thesis.git
8 years agofigures/v-dep: Remove UnFill from plot legend addition master v1.0
W. Trevor King [Fri, 28 Jun 2013 17:07:33 +0000 (13:07 -0400)]
figures/v-dep: Remove UnFill from plot legend addition

It was blanking the plots.

8 years agoblurb/abstract.tex: '\pyafm' -> '\unfoldprotein' in OS-agnostic discussion
W. Trevor King [Fri, 28 Jun 2013 16:16:56 +0000 (12:16 -0400)]
blurb/abstract.tex: '\pyafm' -> '\unfoldprotein' in OS-agnostic discussion

To be consistent with my earlier subject overview a few sentences
earlier.

8 years agohooke/history.tex: Add a nomenclature entry for UI
W. Trevor King [Fri, 28 Jun 2013 15:32:08 +0000 (11:32 -0400)]
hooke/history.tex: Add a nomenclature entry for UI

Thanks, Prof. Yuan.

8 years agoblurb/acknowledgments.tex: Fix 'Louis' -> 'Luis'
W. Trevor King [Fri, 28 Jun 2013 15:21:50 +0000 (11:21 -0400)]
blurb/acknowledgments.tex: Fix 'Louis' -> 'Luis'

Oops, again.

8 years agoapparatus/main.tex: Stick to future tense 'We will discuss'
W. Trevor King [Fri, 28 Jun 2013 12:21:42 +0000 (08:21 -0400)]
apparatus/main.tex: Stick to future tense 'We will discuss'

The rest of this paragraph is all future tense.

8 years agointroduction/main.tex: Fix 'ion strength' -> 'ionic strength'
W. Trevor King [Fri, 28 Jun 2013 12:08:25 +0000 (08:08 -0400)]
introduction/main.tex: Fix 'ion strength' -> 'ionic strength'

8 years agointroduction/main.tex: Mention unfold-protein in the outline
W. Trevor King [Fri, 28 Jun 2013 12:05:54 +0000 (08:05 -0400)]
introduction/main.tex: Mention unfold-protein in the outline

Try to tie the abstract (which just mentions unfold-protein) to the
chapter subject (which just mentions pyafm), while still making it
clear that they are both my work.

8 years agointroduction/main.tex: 'as' -> 'because' for drug-designer consumption
W. Trevor King [Fri, 28 Jun 2013 12:02:04 +0000 (08:02 -0400)]
introduction/main.tex: 'as' -> 'because' for drug-designer consumption

I think this reads a bit more clearly.

8 years agointroduction/main.tex: Only emphasize 'un' in 'unfolding'
W. Trevor King [Fri, 28 Jun 2013 12:01:17 +0000 (08:01 -0400)]
introduction/main.tex: Only emphasize 'un' in 'unfolding'

To emphasize that I'm making the folding/unfolding distinction.

8 years agointroduction/main.tex: Retitle sec:single-molecule to Why single molecule?
W. Trevor King [Fri, 28 Jun 2013 11:54:37 +0000 (07:54 -0400)]
introduction/main.tex: Retitle sec:single-molecule to Why single molecule?

Help focus readers on the point I'm trying to make in this section.

8 years agointroduction/main.tex: Reword sentence about forward/inverse difficulty
W. Trevor King [Fri, 28 Jun 2013 11:50:02 +0000 (07:50 -0400)]
introduction/main.tex: Reword sentence about forward/inverse difficulty

The original was a bit too nested, so I've broken it into more
distinct sections.

8 years agoblurb/abstract.tex: Change pyafm -> unfold-protein and remove Na+
W. Trevor King [Fri, 28 Jun 2013 11:42:02 +0000 (07:42 -0400)]
blurb/abstract.tex: Change pyafm -> unfold-protein and remove Na+

The NaCl data had a small number of noisy unfolding events, which
weren't particularly convincing, so they're not in the final thesis.

Instead of mentioning pyafm here, cut straight to the top-level
unfold-protein package, since that's where the experiment control
happens.

