Merge unfolding and tension chapters back into sawsim chapter.
In order to focus on my contributions, I think it would be clearer to
bundle the theory into the sawsim chapter. They're all very closely
related, and it means I can keep patting myself on the back throughout
the chapter so the reader doesn't loose focus ;).
This commit is mostly a reworking of the sawsim chapter.
Other changes:
* Dissable old SCons asymptote build. I'm using the build-asy.py
script for this now, and I haven't worked out how to wedge that into
SCons yet. The problem is all this scratch-directory linking.
* Add an E. coli index point in apparatus/polymer-synthesis.tex.
* Add blub/gumbel.tex (not currently included) to work out the
different probability distribution nomenclature.
* Add wlc-extension.asy, wlc-model.asy, fjc-extension.asy,
fjc-model.asy, landscape-bell.asy, and wiggle.asy.
* unfolding.asy: pull Wiggle out into wiggle.asy.
* cantilever/theory.tex: flesh out energy landscape caption.
* introduction/main.tex: link rief02 for simulation/experiment
comparison.
* local_cmmds.tex: add \Langevin, \insilico, \invitro, \invivo,
\pysawsim. Comment out \r and \rs (which aren't used?) because they
were colliding with something inside Angstroms (\AA).
* root.bib: Add wikipedia:gumbel, gumbel58, wikipedia:GEV,
wikipedia:gompertz, wikipedia:gumbel-t1, wikipedia:gumbel-t2,
dudko08, baljon96, fisher99a, fisher99b, zlatanova00, viani99,
capitanio02, binnig86, williams86, martin87, and meyer88. Also fix
a few BibTeX markup issues.
* packages.tex: fix struct -> struck typo and import booktabs and
fancyvrb. Also disable lineno usage in final mode.
* root.tex: disable lineno usage in final mode and remove unfolding
chapter.
* sim-hist.asy: smaller size.
* fit-valley.asy, sim-sawtooth.asy: smaller size, more consistent axis
labeling.
* kappa-sawteeth.asy: more consistent axis labeling.
43 files changed: