93 |
|
The actual trajectory, along which a dynamical system may move from |
94 |
|
one point to another within a specified time, is derived by finding |
95 |
|
the path which minimizes the time integral of the difference between |
96 |
< |
the kinetic, $K$, and potential energies, $U$ \cite{tolman79}. |
96 |
> |
the kinetic, $K$, and potential energies, $U$ \cite{Tolman1979}. |
97 |
|
\begin{equation} |
98 |
|
\delta \int_{t_1 }^{t_2 } {(K - U)dt = 0} , |
99 |
|
\label{introEquation:halmitonianPrinciple1} |
189 |
|
Eq.~\ref{introEquation:motionHamiltonianCoordinate} and |
190 |
|
Eq.~\ref{introEquation:motionHamiltonianMomentum} are Hamilton's |
191 |
|
equation of motion. Due to their symmetrical formula, they are also |
192 |
< |
known as the canonical equations of motions \cite{Goldstein01}. |
192 |
> |
known as the canonical equations of motions \cite{Goldstein2001}. |
193 |
|
|
194 |
|
An important difference between Lagrangian approach and the |
195 |
|
Hamiltonian approach is that the Lagrangian is considered to be a |
200 |
|
appropriate for application to statistical mechanics and quantum |
201 |
|
mechanics, since it treats the coordinate and its time derivative as |
202 |
|
independent variables and it only works with 1st-order differential |
203 |
< |
equations\cite{Marion90}. |
203 |
> |
equations\cite{Marion1990}. |
204 |
|
|
205 |
|
In Newtonian Mechanics, a system described by conservative forces |
206 |
|
conserves the total energy \ref{introEquation:energyConservation}. |
470 |
|
many-body system in Statistical Mechanics. Fortunately, Ergodic |
471 |
|
Hypothesis is proposed to make a connection between time average and |
472 |
|
ensemble average. It states that time average and average over the |
473 |
< |
statistical ensemble are identical \cite{Frenkel1996, leach01:mm}. |
473 |
> |
statistical ensemble are identical \cite{Frenkel1996, Leach2001}. |
474 |
|
\begin{equation} |
475 |
|
\langle A(q , p) \rangle_t = \mathop {\lim }\limits_{t \to \infty } |
476 |
|
\frac{1}{t}\int\limits_0^t {A(q(t),p(t))dt = \int\limits_\Gamma |
484 |
|
a properly weighted statistical average. This allows the researcher |
485 |
|
freedom of choice when deciding how best to measure a given |
486 |
|
observable. In case an ensemble averaged approach sounds most |
487 |
< |
reasonable, the Monte Carlo techniques\cite{metropolis:1949} can be |
487 |
> |
reasonable, the Monte Carlo techniques\cite{Metropolis1949} can be |
488 |
|
utilized. Or if the system lends itself to a time averaging |
489 |
|
approach, the Molecular Dynamics techniques in |
490 |
|
Sec.~\ref{introSection:molecularDynamics} will be the best |
498 |
|
within the equations. Since 1990, geometric integrators, which |
499 |
|
preserve various phase-flow invariants such as symplectic structure, |
500 |
|
volume and time reversal symmetry, are developed to address this |
501 |
< |
issue. The velocity verlet method, which happens to be a simple |
502 |
< |
example of symplectic integrator, continues to gain its popularity |
503 |
< |
in molecular dynamics community. This fact can be partly explained |
504 |
< |
by its geometric nature. |
501 |
> |
issue\cite{Dullweber1997, McLachlan1998, Leimkuhler1999}. The |
502 |
> |
velocity verlet method, which happens to be a simple example of |
503 |
> |
symplectic integrator, continues to gain its popularity in molecular |
504 |
> |
dynamics community. This fact can be partly explained by its |
505 |
> |
geometric nature. |
506 |
|
|
507 |
|
\subsection{\label{introSection:symplecticManifold}Symplectic Manifold} |
508 |
|
A \emph{manifold} is an abstract mathematical space. It locally |
566 |
|
\end{equation}In this case, $f$ is |
567 |
|
called a \emph{Hamiltonian vector field}. |
568 |
|
|
569 |
< |
Another generalization of Hamiltonian dynamics is Poisson Dynamics, |
569 |
> |
Another generalization of Hamiltonian dynamics is Poisson |
570 |
> |
Dynamics\cite{Olver1986}, |
571 |
|
\begin{equation} |
572 |
|
\dot x = J(x)\nabla _x H \label{introEquation:poissonHamiltonian} |
573 |
|
\end{equation} |
614 |
|
|
615 |
|
\subsection{\label{introSection:geometricProperties}Geometric Properties} |
616 |
|
|
617 |
< |
The hidden geometric properties of ODE and its flow play important |
618 |
< |
roles in numerical studies. Many of them can be found in systems |
619 |
< |
which occur naturally in applications. |
617 |
> |
The hidden geometric properties\cite{Budd1999, Marsden1998} of ODE |
618 |
> |
and its flow play important roles in numerical studies. Many of them |
619 |
> |
can be found in systems which occur naturally in applications. |
