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\chapter{\label{chapt:introduction}INTRODUCTION AND THEORETICAL BACKGROUND} |
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\section{\label{introSection:molecularDynamics}Molecular Dynamics} |
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\section{\label{introSection:classicalMechanics}Classical |
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Mechanics} |
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As a special discipline of molecular modeling, Molecular dynamics |
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has proven to be a powerful tool for studying the functions of |
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biological systems, providing structural, thermodynamic and |
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dynamical information. |
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\subsection{\label{introSection:classicalMechanics}Classical Mechanics} |
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Closely related to Classical Mechanics, Molecular Dynamics |
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simulations are carried out by integrating the equations of motion |
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for a given system of particles. There are three fundamental ideas |
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when further combine with the laws of mechanics will also be |
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sufficient to predict the future behavior of the system. |
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\subsubsection{\label{introSection:newtonian}Newtonian Mechanics} |
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\subsection{\label{introSection:newtonian}Newtonian Mechanics} |
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The discovery of Newton's three laws of mechanics which govern the |
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motion of particles is the foundation of the classical mechanics. |
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Newton¡¯s first law defines a class of inertial frames. Inertial |
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frames are reference frames where a particle not interacting with |
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other bodies will move with constant speed in the same direction. |
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With respect to inertial frames Newton¡¯s second law has the form |
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\begin{equation} |
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F = \frac {dp}{dt} = \frac {mv}{dt} |
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\label{introEquation:newtonSecondLaw} |
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\end{equation} |
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A point mass interacting with other bodies moves with the |
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acceleration along the direction of the force acting on it. Let |
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$F_ij$ be the force that particle $i$ exerts on particle $j$, and |
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$F_ji$ be the force that particle $j$ exerts on particle $i$. |
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Newton¡¯s third law states that |
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\begin{equation} |
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F_ij = -F_ji |
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\label{introEquation:newtonThirdLaw} |
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\end{equation} |
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\subsubsection{\label{introSection:lagrangian}Lagrangian Mechanics} |
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Conservation laws of Newtonian Mechanics play very important roles |
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in solving mechanics problems. The linear momentum of a particle is |
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conserved if it is free or it experiences no force. The second |
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conservation theorem concerns the angular momentum of a particle. |
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The angular momentum $L$ of a particle with respect to an origin |
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from which $r$ is measured is defined to be |
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\begin{equation} |
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L \equiv r \times p \label{introEquation:angularMomentumDefinition} |
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\end{equation} |
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The torque $\tau$ with respect to the same origin is defined to be |
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\begin{equation} |
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N \equiv r \times F \label{introEquation:torqueDefinition} |
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\end{equation} |
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Differentiating Eq.~\ref{introEquation:angularMomentumDefinition}, |
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\[ |
