\begin{figure}
\vspace{-1in}
\begin{center}
-\subfloat[][]{\includegraphics{sawsim/sim-sawtooth}\label{fig:sawsim:sim-sawtooth}%
+\subfloat[][]{\includegraphics{figures/sim-sawtooth/fig}\label{fig:sawsim:sim-sawtooth}%
}\\
-\subfloat[][]{\includegraphics{sawsim/sim-hist}\label{fig:sawsim:sim-hist}%
+\subfloat[][]{\includegraphics{figures/sim-hist/fig}\label{fig:sawsim:sim-hist}%
}
\caption{(a) Three simulated force curves from pulling a polymer of
eight identical protein molecules. The simulation was carried out
unfolding order and polymer length.
\begin{figure}
-\begin{center}
-\includegraphics{sawsim/order-dep}
-\caption{The dependence of the unfolding force on the temporal
- unfolding order for four polymers with $4$, $8$, $12$, and $16$
- molecules of identical proteins. Each point in the figure is the
- average of $400$ data points. The first point in each curve
- represents the average of only the first peak in each of the $400$
- simulated force curves, the second point represents the average of
- only the second peak, and so on. The solid lines are fits of
- \cref{eq:sawsim:order-dep} to the simulated data, with best fit
- $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$,
- respectively, for lengths $4$ through $16$. The insets show the
- force distributions of the first, fourth, and eighth peaks, left to
- right, for the polymer with eight protein molecules. The parameters
- used for generating the data were the same as those used for
- \cref{fig:sawsim:sim-sawtooth}, except the polymer length, and the
- histograms in the insets were normalized in the same way as in
- \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}}
-\end{center}
+ \begin{center}
+ \includegraphics{figures/order-dep/fig}
+ \caption{The dependence of the unfolding force on the temporal
+ unfolding order for four polymers with $4$, $8$, $12$, and $16$
+ molecules of identical proteins. Each point in the figure is the
+ average of $400$ data points. The first point in each curve
+ represents the average of only the first peak in each of the $400$
+ simulated force curves, the second point represents the average of
+ only the second peak, and so on. The solid lines are fits of
+ \cref{eq:sawsim:order-dep} to the simulated data, with best fit
+ $\kappa_\text{WLC}=203$, $207$, $161$, and $157\U{pN/nm}$,
+ respectively, for lengths $4$ through $16$. The insets show the
+ force distributions of the first, fourth, and eighth peaks, left
+ to right, for the polymer with eight protein molecules. The
+ parameters used for generating the data were the same as those
+ used for \cref{fig:sawsim:sim-sawtooth}, except the polymer
+ length, and the histograms in the insets were normalized in the
+ same way as in
+ \cref{fig:sawsim:sim-hist}.\label{fig:sawsim:order-dep}}
+ \end{center}
\end{figure}
\subsection{The effect of polymer inhomogeneity}
\begin{figure}
\begin{center}
-\includegraphics{sawsim/kappa-sawteeth}
+\includegraphics{figures/kappa-sawteeth/fig}
\caption{Simulated force curves obtained from pulling a polymer with
eight protein molecules using cantilevers with different force
constants $\kappa_c$. Parameters used in generating these curves
about the protein from other sources.
\begin{figure}
-\begin{center}
-\subfloat[][]{\includegraphics{sawsim/v-dep}\label{fig:sawsim:v-dep}%
-} \\
-\subfloat[][]{\includegraphics{sawsim/v-dep-sd}\label{fig:sawsim:width-v-dep}%
-}
-\caption{(a) The dependence of the unfolding forces on the pulling
- speed for three different model protein molecules characterized by
- the parameters $k_{u0}$ and $\Delta x_u$. The polymer length is
- eight molecules, and each symbol is the average of $3200$ data
- points. (b) The dependence of standard deviation of the unfolding
- force distribution on the pulling speed for the simulation data
- shown in (a), using the same symbols. The insets show the force
- distribution histograms for the three proteins at the pulling speed
- of $1\U{$\mu$m/s}$. The left, middle and right histograms are for
- the proteins represented by the top, middle, and bottom lines in (a),
- respectively.\label{fig:sawsim:all-v-dep}}
-\end{center}
+ \begin{center}
+ \subfloat[][]{\includegraphics{figures/v-dep/fig}%
+ \label{fig:sawsim:v-dep}%
+ } \\
+ \subfloat[][]{\includegraphics{figures/v-dep/fig-sd}%
+ \label{fig:sawsim:width-v-dep}%
+ }
+ \caption{(a) The dependence of the unfolding forces on the pulling
+ speed for three different model protein molecules characterized by
+ the parameters $k_{u0}$ and $\Delta x_u$. The polymer length is
+ eight molecules, and each symbol is the average of $3200$ data
+ points. (b) The dependence of standard deviation of the unfolding
+ force distribution on the pulling speed for the simulation data
+ shown in (a), using the same symbols. The insets show the force
+ distribution histograms for the three proteins at the pulling
+ speed of $1\U{$\mu$m/s}$. The left, middle and right histograms
+ are for the proteins represented by the top, middle, and bottom
+ lines in (a), respectively.\label{fig:sawsim:all-v-dep}}
+ \end{center}
\end{figure}
\begin{figure}
-\begin{center}
-\includegraphics{sawsim/fit-space}
-\caption{Fit quality between an experimental data set and simulated
- data sets obtained using various values of unfolding rate parameters
- $k_{u0}$ and $\Delta x_u$. The experimental data are from octameric
- ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04}, and the other
- model parameters are the same as those in \cref{fig:sawsim:sim-all}. The
- best fit parameters are $\Delta x_u=0.17\U{nm}$ and
- $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$. The simulation histograms were
- built from $400$ pulls at for each parameter pair. The color scale
- shown on the right is $log_{10}(D_\text{JS})$.
-\label{fig:sawsim:fit-space}}
-\end{center}
+ \begin{center}
+ \includegraphics{figures/fit-space/fig}
+ \caption{Fit quality between an experimental data set and simulated
+ data sets obtained using various values of unfolding rate
+ parameters $k_{u0}$ and $\Delta x_u$. The experimental data are
+ from octameric ubiquitin pulled at $1\U{$\mu$m/s}$\citep{chyan04},
+ and the other model parameters are the same as those in
+ \cref{fig:sawsim:sim-all}. The best fit parameters are $\Delta
+ x_u=0.17\U{nm}$ and $k_{u0}=1.2\E{-2}\U{s$^{-1}$}$. The
+ simulation histograms were built from $400$ pulls at for each
+ parameter pair. The color scale shown on the right is
+ $log_{10}(D_\text{JS})$.\label{fig:sawsim:fit-space}}
+ \end{center}
\end{figure}
projects / thesis.git / commitdiff