620 |
|
|
621 |
|
Let $\varphi$ be the flow of Hamiltonian vector field, $\varphi$ is |
622 |
|
a \emph{symplectic} flow if it satisfies, |
660 |
|
which is the condition for conserving \emph{first integral}. For a |
661 |
|
canonical Hamiltonian system, the time evolution of an arbitrary |
662 |
|
smooth function $G$ is given by, |
663 |
< |
\begin{equation} |
664 |
< |
\begin{array}{c} |
665 |
< |
\frac{{dG(x(t))}}{{dt}} = [\nabla _x G(x(t))]^T \dot x(t) \\ |
666 |
< |
= [\nabla _x G(x(t))]^T J\nabla _x H(x(t)). \\ |
665 |
< |
\end{array} |
663 |
> |
|
664 |
> |
\begin{eqnarray} |
665 |
> |
\frac{{dG(x(t))}}{{dt}} & = & [\nabla _x G(x(t))]^T \dot x(t) \\ |
666 |
> |
& = & [\nabla _x G(x(t))]^T J\nabla _x H(x(t)). \\ |
667 |
|
\label{introEquation:firstIntegral1} |
668 |
< |
\end{equation} |
668 |
> |
\end{eqnarray} |
669 |
> |
|
670 |
> |
|
671 |
|
Using poisson bracket notion, Equation |
672 |
|
\ref{introEquation:firstIntegral1} can be rewritten as |
673 |
|
\[ |
682 |
|
is a \emph{first integral}, which is due to the fact $\{ H,H\} = |
683 |
|
0$. |
684 |
|
|
685 |
< |
|
683 |
< |
When designing any numerical methods, one should always try to |
685 |
> |
When designing any numerical methods, one should always try to |
686 |
|
preserve the structural properties of the original ODE and its flow. |
687 |
|
|
688 |
|
\subsection{\label{introSection:constructionSymplectic}Construction of Symplectic Methods} |
699 |
|
\item Splitting methods |
700 |
|
\end{enumerate} |
701 |
|
|
702 |
< |
Generating function tends to lead to methods which are cumbersome |
703 |
< |
and difficult to use. In dissipative systems, variational methods |
704 |
< |
can capture the decay of energy accurately. Since their |
705 |
< |
geometrically unstable nature against non-Hamiltonian perturbations, |
706 |
< |
ordinary implicit Runge-Kutta methods are not suitable for |
707 |
< |
Hamiltonian system. Recently, various high-order explicit |
708 |
< |
Runge--Kutta methods have been developed to overcome this |
702 |
> |
Generating function\cite{Channell1990} tends to lead to methods |
703 |
> |
which are cumbersome and difficult to use. In dissipative systems, |
704 |
> |
variational methods can capture the decay of energy |
705 |
> |
accurately\cite{Kane2000}. Since their geometrically unstable nature |
706 |
> |
against non-Hamiltonian perturbations, ordinary implicit Runge-Kutta |
707 |
> |
methods are not suitable for Hamiltonian system. Recently, various |
708 |
> |
high-order explicit Runge-Kutta methods |
709 |
> |
\cite{Owren1992,Chen2003}have been developed to overcome this |
710 |
|
instability. However, due to computational penalty involved in |
711 |
|
implementing the Runge-Kutta methods, they do not attract too much |
712 |
|
attention from Molecular Dynamics community. Instead, splitting have |
713 |
|
been widely accepted since they exploit natural decompositions of |
714 |
< |
the system\cite{Tuckerman92}. |
714 |
> |
the system\cite{Tuckerman1992, McLachlan1998}. |
715 |
|
|
716 |
|
\subsubsection{\label{introSection:splittingMethod}Splitting Method} |
717 |
|
|
847 |
|
\[ |
848 |
|
[X,Y] = XY - YX . |
849 |
|
\] |
850 |
< |
Applying Baker-Campbell-Hausdorff formula to Sprang splitting, we |
851 |
< |
can obtain |
852 |
< |
\begin{eqnarray} |
850 |
> |
Applying Baker-Campbell-Hausdorff formula\cite{Varadarajan1974} to |
851 |
> |
Sprang splitting, we can obtain |
852 |
> |
\begin{eqnarray*} |
853 |
|
\exp (h X/2)\exp (h Y)\exp (h X/2) & = & \exp (h X + h Y + h^2 [X,Y]/4 + h^2 [Y,X]/4 \\ |
854 |
|
& & \mbox{} + h^2 [X,X]/8 + h^2 [Y,Y]/8 \\ |
855 |
< |
& & \mbox{} + h^3 [Y,[Y,X]]/12 - h^3[X,[X,Y]]/24\\ |
856 |
< |
& & \mbox{} + \ldots ) |
854 |
< |
\end{eqnarrary} |
855 |
> |
& & \mbox{} + h^3 [Y,[Y,X]]/12 - h^3[X,[X,Y]]/24 + \ldots ) |
856 |
> |
\end{eqnarray*} |
857 |
|
Since \[ [X,Y] + [Y,X] = 0\] and \[ [X,X] = 0\], the dominant local |
858 |
|
error of Spring splitting is proportional to $h^3$. The same |
859 |
|
procedure can be applied to general splitting, of the form |
861 |
|
\varphi _{b_m h}^2 \circ \varphi _{a_m h}^1 \circ \varphi _{b_{m - |
862 |
|
1} h}^2 \circ \ldots \circ \varphi _{a_1 h}^1 . |
863 |
|
\end{equation} |
864 |
< |
Careful choice of coefficient $a_1 ,\ldot , b_m$ will lead to higher |
864 |
> |
Careful choice of coefficient $a_1 \ldots b_m$ will lead to higher |
865 |
|
order method. Yoshida proposed an elegant way to compose higher |
866 |
< |
order methods based on symmetric splitting. Given a symmetric second |
867 |
< |
order base method $ \varphi _h^{(2)} $, a fourth-order symmetric |
