thesis.git
11 years agocalibcant/discussion.tex: POE is approximate (first order Taylor)
W. Trevor King [Sun, 5 May 2013 18:42:00 +0000 (14:42 -0400)]
calibcant/discussion.tex: POE is approximate (first order Taylor)

11 years agocalibcant/discussion.tex: Cleanup peak-frequency discussion
W. Trevor King [Sun, 5 May 2013 18:36:33 +0000 (14:36 -0400)]
calibcant/discussion.tex: Cleanup peak-frequency discussion

Add $f_\text{max}$ for clarity, and link to this equation from the
vibration figure.

11 years agoroot.bib: Fix math markup in tlusty98 note
W. Trevor King [Sun, 5 May 2013 18:24:48 +0000 (14:24 -0400)]
root.bib: Fix math markup in tlusty98 note

11 years agocalibcant: flesh out calibcant chapter
W. Trevor King [Sun, 5 May 2013 02:04:27 +0000 (22:04 -0400)]
calibcant: flesh out calibcant chapter

Figures, references, theory, etc.

11 years agocalibcant/theory.tex: Increase linking to apparatus/cantilever-calib
W. Trevor King [Fri, 3 May 2013 20:58:29 +0000 (16:58 -0400)]
calibcant/theory.tex: Increase linking to apparatus/cantilever-calib

11 years agocalibcant/theory.tex: Cleanup after de-appendicizing
W. Trevor King [Fri, 3 May 2013 20:42:40 +0000 (16:42 -0400)]
calibcant/theory.tex: Cleanup after de-appendicizing

I added a new command \abs{} for absolute values, which uses \lvert
and \rvert.  This works better than |...|, because the lines stretch
to enclose their argument.  The nomencl package also refuses to add
entries containing the pipe symbol to the nomenclature.

11 years agopyafm/discussion.tex: Fix 'fig:fig:...' -> 'fig:...' typo
W. Trevor King [Fri, 3 May 2013 20:41:47 +0000 (16:41 -0400)]
pyafm/discussion.tex: Fix 'fig:fig:...' -> 'fig:...' typo

11 years agosawsim/discussion.tex: Fix '\ie ' -> '\ie\ ' typo
W. Trevor King [Fri, 3 May 2013 15:18:09 +0000 (11:18 -0400)]
sawsim/discussion.tex: Fix '\ie ' -> '\ie\ ' typo

LaTeX macros gobble the trailing space, unless we escape it with '\ '.

11 years agocalibcant: Move most of the derivation in from the appendix
W. Trevor King [Thu, 2 May 2013 00:23:03 +0000 (20:23 -0400)]
calibcant: Move most of the derivation in from the appendix

Shrink the cantilever-calib appendix down just the bits where I've
added tons of intermediate steps.

11 years agoapparatus/cantilever-calib.tex: Summarize the experiment procedure
W. Trevor King [Wed, 1 May 2013 23:20:11 +0000 (19:20 -0400)]
apparatus/cantilever-calib.tex: Summarize the experiment procedure

Folks might find the raw equation unenlightening.  Hopefully a few
words about the procedure will help this teaser sink in so they're
ready for the calibcant chapter.

11 years agocalibcant/main.tex: Label chapter and sections
W. Trevor King [Wed, 1 May 2013 23:18:35 +0000 (19:18 -0400)]
calibcant/main.tex: Label chapter and sections

Most of the theory derivation (except for the long integrals) will
move here from the current calibration appendix.  The new labels allow
us to link into the calibcant-based chapter (vs. a theory-only
chapter), where I can highlight my work.

11 years agoapparatus/cantilever-calib.tex: Move nomenclature out of paragraph
W. Trevor King [Wed, 1 May 2013 23:12:11 +0000 (19:12 -0400)]
apparatus/cantilever-calib.tex: Move nomenclature out of paragraph

This makes it easier to read the text of the paragraph itself, which
had previously ended a paragraph with a sentence (fixed now).

11 years agosawsim/discussion.tex: Remove Who's who (only I care ;)
W. Trevor King [Wed, 1 May 2013 20:49:23 +0000 (16:49 -0400)]
sawsim/discussion.tex: Remove Who's who (only I care ;)

11 years agopyafm: Fill in the chapter on my control stack
W. Trevor King [Wed, 1 May 2013 20:47:00 +0000 (16:47 -0400)]
pyafm: Fill in the chapter on my control stack

Use minted for syntax highlighting in code excerpts (yay pygments!).

