$ is a $6\times 6$ matrix given by |
104 |
> |
Theoretically, the friction kernel can be determined using the |
105 |
> |
velocity autocorrelation function. However, this approach become |
106 |
> |
impractical when the system become more and more complicate. |
107 |
> |
Instead, various approaches based on hydrodynamics have been |
108 |
> |
developed to calculate the friction coefficients. In general, |
109 |
> |
friction tensor $\Xi$ is a $6\times 6$ matrix given by |
110 |
|
\[ |
111 |
|
\Xi = \left( {\begin{array}{*{20}c} |
112 |
|
{\Xi _{}^{tt} } & {\Xi _{}^{rt} } \\ |
137 |
|
|
138 |
|
\subsubsection{\label{introSection:resistanceTensorRegular}\textbf{The Resistance Tensor for Regular Shape}} |
139 |
|
|
140 |
< |
For a spherical particle, the translational and rotational friction |
141 |
< |
constant can be calculated from Stoke's law, |
140 |
> |
For a spherical particle with slip boundary conditions, the |
141 |
> |
translational and rotational friction constant can be calculated |
142 |
> |
from Stoke's law, |
143 |
|
\[ |
144 |
|
\Xi ^{tt} = \left( {\begin{array}{*{20}c} |
145 |
|
{6\pi \eta R} & 0 & 0 \\ |
161 |
|
Other non-spherical shape, such as cylinder and ellipsoid |
162 |
|
\textit{etc}, are widely used as reference for developing new |
163 |
|
hydrodynamics theory, because their properties can be calculated |
164 |
< |
exactly. In 1936, Perrin extended Stokes's law to general ellipsoid, |
165 |
< |
also called a triaxial ellipsoid, which is given in Cartesian |
166 |
< |
coordinates by\cite{Perrin1934, Perrin1936} |
164 |
> |
exactly. In 1936, Perrin extended Stokes's law to general |
165 |
> |
ellipsoids, also called a triaxial ellipsoid, which is given in |
166 |
> |
Cartesian coordinates by\cite{Perrin1934, Perrin1936} |
167 |
|
\[ |
168 |
|
\frac{{x^2 }}{{a^2 }} + \frac{{y^2 }}{{b^2 }} + \frac{{z^2 }}{{c^2 |
169 |
|
}} = 1 |
198 |
|
\end{array}. |
199 |
|
\] |
200 |
|
|
201 |
< |
\subsubsection{\label{introSection:resistanceTensorRegularArbitrary}\textbf{The Resistance Tensor for Arbitrary Shape}} |
201 |
> |
\subsubsection{\label{introSection:resistanceTensorRegularArbitrary}\textbf{The Resistance Tensor for Arbitrary Shapes}} |
202 |
|
|
203 |
< |
Unlike spherical and other regular shaped molecules, there is not |
204 |
< |
analytical solution for friction tensor of any arbitrary shaped |
203 |
> |
Unlike spherical and other simply shaped molecules, there is no |
204 |
> |
analytical solution for the friction tensor for arbitrarily shaped |
205 |
|
rigid molecules. The ellipsoid of revolution model and general |
206 |
|
triaxial ellipsoid model have been used to approximate the |
207 |
|
hydrodynamic properties of rigid bodies. However, since the mapping |
208 |
< |
from all possible ellipsoidal space, $r$-space, to all possible |
209 |
< |
combination of rotational diffusion coefficients, $D$-space is not |
208 |
> |
from all possible ellipsoidal spaces, $r$-space, to all possible |
209 |
> |
combination of rotational diffusion coefficients, $D$-space, is not |
210 |
|
unique\cite{Wegener1979} as well as the intrinsic coupling between |
211 |
< |
translational and rotational motion of rigid body, general ellipsoid |
212 |
< |
is not always suitable for modeling arbitrarily shaped rigid |
213 |
< |
molecule. A number of studies have been devoted to determine the |
214 |
< |
friction tensor for irregularly shaped rigid bodies using more |
211 |
> |
translational and rotational motion of rigid body, general |
212 |
> |
ellipsoids are not always suitable for modeling arbitrarily shaped |
213 |
> |
rigid molecule. A number of studies have been devoted to determine |
214 |
> |
the friction tensor for irregularly shaped rigid bodies using more |
215 |
|