868 |
< |
method can be constructed by composing, |
866 |
> |
order methods based on symmetric splitting\cite{Yoshida1990}. Given |
867 |
> |
a symmetric second order base method $ \varphi _h^{(2)} $, a |
868 |
> |
fourth-order symmetric method can be constructed by composing, |
869 |
|
\[ |
870 |
|
\varphi _h^{(4)} = \varphi _{\alpha h}^{(2)} \circ \varphi _{\beta |
871 |
|
h}^{(2)} \circ \varphi _{\alpha h}^{(2)} |
914 |
|
\end{enumerate} |
915 |
|
These three individual steps will be covered in the following |
916 |
|
sections. Sec.~\ref{introSec:initialSystemSettings} deals with the |
917 |
< |
initialization of a simulation. Sec.~\ref{introSec:production} will |
918 |
< |
discusses issues in production run. Sec.~\ref{introSection:Analysis} |
919 |
< |
provides the theoretical tools for trajectory analysis. |
917 |
> |
initialization of a simulation. Sec.~\ref{introSection:production} |
918 |
> |
will discusses issues in production run. |
919 |
> |
Sec.~\ref{introSection:Analysis} provides the theoretical tools for |
920 |
> |
trajectory analysis. |
921 |
|
|
922 |
|
\subsection{\label{introSec:initialSystemSettings}Initialization} |
923 |
|
|
987 |
|
|
988 |
|
\subsection{\label{introSection:production}Production} |
989 |
|
|
990 |
< |
Production run is the most important steps of the simulation, in |
990 |
> |
Production run is the most important step of the simulation, in |
991 |
|
which the equilibrated structure is used as a starting point and the |
992 |
|
motions of the molecules are collected for later analysis. In order |
993 |
|
to capture the macroscopic properties of the system, the molecular |
1003 |
|
A natural approach to avoid system size issue is to represent the |
1004 |
|
bulk behavior by a finite number of the particles. However, this |
1005 |
|
approach will suffer from the surface effect. To offset this, |
1006 |
< |
\textit{Periodic boundary condition} is developed to simulate bulk |
1007 |
< |
properties with a relatively small number of particles. In this |
1008 |
< |
method, the simulation box is replicated throughout space to form an |
1009 |
< |
infinite lattice. During the simulation, when a particle moves in |
1010 |
< |
the primary cell, its image in other cells move in exactly the same |
1011 |
< |
direction with exactly the same orientation. Thus, as a particle |
1012 |
< |
leaves the primary cell, one of its images will enter through the |
1013 |
< |
opposite face. |
1014 |
< |
%\begin{figure} |
1015 |
< |
%\centering |
1016 |
< |
%\includegraphics[width=\linewidth]{pbcFig.eps} |
1017 |
< |
%\caption[An illustration of periodic boundary conditions]{A 2-D |
1018 |
< |
%illustration of periodic boundary conditions. As one particle leaves |
1019 |
< |
%the right of the simulation box, an image of it enters the left.} |
1020 |
< |
%\label{introFig:pbc} |
1021 |
< |
%\end{figure} |
1006 |
> |
\textit{Periodic boundary condition} (see Fig.~\ref{introFig:pbc}) |
1007 |
> |
is developed to simulate bulk properties with a relatively small |
1008 |
> |
number of particles. In this method, the simulation box is |
1009 |
> |
replicated throughout space to form an infinite lattice. During the |
1010 |
> |
simulation, when a particle moves in the primary cell, its image in |
1011 |
> |
other cells move in exactly the same direction with exactly the same |
1012 |
> |
orientation. Thus, as a particle leaves the primary cell, one of its |
1013 |
> |
images will enter through the opposite face. |
1014 |
> |
\begin{figure} |
1015 |
> |
\centering |
1016 |
> |
\includegraphics[width=\linewidth]{pbc.eps} |
1017 |
> |
\caption[An illustration of periodic boundary conditions]{A 2-D |
1018 |
> |
illustration of periodic boundary conditions. As one particle leaves |
1019 |
> |
the left of the simulation box, an image of it enters the right.} |
1020 |
> |
\label{introFig:pbc} |
1021 |
> |
\end{figure} |
1022 |
|
|
1023 |
|
%cutoff and minimum image convention |
1024 |
|
Another important technique to improve the efficiency of force |
1036 |
|
reciprocal sums with rapid and absolute convergence, has proved to |
1037 |
|
minimize the periodicity artifacts in liquid simulations. Taking the |
1038 |
|
advantages of the fast Fourier transform (FFT) for calculating |
1039 |
< |
discrete Fourier transforms, the particle mesh-based methods are |
1040 |
< |
accelerated from $O(N^{3/2})$ to $O(N logN)$. An alternative |
1041 |
< |
approach is \emph{fast multipole method}, which treats Coulombic |
1042 |
< |
interaction exactly at short range, and approximate the potential at |
1043 |
< |