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\dot L = \frac{d}{{dt}}(r \times p) = (\dot r \times p) + (r \times |
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\dot p) |
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\] |
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since |
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\[ |
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\dot r \times p = \dot r \times mv = m\dot r \times \dot r \equiv 0 |
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\] |
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thus, |
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\begin{equation} |
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\dot L = r \times \dot p = N |
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\end{equation} |
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If there are no external torques acting on a body, the angular |
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momentum of it is conserved. The last conservation theorem state |
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that if all forces are conservative, Energy |
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\begin{equation}E = T + V \label{introEquation:energyConservation} |
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\end{equation} |
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is conserved. All of these conserved quantities are |
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important factors to determine the quality of numerical integration |
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scheme for rigid body \cite{Dullweber1997}. |
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\subsection{\label{introSection:lagrangian}Lagrangian Mechanics} |
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Newtonian Mechanics suffers from two important limitations: it |
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describes their motion in special cartesian coordinate systems. |
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Another limitation of Newtonian mechanics becomes obvious when we |
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which arise in attempts to apply Newton's equation to complex |
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system, alternative procedures may be developed. |
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\subsubsubsection{\label{introSection:halmiltonPrinciple}Hamilton's |
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\subsubsection{\label{introSection:halmiltonPrinciple}Hamilton's |
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Principle} |
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Hamilton introduced the dynamical principle upon which it is |
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The actual trajectory, along which a dynamical system may move from |
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one point to another within a specified time, is derived by finding |
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the path which minimizes the time integral of the difference between |
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the kinetic, $K$, and potential energies, $U$. |
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the kinetic, $K$, and potential energies, $U$ \cite{tolman79}. |
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\begin{equation} |
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\delta \int_{t_1 }^{t_2 } {(K - U)dt = 0} , |
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\lable{introEquation:halmitonianPrinciple1} |
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\label{introEquation:halmitonianPrinciple1} |
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\end{equation} |
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For simple mechanical systems, where the forces acting on the |
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\end{equation} |
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then Eq.~\ref{introEquation:halmitonianPrinciple1} becomes |
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\begin{equation} |
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\delta \int_{t_1 }^{t_2 } {K dt = 0} , |
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\lable{introEquation:halmitonianPrinciple2} |
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\delta \int_{t_1 }^{t_2 } {L dt = 0} , |
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\label{introEquation:halmitonianPrinciple2} |
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\end{equation} |
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\subsubsubsection{\label{introSection:equationOfMotionLagrangian}The |
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\subsubsection{\label{introSection:equationOfMotionLagrangian}The |
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Equations of Motion in Lagrangian Mechanics} |
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for a holonomic system of $f$ degrees of freedom, the equations of |
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\begin{equation} |
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\frac{d}{{dt}}\frac{{\partial L}}{{\partial \dot q_i }} - |
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\frac{{\partial L}}{{\partial q_i }} = 0,{\rm{ }}i = 1, \ldots,f |
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\lable{introEquation:eqMotionLagrangian} |
