W. Trevor King [Thu, 9 May 2013 20:09:41 +0000 (16:09 -0400)]
introduction/main.tex: Add a lead-in paragraph
Instead of jumping in at the top, Prof. Cruz suggested zooming out
from my work to the big picture before drilling back down. Adding
more context can't hurt ;).
W. Trevor King [Thu, 9 May 2013 02:36:07 +0000 (22:36 -0400)]
Convert existing external references to \xref, \fref, etc.
Hooray consistency!
W. Trevor King [Thu, 9 May 2013 02:17:03 +0000 (22:17 -0400)]
local_cmmds.tex: Add 'section' processing to \fref
Again, matching cleveref's \cref{} formatting
W. Trevor King [Thu, 9 May 2013 02:07:36 +0000 (22:07 -0400)]
local_cmmds.tex: Use `Eq.` instead of `Eqn.` in \fref
For consistency with cleveref's \cref{}.
W. Trevor King [Thu, 9 May 2013 02:03:33 +0000 (22:03 -0400)]
local_cmmds.tex: Only equations need (value) in \iref
We want `Eqn. (a)` and `Fig. b`, not `Fig. (b)`.
W. Trevor King [Thu, 9 May 2013 01:50:49 +0000 (21:50 -0400)]
local_cmmds.tex: Escape whitespace in \xref
Now
(\xref{a}{equation}{c})
is rendered as
(A Eqn. (c))
instead of
( A Eqn. (c) )
W. Trevor King [Thu, 9 May 2013 00:44:23 +0000 (20:44 -0400)]
local_cmmds.tex: Remove posessive in \xref
Because
Name^{ref}'s Eq. (X)
looks silly, and I couldn't find a clean way to get
Name's^{ref} Eq.(X)
W. Trevor King [Thu, 9 May 2013 00:33:19 +0000 (20:33 -0400)]
local_cmmds.tex: Add \iref, \fref, and \xref
This makes it easy to get consistent (and flexible) formatting for
references to external equations, figures, etc. I'm surprised that
this isn't somehow bundled into cleveref or natbib. If I get time, I
may try and pull it out into its own package.
Based Joseph Wright's answer [2] to a question about switch statements
[1].
[1]: http://tex.stackexchange.com/questions/29133/how-to-create-switch-structure-comparing-strings-in-latex
[2]: http://tex.stackexchange.com/a/29139
W. Trevor King [Wed, 8 May 2013 23:18:30 +0000 (19:18 -0400)]
src/pyafm/main.tex: Add missing em-dash in Whitehead epigraph
W. Trevor King [Wed, 8 May 2013 21:47:03 +0000 (17:47 -0400)]
calibcant/discussion.tex: Cite benedetti12 for valid "Lorentzian"
Maybe there is a distinction between "a Lorentzian function" and "the
Lorentzian" that I am unaware of... At least Benedetti uses the right
function.
W. Trevor King [Wed, 8 May 2013 21:41:24 +0000 (17:41 -0400)]
calibcant/theory.tex: Cite benedetti12 for eq:DHO-psd
He has a similar treatment to my theory section in his section 8.2.1
(Spectrum of a cantilever) starting on page 99.
Congratulations on graduating, Fabrizio!
W. Trevor King [Wed, 8 May 2013 19:28:38 +0000 (15:28 -0400)]
blurb/acknowledgments.tex: Flesh out acknowledgements
Thank people :D.
Also add contact info and link to the Git repository for people who
only stumble across the dead-trees version of this thing.
W. Trevor King [Wed, 8 May 2013 17:08:31 +0000 (13:08 -0400)]
README,root.tex: Update drexel.edu to tremily.us
That way they'll point somewhere I can maintain after graduating.
W. Trevor King [Wed, 8 May 2013 16:50:34 +0000 (12:50 -0400)]
src/hooke: Initial work on a Hooke chapter
I'm stopping here and moving on to my buffer-results from February, so
I have something to show at my next committee meeting.
W. Trevor King [Wed, 8 May 2013 15:13:57 +0000 (11:13 -0400)]
apparatus/cantilever-calib.tex: Avoid blank lines before \nomenclature{}
W. Trevor King [Wed, 8 May 2013 15:08:59 +0000 (11:08 -0400)]
calibcant/theory.tex: Rework general derivations to remove G_1 (G_1p -> G_1)
Values for the G constants are more easily calculated from the
equipartition theorem than through chaining G definitions. I removed
G_1 entirely, and renamed G_1p -> G_1.
I also check my results against publishes sources. It would have been
helpful if I had discovered burnham03 earlier :p. They have a general
PSD formula, white and 1/f noise terms, and interference-based piezo
calibration. Institutionalizing knowledge like this (vs. relying on
vast literature searches) is a good reason to consolidate work around
a small numer of open source tools. Sigh.
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 :)
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.
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'
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...
W. Trevor King [Wed, 8 May 2013 01:25:30 +0000 (21:25 -0400)]
pyafm/stack.tex: Fix \citetalias{...} from 'swig' to 'beazley96'
W. Trevor King [Tue, 7 May 2013 20:38:43 +0000 (16:38 -0400)]
local_cmmds.tex: Add \order and \cf commands
W. Trevor King [Tue, 7 May 2013 20:37:30 +0000 (16:37 -0400)]
pyafm/conclusions.tex: Mention materassi09 and aioanei11 as alternatives
W. Trevor King [Tue, 7 May 2013 20:34:18 +0000 (16:34 -0400)]
calibcant/procedure.tex: Mention materassi09's alternative bump technique
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
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.