long range through multipolar expansion. In spite of their wide |
1044 |
< |
acceptances at the molecular simulation community, these two methods |
1045 |
< |
are hard to be implemented correctly and efficiently. Instead, we |
1046 |
< |
use a damped and charge-neutralized Coulomb potential method |
1047 |
< |
developed by Wolf and his coworkers. The shifted Coulomb potential |
1048 |
< |
for particle $i$ and particle $j$ at distance $r_{rj}$ is given by: |
1039 |
> |
discrete Fourier transforms, the particle mesh-based |
1040 |
> |
methods\cite{Hockney1981,Shimada1993, Luty1994} are accelerated from |
1041 |
> |
$O(N^{3/2})$ to $O(N logN)$. An alternative approach is \emph{fast |
1042 |
> |
multipole method}\cite{Greengard1987, Greengard1994}, which treats |
1043 |
> |
Coulombic interaction exactly at short range, and approximate the |
1044 |
> |
potential at long range through multipolar expansion. In spite of |
1045 |
> |
their wide acceptances at the molecular simulation community, these |
1046 |
> |
two methods are hard to be implemented correctly and efficiently. |
1047 |
> |
Instead, we use a damped and charge-neutralized Coulomb potential |
1048 |
> |
method developed by Wolf and his coworkers\cite{Wolf1999}. The |
1049 |
> |
shifted Coulomb potential for particle $i$ and particle $j$ at |
1050 |
> |
distance $r_{rj}$ is given by: |
1051 |
|
\begin{equation} |
1052 |
|
V(r_{ij})= \frac{q_i q_j \textrm{erfc}(\alpha |
1053 |
|
r_{ij})}{r_{ij}}-\lim_{r_{ij}\rightarrow |
1057 |
|
where $\alpha$ is the convergence parameter. Due to the lack of |
1058 |
|
inherent periodicity and rapid convergence,this method is extremely |
1059 |
|
efficient and easy to implement. |
1060 |
< |
%\begin{figure} |
1061 |
< |
%\centering |
1062 |
< |
%\includegraphics[width=\linewidth]{pbcFig.eps} |
1063 |
< |
%\caption[An illustration of shifted Coulomb potential]{An illustration of shifted Coulomb potential.} |
1064 |
< |
%\label{introFigure:shiftedCoulomb} |
1065 |
< |
%\end{figure} |
1060 |
> |
\begin{figure} |
1061 |
> |
\centering |
1062 |
> |
\includegraphics[width=\linewidth]{shifted_coulomb.eps} |
1063 |
> |
\caption[An illustration of shifted Coulomb potential]{An |
1064 |
> |
illustration of shifted Coulomb potential.} |
1065 |
> |
\label{introFigure:shiftedCoulomb} |
1066 |
> |
\end{figure} |
1067 |
|
|
1068 |
|
%multiple time step |
1069 |
|
|
1109 |
|
function}, is of most fundamental importance to liquid-state theory. |
1110 |
|
Pair distribution function can be gathered by Fourier transforming |
1111 |
|
raw data from a series of neutron diffraction experiments and |
1112 |
< |
integrating over the surface factor \cite{Powles73}. The experiment |
1113 |
< |
result can serve as a criterion to justify the correctness of the |
1114 |
< |
theory. Moreover, various equilibrium thermodynamic and structural |
1115 |
< |
properties can also be expressed in terms of radial distribution |
1116 |
< |
function \cite{allen87:csl}. |
1112 |
> |
integrating over the surface factor \cite{Powles1973}. The |
1113 |
> |
experiment result can serve as a criterion to justify the |
1114 |
> |
correctness of the theory. Moreover, various equilibrium |
1115 |
> |
thermodynamic and structural properties can also be expressed in |
1116 |
> |
terms of radial distribution function \cite{Allen1987}. |
1117 |
|
|
1118 |
|
A pair distribution functions $g(r)$ gives the probability that a |
1119 |
|
particle $i$ will be located at a distance $r$ from a another |
1191 |
|
movement of the objects in 3D gaming engine or other physics |
1192 |
|
simulator is governed by the rigid body dynamics. In molecular |
1193 |
|
simulation, rigid body is used to simplify the model in |
1194 |
< |
protein-protein docking study{\cite{Gray03}}. |
1194 |
> |
protein-protein docking study\cite{Gray2003}. |
1195 |
|
|
1196 |
|
It is very important to develop stable and efficient methods to |
1197 |
|
integrate the equations of motion of orientational degrees of |
1199 |
|
rotational degrees of freedom. However, due to its singularity, the |
1200 |
|
numerical integration of corresponding equations of motion is very |
1201 |
|
inefficient and inaccurate. Although an alternative integrator using |
1202 |
< |
different sets of Euler angles can overcome this difficulty\cite{}, |
1203 |
< |
the computational penalty and the lost of angular momentum |
1204 |
< |
conservation still remain. A singularity free representation |
1205 |
< |
utilizing quaternions was developed by Evans in 1977. Unfortunately, |
1206 |
< |
this approach suffer from the nonseparable Hamiltonian resulted from |