advanced method where the molecule of interest was modeled by |
216 |
|
combinations of spheres(beads)\cite{Carrasco1999} and the |
217 |
|
hydrodynamics properties of the molecule can be calculated using the |
273 |
|
B_{ij} = \delta _{ij} \frac{I}{{6\pi \eta R}} + (1 - \delta _{ij} |
274 |
|
)T_{ij} |
275 |
|
\] |
276 |
< |
where $\delta _{ij}$ is Kronecker delta function. Inverting matrix |
277 |
< |
$B$, we obtain |
276 |
> |
where $\delta _{ij}$ is Kronecker delta function. Inverting the $B$ |
277 |
> |
matrix, we obtain |
278 |
|
|
279 |
|
\[ |
280 |
|
C = B^{ - 1} = \left( {\begin{array}{*{20}c} |
306 |
|
|
307 |
|
The resistance tensor depends on the origin to which they refer. The |
308 |
|
proper location for applying friction force is the center of |
309 |
< |
resistance (reaction), at which the trace of rotational resistance |
310 |
< |
tensor, $ \Xi ^{rr}$ reaches minimum. Mathematically, the center of |
311 |
< |
resistance is defined as an unique point of the rigid body at which |
312 |
< |
the translation-rotation coupling tensor are symmetric, |
309 |
> |
resistance (or center of reaction), at which the trace of rotational |
310 |
> |
resistance tensor, $ \Xi ^{rr}$ reaches a minimum value. |
311 |
> |
Mathematically, the center of resistance is defined as an unique |
312 |
> |
point of the rigid body at which the translation-rotation coupling |
313 |
> |
tensor are symmetric, |
314 |
|
\begin{equation} |
315 |
|
\Xi^{tr} = \left( {\Xi^{tr} } \right)^T |
316 |
|
\label{introEquation:definitionCR} |
317 |
|
\end{equation} |
318 |
< |
Form Equation \ref{introEquation:ResistanceTensorArbitraryOrigin}, |
318 |
> |
From Equation \ref{introEquation:ResistanceTensorArbitraryOrigin}, |
319 |
|
we can easily find out that the translational resistance tensor is |
320 |
|
origin independent, while the rotational resistance tensor and |
321 |
|
translation-rotation coupling resistance tensor depend on the |
322 |
< |
origin. Given resistance tensor at an arbitrary origin $O$, and a |
323 |
< |
vector ,$r_{OP}(x_{OP}, y_{OP}, z_{OP})$, from $O$ to $P$, we can |
322 |
> |
origin. Given the resistance tensor at an arbitrary origin $O$, and |
323 |
> |
a vector ,$r_{OP}(x_{OP}, y_{OP}, z_{OP})$, from $O$ to $P$, we can |
324 |
|
obtain the resistance tensor at $P$ by |
325 |
|
\begin{equation} |
326 |
|
\begin{array}{l} |
361 |
|
where $x_OR$, $y_OR$, $z_OR$ are the components of the vector |
362 |
|
joining center of resistance $R$ and origin $O$. |
363 |
|
|
364 |
< |
\subsection{Langevin dynamics for rigid particles of arbitrary shape\label{LDRB}} |
364 |
> |
\subsection{Langevin Dynamics for Rigid Particles of Arbitrary Shape\label{LDRB}} |
365 |
|
|
366 |
|
Consider a Langevin equation of motions in generalized coordinates |
367 |
|
\begin{equation} |
516 |
|
+ \frac{h}{2} {\bf \tau}^b(t + h) . |
517 |
|
\end{align*} |
518 |
|
|
519 |
< |
\section{Results and discussion} |
519 |
> |
\section{Results and Discussion} |
520 |
|
|
521 |
|
The Langevin algorithm described in previous section has been |
522 |
|
implemented in {\sc oopse}\cite{Meineke2005} and applied to the |
523 |
|
studies of kinetics and thermodynamic properties in several systems. |
524 |
|
|
525 |
< |
\subsection{Temperature control} |
525 |
> |
\subsection{Temperature Control} |
526 |
|
|
527 |
|
As shown in Eq.~\ref{randomForce}, random collisions associated with |
528 |
|
the solvent's thermal motions is controlled by the external |
547 |
|
\begin{center} |
548 |
|
\begin{tabular}{|l|l|l|} |
549 |
|
\hline |
550 |
< |
\eta & $\text{T}_{\text{avg}}$ & $\text{T}_{\text{rms}}$ \\ |
550 |
> |
$\eta$ & $\text{T}_{\text{avg}}$ & $\text{T}_{\text{rms}}$ \\ |
551 |
|
1 & 300.47 & 10.99 \\ |
552 |
|
0.1 & 301.19 & 11.136 \\ |
553 |
|
0.01 & 303.04 & 11.796 \\ |
571 |