8 years agoConsistently sentence-case section titles
W. Trevor King [Fri, 28 Jun 2013 11:34:51 +0000 (07:34 -0400)]
Consistently sentence-case section titles

8 years agoDistinguish between glutamine and glutamic acid
W. Trevor King [Thu, 27 Jun 2013 21:03:30 +0000 (17:03 -0400)]
Distinguish between glutamine and glutamic acid

This is important ;).  Thanks, Prof. Cruz.

8 years agocalibcant/procedure.tex: Discuss 14kHz spike in fig:calibcant:vibration
W. Trevor King [Thu, 27 Jun 2013 20:39:37 +0000 (16:39 -0400)]
calibcant/procedure.tex: Discuss 14kHz spike in fig:calibcant:vibration

8 years agosawsim: Shift review of past research into the introduction
W. Trevor King [Thu, 27 Jun 2013 20:20:06 +0000 (16:20 -0400)]
sawsim: Shift review of past research into the introduction

8 years agoAdd prefixes to sort the nomenclature appropriately
W. Trevor King [Thu, 27 Jun 2013 19:54:39 +0000 (15:54 -0400)]
Add prefixes to sort the nomenclature appropriately

In order:
* Operators and functions
* Greek symbols
* Roman symbols
* Text

I also added a bunch of trailing periods, and ensured that the
\nomenclature{} calls were set off from paragraphs by a `%`.

8 years agopackages: Don't use prefixes when sorting nomenclature entries
W. Trevor King [Thu, 27 Jun 2013 18:17:22 +0000 (14:17 -0400)]
packages: Don't use prefixes when sorting nomenclature entries

From the nomencl docs:

  Personally, I like to specify the noprefix option and use the
  optional argument to get exactly the sort order I want.

See also section 5.1 (Subgroups) about distinct groups of entries
(e.g. Greek variables, Roman variables, words).

8 years agoroot.bib: Rename READ notes to wtk_note
W. Trevor King [Thu, 27 Jun 2013 18:09:46 +0000 (14:09 -0400)]
root.bib: Rename READ notes to wtk_note

Not appropriate for my thesis ;).

8 years agoroot.bib: Fix a bunch of markup (e.g. [beta] -> $\beta$)
W. Trevor King [Thu, 27 Jun 2013 17:54:31 +0000 (13:54 -0400)]
root.bib: Fix a bunch of markup (e.g. [beta] -> $\beta$)

Some of the citation exporters I've been using do a pretty bad job
with non-ASCII characters.  This fixes a few of the more obvious
mistakes.

8 years agosalt/main.tex: Cite hofmeister88 and smith13
W. Trevor King [Thu, 27 Jun 2013 17:51:35 +0000 (13:51 -0400)]
salt/main.tex: Cite hofmeister88 and smith13

Additional background and CaCl2 motivation respectively.

8 years agoroot.bib: Add hofmeister88
W. Trevor King [Thu, 27 Jun 2013 17:51:03 +0000 (13:51 -0400)]
root.bib: Add hofmeister88

8 years agosalt/main.tex: Fix 'Amyloid' -> 'amyloid'
W. Trevor King [Wed, 26 Jun 2013 17:39:19 +0000 (13:39 -0400)]
salt/main.tex: Fix 'Amyloid' -> 'amyloid'

It's not a proper noun.

8 years agoroot.bib: Add smith13 as a salt-effect reference
W. Trevor King [Wed, 26 Jun 2013 17:32:51 +0000 (13:32 -0400)]
root.bib: Add smith13 as a salt-effect reference

8 years agoroot.bib: Use the paper's title capitalization in isaacs06
W. Trevor King [Wed, 26 Jun 2013 17:23:00 +0000 (13:23 -0400)]
root.bib: Use the paper's title capitalization in isaacs06

It was published that way, so preserve the capitalization (and use of
\beta) in my BibTeX.

