ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/tengDissertation/Introduction.tex
Revision: 2696
Committed: Thu Apr 6 22:06:50 2006 UTC (18 years, 3 months ago) by tim
Content type: application/x-tex
File size: 21871 byte(s)
Log Message:
adding Generalized Langevin Dynamics and Symplectic Manifold.

File Contents

# Content
1 \chapter{\label{chapt:introduction}INTRODUCTION AND THEORETICAL BACKGROUND}
2
3 \section{\label{introSection:classicalMechanics}Classical
4 Mechanics}
5
6 Closely related to Classical Mechanics, Molecular Dynamics
7 simulations are carried out by integrating the equations of motion
8 for a given system of particles. There are three fundamental ideas
9 behind classical mechanics. Firstly, One can determine the state of
10 a mechanical system at any time of interest; Secondly, all the
11 mechanical properties of the system at that time can be determined
12 by combining the knowledge of the properties of the system with the
13 specification of this state; Finally, the specification of the state
14 when further combine with the laws of mechanics will also be
15 sufficient to predict the future behavior of the system.
16
17 \subsection{\label{introSection:newtonian}Newtonian Mechanics}
18 The discovery of Newton's three laws of mechanics which govern the
19 motion of particles is the foundation of the classical mechanics.
20 Newton¡¯s first law defines a class of inertial frames. Inertial
21 frames are reference frames where a particle not interacting with
22 other bodies will move with constant speed in the same direction.
23 With respect to inertial frames Newton¡¯s second law has the form
24 \begin{equation}
25 F = \frac {dp}{dt} = \frac {mv}{dt}
26 \label{introEquation:newtonSecondLaw}
27 \end{equation}
28 A point mass interacting with other bodies moves with the
29 acceleration along the direction of the force acting on it. Let
30 $F_ij$ be the force that particle $i$ exerts on particle $j$, and
31 $F_ji$ be the force that particle $j$ exerts on particle $i$.
32 Newton¡¯s third law states that
33 \begin{equation}
34 F_ij = -F_ji
35 \label{introEquation:newtonThirdLaw}
36 \end{equation}
37
38 Conservation laws of Newtonian Mechanics play very important roles
39 in solving mechanics problems. The linear momentum of a particle is
40 conserved if it is free or it experiences no force. The second
41 conservation theorem concerns the angular momentum of a particle.
42 The angular momentum $L$ of a particle with respect to an origin
43 from which $r$ is measured is defined to be
44 \begin{equation}
45 L \equiv r \times p \label{introEquation:angularMomentumDefinition}
46 \end{equation}
47 The torque $\tau$ with respect to the same origin is defined to be
48 \begin{equation}
49 N \equiv r \times F \label{introEquation:torqueDefinition}
50 \end{equation}
51 Differentiating Eq.~\ref{introEquation:angularMomentumDefinition},
52 \[
53 \dot L = \frac{d}{{dt}}(r \times p) = (\dot r \times p) + (r \times
54 \dot p)
55 \]
56 since
57 \[
58 \dot r \times p = \dot r \times mv = m\dot r \times \dot r \equiv 0
59 \]
60 thus,
61 \begin{equation}
62 \dot L = r \times \dot p = N
63 \end{equation}
64 If there are no external torques acting on a body, the angular
65 momentum of it is conserved. The last conservation theorem state
66 that if all forces are conservative, Energy
67 \begin{equation}E = T + V \label{introEquation:energyConservation}
68 \end{equation}
69 is conserved. All of these conserved quantities are
70 important factors to determine the quality of numerical integration
71 scheme for rigid body \cite{Dullweber1997}.
72
73 \subsection{\label{introSection:lagrangian}Lagrangian Mechanics}
74
75 Newtonian Mechanics suffers from two important limitations: it
76 describes their motion in special cartesian coordinate systems.
77 Another limitation of Newtonian mechanics becomes obvious when we
78 try to describe systems with large numbers of particles. It becomes
79 very difficult to predict the properties of the system by carrying
80 out calculations involving the each individual interaction between
81 all the particles, even if we know all of the details of the
82 interaction. In order to overcome some of the practical difficulties
83 which arise in attempts to apply Newton's equation to complex
84 system, alternative procedures may be developed.
