thesis.git
11 years agoroot.bib: Confirmation from Bechhoefer about missing 1/pi in A12
W. Trevor King [Wed, 8 May 2013 03:06:33 +0000 (23:06 -0400)]
root.bib: Confirmation from Bechhoefer about missing 1/pi in A12

On Tue, May 07, 2013 at 07:19:32PM -0700, John Bechhoefer wrote:
> Right you are!  And you are the first person in > 10 years to catch
> this :)

11 years agopackages.tex: Don't use footmisc (it doesn't mesh with hyperref)
W. Trevor King [Wed, 8 May 2013 02:05:03 +0000 (22:05 -0400)]
packages.tex: Don't use footmisc (it doesn't mesh with hyperref)

From the footmisc manual:

  User interface---interactions with other packages
  ...
  hyperref

    The hyperref package has ambitions to make hyperlinks from
    footnote marks to the corresponding footnote body; naturally this
    causes grief to footmisc, and unfortunately no remedy is currently
    known. If you use footmisc, suppress hyperref’s hyper-footnotes,
    by loading it as:

    \usepackage[hyperfootnotes=false,...]{hyperref}

    Further work on the interaction between the two packages is
    proposed, but not yet scheduled.

See also:
http://tex.stackexchange.com/questions/71664/why-are-all-of-my-footnotes-hyperlinked-to-the-titlepage

I can't delay the hyperref import until after footmisc, because the
hyperref import happens inside drexel-thesis.

11 years agocalibcant/discussion.tex: Fix 'eq:eq:peak-frequency' -> 'eq:peak-frequency'
W. Trevor King [Wed, 8 May 2013 01:45:59 +0000 (21:45 -0400)]
calibcant/discussion.tex: Fix 'eq:eq:peak-frequency' -> 'eq:peak-frequency'

11 years agoroot.bib: Add livadaru03 and burnham03 and mark typos
W. Trevor King [Wed, 8 May 2013 01:34:12 +0000 (21:34 -0400)]
root.bib: Add livadaru03 and burnham03 and mark typos

Typos in equations listed in bechhoefer02, schlierf06, livadaru03, and
puchner08.  I have contacted the listed author in each case, but so
far there are no published errata :(.  To be fair, I only emailed
Bechhoefer a few hours ago ;).

Excerpts from the relevant emails:

On Tue, Apr 08, 2008 at 07:16:34PM -0400, W. Trevor King wrote:
> ...
> > My double integral is exploding, so I was double checking your formulas.
> I believe you swapped signs in the exponent in your Kramers' rate equation.
>
> It should be
>  k^-1 = 1/D \int_{x_-}^{x_+} e^{  \beta U(x)} [ \int_{0}^{x} e^{- \beta U(x')} dx' ] dx
> not
>  k^-1 = 1/D \int_{x_-}^{x_+} e^{- \beta U(x)} [ \int_{0}^{x} e^{  \beta U(x')} dx' ] dx
>
> See, for example, H\"anggi et al., Rev. Mod. Phys 1990,
>   http://prola.aps.org/abstract/RMP/v62/i2/p251_1
> Equation 4.56b,
> or Socci et al., J Chem Phy 1996
>   http://arxiv.org/pdf/cond-mat/9601091
> Equation 2.

On Wed, Apr 09, 2008 at 09:03:02AM +0200, Michael Schlierf wrote:
> For your second email: So far I am pretty sure about our published
> solution as it worked out. So have you double checked your integral
> borders? Try Kramers first in a simple potential, like a cusp-like or
> flat one. For those some analytical solutions are known and you could
> compare.

On Fri, Sep 07, 2012 at 07:09:17AM -0400, W. Trevor King wrote:
> On Fri, Sep 07, 2012 at 09:28:41AM +0200, Roland Netz wrote:
> > sorry for the confusion: Yes, the formula Eq 46 contains typos, as
> > you correctly point out.
>
> Ah.  Some sort of heads-up on the article page would be useful,
> because at least Puchner [1] quotes the typo-containing version.

