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W. Trevor King [Fri, 12 Mar 2010 05:24:34 +0000 (00:24 -0500)]
Use a bit less negative space for \logp{}
W. Trevor King [Fri, 12 Mar 2010 04:23:19 +0000 (23:23 -0500)]
Fixed the bulk of Mom's remaining typos and clarification requests
W. Trevor King [Thu, 11 Mar 2010 18:34:16 +0000 (13:34 -0500)]
Fixed typos Mom found in the appenidicies + switched cantilver-calib to cref
Use - instead of _ in labels (I think it looks nicer :).
Note that using multiple references in \cref in appendicies
\cref{eq:res-thm,eq:res-simple}
breaks with cleveref v0.14.2 (but works with v0.15.3). The errors were:
! Missing number, treated as zero.
<to be read again>
{
l.94 Applying \cref{eq:res_thm,eq:res_simple}
Caused by \@results like
{
2147483647}\@result
rather than the newer
2147483647,\@result
W. Trevor King [Thu, 11 Mar 2010 17:43:00 +0000 (12:43 -0500)]
Addressed Mom's concerns about WLC indexing and fixed some sawsim typos
W. Trevor King [Thu, 11 Mar 2010 15:07:55 +0000 (10:07 -0500)]
Add Index and Nomenclature sections
W. Trevor King [Thu, 25 Feb 2010 15:35:00 +0000 (10:35 -0500)]
Moved figures/contour/contour.asy to asyfig workflow
W. Trevor King [Thu, 25 Feb 2010 15:23:57 +0000 (10:23 -0500)]
Fix i_dep.d -> i-dep.d
W. Trevor King [Thu, 25 Feb 2010 15:10:10 +0000 (10:10 -0500)]
Add FIGS variable to asyprocess Makefiles to reduce duplication
Also moved the other two schematic ASY figures over from external
builds to asyfig.
W. Trevor King [Thu, 25 Feb 2010 15:09:23 +0000 (10:09 -0500)]
Added labels to cantilever simulation figures
W. Trevor King [Thu, 25 Feb 2010 15:01:00 +0000 (10:01 -0500)]
Pull out cantilever peak index simulation figure.
W. Trevor King [Thu, 25 Feb 2010 14:44:51 +0000 (09:44 -0500)]
Use packages.tex in asyprocess calls
W. Trevor King [Thu, 25 Feb 2010 12:34:31 +0000 (07:34 -0500)]
Working my 2009 Biophys Soc poster into cantilever/
Several large asymptote figures, so rather than using fully external
asy (non-matching fonts, etc) or \usepackage[inline]{asymptote}
(recompiles all asy graphics every time), I've switched to asyfig
http://www.ctan.org/tex-archive/macros/latex/contrib/asyfig/
The current CTAN version is v0.1b, but that wasn't quite flexible
enough, but Will Robertson versions in git, so I cloned his branch
http://github.com/wspr/asyfig
and added what I needed
http://www.physics.drexel.edu/~wking/code/git/asyfig.git/
I don't think it's all working yet, but there's a lot of work since my
last commit, so here's a checkpoint ;).
W. Trevor King [Tue, 23 Feb 2010 20:06:34 +0000 (15:06 -0500)]
Fix other errata listed on wiki.creativecommons.org/Legalcode_errata
W. Trevor King [Tue, 23 Feb 2010 19:27:18 +0000 (14:27 -0500)]
Added I27 introduction to sec:cantilever
W. Trevor King [Tue, 23 Feb 2010 16:19:24 +0000 (11:19 -0500)]
Added Introduction \section{Thesis Outline}.
Spellchecked introduction/main.tex.
Changed title (again :p) to:
"Temperature and cantilever dependent protein unfolding"
W. Trevor King [Tue, 23 Feb 2010 15:09:51 +0000 (10:09 -0500)]
Changed title to "Mechanical protein unfolding analysis"
W. Trevor King [Tue, 23 Feb 2010 15:07:08 +0000 (10:07 -0500)]
Oops. \copyrightCCBYSA -> \copyrighttextCCBYSA
W. Trevor King [Tue, 23 Feb 2010 14:46:10 +0000 (09:46 -0500)]
Move Sawsim into paragraph fully into sawsim/introduction.tex
W. Trevor King [Tue, 23 Feb 2010 14:45:27 +0000 (09:45 -0500)]
GNU FDL too restrictive, use CC-by-sa instead.