8 years agocalibcant/overview.tex: Fix 'calibcant/procedure' -> 'sec:calibcant:procedure'
W. Trevor King [Wed, 26 Jun 2013 12:45:19 +0000 (08:45 -0400)]
calibcant/overview.tex: Fix 'calibcant/procedure' -> 'sec:calibcant:procedure'

This typo landed in fb7a203 (calibcant/overview.tex: Give a road map
for the rest of this chapter, 2013-06-21).

8 years agoDon't specify .png in \includegraphics{}
W. Trevor King [Wed, 26 Jun 2013 12:29:14 +0000 (08:29 -0400)]
Don't specify .png in \includegraphics{}

LaTeX figures out valid extensions automatically.

8 years agofigures/calibcant: Re-render figures using LaTeX labels
W. Trevor King [Wed, 26 Jun 2013 12:26:00 +0000 (08:26 -0400)]
figures/calibcant: Re-render figures using LaTeX labels

This gives better kerning than Matplotlib's built-in rendering.  I
also adjusted the labels to have more consistent capitalization (in
the titles) and less overlap via symbolic representation (for the
statistics y-axis).

8 years agocalibcant/procedure.tex: Add trailing period in no-offset figure
W. Trevor King [Mon, 24 Jun 2013 13:01:14 +0000 (09:01 -0400)]
calibcant/procedure.tex: Add trailing period in no-offset figure

8 years agocalibcant/procedure.tex: Describe colors in fig:calibcant:bump caption
W. Trevor King [Mon, 24 Jun 2013 12:42:17 +0000 (08:42 -0400)]
calibcant/procedure.tex: Describe colors in fig:calibcant:bump caption

Prof. Cruz was unclear about what was what in the first panel, and
didn't notice that the approach/retract doubling also applied to the
first panel.

8 years agopyafm/discussion.tex: Add red/blue comments to all LabVIEW captions
W. Trevor King [Mon, 24 Jun 2013 12:32:24 +0000 (08:32 -0400)]
pyafm/discussion.tex: Add red/blue comments to all LabVIEW captions

Also make it more explicit that it was only these comparison curves
that were not isolated.

8 years agocalibcant/overview.tex: Give a road map for the rest of this chapter
W. Trevor King [Fri, 21 Jun 2013 18:58:42 +0000 (14:58 -0400)]
calibcant/overview.tex: Give a road map for the rest of this chapter

8 years agopyafm/overview.tex: Remove figure references
W. Trevor King [Fri, 21 Jun 2013 18:47:38 +0000 (14:47 -0400)]
pyafm/overview.tex: Remove figure references

Prof. Cruz points out that I don't actually discuss the figures until
later sections.  If I want to refer forward, I could cite the sections
themselves, but it's easier to just remove these references.

8 years agosawsim/discussion.tex: Flesh out testing procedure
W. Trevor King [Fri, 21 Jun 2013 18:45:09 +0000 (14:45 -0400)]
sawsim/discussion.tex: Flesh out testing procedure

Prof. Cruz thought the existing lead in wasn't clear.

8 years agosawsim/discussion.tex: Remove double integral Kramers' testing
W. Trevor King [Fri, 21 Jun 2013 18:39:25 +0000 (14:39 -0400)]
sawsim/discussion.tex: Remove double integral Kramers' testing

I don't have enough detail/support here to let it stand.

8 years agosawsim/discussion.tex: Rework sawsim Monte Carlo review
W. Trevor King [Fri, 21 Jun 2013 17:57:56 +0000 (13:57 -0400)]
sawsim/discussion.tex: Rework sawsim Monte Carlo review

Start with the big picture, and zoom in on the finer points.

8 years agohooke: Promote \subsections to \sections
W. Trevor King [Fri, 21 Jun 2013 17:41:39 +0000 (13:41 -0400)]
hooke: Promote \subsections to \sections

These aren't subsections of the Hooke history section.

