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- % vim: set foldmethod=marker foldmarker=<<<,>>>:
- \section{Mobility problem} %<<<
- \begin{FIframe}{Mobility problem}{} %<<<
- \vspace{-1em}
- \begin{columns}
- \column{0.6\textwidth}
- \begin{itemize}
- \item $n$ rigid bodies ~~$\Omega = \sum\limits_{i=1}^{n} \Omega_i$
- \only<1>{
- with velocities ~$\vct{V}(\vct{x}) = \vct{v}_i + \vct{\omega}_i \times (\vct{x}-\vct{x}^c_i)$,
- }%
- \only<2>{
- with velocities ~{\color{red}$\vct{V}(\vct{x}) = \vct{v}_i + \vct{\omega}_i \times (\vct{x}-\vct{x}^c_i)$},
- }
- \vspace{0.8ex}
- and given forces $\vct{F}_i$, ~torques $\vct{T}_i$ abount $\vct{x}^c_i$.
- \vspace{1.4em}
- \item Stokesian fluid in $\Real^3 \setminus \Omega$
- \vspace{0.7ex}
- \qquad $\displaystyle \Delta \vct{u} - \nabla p = 0, ~~\nabla \cdot \vct{u} = 0,$ \\
- \vspace{0.6ex}
- \qquad $\displaystyle \vct{u} \rightarrow 0$ ~as~ $\vct{x} \rightarrow \infty$.
- \vspace{1.3em}
- \item Boundary conditions on $\partial\Omega$,
- \vspace{0.6ex}
- \only<1>{\qquad $\displaystyle \vct{u} = \vct{V} + \vct{u}_s$.}
- \only<2>{\qquad $\displaystyle \vct{u} = {\color{red}\vct{V}} + \vct{u}_s$.}
- \end{itemize}
- \vspace{1em}
- \qquad\quad
- \only<1>{\phantom{\color{red} unknown: $\vct{V}(\vct{u}_i, \vct{\omega}_i)$}}
- \only<2>{\color{red} unknown: $\vct{V}(\vct{u}_i, \vct{\omega}_i)$}
- \column{0.4\textwidth}
- \resizebox{0.98\textwidth}{!}{\begin{tikzpicture}
- \node[anchor=south west,inner sep=0] at (0,0) {\includegraphics[angle=90,origin=c,width=4cm]{figs/rigid-bodies.png}};
- \draw[ultra thick, ->] (2.19,0.95) to (3,1.5);
- \node at (3.25, 1.5) {$\vct{F}_1$};
- \node (a) at (2.0, 1.3) {};
- \node (b) at (2.08, 1.3) {};
- \draw[thick, ->] (a) to [out=140,in=60, looseness=3] (b);
- \draw[ultra thick, ->] (2.1,1) to (1.85,2.15);
- \node at (1.85, 2.3) {$\vct{T}_1$};
- %\draw[color=red, ultra thick] (2.7,0.9) circle (1pt);
- %\node at (2.5, 0.5) {\color{red} \Large $x$};
- %\draw[ultra thick, ->] (4.3,0.45) to (3.1,0.5);
- %\node [rotate=-6] at (5.55, 0.25) {log singularity};
- %\draw[ultra thick, ->] (10.5,-0.25) to (12.1,-0.2);
- %\node [rotate=-4.5] at (9.5, -0.17) {$|s-s_0|^{-\alpha}$};
- \end{tikzpicture}}
- \end{columns}
- \end{FIframe} %>>>
- \begin{FIframe}{Mobility problem - double-layer formulation}{} %<<<
- Represent fluid velocity: ~~$\displaystyle \vct{u} = \StokesSL[\vct{\nu}(\vct{F}_i, \vct{T}_i)] + \StokesDL[{\color{red}\vct{\sigma}}] $
- \vspace{0.3em}
- and rigid body velocity: ~~$\displaystyle \vct{V} = -\sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}}$
- \vspace{1.5em}
- Applying boundary conditions ~ ($\displaystyle \vct{u} = \vct{V} + \vct{u}_s$ ~on~ $\partial\Omega$),
- \vspace{0.3em}
- \qquad$\qquad\displaystyle
- (I/2 + D) \, {\color{red}\vct{\sigma}} + \sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}} = \vct{u}_s - S \, \vct{\nu}
- $
- \vspace{0.5em}{\em(Pozrikidis - Boundary Integral and Singularity Methods for Linearized Viscous Flow)}
- \vspace{0.5em}
- \only<2->{Second kind integral equation \quad {\color{red} $\cdots$ but doesn't work for slender bodies!}
- %, should be well-conditioned.\\
- %What can possibly go wrong?