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\label{introEquation:eqMotionLagrangian} |
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\end{equation} |
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where $q_{i}$ is generalized coordinate and $\dot{q_{i}}$ is |
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generalized velocity. |
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\subsubsection{\label{introSection:hamiltonian}Hamiltonian Mechanics} |
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\subsection{\label{introSection:hamiltonian}Hamiltonian Mechanics} |
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Arising from Lagrangian Mechanics, Hamiltonian Mechanics was |
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introduced by William Rowan Hamilton in 1833 as a re-formulation of |
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p_i = \frac{\partial L}{\partial \dot q_i} |
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\label{introEquation:generalizedMomenta} |
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\end{equation} |
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With the help of these momenta, we may now define a new quantity $H$ |
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by the equation |
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The Lagrange equations of motion are then expressed by |
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\begin{equation} |
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H = p_1 \dot q_1 + \ldots + p_f \dot q_f - L, |
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p_i = \frac{{\partial L}}{{\partial q_i }} |
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\label{introEquation:generalizedMomentaDot} |
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\end{equation} |
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|
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With the help of the generalized momenta, we may now define a new |
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quantity $H$ by the equation |
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\begin{equation} |
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H = \sum\limits_k {p_k \dot q_k } - L , |
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\label{introEquation:hamiltonianDefByLagrangian} |
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\end{equation} |
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where $ \dot q_1 \ldots \dot q_f $ are generalized velocities and |
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$L$ is the Lagrangian function for the system. |
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Differentiating Eq.~\ref{introEquation:hamiltonianDefByLagrangian}, |
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one can obtain |
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\begin{equation} |
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dH = \sum\limits_k {\left( {p_k d\dot q_k + \dot q_k dp_k - |
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\frac{{\partial L}}{{\partial q_k }}dq_k - \frac{{\partial |
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L}}{{\partial \dot q_k }}d\dot q_k } \right)} - \frac{{\partial |
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L}}{{\partial t}}dt \label{introEquation:diffHamiltonian1} |
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\end{equation} |
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Making use of Eq.~\ref{introEquation:generalizedMomenta}, the |
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second and fourth terms in the parentheses cancel. Therefore, |
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Eq.~\ref{introEquation:diffHamiltonian1} can be rewritten as |
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\begin{equation} |
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dH = \sum\limits_k {\left( {\dot q_k dp_k - \dot p_k dq_k } |
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\right)} - \frac{{\partial L}}{{\partial t}}dt |
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\label{introEquation:diffHamiltonian2} |
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\end{equation} |
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By identifying the coefficients of $dq_k$, $dp_k$ and dt, we can |
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find |
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\begin{equation} |
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\frac{{\partial H}}{{\partial p_k }} = q_k |
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\label{introEquation:motionHamiltonianCoordinate} |
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\end{equation} |
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\begin{equation} |
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\frac{{\partial H}}{{\partial q_k }} = - p_k |
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\label{introEquation:motionHamiltonianMomentum} |
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\end{equation} |
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and |
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\begin{equation} |
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\frac{{\partial H}}{{\partial t}} = - \frac{{\partial L}}{{\partial |