11 years agofigures/labview-comparision: Data and figures comparing control stacks
W. Trevor King [Wed, 1 May 2013 20:44:54 +0000 (16:44 -0400)]
figures/labview-comparision: Data and figures comparing control stacks

This should be automated, but I don't have time now.

11 years agoUpdate to TeXLive 2011 needs protected caption subrefs
W. Trevor King [Sun, 28 Apr 2013 19:59:26 +0000 (15:59 -0400)]
Update to TeXLive 2011 needs protected caption subrefs

To avoid:

  ! Argument of \@caption has an extra }.

fragile \subref{} calls in \caption{} arguments need to be
\protect-ed.  For details, see:

  http://tex.stackexchange.com/questions/31817/texlive-2011-and-subfig

where egreg points out that the change probably happened in the bump
to caption 3.2.

11 years agoroot.bib: Add missing @string definition for APL
W. Trevor King [Sat, 27 Apr 2013 03:47:04 +0000 (23:47 -0400)]
root.bib: Add missing @string definition for APL

11 years agoroot.bib: Add missing commas in martin87 and meyer88
W. Trevor King [Sat, 27 Apr 2013 03:43:35 +0000 (23:43 -0400)]
root.bib: Add missing commas in martin87 and meyer88

11 years agopyafm: Split into per-section files
W. Trevor King [Fri, 26 Apr 2013 16:01:19 +0000 (12:01 -0400)]
pyafm: Split into per-section files

This makes the source for a particular section easier to find.

11 years agoapparatus/cantilever-calib.tex: Use '\cite{...}' instead of '\citep{...}'
W. Trevor King [Thu, 25 Apr 2013 19:36:00 +0000 (15:36 -0400)]
apparatus/cantilever-calib.tex: Use '\cite{...}' instead of '\citep{...}'

\citep doesn't seem to work inside \nomenclature.

11 years agoReplace '\cite{...}' with '\citep{...}'
W. Trevor King [Thu, 25 Apr 2013 19:33:29 +0000 (15:33 -0400)]
Replace '\cite{...}' with '\citep{...}'

This way we get the configured natbib formatting.

11 years agocantilever/discussion.tex: Update sawsim link
W. Trevor King [Thu, 25 Apr 2013 17:24:20 +0000 (13:24 -0400)]
cantilever/discussion.tex: Update sawsim link

Shortly after this thesis is finalized I should graduate ;).  Point
folks reading the thesis to my personal site for sawsim, instead of
the Drexel site that I may no longer control.

Also:
* Add a more informative section title.
* Use \citet{} instead of hardcoding Walton et al.
* Use \url{} for a clickable link.

11 years agocantilever/main.tex: Clarify title with "stiffness effect"
W. Trevor King [Thu, 25 Apr 2013 17:15:47 +0000 (13:15 -0400)]
cantilever/main.tex: Clarify title with "stiffness effect"

11 years agocantilever/simulations.tex: Link to sec:sawsim:cantilever
W. Trevor King [Thu, 25 Apr 2013 17:14:47 +0000 (13:14 -0400)]
cantilever/simulations.tex: Link to sec:sawsim:cantilever

11 years agocantilever/theory.tex: Cite Walton 2008 as motivation
W. Trevor King [Thu, 25 Apr 2013 17:12:52 +0000 (13:12 -0400)]
cantilever/theory.tex: Cite Walton 2008 as motivation

11 years agointroduction/main.tex: Expand on the landscape/pathway distinction
W. Trevor King [Thu, 25 Apr 2013 17:10:31 +0000 (13:10 -0400)]
introduction/main.tex: Expand on the landscape/pathway distinction

11 years agointroduction/main.tex: Tighten single molecule lead-in
W. Trevor King [Thu, 25 Apr 2013 17:07:21 +0000 (13:07 -0400)]
introduction/main.tex: Tighten single molecule lead-in

Replace "imposes certain limitations on" with "limits" ;).

11 years agoMerge remote-tracking branch 'local/master'
W. Trevor King [Thu, 25 Apr 2013 12:48:22 +0000 (08:48 -0400)]
Merge remote-tracking branch 'local/master'

With thesis development distributed over a number of machines, I lost
track of a few repositories.  This pulls in some changes from a
recently rediscovered repo.

