to WLCs\index{WLC} to identify I27 unfolding events. The results were
sorted into two bins according to cantilever stiffness, and then
averaged across each cantilever-stiffness/pulling-speed group to
-produce \cref{fig:plot-splits}.
+produce \cref{fig:cant:v-dep}.
\begin{figure}
- \includegraphics[width=4in]{figures/cantilever-data/plot_splits}
- \caption{Plot splits.\label{fig:plot-splits}}
+ \asyfig{figures/cantilever-data/v-dep}
+ \caption{Pulling speed dependence of I27 for different cantilever
+ stiffnesses. The listed stiffnesses are averages across several
+ individual cantilevers and calibrations. Each box is the average
+ of some number of unfolding events, and the box area is
+ proportional to that number. There are $82$ unfolding events for
+ the stiff cantilevers and $274$ for the soft cantilevers.%
+ \label{fig:cant:v-dep}}
\end{figure}
Unfortunately, the data are not of high enough quality to extract the
unfolding parameters $k$ or $\Delta x$. Note that the increase in
mean unfolding force is not entirely due to the increased loading rate
of the stiffer cantilever, because the difference is still present in
-the loading rate dependence (\cref{fig:cantilever:loading-rate}). The
+the loading rate dependence (\cref{fig:cant:load-dep}). The
loading rates were extracted from the data by taking the slope of the
fit WLC\index{WLC} at unfolding.
\begin{figure}
\asyfig{figures/cantilever-data/loading-rate}
- \caption{Loading rate.\label{fig:cantilever:loading-rate}}
+ \caption{Loading rate.\label{fig:cant:load-dep}}
\end{figure}
void graphFile(picture pic=currentpicture, string file="datafile",
real xscale=1, real yscale=1, pen p=red,
- path mpath=scale(0.8mm)*unitcircle, string t="Title",
+ path mpath=scale(0.8mm)*unitcircle,
+ markroutine markroutine=marknodes,
+ string t="Title",
bool dots=false) {
pen pline=p;
+ marker mk = nomarker;
file fin=input(file).line();
real[][] a=fin.dimension(0,0);
a=transpose(a);
real[] y=a[1];
if (dots == true) {
pline = invisible;
+ mk = marker(mpath, markroutine, p);
}
if (t != "Title") {
- draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, legend=sLabel(t,extra_spaces=1), marker=marker(mpath, p));
+ draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, legend=sLabel(t,extra_spaces=1), marker=mk);
} else {
- draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, marker=marker(mpath, p));
+ draw(pic=pic, graph(pic,xscale*x,yscale*y), p=pline, marker=mk);
}
}
path m8=scale(2mm)*shift(-.5,-.5)*unitsquare;
path m30=scale(1.5mm)*unitcircle;
path mdot=scale(0.2pt)*unitcircle;
+
+markroutine marksize(string file="datafile", pen p=red, path mpath=scale(0.8mm)*unitcircle, real size=1) {
+ return new void(picture pic=currentpicture, frame f, path g) {
+ /* frame f is the marker we setup in graphFile(). We can't scale
+ that directly though, since the drawn line thickness would change.
+ Instead, we give marksize() the same p and mpath that graphFile()
+ got, so it can scale the path and stroke it with the unscaled pen.