On Wed, Sep 12, 2012 at 01:37:23AM +0000, Puchner, Georg Elias Michael wrote:
> thanks for pointing this out, I wasn't aware of this typo and also
> think they should have published and erratum.
>
> I dug into my old data and code (I am not doing force spectroscopy
> andy more since some years) and implemented your corrected
> version. I attached a comparison of my old transformation equation
> (black line with the parameters γ=22° and b=0.4 nm as published) and
> the fixed equation (dashed red line with γ=41° and b=0.11 nm)
>
> As you see, the quality is only slightly increased for some peaks
> but the parameters now make more sense...

On Tue, May 07, 2013 at 07:05:31PM -0400, W. Trevor King wrote:
> I'm citing your thermal spring constant calculation [1] in my thesis
> [2] to confirm my derivation of the overdamped power spectral density
> of a harmonic oscillator.  I was just double-checking my PSD (at the
> end of section 5.2.1 “Highly damped case”, currently around page 48)
> against your equation A12:
>
>   x²(ω) = (2kBTγ) / [k²(1+ω²τ₀²)]       (A12)
>
> It looks like you're missing a factor of 1/π...

11 years agopyafm/stack.tex: Fix \citetalias{...} from 'swig' to 'beazley96'
W. Trevor King [Wed, 8 May 2013 01:25:30 +0000 (21:25 -0400)]
pyafm/stack.tex: Fix \citetalias{...} from 'swig' to 'beazley96'

11 years agolocal_cmmds.tex: Add \order and \cf commands
W. Trevor King [Tue, 7 May 2013 20:38:43 +0000 (16:38 -0400)]
local_cmmds.tex: Add \order and \cf commands

11 years agopyafm/conclusions.tex: Mention materassi09 and aioanei11 as alternatives
W. Trevor King [Tue, 7 May 2013 20:37:30 +0000 (16:37 -0400)]
pyafm/conclusions.tex: Mention materassi09 and aioanei11 as alternatives

11 years agocalibcant/procedure.tex: Mention materassi09's alternative bump technique
W. Trevor King [Tue, 7 May 2013 20:34:18 +0000 (16:34 -0400)]
calibcant/procedure.tex: Mention materassi09's alternative bump technique

11 years agosawsim/discussion.tex: Talk about benedetti11 in relation to my analysis
W. Trevor King [Tue, 7 May 2013 20:09:45 +0000 (16:09 -0400)]
sawsim/discussion.tex: Talk about benedetti11 in relation to my analysis

11 years agoroot.bib: Add kuhn05, materassi09, aioanei11, and benedetti11
W. Trevor King [Tue, 7 May 2013 20:06:00 +0000 (16:06 -0400)]
root.bib: Add kuhn05, materassi09, aioanei11, and benedetti11

The first three include alternatives to Hooke, and the last treats my
king10 theory with a simulation-avoiding bent.

11 years agopyafm: Use 'open source' instead of 'FLOSS'
W. Trevor King [Tue, 7 May 2013 16:16:05 +0000 (12:16 -0400)]
pyafm: Use 'open source' instead of 'FLOSS'

Less jargon, and more consistency (e.g. with my title ;).  The libre
distinction is small, and not particularly critical to this paper.  I
think it is essential that labs let you see their experiment control
software (eakly open source).  Whether or not their license allows for
sharing is less critical, although without significant funding
differences, I expect share-alike software to quickly surpass
no-derivatives software in terms of functionality.

11 years agoFixes suggested by my mom (Lynn Duncan)
W. Trevor King [Tue, 7 May 2013 14:46:35 +0000 (10:46 -0400)]
Fixes suggested by my mom (Lynn Duncan)

Mostly in one of the following categories:
* Fixing typos
* Reducing colloquialism and jargon
* Adding clarification and background

11 years agoblurb/vita.tex: Add a CV using bibunits and currvita
W. Trevor King [Mon, 6 May 2013 18:37:02 +0000 (14:37 -0400)]
blurb/vita.tex: Add a CV using bibunits and currvita

The CV is still commented out (\include{blurb/vita}), but it will be
ready to go once I get into the final drafts.

11 years agoblurb/acknowledgments.tex: Change 'Graphical' -> 'Graphics'
W. Trevor King [Mon, 6 May 2013 16:49:57 +0000 (12:49 -0400)]
blurb/acknowledgments.tex: Change 'Graphical' -> 'Graphics'

Hopefully this makes it clear that these are languages for writing
graphics, not languages where you program via a graphical interface.