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t}} |
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\label{introEquation:motionHamiltonianTime} |
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\end{equation} |
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|
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Eq.~\ref{introEquation:motionHamiltonianCoordinate} and |
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Eq.~\ref{introEquation:motionHamiltonianMomentum} are Hamilton's |
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equation of motion. Due to their symmetrical formula, they are also |
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known as the canonical equations of motions \cite{Goldstein01}. |
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|
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An important difference between Lagrangian approach and the |
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Hamiltonian approach is that the Lagrangian is considered to be a |
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function of the generalized velocities $\dot q_i$ and the |
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appropriate for application to statistical mechanics and quantum |
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mechanics, since it treats the coordinate and its time derivative as |
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independent variables and it only works with 1st-order differential |
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equations. |
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equations\cite{Marion90}. |
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|
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In Newtonian Mechanics, a system described by conservative forces |
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conserves the total energy \ref{introEquation:energyConservation}. |
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It follows that Hamilton's equations of motion conserve the total |
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Hamiltonian. |
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\begin{equation} |
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\frac{{dH}}{{dt}} = \sum\limits_i {\left( {\frac{{\partial |
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H}}{{\partial q_i }}\dot q_i + \frac{{\partial H}}{{\partial p_i |
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}}\dot p_i } \right)} = \sum\limits_i {\left( {\frac{{\partial |
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H}}{{\partial q_i }}\frac{{\partial H}}{{\partial p_i }} - |
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\frac{{\partial H}}{{\partial p_i }}\frac{{\partial H}}{{\partial |
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q_i }}} \right) = 0} |
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\label{introEquation:conserveHalmitonian} |
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\end{equation} |
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|
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\subsubsection{\label{introSection:canonicalTransformation}Canonical Transformation} |
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When studying Hamiltonian system, it is more convenient to use |
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notation |
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\begin{equation} |
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r = r(q,p)^T |
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\end{equation} |
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and to introduce a $2n \times 2n$ canonical structure matrix $J$, |
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\begin{equation} |
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J = \left( {\begin{array}{*{20}c} |
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0 & I \\ |
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{ - I} & 0 \\ |
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\end{array}} \right) |
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\label{introEquation:canonicalMatrix} |
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\end{equation} |
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where $I$ is a $n \times n$ identity matrix and $J$ is a |
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skew-symmetric matrix ($ J^T = - J $). Thus, Hamiltonian system |
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can be rewritten as, |
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\begin{equation} |
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\frac{d}{{dt}}r = J\nabla _r H(r) |
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\label{introEquation:compactHamiltonian} |
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\end{equation} |
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|
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\subsection{\label{introSection:statisticalMechanics}Statistical Mechanics} |
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\section{\label{introSection:geometricIntegratos}Geometric Integrators} |
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|
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The thermodynamic behaviors and properties of Molecular Dynamics |
