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# Line 113 | Line 113 | For a holonomic system of $f$ degrees of freedom, the
113   \subsubsection{\label{introSection:equationOfMotionLagrangian}\textbf{The
114   Equations of Motion in Lagrangian Mechanics}}
115  
116 < For a holonomic system of $f$ degrees of freedom, the equations of
117 < motion in the Lagrangian form is
116 > For a system of $f$ degrees of freedom, the equations of motion in
117 > the Lagrangian form is
118   \begin{equation}
119   \frac{d}{{dt}}\frac{{\partial L}}{{\partial \dot q_i }} -
120   \frac{{\partial L}}{{\partial q_i }} = 0,{\rm{ }}i = 1, \ldots,f
# Line 231 | Line 231 | A microscopic state or microstate of a classical syste
231   ,q_f ,p_1 , \ldots ,p_f )$, with a unique set of values of $6f$
232   coordinates and momenta is a phase space vector.
233  
234 + %%%fix me
235   A microscopic state or microstate of a classical system is
236   specification of the complete phase space vector of a system at any
237   instant in time. An ensemble is defined as a collection of systems
# Line 282 | Line 283 | With the help of Equation(\ref{introEquation:unitProba
283   {\rho (q,p,t)dq_1 } ...dq_f dp_1 } ...dp_f }}.
284   \label{introEquation:unitProbability}
285   \end{equation}
286 < With the help of Equation(\ref{introEquation:unitProbability}) and
287 < the knowledge of the system, it is possible to calculate the average
286 > With the help of Eq.~\ref{introEquation:unitProbability} and the
287 > knowledge of the system, it is possible to calculate the average
288   value of any desired quantity which depends on the coordinates and
289   momenta of the system. Even when the dynamics of the real system is
290   complex, or stochastic, or even discontinuous, the average
# Line 306 | Line 307 | isolated and conserve energy, the Microcanonical ensem
307   thermodynamic equilibrium.
308  
309   As an ensemble of systems, each of which is known to be thermally
310 < isolated and conserve energy, the Microcanonical ensemble(NVE) has a
311 < partition function like,
310 > isolated and conserve energy, the Microcanonical ensemble (NVE) has
311 > a partition function like,
312   \begin{equation}
313   \Omega (N,V,E) = e^{\beta TS} \label{introEquation:NVEPartition}.
314   \end{equation}
315 < A canonical ensemble(NVT)is an ensemble of systems, each of which
315 > A canonical ensemble (NVT)is an ensemble of systems, each of which
316   can share its energy with a large heat reservoir. The distribution
317   of the total energy amongst the possible dynamical states is given
318   by the partition function,
# Line 321 | Line 322 | condition, the isothermal-isobaric ensemble(NPT) plays
322   \end{equation}
323   Here, $A$ is the Helmholtz free energy which is defined as $ A = U -
324   TS$. Since most experiments are carried out under constant pressure
325 < condition, the isothermal-isobaric ensemble(NPT) plays a very
325 > condition, the isothermal-isobaric ensemble (NPT) plays a very
326   important role in molecular simulations. The isothermal-isobaric
327   ensemble allow the system to exchange energy with a heat bath of
328   temperature $T$ and to change the volume as well. Its partition
# Line 337 | Line 338 | $\rho$, we begin from Equation(\ref{introEquation:delt
338   Liouville's theorem is the foundation on which statistical mechanics
339   rests. It describes the time evolution of the phase space
340   distribution function. In order to calculate the rate of change of
341 < $\rho$, we begin from Equation(\ref{introEquation:deltaN}). If we
342 < consider the two faces perpendicular to the $q_1$ axis, which are
343 < located at $q_1$ and $q_1 + \delta q_1$, the number of phase points
344 < leaving the opposite face is given by the expression,
341 > $\rho$, we begin from Eq.~\ref{introEquation:deltaN}. If we consider
342 > the two faces perpendicular to the $q_1$ axis, which are located at
343 > $q_1$ and $q_1 + \delta q_1$, the number of phase points leaving the
344 > opposite face is given by the expression,
345   \begin{equation}
346   \left( {\rho  + \frac{{\partial \rho }}{{\partial q_1 }}\delta q_1 }
347   \right)\left( {\dot q_1  + \frac{{\partial \dot q_1 }}{{\partial q_1
# Line 376 | Line 377 | statistical mechanics, since the number of particles i
377  
378   Liouville's theorem states that the distribution function is
379   constant along any trajectory in phase space. In classical
380 < statistical mechanics, since the number of particles in the system
381 < is huge, we may be able to believe the system is stationary,
380 > statistical mechanics, since the number of members in an ensemble is
381 > huge and constant, we can assume the local density has no reason
382 > (other than classical mechanics) to change,
383   \begin{equation}
384   \frac{{\partial \rho }}{{\partial t}} = 0.