* local/master:
  Relabel src/unfolding/rate.tex as sec:unfolding-rate.
  Consolidate references to cantilever calibration summary as sec:cantilever-calib:intro.
  Remove cruft from SCons generator bodies.

Conflicts:
src/apparatus/main.tex
src/unfolding/rate.tex

11 years agosrc/pyafm/main.tex: Add a space after \pyafm in the header
W. Trevor King [Fri, 19 Apr 2013 21:26:43 +0000 (17:26 -0400)]
src/pyafm/main.tex: Add a space after \pyafm in the header

11 years agosrc/figures/fit-space/extract_fit_valley.py: print -> print()
W. Trevor King [Wed, 17 Apr 2013 23:35:38 +0000 (19:35 -0400)]
src/figures/fit-space/extract_fit_valley.py: print -> print()

11 years agosrc/figures/script/pyfit: print -> print()
W. Trevor King [Wed, 17 Apr 2013 23:34:30 +0000 (19:34 -0400)]
src/figures/script/pyfit: print -> print()

11 years agosrc/figures/cantilever-data/make_v_dep_plots.sh: print -> print()
W. Trevor King [Wed, 17 Apr 2013 23:29:46 +0000 (19:29 -0400)]
src/figures/cantilever-data/make_v_dep_plots.sh: print -> print()

Fix embedded Python syntax to avoid:

  ./make_v_dep_plots.sh
    File "<string>", line 1
      print '%.2f' % 131.97793902439034
                 ^
  SyntaxError: invalid syntax

11 years agosrc/figures/cantilever-data/get_v_dep.sh: print -> print()
W. Trevor King [Wed, 17 Apr 2013 21:57:56 +0000 (17:57 -0400)]
src/figures/cantilever-data/get_v_dep.sh: print -> print()

Fix embedded Python syntax to avoid:

  cd .. && ./get_v_dep.sh
    File "<string>", line 1
      print '%.2f' % 131.97793902439034
                 ^
  SyntaxError: invalid syntax

11 years agosrc/figures/cantilever-data/avg_data.py: Vs.sort() -> sorted()
W. Trevor King [Wed, 17 Apr 2013 21:54:42 +0000 (17:54 -0400)]
src/figures/cantilever-data/avg_data.py: Vs.sort() -> sorted()

Avoid:

  cd .. && python avg_data.py
  Traceback (most recent call last):
    File "avg_data.py", line 78, in <module>
      write_average_file(FofV, avgK)
    File "avg_data.py", line 55, in write_average_file
      Vs.sort()
  AttributeError: 'dict_keys' object has no attribute 'sort'

11 years agosrc/figures/cantilever-data: Modernize print statements
W. Trevor King [Wed, 17 Apr 2013 21:14:52 +0000 (17:14 -0400)]
src/figures/cantilever-data: Modernize print statements

Old                 New
===============     ================
print >> x, ...     x.write(...)
print ...           print(...)
'%s' % (...)        '{}'.format(...)
===============     ================

The old `print >> ` syntax wasn't Python 3 compliant.

11 years agosrc/figures: Use open() instead of file() in Python scripts
W. Trevor King [Wed, 17 Apr 2013 21:04:35 +0000 (17:04 -0400)]
src/figures: Use open() instead of file() in Python scripts

file() is gone in Python 3, and open() was always the prefered method
for opening files.  I just didn't know that when I wrote the original
code ;).

12 years agoroot.bib: add roman12 entry for Marisa's thesis
W. Trevor King [Sat, 17 Nov 2012 14:07:42 +0000 (09:07 -0500)]
root.bib: add roman12 entry for Marisa's thesis

12 years agoStub out pyafm and calibcant chapters.
W. Trevor King [Mon, 2 Jul 2012 16:30:51 +0000 (12:30 -0400)]
Stub out pyafm and calibcant chapters.

Add Prof. Cruz as an advisor.

12 years agoMerge unfolding and tension chapters back into sawsim chapter.
W. Trevor King [Fri, 29 Jun 2012 19:51:54 +0000 (15:51 -0400)]
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.

12 years agoShrink expt-sawtooth.asy to a more reasonable size.
W. Trevor King [Thu, 28 Jun 2012 18:46:57 +0000 (14:46 -0400)]
Shrink expt-sawtooth.asy to a more reasonable size.