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\subsection{\label{introSection:symplecticManifold}Symplectic Manifold} |
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A \emph{manifold} is an abstract mathematical space. It locally |
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looks like Euclidean space, but when viewed globally, it may have |
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more complicate structure. A good example of manifold is the surface |
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of Earth. It seems to be flat locally, but it is round if viewed as |
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a whole. A \emph{differentiable manifold} (also known as |
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\emph{smooth manifold}) is a manifold with an open cover in which |
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the covering neighborhoods are all smoothly isomorphic to one |
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another. In other words,it is possible to apply calculus on |
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\emph{differentiable manifold}. A \emph{symplectic manifold} is |
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defined as a pair $(M, \omega)$ consisting of a \emph{differentiable |
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manifold} $M$ and a close, non-degenerated, bilinear symplectic |
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form, $\omega$. One of the motivation to study \emph{symplectic |
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manifold} in Hamiltonian Mechanics is that a symplectic manifold can |
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represent all possible configurations of the system and the phase |
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space of the system can be described by it's cotangent bundle. Every |
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symplectic manifold is even dimensional. For instance, in Hamilton |
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equations, coordinate and momentum always appear in pairs. |
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|
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A \emph{symplectomorphism} is also known as a \emph{canonical |
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transformation}. |
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|
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Any real-valued differentiable function H on a symplectic manifold |
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can serve as an energy function or Hamiltonian. Associated to any |
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Hamiltonian is a Hamiltonian vector field; the integral curves of |
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the Hamiltonian vector field are solutions to the Hamilton-Jacobi |
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equations. The Hamiltonian vector field defines a flow on the |
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symplectic manifold, called a Hamiltonian flow or symplectomorphism. |
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By Liouville's theorem, Hamiltonian flows preserve the volume form |
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on the phase space. |
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|
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\subsection{\label{Construction of Symplectic Methods}} |
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|
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\section{\label{introSection:statisticalMechanics}Statistical |
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Mechanics} |
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|
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The thermodynamic behaviors and properties of Molecular Dynamics |
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simulation are governed by the principle of Statistical Mechanics. |
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The following section will give a brief introduction to some of the |
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Statistical Mechanics concepts presented in this dissertation. |
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|
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\subsubsection{\label{introSection::ensemble}Ensemble} |
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\subsection{\label{introSection:ensemble}Ensemble and Phase Space} |
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|
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\subsubsection{\label{introSection:ergodic}The Ergodic Hypothesis} |
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\subsection{\label{introSection:ergodic}The Ergodic Hypothesis} |
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|
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\subsection{\label{introSection:rigidBody}Dynamics of Rigid Bodies} |
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|
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\subsection{\label{introSection:correlationFunctions}Correlation Functions} |
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Various thermodynamic properties can be calculated from Molecular |