385   \label{introEquation:stationary}
# Line 430 | Line 432 | Substituting equations of motion in Hamiltonian formal
432   \label{introEquation:poissonBracket}
433   \end{equation}
434   Substituting equations of motion in Hamiltonian formalism(
435 < \ref{introEquation:motionHamiltonianCoordinate} ,
436 < \ref{introEquation:motionHamiltonianMomentum} ) into
437 < (\ref{introEquation:liouvilleTheorem}), we can rewrite Liouville's
438 < theorem using Poisson bracket notion,
435 > Eq.~\ref{introEquation:motionHamiltonianCoordinate} ,
436 > Eq.~\ref{introEquation:motionHamiltonianMomentum} ) into
437 > (Eq.~\ref{introEquation:liouvilleTheorem}), we can rewrite
438 > Liouville's theorem using Poisson bracket notion,
439   \begin{equation}
440   \left( {\frac{{\partial \rho }}{{\partial t}}} \right) =  - \left\{
441   {\rho ,H} \right\}.
# Line 1735 | Line 1737 | or be determined by Stokes' law for regular shaped par
1737   \end{equation}
1738   which is known as the Langevin equation. The static friction
1739   coefficient $\xi _0$ can either be calculated from spectral density
1740 < or be determined by Stokes' law for regular shaped particles.A
1740 > or be determined by Stokes' law for regular shaped particles. A
1741   briefly review on calculating friction tensor for arbitrary shaped
1742   particles is given in Sec.~\ref{introSection:frictionTensor}.
1743  
# Line 1768 | Line 1770 | can model the random force and friction kernel.
1770   \end{equation}
1771   In effect, it acts as a constraint on the possible ways in which one
1772   can model the random force and friction kernel.
1771
1772 \subsection{\label{introSection:frictionTensor} Friction Tensor}
1773 Theoretically, the friction kernel can be determined using velocity
1774 autocorrelation function. However, this approach become impractical
1775 when the system become more and more complicate. Instead, various
1776 approaches based on hydrodynamics have been developed to calculate
1777 the friction coefficients. The friction effect is isotropic in
1778 Equation, $\zeta$ can be taken as a scalar. In general, friction
1779 tensor $\Xi$ is a $6\times 6$ matrix given by
1780 \[
1781 \Xi  = \left( {\begin{array}{*{20}c}
1782   {\Xi _{}^{tt} } & {\Xi _{}^{rt} }  \\
1783   {\Xi _{}^{tr} } & {\Xi _{}^{rr} }  \\
1784 \end{array}} \right).
1785 \]
1786 Here, $ {\Xi^{tt} }$ and $ {\Xi^{rr} }$ are translational friction
1787 tensor and rotational resistance (friction) tensor respectively,
1788 while ${\Xi^{tr} }$ is translation-rotation coupling tensor and $
1789 {\Xi^{rt} }$ is rotation-translation coupling tensor. When a
1790 particle moves in a fluid, it may experience friction force or
1791 torque along the opposite direction of the velocity or angular
1792 velocity,
1793 \[
1794 \left( \begin{array}{l}
1795 F_R  \\
1796 \tau _R  \\
1797 \end{array} \right) =  - \left( {\begin{array}{*{20}c}
1798   {\Xi ^{tt} } & {\Xi ^{rt} }  \\
1799   {\Xi ^{tr} } & {\Xi ^{rr} }  \\
1800 \end{array}} \right)\left( \begin{array}{l}
1801 v \\
1802 w \\
1803 \end{array} \right)
1804 \]
1805 where $F_r$ is the friction force and $\tau _R$ is the friction
1806 toque.
1807
1808 \subsubsection{\label{introSection:resistanceTensorRegular}\textbf{The Resistance Tensor for Regular Shape}}
1809
1810 For a spherical particle, the translational and rotational friction
1811 constant can be calculated from Stoke's law,
1812 \[
1813 \Xi ^{tt}  = \left( {\begin{array}{*{20}c}
1814   {6\pi \eta R} & 0 & 0  \\
1815   0 & {6\pi \eta R} & 0  \\
1816   0 & 0 & {6\pi \eta R}  \\
1817 \end{array}} \right)
1818 \]
1819 and
1820 \[
1821 \Xi ^{rr}  = \left( {\begin{array}{*{20}c}
1822   {8\pi \eta R^3 } & 0 & 0  \\
1823   0 & {8\pi \eta R^3 } & 0  \\
1824   0 & 0 & {8\pi \eta R^3 }  \\
1825 \end{array}} \right)
1826 \]
1827 where $\eta$ is the viscosity of the solvent and $R$ is the
1828 hydrodynamics radius.