Also make the x-axis label more explicit ("Distance" was too vague).

12 years agoConsolidate fig:afm-schematic and fig:piezo-schematic into one figure.
W. Trevor King [Thu, 28 Jun 2012 18:44:18 +0000 (14:44 -0400)]
Consolidate fig:afm-schematic and fig:piezo-schematic into one figure.

Also cite binnig86 (AFM with STM sensor) and meyer88 (AFM with optical
lever) when introducing the AFM.

12 years agoLimit default graphMatrixFile palette to 8192 colors.
W. Trevor King [Thu, 28 Jun 2012 05:17:16 +0000 (01:17 -0400)]
Limit default graphMatrixFile palette to 8192 colors.

For some reason, leaving it at the default 32761 gives me unfilled
color bars for z scaling.

12 years agoUse 1/3 instead of 0.\bar{3} in monte-carlo.asy.
W. Trevor King [Wed, 27 Jun 2012 19:17:12 +0000 (15:17 -0400)]
Use 1/3 instead of 0.\bar{3} in monte-carlo.asy.

I'm already using \bar{} for the complex conjugate.

12 years agoUse kappa for spring constants (k is for rates).
W. Trevor King [Wed, 27 Jun 2012 19:13:49 +0000 (15:13 -0400)]
Use kappa for spring constants (k is for rates).

12 years agoExcape the hash symbol (#) in agilent-sure2 bib entry.
W. Trevor King [Wed, 27 Jun 2012 13:39:59 +0000 (09:39 -0400)]
Excape the hash symbol (#) in agilent-sure2 bib entry.

12 years agoThere is no way to comment out BibTeX values, just use a non-standard name.
W. Trevor King [Wed, 27 Jun 2012 13:35:48 +0000 (09:35 -0400)]
There is no way to comment out BibTeX values, just use a non-standard name.

12 years agoAdd WKing @string to packaging/main.bib.
W. Trevor King [Wed, 27 Jun 2012 13:29:22 +0000 (09:29 -0400)]
Add WKing @string to packaging/main.bib.

Apparently @string definitions are local to a single .bib file.  It's
not picking up my definition in root.bib anyway.

12 years agoAdd a missing comma after the url entry for agilent-sure2.
W. Trevor King [Wed, 27 Jun 2012 13:25:51 +0000 (09:25 -0400)]
Add a missing comma after the url entry for agilent-sure2.

12 years agoSet Asymptote fontsize to 10pt globally, not just for sLabel()s.
W. Trevor King [Wed, 27 Jun 2012 13:20:58 +0000 (09:20 -0400)]
Set Asymptote fontsize to 10pt globally, not just for sLabel()s.

12 years agoAdd packaging bibliography.
W. Trevor King [Wed, 27 Jun 2012 05:40:30 +0000 (01:40 -0400)]
Add packaging bibliography.

I'll add the text for this chapter later, but I need these citations
for the abstract.

12 years agoUse \subref in unfolding schematic image.
W. Trevor King [Wed, 27 Jun 2012 05:02:14 +0000 (01:02 -0400)]
Use \subref in unfolding schematic image.

This is better than hardcoding subfigure references in the caption.

12 years agoAdd I27 length to fig:I27 caption.
W. Trevor King [Wed, 27 Jun 2012 05:00:54 +0000 (01:00 -0400)]
Add I27 length to fig:I27 caption.

12 years agoUse \subref in unfolding pathway vs. landscape image.
W. Trevor King [Tue, 26 Jun 2012 20:34:11 +0000 (16:34 -0400)]
Use \subref in unfolding pathway vs. landscape image.

This is better than hardcoding subfigure references in the caption.

Also reference kellermayer97 as an early example of force spectroscopy
on proteins with laser tweezers (they're right after rief97a in the
journal).

12 years agoConsolidate duplicate I27 nomenclature entries.
W. Trevor King [Tue, 26 Jun 2012 15:18:34 +0000 (11:18 -0400)]
Consolidate duplicate I27 nomenclature entries.

And place the consolidated entry in apparatus/polymer-synthesis.tex
where I27 is introduced.

12 years agoAdd schematics for Kramers' integrand and the unfolding landscape.
W. Trevor King [Tue, 26 Jun 2012 05:52:54 +0000 (01:52 -0400)]
Add schematics for Kramers' integrand and the unfolding landscape.