8 years agohooke/conclusions.tex: Discuss frameworks and automation
W. Trevor King [Fri, 21 Jun 2013 17:36:04 +0000 (13:36 -0400)]
hooke/conclusions.tex: Discuss frameworks and automation

8 years agohooke/ui.tex: Reword fundamental UI description
W. Trevor King [Fri, 21 Jun 2013 16:03:56 +0000 (12:03 -0400)]
hooke/ui.tex: Reword fundamental UI description

Prof. Cruz pointed out that the old wording had the typo 'because at
the a basic', and I thought I'd just rework the whole phrase.

8 years agohooke/drivers.tex: Fix 'Drivers have can' -> 'Drivers can' typo
W. Trevor King [Fri, 21 Jun 2013 16:01:46 +0000 (12:01 -0400)]
hooke/drivers.tex: Fix 'Drivers have can' -> 'Drivers can' typo

Thanks, Prof. Cruz.

8 years agopyafm/frameworks.tex: Remove duplicates in 'in the the general'
W. Trevor King [Fri, 21 Jun 2013 15:59:12 +0000 (11:59 -0400)]
pyafm/frameworks.tex: Remove duplicates in 'in the the general'

Thanks, Prof. Cruz.

8 years agosawsim/discussion.tex: Shift fig:sawsim:order-dep forward
W. Trevor King [Fri, 21 Jun 2013 14:04:47 +0000 (10:04 -0400)]
sawsim/discussion.tex: Shift fig:sawsim:order-dep forward

So it shows up within a page of the first reference to it.

Thanks, Prof. Cruz.

8 years agoroot.bib: Add a direct link to sawsim in as a note in king10
W. Trevor King [Fri, 21 Jun 2013 13:39:33 +0000 (09:39 -0400)]
root.bib: Add a direct link to sawsim in as a note in king10

Thanks, Prof. Cruz.

8 years agosalt/main.tex: Fix '0.5 m' -> '0.5 M' typo
W. Trevor King [Fri, 21 Jun 2013 13:35:37 +0000 (09:35 -0400)]
salt/main.tex: Fix '0.5 m' -> '0.5 M' typo

Thanks, Prof. Cruz.

8 years agosalt/main.tex: Fix 'argenine' -> 'arginine' typo
W. Trevor King [Fri, 21 Jun 2013 13:34:56 +0000 (09:34 -0400)]
salt/main.tex: Fix 'argenine' -> 'arginine' typo

Thanks, Prof. Cruz.

8 years agofigures/order-dep/order-dep.asy: Reduce x ticks on inset histograms
W. Trevor King [Fri, 21 Jun 2013 13:30:37 +0000 (09:30 -0400)]
figures/order-dep/order-dep.asy: Reduce x ticks on inset histograms

Having three ticks (with N=2?) makes for integer tick labels.  The
change from N=3 to N=2 may be due to a regression in Asymptote, but I
don't have the time to track that down now.

Thanks for pointing out the problem, Prof. Cruz.

8 years agosawsim/methods.tex: Plug sec:salt from sec:sawsim:rate:other summary
W. Trevor King [Fri, 21 Jun 2013 12:43:39 +0000 (08:43 -0400)]
sawsim/methods.tex: Plug sec:salt from sec:sawsim:rate:other summary

Remind folks about the end goals, and ease of re-analysis.

Thanks, Prof. Cruz.

8 years agoroot.bib: ScienceDirect links are long, use DOIs instead
W. Trevor King [Fri, 21 Jun 2013 12:33:32 +0000 (08:33 -0400)]
root.bib: ScienceDirect links are long, use DOIs instead

This is a bit redundant, but at least the links are shorter and
stable.

8 years agosawsim/methods.tex: Fix 'effectivly' -> 'effectively' typo
W. Trevor King [Fri, 21 Jun 2013 12:28:01 +0000 (08:28 -0400)]
sawsim/methods.tex: Fix 'effectivly' -> 'effectively' typo

Thanks, Prof. Cruz.

8 years agosawsim/methods.tex: Tighten 'A short chain' -> 'Short chains'
W. Trevor King [Fri, 21 Jun 2013 12:26:58 +0000 (08:26 -0400)]
sawsim/methods.tex: Tighten 'A short chain' -> 'Short chains'

Thanks, Prof. Cruz.