+ */
+ file fin=input(file).line();
+ real[][] a=fin.dimension(0,0);
+ a=transpose(a);
+ real[] s=a[3];
+ for (int i=0; i <= length(g); ++i) {
+ pair z = point(g, i);
+ frame f;
+ draw(f, scale(sqrt(s[i]/size))*mpath, p);
+ add(pic, f, z);
+ }
+ };
+}
--
FIGS = v-dep loading-rate
-DATA = v-dep.d/v_dep_131.98.dat \
+V_DEP_DATA = v-dep.d/v_dep_131.98.dat \
v-dep.d/v_dep_131.98.fit \
v-dep.d/v_dep_24.33.dat \
- v-dep.d/v_dep_24.33.fit \
- loading-rate.d/loading_rate_131.98 \
+ v-dep.d/v_dep_24.33.fit
+LOADING_RATE_DATA = loading-rate.d/loading_rate_131.98 \
loading-rate.d/loading_rate_24.33
+DATA = $(V_DEP_DATA) $(LOADING_RATE_DATA)
DATA_DIRS = data v-dep.d loading-rate.d
all : $(FIGS:%=%_.tex)
clean :
- rm -f $(FIGS:%=%_*) $(FIGS:%=%-*) *.pyc
+ rm -f $(FIGS:%=%_*) $(FIGS:%=%-*) v-dep.asy v-dep.gp *.pyc
#rm -rf $(DATA_DIRS)
%_.tex : %.asy $(DATA)
$(DATA_DIRS) :
mkdir $@
-data/raw : extract_f_v_k_data.sh $(DATA_DIRS)
- ./$< > $@
+#data/raw : extract_f_v_k_data.sh $(DATA_DIRS)
+# ./$< > $@
data/spring-constants data/averaged-data : avg_data.py data/raw
python $<
-v-dep.asy v-dep.gp v-dep.d/v_dep_%.dat : \
- make_plots.sh data/spring-constants data/averaged-data
+v-dep.d/v_dep_%.dat : \
+ get_v_dep.sh data/spring-constants data/averaged-data
./$<
v-dep.d/v_dep_%.fit : fit_data.py v-dep.d/v_dep_%.dat
python $^ > $@
-v-dep.pdf : v-dep.gp v-dep.d/v_dep_*
+v-dep.asy v-dep.gp : make_v_dep_plots.sh $(V_DEP_DATA)
+ ./$<
+
+v-dep.pdf : v-dep.gp $(V_DEP_DATA)
gnuplot $<
v-dep.eps : v-dep.pdf
KFILE='./data/spring-constants'
AVGFILE='./data/averaged-data'
-ASYSPLIT='./v-dep.asy'
-GPSPLIT='./v-dep.gp'
-PLOTS=""
while read LINE
do
Kprecise=`echo "$LINE" | sed 's/.*= \([0-9.]*\) +.*/\1/'`
echo "clearing $FILE"
> "$FILE.dat"
rm -f "$FILE.fit"
- PLOTS="$PLOTS, '$FILE.dat' using 1:2:(sqrt(\$4)) with points pt 6 pointsize variable t '$K (pN/nm)'"
- PLOTS="$PLOTS, '$FILE.fit' using 1:2 with lines notitle"
done < <(tac "$KFILE")
-PLOTS="${PLOTS:2}" # remove leading ' ,'
while read DATA
do
+++ /dev/null
-1.338 107.3
-1.565 140.8
-332.1 329.2
-109.92 230.2
-165.6 323.9
-247.83 391.1
-36.518 179.3
-54.9883 269.9
-47.3663 273.9
-42.0267 264.3
-35.081 259.6
-56.6138 279.9
-39.7415 317
-15.1975 246.8
-15.4771 278.5
-15.3074 216.9
-8.24467 217
-9.5142 256.3
-367.575 348.6
-182.026 325.3
-109.61 295.8
-11.75 271.2
-7.565 273.2
-3.825 215.8
-178.461 321.9
-107.815 302.7
-248.651 319.5
-110.104 378.4
-82.5727 258
-55.7042 276.8
-69.1621 366.8
-46.1427 338.7
-217.6 316.9
-230.8 386
-94.88 284.8
-61.9461 326.7
-49.2637 347.7
-30.8974 247.4
-65.19 444
-32.897 247.8
-45.9736 388.7
-59.6136 505.5
-13.6803 355
-10.9925 342.6
-10.0444 336.5
-8.47166 190.9
-11.28 315.9
-14.0736 357.2
-20.5828 500.8
-101.741 377.5
-73.9691 396
-9.31544 259.9
-12.3903 357.7
-14.4225 410.8
-11.5782 410.4
-35.1063 252.7
-25.7327 282.3
-5.993 269.3
-57.1228 202.3
-70.0795 314.4
-52.5927 303.4
-55.515 339
-62.2298 397.2
-57.7281 402.9
-48.299 397.9
-36.2503 380.4
-35.6355 396.3
-29.8571 374.6
-36.5718 443.3
-146.59 343.5
-146.212 400.8
-294.6 387.4
-255.6 393.2
-227.6 304.9
-224.4 397.7