|
NVE (see green curve in Fig.~\ref{langevin:temperature}) which loses |
572 |
|
the temperature control ability. |
573 |
|
|
573 |
– |
|
574 |
|
\begin{figure} |
575 |
|
\centering |
576 |
|
\includegraphics[width=\linewidth]{temperature.eps} |
578 |
|
temperature fluctuation versus time.} \label{langevin:temperature} |
579 |
|
\end{figure} |
580 |
|
|
581 |
< |
\subsection{Langevin dynamics of banana-shaped molecule} |
581 |
> |
\subsection{Langevin Dynamics of Banana Shaped Molecule} |
582 |
> |
|
583 |
> |
In order to verify that Langevin dynamics can mimic the dynamics of |
584 |
> |
the systems absent of explicit solvents, we carried out two sets of |
585 |
> |
simulations and compare their dynamic properties. |
586 |
|
|
587 |
+ |
\subsubsection{Simulations Contain One Banana Shaped Molecule} |
588 |
+ |
|
589 |
+ |
Fig.~\ref{langevin:oneBanana} shows a snapshot of the simulation |
590 |
+ |
made of 256 pentane molecules and one banana shaped molecule at |
591 |
+ |
273~K. It has an equivalent implicit solvent model containing only |
592 |
+ |
one banana shaped molecule with viscosity of 0.289 center poise. To |
593 |
+ |
calculate the hydrodynamic properties of the banana shaped molecule, |
594 |
+ |
we create a rough shell model (see Fig.~\ref{langevin:roughShell}), |
595 |
+ |
in which the banana shaped molecule is represented as a ``shell'' |
596 |
+ |
made of 2266 small identical beads with size of 0.3 $\AA$ on the |
597 |
+ |
surface. Applying the procedure described in |
598 |
+ |
Sec.~\ref{introEquation:ResistanceTensorArbitraryOrigin}, we |
599 |
+ |
identified the center of resistance at $(0, 0.7482, -0.1988)$, as |
600 |
+ |
well as the resistance tensor, |
601 |
+ |
\[ |
602 |
+ |
\left( {\begin{array}{*{20}c} |
603 |
+ |
0.9261 & 1.310e-14 & -7.292e-15&5.067e-14&0.08585&0.2057\\ |
604 |
+ |
3.968e-14& 0.9270&-0.007063& 0.08585&6.764e-14&4.846e-14\\ |
605 |
+ |
-6.561e-16&-0.007063&0.7494&0.2057&4.846e-14&1.5036e-14\\ |
606 |
+ |
5.067e-14&0.0858&0.2057& 58.64& 8.563e-13&-8.5736\\ |
607 |
+ |
0.08585&6.764e-14&4.846e-14&1.555e-12&48.30&3.219&\\ |
608 |
+ |
0.2057&4.846e-14&1.5036e-14&-3.904e-13&3.219&10.7373\\ |
609 |
+ |
\end{array}} \right). |
610 |
+ |
\] |
611 |
+ |
|
612 |
|
\begin{figure} |
613 |
|
\centering |
614 |
< |
\includegraphics[width=\linewidth]{one_banana.eps} |
615 |
< |
\caption[]{.} \label{langevin:banana} |
614 |
> |
\includegraphics[width=\linewidth]{roughShell.eps} |
615 |
> |
\caption[Rough shell model for banana shaped molecule]{Rough shell |
616 |
> |
model for banana shaped molecule.} \label{langevin:roughShell} |
617 |
|
\end{figure} |
618 |
|
|
619 |
|
\begin{figure} |
620 |
|
\centering |
621 |
< |
\includegraphics[width=\linewidth]{roughShell.eps} |
622 |
< |
\caption[Rough Shell]{Rough Shell.} \label{langevin:roughShell} |
621 |
> |
\includegraphics[width=\linewidth]{oneBanana.eps} |
622 |
> |
\caption[Snapshot from Simulation of One Banana Shaped Molecules and |
623 |
> |
256 Pentane Molecules]{Snapshot from simulation of one Banana shaped |
624 |
> |
molecules and 256 pentane molecules.} \label{langevin:oneBanana} |
625 |
|
\end{figure} |
626 |
|
|
627 |
+ |
\subsubsection{Simulations Contain Two Banana Shaped Molecules} |
628 |
+ |
|
629 |
|
\begin{figure} |
630 |
|
\centering |
631 |
|
\includegraphics[width=\linewidth]{twoBanana.eps} |
632 |
< |
\caption[Two Banana Shaped Molecules]{Two Banana Shaped Molecules.} |
633 |
< |
\label{langevin:twoBanana} |
632 |
> |
\caption[Snapshot from Simulation of Two Banana Shaped Molecules and |
633 |
> |
256 Pentane Molecules]{Snapshot from simulation of two Banana shaped |
634 |
> |
molecules and 256 pentane molecules.} \label{langevin:twoBanana} |
635 |
|
\end{figure} |
636 |
|
|
637 |
|
\section{Conclusions} |