8 years agoapparatus/procedure.tex: Add red/blue examples to sec:sawsim:tension:wlc
W. Trevor King [Fri, 21 Jun 2013 12:25:09 +0000 (08:25 -0400)]
apparatus/procedure.tex: Add red/blue examples to sec:sawsim:tension:wlc

Thanks, Prof. Cruz.

8 years agosawsim/methods.tex: Fix 'forumla' -> 'formula' typo
W. Trevor King [Fri, 21 Jun 2013 12:12:25 +0000 (08:12 -0400)]
sawsim/methods.tex: Fix 'forumla' -> 'formula' typo

Thanks, Prof. Cruz.

8 years agointroduction/main.tex: Fix 'roll' -> 'role' typo
W. Trevor King [Fri, 21 Jun 2013 12:10:49 +0000 (08:10 -0400)]
introduction/main.tex: Fix 'roll' -> 'role' typo

Thanks Prof. Cruz.

8 years agoroot.tex: Fix 'Louis' -> 'Luis' typo
W. Trevor King [Fri, 21 Jun 2013 12:09:42 +0000 (08:09 -0400)]
root.tex: Fix 'Louis' -> 'Luis' typo

Oops.  Thanks for pointing this out, Prof. Cruz :p.

8 years agofuture/software.tex: Add 'tarball' to the nomenclature
W. Trevor King [Sat, 15 Jun 2013 20:47:07 +0000 (16:47 -0400)]
future/software.tex: Add 'tarball' to the nomenclature

Additional software jargon.  Thanks Mom!

8 years agofuture: Fix some typos that Mom found
W. Trevor King [Sat, 15 Jun 2013 20:46:36 +0000 (16:46 -0400)]
future: Fix some typos that Mom found

8 years agohooke/main.tex: Remove the discussion section
W. Trevor King [Sat, 15 Jun 2013 16:10:33 +0000 (12:10 -0400)]
hooke/main.tex: Remove the discussion section

There's not much wrap up to do, so I'll put it all in the conlusions
section.

8 years agohooke/ui.tex: Fill in user interface section
W. Trevor King [Sat, 15 Jun 2013 16:09:51 +0000 (12:09 -0400)]
hooke/ui.tex: Fill in user interface section

Also add a screenshot of the GUI.

8 years agosawsim/discussion.tex: Link to sec:hooke:plugins for unfolding force
W. Trevor King [Fri, 14 Jun 2013 19:08:53 +0000 (15:08 -0400)]
sawsim/discussion.tex: Link to sec:hooke:plugins for unfolding force

Not a great fit, but I don't have a whole section devoted to unfolding
force extraction.

8 years agoapparatus/main.tex: Remove link to sec:temperature
W. Trevor King [Fri, 14 Jun 2013 19:06:47 +0000 (15:06 -0400)]
apparatus/main.tex: Remove link to sec:temperature

... since we no longer include that chapter.

8 years agopyafm/auxiliary.tex: Add an 'and' for the last Z-N tuning rule
W. Trevor King [Fri, 14 Jun 2013 19:01:41 +0000 (15:01 -0400)]
pyafm/auxiliary.tex: Add an 'and' for the last Z-N tuning rule

8 years agopyafm/auxiliary.tex: Fix reference to fig:stepper:backlash
W. Trevor King [Fri, 14 Jun 2013 18:56:12 +0000 (14:56 -0400)]
pyafm/auxiliary.tex: Fix reference to fig:stepper:backlash

8 years agoroot.bib: Remove some TODOs from the notes
W. Trevor King [Fri, 14 Jun 2013 18:54:16 +0000 (14:54 -0400)]
root.bib: Remove some TODOs from the notes

8 years agosawsim/discussion.tex: No time to mathematically define l_{ts}
W. Trevor King [Fri, 14 Jun 2013 18:44:29 +0000 (14:44 -0400)]
sawsim/discussion.tex: No time to mathematically define l_{ts}

8 years agosawsim/discussion.tex: No time to flesh out my interpolating tree
W. Trevor King [Fri, 14 Jun 2013 18:42:37 +0000 (14:42 -0400)]
sawsim/discussion.tex: No time to flesh out my interpolating tree

I love it, but there's only so much time (or reader interest).