1207 |
< |
quaternion representation, which prevents the symplectic algorithm |
1208 |
< |
to be utilized. Another different approach is to apply holonomic |
1209 |
< |
constraints to the atoms belonging to the rigid body. Each atom |
1210 |
< |
moves independently under the normal forces deriving from potential |
1211 |
< |
energy and constraint forces which are used to guarantee the |
1212 |
< |
rigidness. However, due to their iterative nature, SHAKE and Rattle |
1213 |
< |
algorithm converge very slowly when the number of constraint |
1214 |
< |
increases. |
1202 |
> |
different sets of Euler angles can overcome this |
1203 |
> |
difficulty\cite{Barojas1973}, the computational penalty and the lost |
1204 |
> |
of angular momentum conservation still remain. A singularity free |
1205 |
> |
representation utilizing quaternions was developed by Evans in |
1206 |
> |
1977\cite{Evans1977}. Unfortunately, this approach suffer from the |
1207 |
> |
nonseparable Hamiltonian resulted from quaternion representation, |
1208 |
> |
which prevents the symplectic algorithm to be utilized. Another |
1209 |
> |
different approach is to apply holonomic constraints to the atoms |
1210 |
> |
belonging to the rigid body. Each atom moves independently under the |
1211 |
> |
normal forces deriving from potential energy and constraint forces |
1212 |
> |
which are used to guarantee the rigidness. However, due to their |
1213 |
> |
iterative nature, SHAKE and Rattle algorithm converge very slowly |
1214 |
> |
when the number of constraint increases\cite{Ryckaert1977, |
1215 |
> |
Andersen1983}. |
1216 |
|
|
1217 |
|
The break through in geometric literature suggests that, in order to |
1218 |
|
develop a long-term integration scheme, one should preserve the |
1219 |
|
symplectic structure of the flow. Introducing conjugate momentum to |
1220 |
|
rotation matrix $Q$ and re-formulating Hamiltonian's equation, a |
1221 |
< |
symplectic integrator, RSHAKE, was proposed to evolve the |
1222 |
< |
Hamiltonian system in a constraint manifold by iteratively |
1221 |
> |
symplectic integrator, RSHAKE\cite{Kol1997}, was proposed to evolve |
1222 |
> |
the Hamiltonian system in a constraint manifold by iteratively |
1223 |
|
satisfying the orthogonality constraint $Q_T Q = 1$. An alternative |
1224 |
< |
method using quaternion representation was developed by Omelyan. |
1225 |
< |
However, both of these methods are iterative and inefficient. In |
1226 |
< |
this section, we will present a symplectic Lie-Poisson integrator |
1227 |
< |
for rigid body developed by Dullweber and his |
1228 |
< |
coworkers\cite{Dullweber1997} in depth. |
1224 |
> |
method using quaternion representation was developed by |
1225 |
> |
Omelyan\cite{Omelyan1998}. However, both of these methods are |
1226 |
> |
iterative and inefficient. In this section, we will present a |
1227 |
> |
symplectic Lie-Poisson integrator for rigid body developed by |
1228 |
> |
Dullweber and his coworkers\cite{Dullweber1997} in depth. |
1229 |
|
|
1230 |
|
\subsection{\label{introSection:constrainedHamiltonianRB}Constrained Hamiltonian for Rigid Body} |
1231 |
|
The motion of the rigid body is Hamiltonian with the Hamiltonian |
1257 |
|
Using Equation (\ref{introEquation:motionHamiltonianCoordinate}, |
1258 |
|
\ref{introEquation:motionHamiltonianMomentum}), one can write down |
1259 |
|
the equations of motion, |
1260 |
< |
\[ |
1261 |
< |
\begin{array}{c} |
1262 |
< |
\frac{{dq}}{{dt}} = \frac{p}{m} \label{introEquation:RBMotionPosition}\\ |
1263 |
< |
\frac{{dp}}{{dt}} = - \nabla _q V(q,Q) \label{introEquation:RBMotionMomentum}\\ |
1264 |
< |
\frac{{dQ}}{{dt}} = PJ^{ - 1} \label{introEquation:RBMotionRotation}\\ |
1265 |
< |
\frac{{dP}}{{dt}} = - \nabla _Q V(q,Q) - 2Q\Lambda . \label{introEquation:RBMotionP}\\ |
1266 |
< |
\end{array} |
1260 |
< |
\] |
1260 |
> |
|
1261 |
> |
\begin{eqnarray} |
1262 |
> |
\frac{{dq}}{{dt}} & = & \frac{p}{m} \label{introEquation:RBMotionPosition}\\ |
1263 |
> |
\frac{{dp}}{{dt}} & = & - \nabla _q V(q,Q) \label{introEquation:RBMotionMomentum}\\ |
1264 |
> |
\frac{{dQ}}{{dt}} & = & PJ^{ - 1} \label{introEquation:RBMotionRotation}\\ |
1265 |
> |
\frac{{dP}}{{dt}} & = & - \nabla _Q V(q,Q) - 2Q\Lambda . \label{introEquation:RBMotionP} |
1266 |
> |
\end{eqnarray} |
1267 |
|
|
1268 |
|
In general, there are two ways to satisfy the holonomic constraints. |
1269 |
|
We can use constraint force provided by lagrange multiplier on the |
1344 |
|
\[ |
1345 |
|
\hat vu = v \times u |
1346 |
|
\] |
1341 |
– |
|
1347 |
|
Using \ref{introEqaution:RBMotionPI}, one can construct a skew |