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.
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
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.
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.
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.
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.
W. Trevor King [Mon, 6 May 2013 13:57:02 +0000 (09:57 -0400)]
sawsim/discussion.tex: Fix '1li00' -> 'li00' typo
W. Trevor King [Mon, 6 May 2013 13:55:46 +0000 (09:55 -0400)]
packaging/main.bib: Python prefers the '' prefix
W. Trevor King [Mon, 6 May 2013 13:55:07 +0000 (09:55 -0400)]
pyafm/main.bib: Add reference for OMEGA
W. Trevor King [Mon, 6 May 2013 13:38:15 +0000 (09:38 -0400)]
sawsim/discussion.tex: Fix minted markup for sawsim snippets
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.
W. Trevor King [Mon, 6 May 2013 12:17:39 +0000 (08:17 -0400)]
src/root.bib: Fix 'HJHudspeth' -> 'AJHudspeth' typo
W. Trevor King [Mon, 6 May 2013 12:15:25 +0000 (08:15 -0400)]
sawsim/discussion.tex: Fix Python citetalias
W. Trevor King [Sun, 5 May 2013 19:55:58 +0000 (15:55 -0400)]
calibcant/discussion.tex: Fill in section on data archival
W. Trevor King [Sun, 5 May 2013 19:14:32 +0000 (15:14 -0400)]
calibcant/discussion.tex: Pluralize 'formulae'
W. Trevor King [Sun, 5 May 2013 19:03:16 +0000 (15:03 -0400)]
calibcant/discussion.tex: Fix 'florian95' -> 'florin95' typo
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.
W. Trevor King [Sun, 5 May 2013 18:48:50 +0000 (14:48 -0400)]
sawsim/discussion.tex: Fix 'Propogation' -> 'Propagation' typo
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 ;).
W. Trevor King [Sun, 5 May 2013 18:42:00 +0000 (14:42 -0400)]
calibcant/discussion.tex: POE is approximate (first order Taylor)
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.
W. Trevor King [Sun, 5 May 2013 18:24:48 +0000 (14:24 -0400)]
root.bib: Fix math markup in tlusty98 note
W. Trevor King [Sun, 5 May 2013 02:04:27 +0000 (22:04 -0400)]
calibcant: flesh out calibcant chapter
Figures, references, theory, etc.
W. Trevor King [Fri, 3 May 2013 20:58:29 +0000 (16:58 -0400)]
calibcant/theory.tex: Increase linking to apparatus/cantilever-calib
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.
W. Trevor King [Fri, 3 May 2013 20:41:47 +0000 (16:41 -0400)]
pyafm/discussion.tex: Fix 'fig:fig:...' -> 'fig:...' 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 '\ '.
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.
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.
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.
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).
W. Trevor King [Wed, 1 May 2013 20:49:23 +0000 (16:49 -0400)]
sawsim/discussion.tex: Remove Who's who (only I care ;)
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!).
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.
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.
W. Trevor King [Sat, 27 Apr 2013 03:47:04 +0000 (23:47 -0400)]
root.bib: Add missing @string definition for APL
W. Trevor King [Sat, 27 Apr 2013 03:43:35 +0000 (23:43 -0400)]
root.bib: Add missing commas in martin87 and meyer88
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.
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.
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.
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.
W. Trevor King [Thu, 25 Apr 2013 17:15:47 +0000 (13:15 -0400)]
cantilever/main.tex: Clarify title with "stiffness effect"
W. Trevor King [Thu, 25 Apr 2013 17:14:47 +0000 (13:14 -0400)]
cantilever/simulations.tex: Link to sec:sawsim:cantilever
W. Trevor King [Thu, 25 Apr 2013 17:12:52 +0000 (13:12 -0400)]
cantilever/theory.tex: Cite Walton 2008 as motivation
W. Trevor King [Thu, 25 Apr 2013 17:10:31 +0000 (13:10 -0400)]
introduction/main.tex: Expand on the landscape/pathway distinction
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" ;).
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
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
W. Trevor King [Wed, 17 Apr 2013 23:35:38 +0000 (19:35 -0400)]
src/figures/fit-space/extract_fit_valley.py: print -> print()
W. Trevor King [Wed, 17 Apr 2013 23:34:30 +0000 (19:34 -0400)]
src/figures/script/pyfit: 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
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
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'
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.
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 ;).
W. Trevor King [Sat, 17 Nov 2012 14:07:42 +0000 (09:07 -0500)]
root.bib: add roman12 entry for Marisa's thesis
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.
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.
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).
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.
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.
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.
W. Trevor King [Wed, 27 Jun 2012 19:13:49 +0000 (15:13 -0400)]
Use kappa for spring constants (k is for rates).
W. Trevor King [Wed, 27 Jun 2012 13:39:59 +0000 (09:39 -0400)]
Excape the hash symbol (#) in agilent-sure2 bib entry.
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.
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.
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.
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.
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.
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.
W. Trevor King [Wed, 27 Jun 2012 05:00:54 +0000 (01:00 -0400)]
Add I27 length to fig:I27 caption.
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).
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.
W. Trevor King [Tue, 26 Jun 2012 05:52:54 +0000 (01:52 -0400)]
Add schematics for Kramers' integrand and the unfolding landscape.