11 years agoblurb/acknowledgments.tex: Link to GNU, Linux, and Gentoo separately
W. Trevor King [Mon, 6 May 2013 16:48:15 +0000 (12:48 -0400)]
blurb/acknowledgments.tex: Link to GNU, Linux, and Gentoo separately

It doesn't take up any more space, and it gives folks who may not
recognize the names easy access to more context.

11 years agoroot.tex: Add commented out 'approvalform' option
W. Trevor King [Mon, 6 May 2013 16:41:42 +0000 (12:41 -0400)]
root.tex: Add commented out 'approvalform' option

So I don't forget when I produce the final copy.

11 years agosawsim/discussion.tex: Fix '1li00' -> 'li00' typo
W. Trevor King [Mon, 6 May 2013 13:57:02 +0000 (09:57 -0400)]
sawsim/discussion.tex: Fix '1li00' -> 'li00' typo

11 years agopackaging/main.bib: Python prefers the 'www.' prefix
W. Trevor King [Mon, 6 May 2013 13:55:46 +0000 (09:55 -0400)]
packaging/main.bib: Python prefers the '' prefix

11 years agopyafm/main.bib: Add reference for OMEGA
W. Trevor King [Mon, 6 May 2013 13:55:07 +0000 (09:55 -0400)]
pyafm/main.bib: Add reference for OMEGA

11 years agosawsim/discussion.tex: Fix minted markup for sawsim snippets
W. Trevor King [Mon, 6 May 2013 13:38:15 +0000 (09:38 -0400)]
sawsim/discussion.tex: Fix minted markup for sawsim snippets

11 years agosrc/root.bib: Fix 'RWTillamnn' -> 'RWTillmann' typo
W. Trevor King [Mon, 6 May 2013 12:18:33 +0000 (08:18 -0400)]
src/root.bib: Fix 'RWTillamnn' -> 'RWTillmann' typo

This was a typo in the metadata at Science.  I sent them an email
suggesting they correct their data, but didn't fix all of my own :p.

11 years agosrc/root.bib: Fix 'HJHudspeth' -> 'AJHudspeth' typo
W. Trevor King [Mon, 6 May 2013 12:17:39 +0000 (08:17 -0400)]
src/root.bib: Fix 'HJHudspeth' -> 'AJHudspeth' typo

11 years agosawsim/discussion.tex: Fix Python citetalias
W. Trevor King [Mon, 6 May 2013 12:15:25 +0000 (08:15 -0400)]
sawsim/discussion.tex: Fix Python citetalias

11 years agocalibcant/discussion.tex: Fill in section on data archival
W. Trevor King [Sun, 5 May 2013 19:55:58 +0000 (15:55 -0400)]
calibcant/discussion.tex: Fill in section on data archival

11 years agocalibcant/discussion.tex: Pluralize 'formulae'
W. Trevor King [Sun, 5 May 2013 19:14:32 +0000 (15:14 -0400)]
calibcant/discussion.tex: Pluralize 'formulae'

11 years agocalibcant/discussion.tex: Fix 'florian95' -> 'florin95' typo
W. Trevor King [Sun, 5 May 2013 19:03:16 +0000 (15:03 -0400)]
calibcant/discussion.tex: Fix 'florian95' -> 'florin95' typo

11 years agoroot.bib: Fix markup issues for BDrake, YMartin, and HKWickramasinghe
W. Trevor King [Sun, 5 May 2013 18:53:29 +0000 (14:53 -0400)]
root.bib: Fix markup issues for BDrake, YMartin, and HKWickramasinghe

Also remove a duplicate martin87 entry.

11 years agosawsim/discussion.tex: Fix 'Propogation' -> 'Propagation' typo
W. Trevor King [Sun, 5 May 2013 18:48:50 +0000 (14:48 -0400)]
sawsim/discussion.tex: Fix 'Propogation' -> 'Propagation' typo

11 years agocalibcant/discussion.tex: Fix simplifying multiplication for eq:peak-frequency
W. Trevor King [Sun, 5 May 2013 18:45:34 +0000 (14:45 -0400)]
calibcant/discussion.tex: Fix simplifying multiplication for eq:peak-frequency

We can divide out all the things that *aren't* zero, and still have
the right hand side be equal to zero.  However, that doesn't mean that
the new right hand side is the same as the old right hand side ;).

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.