1829
1830 Other non-spherical shape, such as cylinder and ellipsoid
1831 \textit{etc}, are widely used as reference for developing new
1832 hydrodynamics theory, because their properties can be calculated
1833 exactly. In 1936, Perrin extended Stokes's law to general ellipsoid,
1834 also called a triaxial ellipsoid, which is given in Cartesian
1835 coordinates by\cite{Perrin1934, Perrin1936}
1836 \[
1837 \frac{{x^2 }}{{a^2 }} + \frac{{y^2 }}{{b^2 }} + \frac{{z^2 }}{{c^2
1838 }} = 1
1839 \]
1840 where the semi-axes are of lengths $a$, $b$, and $c$. Unfortunately,
1841 due to the complexity of the elliptic integral, only the ellipsoid
1842 with the restriction of two axes having to be equal, \textit{i.e.}
1843 prolate($ a \ge b = c$) and oblate ($ a < b = c $), can be solved
1844 exactly. Introducing an elliptic integral parameter $S$ for prolate,
1845 \[
1846 S = \frac{2}{{\sqrt {a^2  - b^2 } }}\ln \frac{{a + \sqrt {a^2  - b^2
1847 } }}{b},
1848 \]
1849 and oblate,
1850 \[
1851 S = \frac{2}{{\sqrt {b^2  - a^2 } }}arctg\frac{{\sqrt {b^2  - a^2 }
1852 }}{a}
1853 \],
1854 one can write down the translational and rotational resistance
1855 tensors
1856 \[
1857 \begin{array}{l}
1858 \Xi _a^{tt}  = 16\pi \eta \frac{{a^2  - b^2 }}{{(2a^2  - b^2 )S - 2a}} \\
1859 \Xi _b^{tt}  = \Xi _c^{tt}  = 32\pi \eta \frac{{a^2  - b^2 }}{{(2a^2  - 3b^2 )S + 2a}} \\
1860 \end{array},
1861 \]
1862 and
1863 \[
1864 \begin{array}{l}
1865 \Xi _a^{rr}  = \frac{{32\pi }}{3}\eta \frac{{(a^2  - b^2 )b^2 }}{{2a - b^2 S}} \\
1866 \Xi _b^{rr}  = \Xi _c^{rr}  = \frac{{32\pi }}{3}\eta \frac{{(a^4  - b^4 )}}{{(2a^2  - b^2 )S - 2a}} \\
1867 \end{array}.
1868 \]
1869
1870 \subsubsection{\label{introSection:resistanceTensorRegularArbitrary}\textbf{The Resistance Tensor for Arbitrary Shape}}
1871
1872 Unlike spherical and other regular shaped molecules, there is not
1873 analytical solution for friction tensor of any arbitrary shaped
1874 rigid molecules. The ellipsoid of revolution model and general
1875 triaxial ellipsoid model have been used to approximate the
1876 hydrodynamic properties of rigid bodies. However, since the mapping
1877 from all possible ellipsoidal space, $r$-space, to all possible
1878 combination of rotational diffusion coefficients, $D$-space is not
1879 unique\cite{Wegener1979} as well as the intrinsic coupling between
1880 translational and rotational motion of rigid body, general ellipsoid
1881 is not always suitable for modeling arbitrarily shaped rigid
1882 molecule. A number of studies have been devoted to determine the
1883 friction tensor for irregularly shaped rigid bodies using more
1884 advanced method where the molecule of interest was modeled by
1885 combinations of spheres(beads)\cite{Carrasco1999} and the
1886 hydrodynamics properties of the molecule can be calculated using the
1887 hydrodynamic interaction tensor. Let us consider a rigid assembly of
1888 $N$ beads immersed in a continuous medium. Due to hydrodynamics
1889 interaction, the ``net'' velocity of $i$th bead, $v'_i$ is different
1890 than its unperturbed velocity $v_i$,
1891 \[
1892 v'_i  = v_i  - \sum\limits_{j \ne i} {T_{ij} F_j }
1893 \]