-45.9736 248.1
-39.167 313.3
-76.624 373.6
-117.934 449.6
-49.519 346.7
-40.4399 332.2
-43.8257 396.2
+++ /dev/null
-34.7853 231.2
-28.9221 232.8
-31.2565 249.9
-139.467 271
-109.651 264.6
-144.445 246.3
-180.185 256.2
-361.617 215.3
-222.571 246.7
-153.55 234.3
-168.992 250.6
-162.258 268.8
-153.291 279.3
-57.1724 186.1
-149.829 229.3
-51.8646 193
-121.807 243.6
-67.6845 193.9
-12.581 199
-17.8712 253.4
-10.4774 228.6
-12.4557 283.4
-318.404 208.1
-190.477 255.8
-6.0015 173
-6.74572 171.5
-241.836 267.4
-60.7929 174.6
-101.058 283.3
-225.126 221.9
-128.032 200.2
-6.09452 129.2
-4.63947 151.9
-1.87368 100.2
-541.616 221.2
-392.696 258.1
-123.863 209.4
-88.0571 181.6
-154.779 199.1
-67.8731 165.4
-123.484 214.2
-6.10522 187
-111.074 181.9
-65.4039 150.3
-44.6793 178.1
-29.0171 195.4
-25.6648 179
-9.425 221.8
-2566.5 315.1
-698.5 311.1
-266.35 248.1
-242.95 225.7
-254 249.4
-183.832 174.1
-84.789 186
-130.296 237.7
-130.82 272.1
-62.6328 223.3
-65.0224 240.8
-239.17 215.4
-8.40114 169.2
-426.146 224.5
-293.5 210.6
-235.2 242.9
-58.8245 219.9
-27.3032 208.4
-11.8766 219.2
-7.71178 202.1
-139.834 197.5
-155.911 217.1
-87.8494 199.4
-52.6342 227.8
-56.8893 264.2
-691.5 228.2
-10.8421 177.9
-7.97246 194.6
-4.96078 197.2
-5.58474 222.7
-3.5507 203.5
-6.584 184.4
-2.92828 205.3
-2.79546 228
-109.618 194.1
-128.589 216.4
-170.967 264.8
-296.55 178.9
-295.55 234.7
-79.4103 206.7
-86.4271 204.8
-12.7162 176.1
-3.90479 108.5
-8.95931 213.2
-4.618 162.1
-8.41784 233.3
-33.1431 206.1
-23.8574 220
-13.9742 181.6
-13.4052 206.2
-17.8148 206.6
-28.2662 219.7
-14.7366 208.7
-16.4421 267.4
-65.2442 177.6
-79.7593 236.3
-305.643 374.5
-119.529 256
-147.529 287.4
-130.292 221.7
-103.962 236.1
-97.8843 273
-85.2586 244.1
-55.411 283.7
-185.46 321
-71.6683 250
-12.5468 225.5
-5.98895 169.1
-7.68286 221
-8.2052 284.7
-14.2174 230.7
-19.4 226.3
-8.418 221.2
-6.458 213.7
-5.068 235.7
-3.153 220.8
-3.118 236.4
-280.602 289.4
-108.477 270.7
-82.9888 274
-205.003 414.4
-197.282 238
-150.657 295
-15.1 198.4
-9.036 207.7
-4.502 212.1
-2.738 181.8
-3.672 250.7
-178.93 224.4
-56.0359 217.4
-83.0476 210.9
-108.315 282.4
-47.0469 268.7
-33.0893 264.6
-153.439 310.6
-92.931 327.6
-83.5395 412.5
-119.048 228.9
-57.0645 233.7
-199.268 242.1
-74.4677 234.9
-90.8007 307.3
-42.7389 168
-24.4887 193.7
-18.6563 253.6
-58.5149 234.6
-29.7544 265.5
-116.894 203.9
-147.063 262.8
-58.2009 235.1
-60.6315 302.9
-40.8088 253.2
-32.2687 258.7
-111.881 204.2
-71.9899 259.5
-55.2881 268
-45.6699 255.2
-42.1422 291.1
-17.5799 239.1
-13.7585 252.7
-13.7924 303.5
-54.7112 212.5
-35.6734 230.8
-28.4006 200.4
-25.1756 217.7
-30.2637 263.9
-26.2443 244.5
-29.2045 277.2
-13.8646 203.9
-15.5764 233.2
-19.0189 275.6
-98.9684 194.3
-63.1913 247.7
-41.1392 258.5
-33.8809 260.7
-34.3192 331
-13.5026 231.5
-9.74262 231.6
-10.0387 255.3
-6.97865 243.3
-253.364 227
-110.652 259.4
-62.4379 255.2
-1154.4 257.3
-369 246.8
-332.4 298.4
-12.8306 193.7
-13.5327 243.1
-6.90051 180
-5.8898 177.6
-7.81729 222.7
-8.20637 241.5
-6.29677 222.7
-8.44339 261.9
-8.13482 288.3
-55.6781 262.8
-48.5227 271.9