12 years agoClean up lattice and off-latice references in the sawsim intro.
W. Trevor King [Tue, 26 Jun 2012 01:12:27 +0000 (21:12 -0400)]
Clean up lattice and off-latice references in the sawsim intro.

Also reference the snippet about simulation timescales in
introduction/main.tex.

12 years agoDon't wrap lu99 url in root.bib.
W. Trevor King [Tue, 26 Jun 2012 00:58:50 +0000 (20:58 -0400)]
Don't wrap lu99 url in root.bib.

12 years agoAdd citations for lu98 and lu99 to introduction MD discussion.
W. Trevor King [Tue, 26 Jun 2012 00:56:32 +0000 (20:56 -0400)]
Add citations for lu98 and lu99 to introduction MD discussion.

These papers are probably the earliest examples of molecular dynamics
simulations of velocity-clamp unfolding.

12 years agoAdd build-asy.py script to build Asymptote figures.
W. Trevor King [Tue, 26 Jun 2012 00:45:38 +0000 (20:45 -0400)]
Add build-asy.py script to build Asymptote figures.

12 years agoAdd figure 2 from kempe85.
W. Trevor King [Tue, 26 Jun 2012 00:45:05 +0000 (20:45 -0400)]
Add figure 2 from kempe85.

12 years agoInclude apparatus/main.bib bibliography (equipment).
W. Trevor King [Mon, 25 Jun 2012 23:38:52 +0000 (19:38 -0400)]
Include apparatus/main.bib bibliography (equipment).

12 years agoComment out some personal stuff to make shorter drafts.
W. Trevor King [Mon, 25 Jun 2012 23:37:41 +0000 (19:37 -0400)]
Comment out some personal stuff to make shorter drafts.

At least while I'm working on major edits.

12 years agoBump copyright year in root.tex.
W. Trevor King [Mon, 25 Jun 2012 23:36:42 +0000 (19:36 -0400)]
Bump copyright year in root.tex.

12 years agoPoint out some early DNA work before introducing titin.
W. Trevor King [Mon, 25 Jun 2012 23:34:47 +0000 (19:34 -0400)]
Point out some early DNA work before introducing titin.

12 years agoFlesh out apparatus chapter.
W. Trevor King [Mon, 25 Jun 2012 23:28:48 +0000 (19:28 -0400)]
Flesh out apparatus chapter.

Move I27 figure in from cantilever/methods, because we introduce I27
in the polymer-synthesis section.

Additions:
* Discussion of the piezo portion of an AFM.
* Discuss history of force spectroscopy.
* Add entire text of polymer synthesis and sample preparation sections.
* Lots of little things.

12 years agoMake piezo schematic smaller.
W. Trevor King [Mon, 25 Jun 2012 23:28:03 +0000 (19:28 -0400)]
Make piezo schematic smaller.

12 years agoAdd berkemeier11 as another paper discussing molecular dynamics speeds.
W. Trevor King [Mon, 25 Jun 2012 23:27:30 +0000 (19:27 -0400)]
Add berkemeier11 as another paper discussing molecular dynamics speeds.

12 years agoAdd several new citations to root.bib (mostly for the apparatus chapter).
W. Trevor King [Mon, 25 Jun 2012 23:24:10 +0000 (19:24 -0400)]
Add several new citations to root.bib (mostly for the apparatus chapter).

New keys:
 bartels03,
 berkemeier11,
 hager02
 honda08
 itoh04,
 kempe85,
 lo01,
 ma10,
 sakaki05,
 schmidt02,
 schmitt00,
 sundberg03,
 ulman96,

12 years agoAdd \diNaHPO (Na2HPO4) and \NadiHPO (NaH2PO4) commands to local_cmmds.tex.
W. Trevor King [Mon, 25 Jun 2012 23:21:44 +0000 (19:21 -0400)]
Add \diNaHPO (Na2HPO4) and \NadiHPO (NaH2PO4) commands to local_cmmds.tex.

Import fixltx2e in packages.tex to get \textsubscript used in defining
these commands.

12 years agoFix redundant 'review' and 'discussed' in apparatus/main.tex.
W. Trevor King [Sun, 24 Jun 2012 07:00:15 +0000 (03:00 -0400)]
Fix redundant 'review' and 'discussed' in apparatus/main.tex.