85
86 \subsubsection{\label{introSection:halmiltonPrinciple}Hamilton's
87 Principle}
88
89 Hamilton introduced the dynamical principle upon which it is
90 possible to base all of mechanics and, indeed, most of classical
91 physics. Hamilton's Principle may be stated as follow,
92
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}.
97 \begin{equation}
98 \delta \int_{t_1 }^{t_2 } {(K - U)dt = 0} ,
99 \label{introEquation:halmitonianPrinciple1}
100 \end{equation}
101
102 For simple mechanical systems, where the forces acting on the
103 different part are derivable from a potential and the velocities are
104 small compared with that of light, the Lagrangian function $L$ can
105 be define as the difference between the kinetic energy of the system
106 and its potential energy,
107 \begin{equation}
108 L \equiv K - U = L(q_i ,\dot q_i ) ,
109 \label{introEquation:lagrangianDef}
110 \end{equation}
111 then Eq.~\ref{introEquation:halmitonianPrinciple1} becomes
112 \begin{equation}
113 \delta \int_{t_1 }^{t_2 } {L dt = 0} ,
114 \label{introEquation:halmitonianPrinciple2}
115 \end{equation}
116
117 \subsubsection{\label{introSection:equationOfMotionLagrangian}The
118 Equations of Motion in Lagrangian Mechanics}
119
120 for a holonomic system of $f$ degrees of freedom, the equations of
121 motion in the Lagrangian form is
122 \begin{equation}
123 \frac{d}{{dt}}\frac{{\partial L}}{{\partial \dot q_i }} -
124 \frac{{\partial L}}{{\partial q_i }} = 0,{\rm{ }}i = 1, \ldots,f
125 \label{introEquation:eqMotionLagrangian}
126 \end{equation}
127 where $q_{i}$ is generalized coordinate and $\dot{q_{i}}$ is
128 generalized velocity.
129
130 \subsection{\label{introSection:hamiltonian}Hamiltonian Mechanics}
131
132 Arising from Lagrangian Mechanics, Hamiltonian Mechanics was
133 introduced by William Rowan Hamilton in 1833 as a re-formulation of
134 classical mechanics. If the potential energy of a system is
135 independent of generalized velocities, the generalized momenta can
136 be defined as
137 \begin{equation}
138 p_i = \frac{\partial L}{\partial \dot q_i}
139 \label{introEquation:generalizedMomenta}
140 \end{equation}
141 The Lagrange equations of motion are then expressed by
142 \begin{equation}
143 p_i = \frac{{\partial L}}{{\partial q_i }}
144 \label{introEquation:generalizedMomentaDot}
145 \end{equation}
146
147 With the help of the generalized momenta, we may now define a new
148 quantity $H$ by the equation
149 \begin{equation}
150 H = \sum\limits_k {p_k \dot q_k } - L ,
151 \label{introEquation:hamiltonianDefByLagrangian}
152 \end{equation}
153 where $ \dot q_1 \ldots \dot q_f $ are generalized velocities and
154 $L$ is the Lagrangian function for the system.
155
156 Differentiating Eq.~\ref{introEquation:hamiltonianDefByLagrangian},
157 one can obtain
158 \begin{equation}
159 dH = \sum\limits_k {\left( {p_k d\dot q_k + \dot q_k dp_k -
160 \frac{{\partial L}}{{\partial q_k }}dq_k - \frac{{\partial
161 L}}{{\partial \dot q_k }}d\dot q_k } \right)} - \frac{{\partial
162 L}}{{\partial t}}dt \label{introEquation:diffHamiltonian1}
163 \end{equation}
164 Making use of Eq.~\ref{introEquation:generalizedMomenta}, the
165 second and fourth terms in the parentheses cancel. Therefore,
166 Eq.~\ref{introEquation:diffHamiltonian1} can be rewritten as
167 \begin{equation}
168 dH = \sum\limits_k {\left( {\dot q_k dp_k - \dot p_k dq_k }
169 \right)} - \frac{{\partial L}}{{\partial t}}dt
170 \label{introEquation:diffHamiltonian2}
171 \end{equation}
172 By identifying the coefficients of $dq_k$, $dp_k$ and dt, we can
173 find
174 \begin{equation}
175 \frac{{\partial H}}{{\partial p_k }} = q_k
176 \label{introEquation:motionHamiltonianCoordinate}
177 \end{equation}
178 \begin{equation}
179 \frac{{\partial H}}{{\partial q_k }} = - p_k
180 \label{introEquation:motionHamiltonianMomentum}
181 \end{equation}
182 and
183 \begin{equation}
184 \frac{{\partial H}}{{\partial t}} = - \frac{{\partial L}}{{\partial
185 t}}
186 \label{introEquation:motionHamiltonianTime}
187 \end{equation}
188
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}.