-18.356 232
-9.235 195.4
-15.22 235.5
-27.1956 196
-12.5298 195.3
-9.04264 199.3
-6.31462 202.1
-129.692 187.7
-31.8506 164.7
-9.703 213.1
-6.617 217.2
-4.691 230.8
-3.34 212.5
-264.619 258
-146.117 273.1
-46.4186 212.5
-29.8602 267.5
-118.029 270.5
-103.37 277
-63.0904 263.6
-1.764 116.7
-4.17 223.7
-2.992 225.4
-2.322 204.6
-2.555 236.2
-149.012 272.5
-42.0068 293.8
-402.8 206.4
-257.4 266.6
-171.62 287.1
-101.3 238.2
-3.66463 118.5
-1.86042 93.12
-2.5531 129.7
-2.02587 123.5
-2.12404 141.1
-32.4106 146.3
-24.0218 167.6
-17.2125 157.2
-16.0114 173.1
-18.9527 150.1
-16.6167 166
-13.4201 159.6
-10.0249 143.4
-156.58 215.8
-58.26 184.2
-64.5847 150.6
-44.7525 174.1
-20.8252 161.7
-16.2478 159.5
-14.5346 274.7
-9.52903 264.2
-4.16181 153.6
-8.0762 263.3
-5.88321 255.7
-5.30377 246.6
-5.94243 292.4
-6.2829 289.4
-20.864 230.8
-19.0898 256
-10.3707 207.5
-7.34662 215.8
-6.23003 225.7
-7.82243 298.8
-8.23481 324.5
-248.163 201.5
-134.579 262.9
-627.121 237.2
-259.133 299.1
--- /dev/null
+#!/bin/bash
+
+KFILE='./data/spring-constants'
+AVGFILE='./data/averaged-data'
+ASYFILE='./v-dep.asy'
+GPFILE='./v-dep.gp'
+
+ASYPLOTS=""
+GPPLOTS=""
+while read LINE
+do
+ Kprecise=`echo "$LINE" | sed 's/.*= \([0-9.]*\) +.*/\1/'`
+ K=`python -c "print '%.2f' % $Kprecise"`
+ FILE="v-dep.d/v_dep_$K"
+ Kindex=`echo "$LINE" | sed 's/K(\([0-9.]*\)) =.*/\1/'`
+ case "$Kindex" in
+ 0)
+ PEN="psoft"
+ ;;
+ 1)
+ PEN="pmed"
+ ;;
+ 2)
+ PEN="phard"
+ ;;
+ esac
+ ASYPLOTS=$(echo -e "$ASYPLOTS\ngraphFile(\"$FILE.dat\", xscale, yscale, $PEN, m8,
+ markroutine=marksize(\"$FILE.dat\", $PEN, m8, 10), t=units(\"$K\",\"pN/nm\"), dots=true);")
+ ASYPLOTS=$(echo -e "$ASYPLOTS\ngraphFile(\"$FILE.fit\", xscale, yscale, $PEN,
+ t=units(\"$K\",\"pN/nm\"));")
+ GPPLOTS="$GPPLOTS, '$FILE.dat' using 1:2:(sqrt(\$4)) with points pt 6 pointsize variable t '$K (pN/nm)'"
+ GPPLOTS="$GPPLOTS, '$FILE.fit' using 1:2 with lines notitle"
+done < <(tac "$KFILE")
+GPPLOTS="${GPPLOTS:2}" # remove leading ' ,'
+
+cat > "$ASYFILE" <<HEREDOC
+import wtk_graph;
+
+size(15cm,10cm,IgnoreAspect);
+
+scale(Log, Linear);
+real xscale=1;
+real yscale=1;
+$ASYPLOTS
+
+//xlimits(1,3e3);
+//ylimits(90,620);
+
+label(sLabel("Pulling speed dependence"), point(N),N);
+xaxis(sLabel("Pulling speed (nm/s)"),BottomTop,LeftTicks);
+yaxis(sLabel("Unfolding force (pN)"),LeftRight,RightTicks);
+
+add(legend(),point(E),20E,UnFill);
+HEREDOC
+
+cat > "$GPFILE" <<HEREDOC
+set xlabel 'Pulling speed (nm/s)'
+set ylabel 'Unfolding force (pN)'
+set logscale x;
+plot $GPPLOTS
+HEREDOC
--- /dev/null
+../asy/wtk_graph.asy
\ No newline at end of file
real xscale=1e12;
real yscale=1e12;
-graphFile(file="sim-loading-rate.d/loading_rate_dep_127_8",
+graphFile(file="loading-rate.d/loading_rate_dep_127_8",
xscale=xscale, yscale=yscale, p=phard, mpath=mdot,
t=units("127","pN/nm"), dots=true);
-graphFile(file="sim-loading-rate.d/loading_rate_dep_27_8",
+graphFile(file="loading-rate.d/loading_rate_dep_27_8",
xscale=xscale, yscale=yscale, p=red, mpath=mdot,
t=units("27","pN/nm"), dots=true);
projects / thesis.git / commitdiff