12 years agoFlesh out motivation to distinguish pathway vs. funnel in intro.
W. Trevor King [Sun, 24 Jun 2012 06:57:12 +0000 (02:57 -0400)]
Flesh out motivation to distinguish pathway vs. funnel in intro.

Also mention:
* difficulties comparing with molecular dynamics simulation.
* large span of ranges amoung available single molecule techniques.

12 years agoAdd citealiases and shorthand commands for a bunch of software packages.
W. Trevor King [Sun, 24 Jun 2012 06:55:16 +0000 (02:55 -0400)]
Add citealiases and shorthand commands for a bunch of software packages.

12 years agoAdd abstract text.
W. Trevor King [Sun, 24 Jun 2012 06:52:26 +0000 (02:52 -0400)]
Add abstract text.

12 years agoAdd labeit95 and sandal09 to root.bib.
W. Trevor King [Sun, 24 Jun 2012 06:51:45 +0000 (02:51 -0400)]
Add labeit95 and sandal09 to root.bib.

12 years agoAdd apparatus/main.bib with vendor references.
W. Trevor King [Sun, 24 Jun 2012 06:49:58 +0000 (02:49 -0400)]
Add apparatus/main.bib with vendor references.

12 years agoAdd piezo.asy for explaining how a tubular piezo works.
W. Trevor King [Sun, 24 Jun 2012 06:49:07 +0000 (02:49 -0400)]
Add piezo.asy for explaining how a tubular piezo works.

12 years agoAdd skeletal_muscle.jpg (modified from Wikipedia).
W. Trevor King [Fri, 22 Jun 2012 12:04:22 +0000 (08:04 -0400)]
Add skeletal_muscle.jpg (modified from Wikipedia).

12 years agoWhitespace cleanups in the rest of the figures/*/*.asy files.
W. Trevor King [Sun, 17 Jun 2012 20:24:06 +0000 (16:24 -0400)]
Whitespace cleanups in the rest of the figures/*/*.asy files.

Used sed to replace tabs with spaces and strip trailing spaces.

12 years agoWhitespace cleanups in base_afm.asy and monte-carlo.asy.
W. Trevor King [Sun, 17 Jun 2012 20:21:24 +0000 (16:21 -0400)]
Whitespace cleanups in base_afm.asy and monte-carlo.asy.

12 years agoConvert tabs to spaces in expt-sawtooth.asy.
W. Trevor King [Sun, 17 Jun 2012 20:18:03 +0000 (16:18 -0400)]
Convert tabs to spaces in expt-sawtooth.asy.

12 years agoRelabel unfolding/rate.tex to sec:rate.
W. Trevor King [Sun, 17 Jun 2012 20:12:12 +0000 (16:12 -0400)]
Relabel unfolding/rate.tex to sec:rate.

This fixes a label-collision with unfolding/distributions.tex on
sec:unfolding-distributions.

12 years agoRemove asyprocess references from SConscript files.
W. Trevor King [Sun, 17 Jun 2012 20:07:10 +0000 (16:07 -0400)]
Remove asyprocess references from SConscript files.

12 years agoWhitespace cleanups in schematic/unfolding.asy.
W. Trevor King [Sun, 17 Jun 2012 18:23:33 +0000 (14:23 -0400)]
Whitespace cleanups in schematic/unfolding.asy.

12 years agoFix sec:cantilever-calib-intro -> sec:cantilever-calib:intro reference.
W. Trevor King [Sun, 17 Jun 2012 17:54:23 +0000 (13:54 -0400)]
Fix sec:cantilever-calib-intro -> sec:cantilever-calib:intro reference.

12 years agoRemove unused asyprocess script (leftover from asyfig framework).
W. Trevor King [Sun, 17 Jun 2012 17:54:15 +0000 (13:54 -0400)]
Remove unused asyprocess script (leftover from asyfig framework).

12 years agoCreate figures/scratch immediately, so it's there by the time we run LaTeX.
W. Trevor King [Sat, 16 Jun 2012 18:52:46 +0000 (14:52 -0400)]
Create figures/scratch immediately, so it's there by the time we run LaTeX.

12 years agoRemove unused asyfig packages.
W. Trevor King [Sat, 16 Jun 2012 18:51:57 +0000 (14:51 -0400)]
Remove unused asyfig packages.