8 years agoroot.bib: I haven't tracked down a copy of gumbel58 yet
W. Trevor King [Fri, 14 Jun 2013 18:39:50 +0000 (14:39 -0400)]
root.bib: I haven't tracked down a copy of gumbel58 yet

8 years agosawsim/introduction.tex: Hide parameter TODO (no time to look this up)
W. Trevor King [Fri, 14 Jun 2013 18:38:32 +0000 (14:38 -0400)]
sawsim/introduction.tex: Hide parameter TODO (no time to look this up)

8 years agosawsim/methods.tex: Fix (or hide) outstanding TODO issues
W. Trevor King [Fri, 14 Jun 2013 18:37:13 +0000 (14:37 -0400)]
sawsim/methods.tex: Fix (or hide) outstanding TODO issues

8 years agopyafm/auxiliary.tex: I can't find a source for bang-bang tuning
W. Trevor King [Fri, 14 Jun 2013 18:30:07 +0000 (14:30 -0400)]
pyafm/auxiliary.tex: I can't find a source for bang-bang tuning

I wonder where the algorithm is from? :p

8 years agopyafm/auxiliary.tex: Add a Peltier figure with a caption from my oral
W. Trevor King [Fri, 14 Jun 2013 18:28:46 +0000 (14:28 -0400)]
pyafm/auxiliary.tex: Add a Peltier figure with a caption from my oral

8 years agofigures/asy/ElectroMag.asy: Add the E&M library from my course project
W. Trevor King [Fri, 14 Jun 2013 17:37:40 +0000 (13:37 -0400)]
figures/asy/ElectroMag.asy: Add the E&M library from my course project

For drawing a Peltier.

8 years agofigures/asy/Mechanics.asy: Add the mechanics library from my course project
W. Trevor King [Fri, 14 Jun 2013 11:24:12 +0000 (07:24 -0400)]
figures/asy/Mechanics.asy: Add the mechanics library from my course project

For drawing a Peltier.

8 years agofigures/asy/Circ.asy: Add the circuit library from my course project
W. Trevor King [Fri, 14 Jun 2013 11:22:53 +0000 (07:22 -0400)]
figures/asy/Circ.asy: Add the circuit library from my course project

For drawing a Peltier.

8 years agofigures/asy/wtk_graph.asy: Add mcross for stepper graphs
W. Trevor King [Fri, 14 Jun 2013 11:21:32 +0000 (07:21 -0400)]
figures/asy/wtk_graph.asy: Add mcross for stepper graphs

A marker in the shape of a small cross.  With this marker, there's
less overlap between successive points that trend in horizontal or
vertical directions.

8 years agopyafm/auxiliary.tex: Bring in some text and figures from my oral
W. Trevor King [Fri, 14 Jun 2013 11:14:10 +0000 (07:14 -0400)]
pyafm/auxiliary.tex: Bring in some text and figures from my oral

Back in 2007-07-01 ;).

8 years agofigures/stepper/step-size.asy: Restore piezo-approach labeling
W. Trevor King [Fri, 14 Jun 2013 11:11:04 +0000 (07:11 -0400)]
figures/stepper/step-size.asy: Restore piezo-approach labeling

I'd had this in the old MetaPost version, but now the positions are
automatic :).

8 years agofigures/stepper: Translate stepper-calibration figures to Asymptote
W. Trevor King [Fri, 14 Jun 2013 08:03:19 +0000 (04:03 -0400)]
figures/stepper: Translate stepper-calibration figures to Asymptote

These figures were from my oral qualifier oh-so-many years ago.  I've
translated them into a modern language, which makes them quite a bit
cleaner than the old format which involved layers of processing in
Bash ;).