1348 |
|
matrix, |
1349 |
|
\begin{equation} |
1350 |
< |
(\mathop \Pi \limits^ \bullet - \mathop \Pi \limits^ \bullet ^T |
1350 |
> |
(\mathop \Pi \limits^ \bullet - \mathop \Pi \limits^ {\bullet ^T} |
1351 |
|
){\rm{ }} = {\rm{ }}(\Pi - \Pi ^T ){\rm{ }}(J^{ - 1} \Pi + \Pi J^{ |
1352 |
|
- 1} ) + \sum\limits_i {[Q^T F_i (r,Q)X_i^T - X_i F_i (r,Q)^T Q]} - |
1353 |
|
(\Lambda - \Lambda ^T ) . \label{introEquation:skewMatrixPI} |
1356 |
|
\ref{introEquation:skewMatrixPI} is zero, which implies the Lagrange |
1357 |
|
multiplier $\Lambda$ is absent from the equations of motion. This |
1358 |
|
unique property eliminate the requirement of iterations which can |
1359 |
< |
not be avoided in other methods\cite{}. |
1359 |
> |
not be avoided in other methods\cite{Kol1997, Omelyan1998}. |
1360 |
|
|
1361 |
|
Applying hat-map isomorphism, we obtain the equation of motion for |
1362 |
|
angular momentum on body frame |
1376 |
|
|
1377 |
|
If there is not external forces exerted on the rigid body, the only |
1378 |
|
contribution to the rotational is from the kinetic potential (the |
1379 |
< |
first term of \ref{ introEquation:bodyAngularMotion}). The free |
1380 |
< |
rigid body is an example of Lie-Poisson system with Hamiltonian |
1376 |
< |
function |
1379 |
> |
first term of \ref{introEquation:bodyAngularMotion}). The free rigid |
1380 |
> |
body is an example of Lie-Poisson system with Hamiltonian function |
1381 |
|
\begin{equation} |
1382 |
|
T^r (\pi ) = T_1 ^r (\pi _1 ) + T_2^r (\pi _2 ) + T_3^r (\pi _3 ) |
1383 |
|
\label{introEquation:rotationalKineticRB} |
1622 |
|
\] |
1623 |
|
where $p$ is real and $L$ is called the Laplace Transform |
1624 |
|
Operator. Below are some important properties of Laplace transform |
1625 |
< |
\begin{equation} |
1626 |
< |
\begin{array}{c} |
1627 |
< |
L(x + y) = L(x) + L(y) \\ |
1628 |
< |
L(ax) = aL(x) \\ |
1629 |
< |
L(\dot x) = pL(x) - px(0) \\ |
1630 |
< |
L(\ddot x) = p^2 L(x) - px(0) - \dot x(0) \\ |
1631 |
< |
L\left( {\int_0^t {g(t - \tau )h(\tau )d\tau } } \right) = G(p)H(p) \\ |
1632 |
< |
\end{array} |
1629 |
< |
\end{equation} |
1625 |
> |
|
1626 |
> |
\begin{eqnarray*} |
1627 |
> |
L(x + y) & = & L(x) + L(y) \\ |
1628 |
> |
L(ax) & = & aL(x) \\ |
1629 |
> |
L(\dot x) & = & pL(x) - px(0) \\ |
1630 |
> |
L(\ddot x)& = & p^2 L(x) - px(0) - \dot x(0) \\ |
1631 |
> |
L\left( {\int_0^t {g(t - \tau )h(\tau )d\tau } } \right)& = & G(p)H(p) \\ |
1632 |
> |
\end{eqnarray*} |
1633 |
|
|
1634 |
+ |
|
1635 |
|
Applying Laplace transform to the bath coordinates, we obtain |
1636 |
< |
\[ |
1637 |
< |
\begin{array}{c} |
1638 |
< |
p^2 L(x_\alpha ) - px_\alpha (0) - \dot x_\alpha (0) = - \omega _\alpha ^2 L(x_\alpha ) + \frac{{g_\alpha }}{{\omega _\alpha }}L(x) \\ |
1639 |
< |
L(x_\alpha ) = \frac{{\frac{{g_\alpha }}{{\omega _\alpha }}L(x) + px_\alpha (0) + \dot x_\alpha (0)}}{{p^2 + \omega _\alpha ^2 }} \\ |
1640 |
< |
\end{array} |
1637 |
< |
\] |
1636 |
> |
\begin{eqnarray*} |
1637 |
> |
p^2 L(x_\alpha ) - px_\alpha (0) - \dot x_\alpha (0) & = & - \omega _\alpha ^2 L(x_\alpha ) + \frac{{g_\alpha }}{{\omega _\alpha }}L(x) \\ |
1638 |
> |
L(x_\alpha ) & = & \frac{{\frac{{g_\alpha }}{{\omega _\alpha }}L(x) + px_\alpha (0) + \dot x_\alpha (0)}}{{p^2 + \omega _\alpha ^2 }} \\ |
1639 |
> |
\end{eqnarray*} |
1640 |
> |
|
1641 |
|
By the same way, the system coordinates become |
1642 |
< |
\[ |
1643 |
< |
\begin{array}{c} |
1644 |
< |
mL(\ddot x) = - \frac{1}{p}\frac{{\partial W(x)}}{{\partial x}} \\ |
1645 |
< |
- \sum\limits_{\alpha = 1}^N {\left\{ { - \frac{{g_\alpha ^2 }}{{m_\alpha \omega _\alpha ^2 }}\frac{p}{{p^2 + \omega _\alpha ^2 }}pL(x) - \frac{p}{{p^2 + \omega _\alpha ^2 }}g_\alpha x_\alpha (0) - \frac{1}{{p^2 + \omega _\alpha ^2 }}g_\alpha \dot x_\alpha (0)} \right\}} \\ |
1643 |
< |
\end{array} |
1644 |
< |
\] |
1642 |
> |
\begin{eqnarray*} |
1643 |
> |
mL(\ddot x) & = & - \frac{1}{p}\frac{{\partial W(x)}}{{\partial x}} \\ |
1644 |
> |
& & \mbox{} - \sum\limits_{\alpha = 1}^N {\left\{ { - \frac{{g_\alpha ^2 }}{{m_\alpha \omega _\alpha ^2 }}\frac{p}{{p^2 + \omega _\alpha ^2 }}pL(x) - \frac{p}{{p^2 + \omega _\alpha ^2 }}g_\alpha x_\alpha (0) - \frac{1}{{p^2 + \omega _\alpha ^2 }}g_\alpha \dot x_\alpha (0)} \right\}} \\ |
1645 |
> |
\end{eqnarray*} |
1646 |
|
|
1647 |
|
With the help of some relatively important inverse Laplace |
1648 |
|
transformations: |
1654 |
|
\end{array} |
1655 |
|
\] |
1656 |
|
, we obtain |
1657 |
< |
\begin{align} |
1658 |
< |
m\ddot x &= - \frac{{\partial W(x)}}{{\partial x}} - |
1657 |
> |
\begin{eqnarray*} |
1658 |
> |