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Dynamics simulation. By comparing experimental values with the |
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calculated properties, one can determine the accuracy of the |
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simulation and the quality of the underlying model. However, both of |
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experiment and computer simulation are usually performed during a |
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certain time interval and the measurements are averaged over a |
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period of them which is different from the average behavior of |
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many-body system in Statistical Mechanics. Fortunately, Ergodic |
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Hypothesis is proposed to make a connection between time average and |
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ensemble average. It states that time average and average over the |
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statistical ensemble are identical \cite{Frenkel1996, leach01:mm}. |
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\begin{equation} |
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\langle A \rangle_t = \mathop {\lim }\limits_{t \to \infty } |
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\frac{1}{t}\int\limits_0^t {A(p(t),q(t))dt = \int\limits_\Gamma |
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{A(p(t),q(t))} } \rho (p(t), q(t)) dpdq |
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\end{equation} |
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where $\langle A \rangle_t$ is an equilibrium value of a physical |
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quantity and $\rho (p(t), q(t))$ is the equilibrium distribution |
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function. If an observation is averaged over a sufficiently long |
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time (longer than relaxation time), all accessible microstates in |
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phase space are assumed to be equally probed, giving a properly |
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weighted statistical average. This allows the researcher freedom of |
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choice when deciding how best to measure a given observable. In case |
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an ensemble averaged approach sounds most reasonable, the Monte |
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Carlo techniques\cite{metropolis:1949} can be utilized. Or if the |
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system lends itself to a time averaging approach, the Molecular |
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Dynamics techniques in Sec.~\ref{introSection:molecularDynamics} |
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will be the best choice\cite{Frenkel1996}. |
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|
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\section{\label{introSection:molecularDynamics}Molecular Dynamics} |
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|
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As a special discipline of molecular modeling, Molecular dynamics |
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has proven to be a powerful tool for studying the functions of |
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biological systems, providing structural, thermodynamic and |
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dynamical information. |
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|
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\subsection{\label{introSec:mdInit}Initialization} |
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|
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\subsection{\label{introSection:mdIntegration} Integration of the Equations of Motion} |
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|
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\section{\label{introSection:rigidBody}Dynamics of Rigid Bodies} |
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|
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A rigid body is a body in which the distance between any two given |
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points of a rigid body remains constant regardless of external |
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forces exerted on it. A rigid body therefore conserves its shape |
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during its motion. |
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|
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Applications of dynamics of rigid bodies. |
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|
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\subsection{\label{introSection:lieAlgebra}Lie Algebra} |
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|
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\subsection{\label{introSection:DLMMotionEquation}The Euler Equations of Rigid Body Motion} |
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|
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\subsection{\label{introSection:otherRBMotionEquation}Other Formulations for Rigid Body Motion} |