193
194 An important difference between Lagrangian approach and the
195 Hamiltonian approach is that the Lagrangian is considered to be a
196 function of the generalized velocities $\dot q_i$ and the
197 generalized coordinates $q_i$, while the Hamiltonian is considered
198 to be a function of the generalized momenta $p_i$ and the conjugate
199 generalized coordinate $q_i$. Hamiltonian Mechanics is more
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}.
204
205 In Newtonian Mechanics, a system described by conservative forces
206 conserves the total energy \ref{introEquation:energyConservation}.
207 It follows that Hamilton's equations of motion conserve the total
208 Hamiltonian.
209 \begin{equation}
210 \frac{{dH}}{{dt}} = \sum\limits_i {\left( {\frac{{\partial
211 H}}{{\partial q_i }}\dot q_i + \frac{{\partial H}}{{\partial p_i
212 }}\dot p_i } \right)} = \sum\limits_i {\left( {\frac{{\partial
213 H}}{{\partial q_i }}\frac{{\partial H}}{{\partial p_i }} -
214 \frac{{\partial H}}{{\partial p_i }}\frac{{\partial H}}{{\partial
215 q_i }}} \right) = 0}
216 \label{introEquation:conserveHalmitonian}
217 \end{equation}
218
219 When studying Hamiltonian system, it is more convenient to use
220 notation
221 \begin{equation}
222 r = r(q,p)^T
223 \end{equation}
224 and to introduce a $2n \times 2n$ canonical structure matrix $J$,
225 \begin{equation}
226 J = \left( {\begin{array}{*{20}c}
227 0 & I \\
228 { - I} & 0 \\
229 \end{array}} \right)
230 \label{introEquation:canonicalMatrix}
231 \end{equation}
232 where $I$ is a $n \times n$ identity matrix and $J$ is a
233 skew-symmetric matrix ($ J^T = - J $). Thus, Hamiltonian system
234 can be rewritten as,
235 \begin{equation}
236 \frac{d}{{dt}}r = J\nabla _r H(r)
237 \label{introEquation:compactHamiltonian}
238 \end{equation}
239
240 \section{\label{introSection:geometricIntegratos}Geometric Integrators}
241
242 \subsection{\label{introSection:symplecticManifold}Symplectic Manifold}
243 A \emph{manifold} is an abstract mathematical space. It locally
244 looks like Euclidean space, but when viewed globally, it may have
245 more complicate structure. A good example of manifold is the surface
246 of Earth. It seems to be flat locally, but it is round if viewed as
247 a whole. A \emph{differentiable manifold} (also known as
248 \emph{smooth manifold}) is a manifold with an open cover in which
249 the covering neighborhoods are all smoothly isomorphic to one
250 another. In other words,it is possible to apply calculus on
251 \emph{differentiable manifold}. A \emph{symplectic manifold} is
252 defined as a pair $(M, \omega)$ consisting of a \emph{differentiable
253 manifold} $M$ and a close, non-degenerated, bilinear symplectic
254 form, $\omega$. One of the motivation to study \emph{symplectic
255 manifold} in Hamiltonian Mechanics is that a symplectic manifold can
256 represent all possible configurations of the system and the phase
257 space of the system can be described by it's cotangent bundle. Every
258 symplectic manifold is even dimensional. For instance, in Hamilton
259 equations, coordinate and momentum always appear in pairs.
260
261 A \emph{symplectomorphism} is also known as a \emph{canonical
262 transformation}.
263
264 Any real-valued differentiable function H on a symplectic manifold
265 can serve as an energy function or Hamiltonian. Associated to any
266 Hamiltonian is a Hamiltonian vector field; the integral curves of
267 the Hamiltonian vector field are solutions to the Hamilton-Jacobi
268 equations. The Hamiltonian vector field defines a flow on the
269 symplectic manifold, called a Hamiltonian flow or symplectomorphism.
270 By Liouville's theorem, Hamiltonian flows preserve the volume form
271 on the phase space.