- \vspace{1em}
- \only<3->{\color{red} $\kappa(I/2 + D) ~\sim~ 1/(\varepsilon^{2} \log \varepsilon^{-1})$}
- }
- \end{FIframe} %>>>
- %\begin{FIframe}{Boundary Integral Formulation}{Dirichlet BVP} %<<<
- % \begin{columns}
- % \column{0.5\textwidth}
- % \quad$\displaystyle \nabla^2 u - \nabla p = 0$ ~~in~~ $\mathbb{R}^3 \setminus \Omega$
- % \quad$\displaystyle u |_{\Gamma} = u_0$
- % \quad $\displaystyle u(x) \rightarrow 0 ~\text{as}~ |x|\rightarrow \infty$
- % \column{0.5\textwidth}
- % \includegraphics[width=0.99\textwidth]{figs/biest-conv}
- % \end{columns}
- % {\bf Integral equation formulation:}
- % \begin{columns}
- % \column{0.75\textwidth}
- % \vspace{1em}
- % $u = \frac{\sigma}{2} + \StokesDL[\sigma] \text{~~~~on~~~~} \Gamma$ \hfill $\kappa \sim 324$
- % \vspace{1em}
- % $u = \StokesSL[\sigma] \text{~~~~on~~~~} \Gamma$ \hfill $\kappa \sim 651$
- % \vspace{1em}
- % $u = \frac{\sigma}{2} + \StokesDL[\sigma] + \StokesSL[\sigma] \text{~~~~on~~~~} \Gamma$ \hfill $\kappa \sim 9$
- % \end{columns}
- %\end{FIframe} %>>>
- %\begin{FIframe}{Conditioning of layer-potential operators}{} %<<<
- % \vspace{1em}
- % \begin{columns}
- % \column{0.05\textwidth}
- % \column{0.35\textwidth}
- % %\quad$\displaystyle \nabla^2 u - \nabla p = 0$ ~~in~~ $\mathbb{R}^3 \setminus \Omega$
- % %\quad$\displaystyle u |_{\Gamma} = u_0$
- % %\quad $\displaystyle u(x) \rightarrow 0 ~\text{as}~ |x|\rightarrow \infty$
- % \vspace{1em}
- % $\kappa(S)$ \hfill $\sim 2.6e6$
- % \vspace{1em}
- % $\kappa(I/2 + D)$ \hfill $\sim 4.3e6$
- % \vspace{1em}
- % $\kappa(I/2 + D + 16 S)$ \hfill $\sim 80$
- % \column{0.1\textwidth}
- % \column{0.50\textwidth}
- % \includegraphics[width=0.99\textwidth]{figs/slender-torus}
- % \end{columns}
- % \vspace{3em}
- % \begin{itemize}
- % \item For infinite cylinder (Laplace case): ~~ $\kappa(I/2 + D) ~\sim~ 1/(\varepsilon^{2} \log \varepsilon^{-1})$
- % \vspace{0.5em}
- % \item Combined field operator well-conditioned: ~~ $I/2 + D + S ~/~ (2\varepsilon \log \varepsilon^{-1})$
- % \end{itemize}
- %\end{FIframe} %>>>
- \begin{FIframe}{Mobility problem - combined field formulation}{} %<<<
- \only<1>{
- Represent fluid velocity: ~~$\displaystyle \vct{u} = \StokesSL[\vct{\nu}(\vct{F}_i, \vct{T}_i)] + \StokesCF[{\color{red}\vct{\sigma}} ] $
- }
- \only<2->{
- \vspace{-0.7em}
- Represent fluid velocity: ~~$\displaystyle \vct{u} = \StokesSL[\vct{\nu}(\vct{F}_i, \vct{T}_i)] + \StokesCF[{\color{red}\vct{\sigma}} - \sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}} ] $
- }
- \only<1>{\vspace{0.5em}}%
- \only<2->{\vspace{-0.65em}}%
- and rigid body velocity: ~~$\displaystyle \vct{V} = -\sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}}$
- \vspace{0.3em}
- where, ~$\displaystyle \StokesCF = \StokesDL + \StokesSL / (2 \varepsilon \log \varepsilon^{-1}) $.