1894 where $F_i$ is the frictional force, and $T_{ij}$ is the
1895 hydrodynamic interaction tensor. The friction force of $i$th bead is
1896 proportional to its ``net'' velocity
1897 \begin{equation}
1898 F_i  = \zeta _i v_i  - \zeta _i \sum\limits_{j \ne i} {T_{ij} F_j }.
1899 \label{introEquation:tensorExpression}
1900 \end{equation}
1901 This equation is the basis for deriving the hydrodynamic tensor. In
1902 1930, Oseen and Burgers gave a simple solution to Equation
1903 \ref{introEquation:tensorExpression}
1904 \begin{equation}
1905 T_{ij}  = \frac{1}{{8\pi \eta r_{ij} }}\left( {I + \frac{{R_{ij}
1906 R_{ij}^T }}{{R_{ij}^2 }}} \right).
1907 \label{introEquation:oseenTensor}
1908 \end{equation}
1909 Here $R_{ij}$ is the distance vector between bead $i$ and bead $j$.
1910 A second order expression for element of different size was
1911 introduced by Rotne and Prager\cite{Rotne1969} and improved by
1912 Garc\'{i}a de la Torre and Bloomfield\cite{Torre1977},
1913 \begin{equation}
1914 T_{ij}  = \frac{1}{{8\pi \eta R_{ij} }}\left[ {\left( {I +
1915 \frac{{R_{ij} R_{ij}^T }}{{R_{ij}^2 }}} \right) + R\frac{{\sigma
1916 _i^2  + \sigma _j^2 }}{{r_{ij}^2 }}\left( {\frac{I}{3} -
1917 \frac{{R_{ij} R_{ij}^T }}{{R_{ij}^2 }}} \right)} \right].
1918 \label{introEquation:RPTensorNonOverlapped}
1919 \end{equation}
1920 Both of the Equation \ref{introEquation:oseenTensor} and Equation
1921 \ref{introEquation:RPTensorNonOverlapped} have an assumption $R_{ij}
1922 \ge \sigma _i  + \sigma _j$. An alternative expression for
1923 overlapping beads with the same radius, $\sigma$, is given by
1924 \begin{equation}
1925 T_{ij}  = \frac{1}{{6\pi \eta R_{ij} }}\left[ {\left( {1 -
1926 \frac{2}{{32}}\frac{{R_{ij} }}{\sigma }} \right)I +
1927 \frac{2}{{32}}\frac{{R_{ij} R_{ij}^T }}{{R_{ij} \sigma }}} \right]
1928 \label{introEquation:RPTensorOverlapped}
1929 \end{equation}
1930
1931 To calculate the resistance tensor at an arbitrary origin $O$, we
1932 construct a $3N \times 3N$ matrix consisting of $N \times N$
1933 $B_{ij}$ blocks
1934 \begin{equation}
1935 B = \left( {\begin{array}{*{20}c}
1936   {B_{11} } &  \ldots  & {B_{1N} }  \\
1937    \vdots  &  \ddots  &  \vdots   \\
1938   {B_{N1} } &  \cdots  & {B_{NN} }  \\
1939 \end{array}} \right),
1940 \end{equation}
1941 where $B_{ij}$ is given by
1942 \[
1943 B_{ij}  = \delta _{ij} \frac{I}{{6\pi \eta R}} + (1 - \delta _{ij}
1944 )T_{ij}
1945 \]
1946 where $\delta _{ij}$ is Kronecker delta function. Inverting matrix
1947 $B$, we obtain
1948
1949 \[
1950 C = B^{ - 1}  = \left( {\begin{array}{*{20}c}
1951   {C_{11} } &  \ldots  & {C_{1N} }  \\
1952    \vdots  &  \ddots  &  \vdots   \\
1953   {C_{N1} } &  \cdots  & {C_{NN} }  \\
1954 \end{array}} \right)
1955 \]
1956 , which can be partitioned into $N \times N$ $3 \times 3$ block
1957 $C_{ij}$. With the help of $C_{ij}$ and skew matrix $U_i$
1958 \[
1959 U_i  = \left( {\begin{array}{*{20}c}
1960   0 & { - z_i } & {y_i }  \\
1961   {z_i } & 0 & { - x_i }  \\
1962   { - y_i } & {x_i } & 0  \\
1963 \end{array}} \right)
1964 \]
1965 where $x_i$, $y_i$, $z_i$ are the components of the vector joining
1966 bead $i$ and origin $O$. Hence, the elements of resistance tensor at