m\ddot x & = & - \frac{{\partial W(x)}}{{\partial x}} - |
1659 |
|
\sum\limits_{\alpha = 1}^N {\left\{ {\left( { - \frac{{g_\alpha ^2 |
1660 |
|
}}{{m_\alpha \omega _\alpha ^2 }}} \right)\int_0^t {\cos (\omega |
1661 |
< |
_\alpha t)\dot x(t - \tau )d\tau - \left[ {g_\alpha x_\alpha (0) |
1662 |
< |
- \frac{{g_\alpha }}{{m_\alpha \omega _\alpha }}} \right]\cos |
1663 |
< |
(\omega _\alpha t) - \frac{{g_\alpha \dot x_\alpha (0)}}{{\omega |
1664 |
< |
_\alpha }}\sin (\omega _\alpha t)} } \right\}} |
1665 |
< |
% |
1666 |
< |
&= - \frac{{\partial W(x)}}{{\partial x}} - \int_0^t |
1661 |
> |
_\alpha t)\dot x(t - \tau )d\tau } } \right\}} \\ |
1662 |
> |
& & + \sum\limits_{\alpha = 1}^N {\left\{ {\left[ {g_\alpha |
1663 |
> |
x_\alpha (0) - \frac{{g_\alpha }}{{m_\alpha \omega _\alpha }}} |
1664 |
> |
\right]\cos (\omega _\alpha t) + \frac{{g_\alpha \dot x_\alpha |
1665 |
> |
(0)}}{{\omega _\alpha }}\sin (\omega _\alpha t)} \right\}} |
1666 |
> |
\end{eqnarray*} |
1667 |
> |
\begin{eqnarray*} |
1668 |
> |
m\ddot x & = & - \frac{{\partial W(x)}}{{\partial x}} - \int_0^t |
1669 |
|
{\sum\limits_{\alpha = 1}^N {\left( { - \frac{{g_\alpha ^2 |
1670 |
|
}}{{m_\alpha \omega _\alpha ^2 }}} \right)\cos (\omega _\alpha |
1671 |
< |
t)\dot x(t - \tau )d} \tau } + \sum\limits_{\alpha = 1}^N {\left\{ |
1672 |
< |
{\left[ {g_\alpha x_\alpha (0) - \frac{{g_\alpha }}{{m_\alpha |
1673 |
< |
\omega _\alpha }}} \right]\cos (\omega _\alpha t) + |
1674 |
< |
\frac{{g_\alpha \dot x_\alpha (0)}}{{\omega _\alpha }}\sin |
1675 |
< |
(\omega _\alpha t)} \right\}} |
1676 |
< |
\end{align} |
1674 |
< |
|
1671 |
> |
t)\dot x(t - \tau )d} \tau } \\ |
1672 |
> |
& & + \sum\limits_{\alpha = 1}^N {\left\{ {\left[ {g_\alpha |
1673 |
> |
x_\alpha (0) - \frac{{g_\alpha }}{{m_\alpha \omega _\alpha }}} |
1674 |
> |
\right]\cos (\omega _\alpha t) + \frac{{g_\alpha \dot x_\alpha |
1675 |
> |
(0)}}{{\omega _\alpha }}\sin (\omega _\alpha t)} \right\}} |
1676 |
> |
\end{eqnarray*} |
1677 |
|
Introducing a \emph{dynamic friction kernel} |
1678 |
|
\begin{equation} |
1679 |
|
\xi (t) = \sum\limits_{\alpha = 1}^N {\left( { - \frac{{g_\alpha ^2 |
1767 |
|
R(t) = \sum\limits_{\alpha = 1}^N {g_\alpha q_\alpha (t)}. |
1768 |
|
\] |
1769 |
|
And since the $q$ coordinates are harmonic oscillators, |
1770 |
< |
\[ |
1771 |
< |
\begin{array}{c} |
1772 |
< |
\left\langle {q_\alpha ^2 } \right\rangle = \frac{{kT}}{{m_\alpha \omega _\alpha ^2 }} \\ |
1773 |
< |
\left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle = \left\langle {q_\alpha ^2 (0)} \right\rangle \cos (\omega _\alpha t) \\ |
1774 |
< |
\left\langle {q_\alpha (t)q_\beta (0)} \right\rangle = \delta _{\alpha \beta } \left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle \\ |
1775 |
< |
\left\langle {R(t)R(0)} \right\rangle = \sum\limits_\alpha {\sum\limits_\beta {g_\alpha g_\beta \left\langle {q_\alpha (t)q_\beta (0)} \right\rangle } } \\ |
1776 |
< |
= \sum\limits_\alpha {g_\alpha ^2 \left\langle {q_\alpha ^2 (0)} \right\rangle \cos (\omega _\alpha t)} \\ |
1777 |
< |
= kT\xi (t) \\ |
1778 |
< |
\end{array} |
1779 |
< |
\] |
1770 |
> |
|
1771 |
> |
\begin{eqnarray*} |
1772 |
> |
\left\langle {q_\alpha ^2 } \right\rangle & = & \frac{{kT}}{{m_\alpha \omega _\alpha ^2 }} \\ |
1773 |
> |
\left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle & = & \left\langle {q_\alpha ^2 (0)} \right\rangle \cos (\omega _\alpha t) \\ |
1774 |
> |
\left\langle {q_\alpha (t)q_\beta (0)} \right\rangle & = &\delta _{\alpha \beta } \left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle \\ |
1775 |
> |
\left\langle {R(t)R(0)} \right\rangle & = & \sum\limits_\alpha {\sum\limits_\beta {g_\alpha g_\beta \left\langle {q_\alpha (t)q_\beta (0)} \right\rangle } } \\ |
1776 |
> |
& = &\sum\limits_\alpha {g_\alpha ^2 \left\langle {q_\alpha ^2 (0)} \right\rangle \cos (\omega _\alpha t)} \\ |
1777 |
> |
& = &kT\xi (t) \\ |
1778 |
> |
\end{eqnarray*} |
1779 |
> |
|
1780 |
|
Thus, we recover the \emph{second fluctuation dissipation theorem} |
1781 |
|
\begin{equation} |
1782 |
|
\xi (t) = \left\langle {R(t)R(0)} \right\rangle |
1848 |
|
hydrodynamics theory, because their properties can be calculated |
1849 |
|
exactly. In 1936, Perrin extended Stokes's law to general ellipsoid, |
1850 |
|
also called a triaxial ellipsoid, which is given in Cartesian |
1851 |
< |
coordinates by |
1851 |
> |
coordinates by\cite{Perrin1934, Perrin1936} |
1852 |
|
\[ |
1853 |
|
\frac{{x^2 }}{{a^2 }} + \frac{{y^2 }}{{b^2 }} + \frac{{z^2 }}{{c^2 |
1854 |
|
}} = 1 |
1892 |
|
hydrodynamic properties of rigid bodies. However, since the mapping |
1893 |
|