- \only<3>{
- \vspace{2.5em}
- Applying boundary conditions,
- \vspace{0.3em}
- \qquad$\qquad\displaystyle
- (\convop{I}/2 + \StokesCF)[{\color{red}\vct{\sigma}} - \sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}} ] + \sum_{i=1}^{6n} \mathfrak{v}_i \mathfrak{v}_i^T {\color{red}\vct{\sigma}} = \vct{u}_s - \StokesSL[\vct{\nu}]
- $
- \vspace{1em}
- Second kind integral equation and well-conditioned!
- }
- \end{FIframe} %>>>
- \begin{FIframe}{Numerical Results - Sedimentation Flow}{} %<<<
- \vspace{-1.5em}
- \begin{columns}[t]
- \column{0.7\textwidth}
- \vspace{1ex}
- {\bf Time-stepping:} 5-th order adaptive SDC
- \vspace{1ex}
- {\bf 8-digits accuracy} in quadratures, GMRES solve, \\
- and time-stepping.
- \vspace{1ex}
- {\bf 40 CPU cores}
- \only<2>{
- \embedvideo{\includegraphics[width=0.99\textwidth]{videos/sed2-top-zoom1}}{videos/sed2-top-zoom1.avi}
- }
- \column{0.4\textwidth}
- \vspace{-0.5em}
- \only<1>{
- \embedvideo{\includegraphics[width=0.99\textwidth]{videos/sed2-side-color}}{videos/sed2-side-color.mov}
- }
- \only<2>{
- \includegraphics[width=0.99\textwidth]{videos/sed2-side-color}
- }
- \end{columns}
- %\embedvideo{\includegraphics[width=0.25\textwidth]{videos/mesh}}{videos/mesh.avi}
- % 5-th order SDC time-stepping
- % 7 - digits accuracy
- % adaptively refined mesh
- % block diagonal preconditioner - plot of GMRES iterations
- \end{FIframe} %>>>
- %\begin{FIframe}{Numerical Results - Sedimentation Flow}{} %<<<
- % \vspace{-2.0em}
- % \begin{center}
- % \resizebox{0.85\textwidth}{!}{\begin{tikzpicture}
- % \pgfplotsset{
- % xmin=0, xmax=250,
- % width=12cm, height=7cm,
- % xlabel={$T$}, xtick distance=50,
- % }
- % \begin{axis}[ymin=0, ymax=110, ylabel={$N_{iter}$}, legend style={draw=none,at={(0,1)},anchor=north west}]
- % \addplot [thick,color=blue] table [x={t},y={noprecond}] {data/sed2}; \addlegendentry{no-preconditioner};
- % \addplot [thick,color=red] table [x={t},y={precond}] {data/sed2}; \addlegendentry{block-preconditioner};
- % %\addplot [thick,color=green] table [x={t},y={KSPprecond}] {data/sed2}; \addlegendentry{Krylov-preconditioner};
- % \end{axis}
- % \begin{axis}[axis y line*=right, ymin=0, ymax=65000, ylabel={$N$}, legend style={draw=none,at={(0.97,0.97)},anchor=north east}]
- % \addplot [thick,dashed,color=black] table [x={t},y={N}] {data/sed2}; \addlegendentry{$N$};
- % \end{axis}
- % \end{tikzpicture}}
- % \end{center}
- % \vspace{-1em}
- % {\bf Close-to-touching:} ~~smaller time-steps, ~~more unknowns ($N$), \\
- % high GMRES iteration count (one-body preconditioner doesn't help). \\
- % {\color{red} $\sim 125 \times$ more expensive!}
- %\end{FIframe} %>>>
- %\begin{FIframe}{Accelerating GMRES Solves}{} %<<<
- % \vspace{0.5em}