W. Trevor King [Tue, 23 Feb 2010 02:25:23 +0000 (21:25 -0500)]
Tied unfolding model paragraph into single molecule methods paragraph
W. Trevor King [Tue, 23 Feb 2010 01:30:00 +0000 (20:30 -0500)]
Fix drexe -> drexel typos in README URLs
W. Trevor King [Tue, 23 Feb 2010 01:23:50 +0000 (20:23 -0500)]
Use \chapter{}, \section{}, and \ref{} in fdl.txt.
Also revert bustamante08 -> betterment08 spellcheck error introduced
in
96237f4dfe4fe90895e36f36199235cfb8282560
W. Trevor King [Mon, 22 Feb 2010 23:29:18 +0000 (18:29 -0500)]
Added FDL appendix
W. Trevor King [Mon, 22 Feb 2010 23:19:35 +0000 (18:19 -0500)]
Added README and COPYING (GNU FDL)
W. Trevor King [Mon, 22 Feb 2010 23:01:12 +0000 (18:01 -0500)]
Added "Double T" folding pathway example
W. Trevor King [Mon, 22 Feb 2010 21:36:25 +0000 (16:36 -0500)]
Added pathway / landscape folding model paragraph
W. Trevor King [Mon, 22 Feb 2010 15:57:35 +0000 (10:57 -0500)]
Working through ligand/receptor figure
W. Trevor King [Mon, 22 Feb 2010 01:16:37 +0000 (20:16 -0500)]
Working through introductory citations, HGP and Levinthal.
W. Trevor King [Thu, 18 Feb 2010 21:53:01 +0000 (16:53 -0500)]
Fix figure 1.1 referencing/labeling
W. Trevor King [Thu, 18 Feb 2010 20:51:49 +0000 (15:51 -0500)]
Merge branch 'master' of yang:./rsrch/notes/thesis
W. Trevor King [Thu, 18 Feb 2010 20:50:53 +0000 (15:50 -0500)]
Some work cleaning up the introductory text
W. Trevor King [Thu, 18 Feb 2010 20:35:53 +0000 (15:35 -0500)]
Draw Laser and Photodiode in AFM schematic.
W. Trevor King [Thu, 18 Feb 2010 17:34:14 +0000 (12:34 -0500)]
Moved AFM-drawing functions from unfolding.asy to base_afm.asy & made substrate motion controllable
W. Trevor King [Thu, 18 Feb 2010 00:22:21 +0000 (19:22 -0500)]
Broke the figures out into their own src subdirectory.
They used to live under the different chapters, but the new structure
will make it easier to share figure-generation code between chapters.
W. Trevor King [Wed, 17 Feb 2010 23:53:33 +0000 (18:53 -0500)]
Broke sawsim chapter into sections and added local_words
W. Trevor King [Wed, 17 Feb 2010 23:33:04 +0000 (18:33 -0500)]
Updated unfolding-distributions input paths in u..-d../main.tex
W. Trevor King [Tue, 9 Feb 2010 22:25:13 +0000 (17:25 -0500)]
Added rough chapter outlines
W. Trevor King [Tue, 9 Feb 2010 20:15:05 +0000 (15:15 -0500)]
Fix linenumbers handling and use 'subfig' drexel-thesis option
W. Trevor King [Tue, 9 Feb 2010 12:33:23 +0000 (07:33 -0500)]
Moved chapter files to */main.tex
W. Trevor King [Thu, 14 Jan 2010 19:13:51 +0000 (14:13 -0500)]
Merged viscocity notes
W. Trevor King [Thu, 14 Jan 2010 18:43:56 +0000 (13:43 -0500)]
Merged my hyeon03 equation derivation
W. Trevor King [Thu, 14 Jan 2010 17:19:01 +0000 (12:19 -0500)]
Brought in unfolding_distributions
W. Trevor King [Thu, 14 Jan 2010 02:20:44 +0000 (21:20 -0500)]
Merged sawsim paper.
W. Trevor King [Thu, 14 Jan 2010 00:28:48 +0000 (19:28 -0500)]
Converted to drexel-thesis class, compiles at home, multiple bibs.
W. Trevor King [Sat, 19 Dec 2009 00:00:07 +0000 (19:00 -0500)]
Transitioned contour figure from MetaPost to Asymptote
W. Trevor King [Wed, 2 Dec 2009 20:22:15 +0000 (15:22 -0500)]
Added latex framework and cantilever_calib appendix.
W. Trevor King [Wed, 2 Dec 2009 07:51:22 +0000 (02:51 -0500)]
Began versioning