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|
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%\subsection{\label{introSection:poissonBrackets}Poisson Brackets} |
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|
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\section{\label{introSection:correlationFunctions}Correlation Functions} |
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|
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\section{\label{introSection:langevinDynamics}Langevin Dynamics} |
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|
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\subsection{\label{introSection:LDIntroduction}Introduction and application of Langevin Dynamics} |
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|
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\subsection{\label{introSection:generalizedLangevinDynamics}Generalized Langevin Dynamics} |
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|
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\subsection{\label{introSection:hydroynamics}Hydrodynamics} |
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\begin{equation} |
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H = \frac{{p^2 }}{{2m}} + U(x) + H_B + \Delta U(x,x_1 , \ldots x_N) |
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\label{introEquation:bathGLE} |
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\end{equation} |
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where $H_B$ is harmonic bath Hamiltonian, |
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\[ |
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H_B =\sum\limits_{\alpha = 1}^N {\left\{ {\frac{{p_\alpha ^2 |
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}}{{2m_\alpha }} + \frac{1}{2}m_\alpha w_\alpha ^2 } \right\}} |
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> |
\] |
| 361 |
> |
and $\Delta U$ is bilinear system-bath coupling, |
| 362 |
> |
\[ |
| 363 |
> |
\Delta U = - \sum\limits_{\alpha = 1}^N {g_\alpha x_\alpha x} |
| 364 |
> |
\] |
| 365 |
> |
Completing the square, |
| 366 |
> |
\[ |
| 367 |
> |
H_B + \Delta U = \sum\limits_{\alpha = 1}^N {\left\{ |
| 368 |
> |
{\frac{{p_\alpha ^2 }}{{2m_\alpha }} + \frac{1}{2}m_\alpha |
| 369 |
> |
w_\alpha ^2 \left( {x_\alpha - \frac{{g_\alpha }}{{m_\alpha |
| 370 |
> |
w_\alpha ^2 }}x} \right)^2 } \right\}} - \sum\limits_{\alpha = |
| 371 |
> |
1}^N {\frac{{g_\alpha ^2 }}{{2m_\alpha w_\alpha ^2 }}} x^2 |
| 372 |
> |
\] |
| 373 |
> |
and putting it back into Eq.~\ref{introEquation:bathGLE}, |
| 374 |
> |
\[ |
| 375 |
> |
H = \frac{{p^2 }}{{2m}} + W(x) + \sum\limits_{\alpha = 1}^N |
| 376 |
> |
{\left\{ {\frac{{p_\alpha ^2 }}{{2m_\alpha }} + \frac{1}{2}m_\alpha |
| 377 |
> |
w_\alpha ^2 \left( {x_\alpha - \frac{{g_\alpha }}{{m_\alpha |
| 378 |
> |
w_\alpha ^2 }}x} \right)^2 } \right\}} |
| 379 |
> |
\] |
| 380 |
> |
where |
| 381 |
> |
\[ |
| 382 |
> |
W(x) = U(x) - \sum\limits_{\alpha = 1}^N {\frac{{g_\alpha ^2 |
| 383 |
> |
}}{{2m_\alpha w_\alpha ^2 }}} x^2 |
| 384 |
> |
\] |
| 385 |
> |
Since the first two terms of the new Hamiltonian depend only on the |
| 386 |
> |
system coordinates, we can get the equations of motion for |
| 387 |
> |
Generalized Langevin Dynamics by Hamilton's equations |
| 388 |
> |
\ref{introEquation:motionHamiltonianCoordinate, |
| 389 |
> |
introEquation:motionHamiltonianMomentum}, |
| 390 |
> |
\begin{align} |
| 391 |
> |
\dot p &= - \frac{{\partial H}}{{\partial x}} |
| 392 |
> |
&= m\ddot x |
| 393 |
> |
&= - \frac{{\partial W(x)}}{{\partial x}} - \sum\limits_{\alpha = 1}^N {g_\alpha \left( {x_\alpha - \frac{{g_\alpha }}{{m_\alpha w_\alpha ^2 }}x} \right)} |
| 394 |
> |
\label{introEq:Lp5} |
| 395 |
> |
\end{align} |
| 396 |
> |
, and |
| 397 |
> |
\begin{align} |
| 398 |
> |
\dot p_\alpha &= - \frac{{\partial H}}{{\partial x_\alpha }} |
| 399 |
> |
&= m\ddot x_\alpha |
| 400 |
> |
&= \- m_\alpha w_\alpha ^2 \left( {x_\alpha - \frac{{g_\alpha}}{{m_\alpha w_\alpha ^2 }}x} \right) |
| 401 |
> |
\end{align} |
| 402 |
> |
|
| 403 |
> |
\subsection{\label{introSection:laplaceTransform}The Laplace Transform} |
| 404 |
> |
|
| 405 |
> |
\[ |
| 406 |
> |
L(x) = \int_0^\infty {x(t)e^{ - pt} dt} |
| 407 |
> |
\] |
| 408 |
> |
|
| 409 |
> |
\[ |
| 410 |
> |
L(x + y) = L(x) + L(y) |
| 411 |
> |
\] |
| 412 |
> |
|
| 413 |
> |
\[ |
| 414 |
> |
L(ax) = aL(x) |
| 415 |
> |
\] |
| 416 |
> |
|
| 417 |
> |
\[ |
| 418 |
> |
L(\dot x) = pL(x) - px(0) |
| 419 |
> |
\] |
| 420 |
> |
|
| 421 |
> |
\[ |
| 422 |
> |
L(\ddot x) = p^2 L(x) - px(0) - \dot x(0) |
| 423 |
> |
\] |
| 424 |
> |
|
| 425 |
> |
\[ |
| 426 |
> |
L\left( {\int_0^t {g(t - \tau )h(\tau )d\tau } } \right) = G(p)H(p) |
| 427 |
> |
\] |
| 428 |
> |
|
| 429 |
> |
Some relatively important transformation, |
| 430 |
> |
\[ |
| 431 |
> |
L(\cos at) = \frac{p}{{p^2 + a^2 }} |
| 432 |
> |
\] |
| 433 |
> |
|
| 434 |
> |
\[ |
| 435 |
> |
L(\sin at) = \frac{a}{{p^2 + a^2 }} |
| 436 |
> |
\] |
| 437 |
> |
|
| 438 |
> |
\[ |
| 439 |
> |
L(1) = \frac{1}{p} |
| 440 |
> |
\] |
| 441 |
> |
|
| 442 |
> |
First, the bath coordinates, |
| 443 |
> |
\[ |
| 444 |
> |
p^2 L(x_\alpha ) - px_\alpha (0) - \dot x_\alpha (0) = - \omega |
| 445 |
> |
_\alpha ^2 L(x_\alpha ) + \frac{{g_\alpha }}{{\omega _\alpha |
| 446 |
> |
}}L(x) |
| 447 |
> |
\] |
| 448 |
> |
\[ |
| 449 |
> |