- % \resizebox{.9\textwidth}{!}{\begin{tikzpicture}%<<<
- % % draw horizontal line
- % \draw[ultra thick, ->] (0,0) -- (14,0);
- % % draw vertical lines
- % \foreach \x in {2,4,6,8,10,12}
- % \draw[ultra thick] (\x cm,3pt) -- (\x cm,-3pt);
- % % draw node
- % \draw[ultra thick] ( 4,0) node[below=3pt] {$t_{n-2}$};
- % \draw[ultra thick] ( 6,0) node[below=3pt] {$t_{n-1}$};
- % \draw[ultra thick] ( 8,0) node[below=3pt] {$t_{n}$};
- % \draw[ultra thick] (10,0) node[below=3pt] {$t_{n+1}$};
- % \end{tikzpicture}}%>>>
- % \vspace{0.5em}
- % \begin{itemize}
- % \setlength\itemsep{0.5em}
- % \item Forward Euler: ~$n\text{-}{th}$~ time step
- % \begin{itemize}
- % \item solve BIE using GMRES:~~ $A_{y_n} \sigma_{\!n} = b_{y_n}$
- % \item advance to $t_{n+1}$:~~~ $y_{n+1} = y_{n} + h\, v(\sigma_{\!n})$
- % \end{itemize}
- % \only<2->{\item Use ~$\sigma_{\!n-1}$~ as initial guess to GMRES}
- % \only<3->{: {\color{red} doesn't work well}}
- % \end{itemize}
- % \only<4->{
- % \vspace{0.5em}
- % \begin{itemize}
- % \item Re-use Krylov subspace from previous time step?
- % \only<5->{
- % \begin{itemize}
- % \item Krylov subspace: ~~$X \leftarrow [b, ~A b, ~\cdots, ~A^{k\shortminus\!1} b]$
- % \item Compute QR decomposition: ~ $QR \leftarrow AX$
- % \item Preconditioner: ~ $P \coloneq I - Q Q^{T} + X R^{-1} Q^{T}$
- % \vspace{0.5em}
- % \item[] \qquad $P \, Ax = x$ \quad for all~~ $x \in span(X)$
- % \item[] \qquad ~\, $P \, y = y$ \quad for all~~ $y \perp span(X)$
- % \end{itemize}
- % }
- % \end{itemize}}
- %\end{FIframe} %>>>
- %\begin{FIframe}{Krylov Preconditioning with SDC}{} %<<<
- % \vspace{-1em}
- % \resizebox{.9\textwidth}{!}{\begin{tikzpicture}%<<<
- % % draw horizontal line
- % \draw[ultra thick, ->] (0,0) -- (14,0);
- % % draw vertical lines
- % \foreach \x in {1.7, 12.3}
- % \draw[ultra thick] (\x cm,6pt) -- (\x cm,-6pt);
- % \draw[ultra thick] (1.7000 ,0) node[above=5pt] {$a$};
- % \draw[ultra thick] (12.3000,0) node[above=5pt] {$b$};
- % \foreach \x in {1.9000, 2.6699, 4.5000, 7.0000, 9.5000, 11.3301, 12.1000}
- % \draw[ultra thick, blue] (\x cm,3pt) -- (\x cm,-3pt);
- % % draw node
- % \draw[ultra thick, blue] (1.9000 ,0) node[below=3pt] {$t_1$};
- % \draw[ultra thick, blue] (2.6699 ,0) node[below=3pt] {$t_2$};
- % \draw[ultra thick, blue] (4.5000 ,0) node[below=3pt] {$t_3$};
- % %\draw[ultra thick, blue] (7.0000 ,0) node[below=3pt] {$t_4$};
- % %\draw[ultra thick, blue] (9.5000 ,0) node[below=3pt] {$t_5$};
- % \draw[ultra thick, blue] (8.5,0) node[below=3pt] {$\cdots$};
- % %\draw[ultra thick, blue] (11.3301,0) node[below=3pt] {$t_6$};
- % \draw[ultra thick, blue] (12.1000,0) node[below=3pt] {$t_m$};
- % \only<2->{%<<<
- % \draw[ultra thick, DarkGreen] (1.9000 ,-1) node {$P_1$};