272
273 \subsection{\label{Construction of Symplectic Methods}}
274
275 \section{\label{introSection:statisticalMechanics}Statistical
276 Mechanics}
277
278 The thermodynamic behaviors and properties of Molecular Dynamics
279 simulation are governed by the principle of Statistical Mechanics.
280 The following section will give a brief introduction to some of the
281 Statistical Mechanics concepts presented in this dissertation.
282
283 \subsection{\label{introSection:ensemble}Ensemble and Phase Space}
284
285 \subsection{\label{introSection:ergodic}The Ergodic Hypothesis}
286
287 Various thermodynamic properties can be calculated from Molecular
288 Dynamics simulation. By comparing experimental values with the
289 calculated properties, one can determine the accuracy of the
290 simulation and the quality of the underlying model. However, both of
291 experiment and computer simulation are usually performed during a
292 certain time interval and the measurements are averaged over a
293 period of them which is different from the average behavior of
294 many-body system in Statistical Mechanics. Fortunately, Ergodic
295 Hypothesis is proposed to make a connection between time average and
296 ensemble average. It states that time average and average over the
297 statistical ensemble are identical \cite{Frenkel1996, leach01:mm}.
298 \begin{equation}
299 \langle A \rangle_t = \mathop {\lim }\limits_{t \to \infty }
300 \frac{1}{t}\int\limits_0^t {A(p(t),q(t))dt = \int\limits_\Gamma
301 {A(p(t),q(t))} } \rho (p(t), q(t)) dpdq
302 \end{equation}
303 where $\langle A \rangle_t$ is an equilibrium value of a physical
304 quantity and $\rho (p(t), q(t))$ is the equilibrium distribution
305 function. If an observation is averaged over a sufficiently long
306 time (longer than relaxation time), all accessible microstates in
307 phase space are assumed to be equally probed, giving a properly
308 weighted statistical average. This allows the researcher freedom of
309 choice when deciding how best to measure a given observable. In case
310 an ensemble averaged approach sounds most reasonable, the Monte
311 Carlo techniques\cite{metropolis:1949} can be utilized. Or if the
312 system lends itself to a time averaging approach, the Molecular
313 Dynamics techniques in Sec.~\ref{introSection:molecularDynamics}
314 will be the best choice\cite{Frenkel1996}.
315
316 \section{\label{introSection:molecularDynamics}Molecular Dynamics}
317
318 As a special discipline of molecular modeling, Molecular dynamics
319 has proven to be a powerful tool for studying the functions of
320 biological systems, providing structural, thermodynamic and
321 dynamical information.
322
323 \subsection{\label{introSec:mdInit}Initialization}
324
325 \subsection{\label{introSection:mdIntegration} Integration of the Equations of Motion}
326
327 \section{\label{introSection:rigidBody}Dynamics of Rigid Bodies}
328
329 A rigid body is a body in which the distance between any two given
330 points of a rigid body remains constant regardless of external
331 forces exerted on it. A rigid body therefore conserves its shape
332 during its motion.
333
334 Applications of dynamics of rigid bodies.
335
336 \subsection{\label{introSection:lieAlgebra}Lie Algebra}
337
338 \subsection{\label{introSection:DLMMotionEquation}The Euler Equations of Rigid Body Motion}
339
340 \subsection{\label{introSection:otherRBMotionEquation}Other Formulations for Rigid Body Motion}
341
342 %\subsection{\label{introSection:poissonBrackets}Poisson Brackets}
343
344 \section{\label{introSection:correlationFunctions}Correlation Functions}
345
346 \section{\label{introSection:langevinDynamics}Langevin Dynamics}
347
348 \subsection{\label{introSection:LDIntroduction}Introduction and application of Langevin Dynamics}
349
350 \subsection{\label{introSection:generalizedLangevinDynamics}Generalized Langevin Dynamics}
351
352 \begin{equation}
353 H = \frac{{p^2 }}{{2m}} + U(x) + H_B + \Delta U(x,x_1 , \ldots x_N)
354 \label{introEquation:bathGLE}
355 \end{equation}
356 where $H_B$ is harmonic bath Hamiltonian,
357 \[
358 H_B =\sum\limits_{\alpha = 1}^N {\left\{ {\frac{{p_\alpha ^2
359 }}{{2m_\alpha }} + \frac{1}{2}m_\alpha w_\alpha ^2 } \right\}}
360 \]
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}