from all possible ellipsoidal space, $r$-space, to all possible |
1894 |
|
combination of rotational diffusion coefficients, $D$-space is not |
1895 |
< |
unique\cite{Wegener79} as well as the intrinsic coupling between |
1896 |
< |
translational and rotational motion of rigid body\cite{}, general |
1897 |
< |
ellipsoid is not always suitable for modeling arbitrarily shaped |
1898 |
< |
rigid molecule. A number of studies have been devoted to determine |
1899 |
< |
the friction tensor for irregularly shaped rigid bodies using more |
1900 |
< |
advanced method\cite{} where the molecule of interest was modeled by |
1901 |
< |
combinations of spheres(beads)\cite{} and the hydrodynamics |
1902 |
< |
properties of the molecule can be calculated using the hydrodynamic |
1903 |
< |
interaction tensor. Let us consider a rigid assembly of $N$ beads |
1904 |
< |
immersed in a continuous medium. Due to hydrodynamics interaction, |
1905 |
< |
the ``net'' velocity of $i$th bead, $v'_i$ is different than its |
1906 |
< |
unperturbed velocity $v_i$, |
1895 |
> |
unique\cite{Wegener1979} as well as the intrinsic coupling between |
1896 |
> |
translational and rotational motion of rigid body, general ellipsoid |
1897 |
> |
is not always suitable for modeling arbitrarily shaped rigid |
1898 |
> |
molecule. A number of studies have been devoted to determine the |
1899 |
> |
friction tensor for irregularly shaped rigid bodies using more |
1900 |
> |
advanced method where the molecule of interest was modeled by |
1901 |
> |
combinations of spheres(beads)\cite{Carrasco1999} and the |
1902 |
> |
hydrodynamics properties of the molecule can be calculated using the |
1903 |
> |
hydrodynamic interaction tensor. Let us consider a rigid assembly of |
1904 |
> |
$N$ beads immersed in a continuous medium. Due to hydrodynamics |
1905 |
> |
interaction, the ``net'' velocity of $i$th bead, $v'_i$ is different |
1906 |
> |
than its unperturbed velocity $v_i$, |
1907 |
|
\[ |
1908 |
|
v'_i = v_i - \sum\limits_{j \ne i} {T_{ij} F_j } |
1909 |
|
\] |
1924 |
|
\end{equation} |
1925 |
|
Here $R_{ij}$ is the distance vector between bead $i$ and bead $j$. |
1926 |
|
A second order expression for element of different size was |
1927 |
< |
introduced by Rotne and Prager\cite{} and improved by Garc\'{i}a de |
1928 |
< |
la Torre and Bloomfield, |
1927 |
> |
introduced by Rotne and Prager\cite{Rotne1969} and improved by |
1928 |
> |
Garc\'{i}a de la Torre and Bloomfield\cite{Torre1977}, |
1929 |
|
\begin{equation} |
1930 |
|
T_{ij} = \frac{1}{{8\pi \eta R_{ij} }}\left[ {\left( {I + |
1931 |
|
\frac{{R_{ij} R_{ij}^T }}{{R_{ij}^2 }}} \right) + R\frac{{\sigma |
2011 |
|
\begin{array}{l} |
2012 |
|
\Xi _P^{tt} = \Xi _O^{tt} \\ |
2013 |
|
\Xi _P^{tr} = \Xi _P^{rt} = \Xi _O^{tr} - U_{OP} \Xi _O^{tt} \\ |
2014 |
< |
\Xi _P^{rr} = \Xi _O^{rr} - U_{OP} \Xi _O^{tt} U_{OP} + \Xi _O^{tr} U_{OP} - U_{OP} \Xi _O^{tr} ^{^T } \\ |
2014 |
> |
\Xi _P^{rr} = \Xi _O^{rr} - U_{OP} \Xi _O^{tt} U_{OP} + \Xi _O^{tr} U_{OP} - U_{OP} \Xi _O^{{tr} ^{^T }} \\ |
2015 |
|
\end{array} |
2016 |
|
\label{introEquation:resistanceTensorTransformation} |
2017 |
|
\end{equation} |
2026 |
|
Using Equations \ref{introEquation:definitionCR} and |
2027 |
|
\ref{introEquation:resistanceTensorTransformation}, one can locate |
2028 |
|
the position of center of resistance, |
2029 |
< |
\[ |
2030 |
< |
\left( \begin{array}{l} |
2029 |
> |
\begin{eqnarray*} |
2030 |
> |
\left( \begin{array}{l} |
2031 |
|
x_{OR} \\ |
2032 |
|
y_{OR} \\ |
2033 |
|
z_{OR} \\ |
2034 |
< |
\end{array} \right) = \left( {\begin{array}{*{20}c} |
2034 |
> |
\end{array} \right) & = &\left( {\begin{array}{*{20}c} |
2035 |
|
{(\Xi _O^{rr} )_{yy} + (\Xi _O^{rr} )_{zz} } & { - (\Xi _O^{rr} )_{xy} } & { - (\Xi _O^{rr} )_{xz} } \\ |
2036 |
|
{ - (\Xi _O^{rr} )_{xy} } & {(\Xi _O^{rr} )_{zz} + (\Xi _O^{rr} )_{xx} } & { - (\Xi _O^{rr} )_{yz} } \\ |
2037 |
|
{ - (\Xi _O^{rr} )_{xz} } & { - (\Xi _O^{rr} )_{yz} } & {(\Xi _O^{rr} )_{xx} + (\Xi _O^{rr} )_{yy} } \\ |
2038 |
< |
\end{array}} \right)^{ - 1} \left( \begin{array}{l} |
2038 |
> |
\end{array}} \right)^{ - 1} \\ |
2039 |
> |
& & \left( \begin{array}{l} |
2040 |
|
(\Xi _O^{tr} )_{yz} - (\Xi _O^{tr} )_{zy} \\ |
2041 |
|
(\Xi _O^{tr} )_{zx} - (\Xi _O^{tr} )_{xz} \\ |
2042 |
|
(\Xi _O^{tr} )_{xy} - (\Xi _O^{tr} )_{yx} \\ |
2043 |
< |
\end{array} \right). |
2044 |
< |
\] |
2043 |
> |
\end{array} \right) \\ |
2044 |
> |
\end{eqnarray*} |
2045 |
> |
|
2046 |
> |
|
2047 |
> |
|
2048 |
|
where $x_OR$, $y_OR$, $z_OR$ are the components of the vector |
2049 |
|
joining center of resistance $R$ and origin $O$. |