Merge unfolding and tension chapters back into sawsim chapter.
authorW. Trevor King <wking@tremily.us>
Fri, 29 Jun 2012 19:51:54 +0000 (15:51 -0400)
committerW. Trevor King <wking@tremily.us>
Fri, 29 Jun 2012 20:08:28 +0000 (16:08 -0400)
commita65847561caf928e9f846c94969e9866d3e217d3
tree9e1736624966508ff122f8fa584817cfde03a26d
parentfa39144b19bc44829857d19815fc94465b6002a9
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:
site_cons/site_tools/asymptote.py
src/apparatus/polymer-synthesis.tex
src/blurb/gumbel.tex [new file with mode: 0644]
src/cantilever/theory.tex
src/figures/fit-space/fit-valley.asy
src/figures/kappa-sawteeth/kappa-sawteeth.asy
src/figures/schematic/SConscript
src/figures/schematic/fjc-extension.asy [new file with mode: 0644]
src/figures/schematic/fjc-model.asy [new file with mode: 0644]
src/figures/schematic/landscape-bell.asy [new file with mode: 0644]
src/figures/schematic/unfolding.asy
src/figures/schematic/wiggle.asy [new file with mode: 0644]
src/figures/schematic/wlc-extension.asy [new file with mode: 0644]
src/figures/schematic/wlc-model.asy [new file with mode: 0644]
src/figures/sim-hist/sim-hist.asy
src/figures/sim-sawtooth/sim-sawtooth.asy
src/introduction/main.tex
src/local_cmmds.tex
src/packages.tex
src/root.bib
src/root.tex
src/sawsim/discussion.tex
src/sawsim/introduction.tex
src/sawsim/methods.tex
src/tension/folded.tex [deleted file]
src/tension/main.tex [deleted file]
src/tension/polymer.tex [deleted file]
src/unfolding/distributions-kramers.tex [deleted file]
src/unfolding/distributions-overview.tex [deleted file]
src/unfolding/distributions-review.tex [deleted file]
src/unfolding/distributions-single_domain-constant_loading.tex [deleted file]
src/unfolding/distributions.tex [deleted file]
src/unfolding/main.tex [deleted file]
src/unfolding/rate-bell.tex [deleted file]
src/unfolding/rate-kramers-saddle.tex [deleted file]
src/unfolding/rate-kramers.tex [deleted file]
src/unfolding/rate-overview.tex [deleted file]
src/unfolding/rate-stiff-bell.tex [deleted file]
src/unfolding/rate.tex [deleted file]
src/unfolding/tension-fjc.tex [deleted file]
src/unfolding/tension-folded.tex [deleted file]
src/unfolding/tension-wlc.tex [deleted file]
src/unfolding/tension.tex [deleted file]