- % \draw[ultra thick, DarkGreen] (2.6699 ,-1) node {$P_2$};
- % \draw[ultra thick, DarkGreen] (4.5000 ,-1) node {$P_3$};
- % \draw[ultra thick, DarkGreen] (8.5000 ,-1) node {$\cdots$};
- % \draw[ultra thick, DarkGreen] (12.1000,-1) node {$P_m$};
- % \draw[ultra thick, DarkGreen, ->] (2.10 ,-1) -- (2.40 ,-1);
- % \draw[ultra thick, DarkGreen, ->] (3.00 ,-1) -- (3.50 ,-1);
- % \draw[ultra thick, DarkGreen, ->] (4.86 ,-1) -- (5.40 ,-1);
- % }%>>>
- % \only<3->{%<<<
- % \draw[ultra thick, DarkGreen, ->] (1.9000 ,-1.25) -- (1.9000 ,-1.8);
- % \draw[ultra thick, DarkGreen, ->] (2.6699 ,-1.25) -- (2.6699 ,-1.8);
- % \draw[ultra thick, DarkGreen, ->] (4.5000 ,-1.25) -- (4.5000 ,-1.8);
- % \draw[ultra thick, DarkGreen, ->] (12.100 ,-1.25) -- (12.100 ,-1.8);
- % \draw[ultra thick, DarkGreen] (1.9000 ,-2.1) node {~~\,$P^{(1)}_1$};
- % \draw[ultra thick, DarkGreen] (2.6699 ,-2.1) node {~~\,$P^{(1)}_2$};
- % \draw[ultra thick, DarkGreen] (4.5000 ,-2.1) node {~~\,$P^{(1)}_3$};
- % \draw[ultra thick, DarkGreen] (8.5000 ,-2.1) node {$\cdots$};
- % \draw[ultra thick, DarkGreen] (12.100 ,-2.1) node {~~\,$P^{(1)}_m$};
- % \draw[ultra thick, black, ->] (0.75 ,-0.5) -- (0.75 ,-3.5);
- % \draw[ultra thick, black] (0.5,-2) node[rotate=-90] {corrections};
- % }%>>>
- % \only<4->{%<<<
- % \draw[ultra thick, DarkGreen, ->] (1.9000 ,-2.5) -- (1.9000 ,-3.0);
- % \draw[ultra thick, DarkGreen, ->] (2.6699 ,-2.5) -- (2.6699 ,-3.0);
- % \draw[ultra thick, DarkGreen, ->] (4.5000 ,-2.5) -- (4.5000 ,-3.0);
- % \draw[ultra thick, DarkGreen, ->] (12.100 ,-2.5) -- (12.100 ,-3.0);
- % \draw[ultra thick, DarkGreen] (1.9000 ,-3.3) node {~~\,$P^{(2)}_1$};
- % \draw[ultra thick, DarkGreen] (2.6699 ,-3.3) node {~~\,$P^{(2)}_2$};
- % \draw[ultra thick, DarkGreen] (4.5000 ,-3.3) node {~~\,$P^{(2)}_3$};
- % \draw[ultra thick, DarkGreen] (8.5000 ,-3.3) node {$\cdots$};
- % \draw[ultra thick, DarkGreen] (12.100 ,-3.3) node {~~\,$P^{(2)}_m$};
- % %\draw[ultra thick, DarkGreen, ->] (1.9000 ,-3.7) -- (1.9000 ,-4.2);
- % %\draw[ultra thick, DarkGreen, ->] (2.6699 ,-3.7) -- (2.6699 ,-4.2);
- % %\draw[ultra thick, DarkGreen, ->] (4.5000 ,-3.7) -- (4.5000 ,-4.2);
- % %\draw[ultra thick, DarkGreen, ->] (12.100 ,-3.7) -- (12.100 ,-4.2);
- % }%>>>
- % \end{tikzpicture}}%>>>
- % \only<5->{
- % \vspace{1.4em}
- % \begin{columns}
- % \column{0.05\textwidth}
- % \column{0.45\textwidth}
- % GMRES iter without preconditioner:
- % \vspace{0.5em}
- % \begin{tabular}{r | r r r r r}
- % \parbox[t]{2mm}{\multirow{5}{*}{\rotatebox[origin=c]{-90}{correction $\rightarrow$}}}
- % & \multicolumn{5}{c}{sub-step $\rightarrow$} \\
- % \hline
- % & 66 & 66 & 66 & 66 & 66 \\
- % & 66 & 66 & 66 & 66 & 66 \\
- % & 66 & 66 & 66 & 66 & 66 \\