1967 arbitrary origin $O$ can be written as
1968 \begin{equation}
1969 \begin{array}{l}
1970 \Xi _{}^{tt}  = \sum\limits_i {\sum\limits_j {C_{ij} } } , \\
1971 \Xi _{}^{tr}  = \Xi _{}^{rt}  = \sum\limits_i {\sum\limits_j {U_i C_{ij} } } , \\
1972 \Xi _{}^{rr}  =  - \sum\limits_i {\sum\limits_j {U_i C_{ij} } } U_j  \\
1973 \end{array}
1974 \label{introEquation:ResistanceTensorArbitraryOrigin}
1975 \end{equation}
1976
1977 The resistance tensor depends on the origin to which they refer. The
1978 proper location for applying friction force is the center of
1979 resistance (reaction), at which the trace of rotational resistance
1980 tensor, $ \Xi ^{rr}$ reaches minimum. Mathematically, the center of
1981 resistance is defined as an unique point of the rigid body at which
1982 the translation-rotation coupling tensor are symmetric,
1983 \begin{equation}
1984 \Xi^{tr}  = \left( {\Xi^{tr} } \right)^T
1985 \label{introEquation:definitionCR}
1986 \end{equation}
1987 Form Equation \ref{introEquation:ResistanceTensorArbitraryOrigin},
1988 we can easily find out that the translational resistance tensor is
1989 origin independent, while the rotational resistance tensor and
1990 translation-rotation coupling resistance tensor depend on the
1991 origin. Given resistance tensor at an arbitrary origin $O$, and a
1992 vector ,$r_{OP}(x_{OP}, y_{OP}, z_{OP})$, from $O$ to $P$, we can
1993 obtain the resistance tensor at $P$ by
1994 \begin{equation}
1995 \begin{array}{l}
1996 \Xi _P^{tt}  = \Xi _O^{tt}  \\
1997 \Xi _P^{tr}  = \Xi _P^{rt}  = \Xi _O^{tr}  - U_{OP} \Xi _O^{tt}  \\
1998 \Xi _P^{rr}  = \Xi _O^{rr}  - U_{OP} \Xi _O^{tt} U_{OP}  + \Xi _O^{tr} U_{OP}  - U_{OP} \Xi _O^{{tr} ^{^T }}  \\
1999 \end{array}
2000 \label{introEquation:resistanceTensorTransformation}
2001 \end{equation}
2002 where
2003 \[
2004 U_{OP}  = \left( {\begin{array}{*{20}c}
2005   0 & { - z_{OP} } & {y_{OP} }  \\
2006   {z_i } & 0 & { - x_{OP} }  \\
2007   { - y_{OP} } & {x_{OP} } & 0  \\
2008 \end{array}} \right)
2009 \]
2010 Using Equations \ref{introEquation:definitionCR} and
2011 \ref{introEquation:resistanceTensorTransformation}, one can locate
2012 the position of center of resistance,
2013 \begin{eqnarray*}
2014 \left( \begin{array}{l}
2015 x_{OR}  \\
2016 y_{OR}  \\
2017 z_{OR}  \\
2018 \end{array} \right) & = &\left( {\begin{array}{*{20}c}
2019   {(\Xi _O^{rr} )_{yy}  + (\Xi _O^{rr} )_{zz} } & { - (\Xi _O^{rr} )_{xy} } & { - (\Xi _O^{rr} )_{xz} }  \\
2020   { - (\Xi _O^{rr} )_{xy} } & {(\Xi _O^{rr} )_{zz}  + (\Xi _O^{rr} )_{xx} } & { - (\Xi _O^{rr} )_{yz} }  \\
2021   { - (\Xi _O^{rr} )_{xz} } & { - (\Xi _O^{rr} )_{yz} } & {(\Xi _O^{rr} )_{xx}  + (\Xi _O^{rr} )_{yy} }  \\
2022 \end{array}} \right)^{ - 1}  \\
2023  & & \left( \begin{array}{l}
2024 (\Xi _O^{tr} )_{yz}  - (\Xi _O^{tr} )_{zy}  \\
2025 (\Xi _O^{tr} )_{zx}  - (\Xi _O^{tr} )_{xz}  \\
2026 (\Xi _O^{tr} )_{xy}  - (\Xi _O^{tr} )_{yx}  \\
2027 \end{array} \right) \\
2028 \end{eqnarray*}
2029
2030
2031
2032 where $x_OR$, $y_OR$, $z_OR$ are the components of the vector
2033 joining center of resistance $R$ and origin $O$.

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