12 years agoAdd hong10, zhao10, liu10, measey09, shan09, yuan08, liu08, ... to root.bib.
W. Trevor King [Sat, 16 Jun 2012 16:23:05 +0000 (12:23 -0400)]
Add hong10, zhao10, liu10, measey09, shan09, yuan08, liu08, ... to root.bib.

Papers by Prof. Yang.

12 years agoChange my email address from drexel.edu to tremily.us.
W. Trevor King [Wed, 18 Apr 2012 17:24:26 +0000 (13:24 -0400)]
Change my email address from drexel.edu to tremily.us.

12 years agoAdd new citation ng07b and change ng07 to ng07a.
W. Trevor King [Thu, 2 Feb 2012 16:46:06 +0000 (11:46 -0500)]
Add new citation ng07b and change ng07 to ng07a.

12 years agoAdd comments referenceing Brockwell's 2002 paper with respect to Gumbel dist.
W. Trevor King [Thu, 2 Feb 2012 15:27:35 +0000 (10:27 -0500)]
Add comments referenceing Brockwell's 2002 paper with respect to Gumbel dist.

13 years agoRelabel src/unfolding/rate.tex as sec:unfolding-rate.
W. Trevor King [Sat, 14 May 2011 20:40:48 +0000 (16:40 -0400)]
Relabel src/unfolding/rate.tex as sec:unfolding-rate.

13 years agoConsolidate references to cantilever calibration summary as sec:cantilever-calib...
W. Trevor King [Sat, 14 May 2011 20:36:16 +0000 (16:36 -0400)]
Consolidate references to cantilever calibration summary as sec:cantilever-calib:intro.

13 years agoRemove cruft from SCons generator bodies.
W. Trevor King [Sat, 14 May 2011 19:11:15 +0000 (15:11 -0400)]
Remove cruft from SCons generator bodies.

13 years agoRemove src/unfolding-distributions/* which were moved to src/unfolding/distributions-*.
W. Trevor King [Sat, 14 May 2011 19:02:07 +0000 (15:02 -0400)]
Remove src/unfolding-distributions/* which were moved to src/unfolding/distributions-*.

13 years agoUpdate to \DUTmonth and \DUTyear to work with >=drexel-thesis-0.10.
W. Trevor King [Sat, 14 May 2011 18:57:59 +0000 (14:57 -0400)]
Update to \DUTmonth and \DUTyear to work with >=drexel-thesis-0.10.

13 years agoRemove silly tex/ directory.
W. Trevor King [Sat, 14 May 2011 18:44:44 +0000 (14:44 -0400)]
Remove silly tex/ directory.

13 years agoAdd a PyMOL builder to SCons and generalize PYMOL_PATH setup.
W. Trevor King [Sat, 14 May 2011 18:42:12 +0000 (14:42 -0400)]
Add a PyMOL builder to SCons and generalize PYMOL_PATH setup.

13 years agoAdjust asymptote and gnuplot doctests to be directory independent.
W. Trevor King [Sat, 14 May 2011 18:11:50 +0000 (14:11 -0400)]
Adjust asymptote and gnuplot doctests to be directory independent.

Now you can run the doctests from any directory and they will still
find the files they are scanning to test.  Note that SCons may not be
installed in your PYTHONPATH by default:

> From: Steven Knight
> Date: May 28, 2008; 10:01am
> Subject: Re: easy_installed scons not working
>
> ...
>
> In essence, we've tried to make SCons more like a standalone
> application that happens to use Python, instead of a Python
> application that only exists "within" the Python installation itself.
> This separation also allows you, for example, to experiment with
> upgrading your Python version without having to re-install SCons.
>
> ...
>
> Note that the hacking we've done on our setup.py does allow you to
> install into the site-package/ subdirectory if you wish, using an
> extended --standard-lib option.
>
> ...

So you may need to try something like:
  PYTHONPATH=/usr/lib/scons-2.0.1/ python site_cons/site_tools/asymptote.py
to run the tests.

13 years agoCorrect GNUPLOTLAGS -> GNUPLOTFLAGS typo in site_cons/site_tools/gnuplot.py.
W. Trevor King [Sat, 14 May 2011 18:02:01 +0000 (14:02 -0400)]
Correct GNUPLOTLAGS -> GNUPLOTFLAGS typo in site_cons/site_tools/gnuplot.py.