- % & 66 & 66 & 66 & 66 & 66 \\
- % \end{tabular}
- % \column{0.05\textwidth}
- % \column{0.44\textwidth}
- % \only<6->{
- % GMRES iter with preconditioner:
- % \vspace{0.5em}
- % \begin{tabular}{r | r r r r r}
- % \parbox[t]{2mm}{\multirow{5}{*}{\rotatebox[origin=c]{-90}{correction $\rightarrow$}}}
- % & \multicolumn{5}{c}{sub-step $\rightarrow$} \\
- % \hline
- % & 66 & 30 & 22 & 45 & 30 \\
- % & 35 & 17 & 33 & 28 & 24 \\
- % & 8 & 4 & 14 & 5 & 12 \\
- % & 1 & 1 & 2 & 2 & 4 \\
- % \end{tabular}}
- % \end{columns}
- % }
- %\end{FIframe} %>>>
- \begin{FIframe}{Numerical Results - Sedimentation Flow}{} %<<<
- \vspace{-2.0em}
- \begin{center}
- \resizebox{0.95\textwidth}{!}{\begin{tikzpicture}
- \pgfplotsset{
- xmin=0, xmax=250,
- width=12cm, height=7cm,
- xlabel={$T$}, xtick distance=50,
- }
- \begin{axis}[ymin=0, ymax=110, ylabel={$N_{iter}$}, legend style={draw=none,at={(0,1)},anchor=north west}]
- \addplot [thick,color=blue] table [x={t},y={noprecond}] {data/sed2}; \addlegendentry{no-preconditioner};
- \addplot [thick,color=red] table [x={t},y={precond}] {data/sed2}; \addlegendentry{block-preconditioner};
- \addplot [thick,color=DarkGreen] table [x={t},y={KSPprecond}] {data/sed2}; \addlegendentry{Krylov-preconditioner};
- \end{axis}
- \begin{axis}[axis y line*=right, ymin=0, ymax=65000, ylabel={$N$}, legend style={draw=none,at={(0.97,0.97)},anchor=north east}]
- \addplot [thick,dashed,color=black] table [x={t},y={N}] {data/sed2}; \addlegendentry{$N$};
- \end{axis}
- \end{tikzpicture}}
- \end{center}
- %\vspace{-1em}
- %{\bf Close-to-touching:} ~~smaller time-steps, ~~more unknowns ($N$), \\
- %high GMRES iteration count (block preconditioner doesn't help). \\
- %{\color{red} $\sim 125 \times$ more expensive!}
- \end{FIframe} %>>>
- %>>>
- %<<< Sedimentation flow
- \begin{FIframe}{Numerical Results - Sedimentation Flow}{} %<<<
- \begin{columns}
- \column{0.35\textwidth}
- \vspace{1ex}
- {\bf 5-th order adaptive SDC}
- \vspace{1ex}
- {\bf 8-digits accuracy} in quadratures, GMRES solve, \\
- and time-stepping.
- \vspace{1ex}
- {\bf 0.5 million unknowns} \\
- 64 rings.
- \vspace{1ex}
- {\bf 160 CPU cores}
- \column{0.65\textwidth}
- \embedvideo{\includegraphics[width=0.99\textwidth]{videos/sed64}}{videos/sed64.mov}
- \end{columns}
- \end{FIframe} %>>>
- %\begin{FIframe}{Numerical Results - Sedimentation Flow}{} %<<<
- % \vspace{-1.9em}
- % \centering
- % \only<1>{ \embedvideo{\includegraphics[width=0.94\textwidth]{videos/bacteria2_.png}}{videos/bacteria2_.mov} }%
- % \only<2>{ \embedvideo{\includegraphics[width=0.47\textwidth]{videos/bacteria64-density.png}}{videos/bacteria64-density.mov} }
- %\end{FIframe} %>>>
- %>>>
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