L(x_\alpha ) = \frac{{\frac{{g_\alpha }}{{\omega _\alpha }}L(x) + |
| 450 |
> |
px_\alpha (0) + \dot x_\alpha (0)}}{{p^2 + \omega _\alpha ^2 }} |
| 451 |
> |
\] |
| 452 |
> |
Then, the system coordinates, |
| 453 |
> |
\begin{align} |
| 454 |
> |
mL(\ddot x) &= - \frac{1}{p}\frac{{\partial W(x)}}{{\partial x}} - |
| 455 |
> |
\sum\limits_{\alpha = 1}^N {\left\{ {\frac{{\frac{{g_\alpha |
| 456 |
> |
}}{{\omega _\alpha }}L(x) + px_\alpha (0) + \dot x_\alpha |
| 457 |
> |
(0)}}{{p^2 + \omega _\alpha ^2 }} - \frac{{g_\alpha ^2 }}{{m_\alpha |
| 458 |
> |
}}\omega _\alpha ^2 L(x)} \right\}} |
| 459 |
> |
% |
| 460 |
> |
&= - \frac{1}{p}\frac{{\partial W(x)}}{{\partial x}} - |
| 461 |
> |
\sum\limits_{\alpha = 1}^N {\left\{ { - \frac{{g_\alpha ^2 }}{{m_\alpha \omega _\alpha ^2 }}\frac{p}{{p^2 + \omega _\alpha ^2 }}pL(x) |
| 462 |
> |
- \frac{p}{{p^2 + \omega _\alpha ^2 }}g_\alpha x_\alpha (0) |
| 463 |
> |
- \frac{1}{{p^2 + \omega _\alpha ^2 }}g_\alpha \dot x_\alpha (0)} \right\}} |
| 464 |
> |
\end{align} |
| 465 |
> |
Then, the inverse transform, |
| 466 |
> |
|
| 467 |
> |
\begin{align} |
| 468 |
> |
m\ddot x &= - \frac{{\partial W(x)}}{{\partial x}} - |
| 469 |
> |
\sum\limits_{\alpha = 1}^N {\left\{ {\left( { - \frac{{g_\alpha ^2 |
| 470 |
> |
}}{{m_\alpha \omega _\alpha ^2 }}} \right)\int_0^t {\cos (\omega |
| 471 |
> |
_\alpha t)\dot x(t - \tau )d\tau - \left[ {g_\alpha x_\alpha (0) |
| 472 |
> |
- \frac{{g_\alpha }}{{m_\alpha \omega _\alpha }}} \right]\cos |
| 473 |
> |
(\omega _\alpha t) - \frac{{g_\alpha \dot x_\alpha (0)}}{{\omega |
| 474 |
> |
_\alpha }}\sin (\omega _\alpha t)} } \right\}} |
| 475 |
> |
% |
| 476 |
> |
&= - \frac{{\partial W(x)}}{{\partial x}} - \int_0^t |
| 477 |
> |
{\sum\limits_{\alpha = 1}^N {\left( { - \frac{{g_\alpha ^2 |
| 478 |
> |
}}{{m_\alpha \omega _\alpha ^2 }}} \right)\cos (\omega _\alpha |
| 479 |
> |
t)\dot x(t - \tau )d} \tau } + \sum\limits_{\alpha = 1}^N {\left\{ |
| 480 |
> |
{\left[ {g_\alpha x_\alpha (0) - \frac{{g_\alpha }}{{m_\alpha |
| 481 |
> |
\omega _\alpha }}} \right]\cos (\omega _\alpha t) + |
| 482 |
> |
\frac{{g_\alpha \dot x_\alpha (0)}}{{\omega _\alpha }}\sin |
| 483 |
> |
(\omega _\alpha t)} \right\}} |
| 484 |
> |
\end{align} |
| 485 |
> |
|
| 486 |
> |
\begin{equation} |
| 487 |
> |
m\ddot x = - \frac{{\partial W}}{{\partial x}} - \int_0^t {\xi |
| 488 |
> |
(t)\dot x(t - \tau )d\tau } + R(t) |
| 489 |
> |
\label{introEuqation:GeneralizedLangevinDynamics} |
| 490 |
> |
\end{equation} |
| 491 |
> |
%where $ {\xi (t)}$ is friction kernel, $R(t)$ is random force and |
| 492 |
> |
%$W$ is the potential of mean force. $W(x) = - kT\ln p(x)$ |
| 493 |
> |
\[ |
| 494 |
> |
\xi (t) = \sum\limits_{\alpha = 1}^N {\left( { - \frac{{g_\alpha ^2 |
| 495 |
> |
}}{{m_\alpha \omega _\alpha ^2 }}} \right)\cos (\omega _\alpha t)} |
| 496 |
> |
\] |
| 497 |
> |
For an infinite harmonic bath, we can use the spectral density and |
| 498 |
> |
an integral over frequencies. |
| 499 |
> |
|
| 500 |
> |
\[ |
| 501 |
> |
R(t) = \sum\limits_{\alpha = 1}^N {\left( {g_\alpha x_\alpha (0) |
| 502 |
> |
- \frac{{g_\alpha ^2 }}{{m_\alpha \omega _\alpha ^2 }}x(0)} |
| 503 |
> |
\right)\cos (\omega _\alpha t)} + \frac{{\dot x_\alpha |
| 504 |
> |
(0)}}{{\omega _\alpha }}\sin (\omega _\alpha t) |
| 505 |
> |
\] |
| 506 |
> |
The random forces depend only on initial conditions. |
| 507 |
> |
|
| 508 |
> |
\subsubsection{\label{introSection:secondFluctuationDissipation}The Second Fluctuation Dissipation Theorem} |
| 509 |
> |
So we can define a new set of coordinates, |
| 510 |
> |
\[ |
| 511 |
> |
q_\alpha (t) = x_\alpha (t) - \frac{1}{{m_\alpha \omega _\alpha |
| 512 |
> |
^2 }}x(0) |
| 513 |
> |
\] |
| 514 |
> |
This makes |
| 515 |
> |
\[ |
| 516 |
> |
R(t) = \sum\limits_{\alpha = 1}^N {g_\alpha q_\alpha (t)} |
| 517 |
> |
\] |
| 518 |
> |
And since the $q$ coordinates are harmonic oscillators, |
| 519 |
> |
\[ |
| 520 |
> |
\begin{array}{l} |
| 521 |
> |
\left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle = \left\langle {q_\alpha ^2 (0)} \right\rangle \cos (\omega _\alpha t) \\ |
| 522 |
> |
\left\langle {q_\alpha (t)q_\beta (0)} \right\rangle = \delta _{\alpha \beta } \left\langle {q_\alpha (t)q_\alpha (0)} \right\rangle \\ |
| 523 |
> |
\end{array} |
| 524 |
> |
\] |
| 525 |
> |
|
| 526 |
> |
\begin{align} |
| 527 |
> |
\left\langle {R(t)R(0)} \right\rangle &= \sum\limits_\alpha |
| 528 |
> |
{\sum\limits_\beta {g_\alpha g_\beta \left\langle {q_\alpha |
| 529 |
> |
(t)q_\beta (0)} \right\rangle } } |
| 530 |
> |
% |
| 531 |
> |
&= \sum\limits_\alpha {g_\alpha ^2 \left\langle {q_\alpha ^2 (0)} |
| 532 |
> |
\right\rangle \cos (\omega _\alpha t)} |
| 533 |
> |
% |
| 534 |
> |
&= kT\xi (t) |
| 535 |
> |
\end{align} |
| 536 |
> |
|
| 537 |
> |
\begin{equation} |
| 538 |
> |
\xi (t) = \left\langle {R(t)R(0)} \right\rangle |
| 539 |
> |
\label{introEquation:secondFluctuationDissipation} |
| 540 |
> |
\end{equation} |
| 541 |
> |
|
| 542 |
> |
\section{\label{introSection:hydroynamics}Hydrodynamics} |
| 543 |
> |
|
| 544 |
> |
\subsection{\label{introSection:frictionTensor} Friction Tensor} |
| 545 |
> |
\subsection{\label{introSection:analyticalApproach}Analytical |
| 546 |
> |
Approach} |
| 547 |
> |
|
| 548 |
> |
\subsection{\label{introSection:approximationApproach}Approximation |
| 549 |
> |
Approach} |
| 550 |
> |
|
| 551 |
> |
\subsection{\label{introSection:centersRigidBody}Centers of Rigid |
| 552 |
> |
Body} |