8 years agoroot.bib: Add lee05 for EDC/linker background
W. Trevor King [Fri, 14 Jun 2013 04:05:14 +0000 (00:05 -0400)]
root.bib: Add lee05 for EDC/linker background

8 years agoroot.bib: Fix 'μ' -> '$\mu$' in jaschke95 abstract
W. Trevor King [Fri, 14 Jun 2013 04:03:06 +0000 (00:03 -0400)]
root.bib: Fix 'μ' -> '$\mu$' in jaschke95 abstract

pdflatex doesn't deal with non-ASCII input very gracefully.  Not that
I'm rendering the abstracts, but still ;).

8 years agoroot.bib: Add gittes98 and berg-sorensen04
W. Trevor King [Fri, 14 Jun 2013 04:02:09 +0000 (00:02 -0400)]
root.bib: Add gittes98 and berg-sorensen04

Both talk about extremely overdamped power spectra.

8 years agocalibcant/main.bib: Add dates to mathworld-lorentzian
W. Trevor King [Fri, 14 Jun 2013 03:30:55 +0000 (23:30 -0400)]
calibcant/main.bib: Add dates to mathworld-lorentzian

And wikipedia-wiener-khinchin.  They still say what I quoted them as
saying back in 2010.

8 years agocalibcant/overview.tex: Flesh out related work
W. Trevor King [Fri, 14 Jun 2013 03:24:05 +0000 (23:24 -0400)]
calibcant/overview.tex: Flesh out related work

Also, cite roters96 for using the proper form but calling it a
Lorentzian.

8 years agocalibcant/overview.tex: Fix 'formula' -> 'formulas' typo
W. Trevor King [Fri, 14 Jun 2013 03:22:06 +0000 (23:22 -0400)]
calibcant/overview.tex: Fix 'formula' -> 'formulas' typo

Wikipedia says that both 'formulas' and 'formulae' are acceptable
plural forms [1], but I have a few 'formulas' occurences in here
already.

[1]: http://en.wikipedia.org/wiki/Formula

8 years agopyafm/main.bib: Curly-brace 'HDF' in entry titles
W. Trevor King [Thu, 13 Jun 2013 23:13:53 +0000 (19:13 -0400)]
pyafm/main.bib: Curly-brace 'HDF' in entry titles

Otherwise it is automatically sentence-cased by bibtex.

8 years agosrc/root.bib: Fix MPCHong -> NPCHong in aruliah12 authors
W. Trevor King [Thu, 13 Jun 2013 23:13:19 +0000 (19:13 -0400)]
src/root.bib: Fix MPCHong -> NPCHong in aruliah12 authors

8 years agocalibcant/discussion.tex: Cite PNAS and Nature for data archival
W. Trevor King [Thu, 13 Jun 2013 23:11:36 +0000 (19:11 -0400)]
calibcant/discussion.tex: Cite PNAS and Nature for data archival

8 years agocalibcant/procedure.tex: Over-estimate port-to-chip distance
W. Trevor King [Thu, 13 Jun 2013 22:20:56 +0000 (18:20 -0400)]
calibcant/procedure.tex: Over-estimate port-to-chip distance

I'd like to actually measure this, but I forget when I'm in lab.  The
whole fluid chamber is about a centimeter in diameter, so 3 mm seems
like a safe upper bound.

8 years agocalibcant/discussion.tex: Finish error propogation paragraph
W. Trevor King [Thu, 13 Jun 2013 22:17:36 +0000 (18:17 -0400)]
calibcant/discussion.tex: Finish error propogation paragraph

Replace "TODO" with "kappa shouldn't change", since I go right into
quoting numbers later on.

8 years agoapparatus/sample-preparation.tex: Comment out epoxy TODO
W. Trevor King [Thu, 13 Jun 2013 22:15:02 +0000 (18:15 -0400)]
apparatus/sample-preparation.tex: Comment out epoxy TODO

I'm not sure what brand it is, and I don't have time to look it up
now.  I'll try to get around to it the next time I'm in the lab.

8 years agoapparatus/afm.tex: Add range of the 2253E piezo
W. Trevor King [Thu, 13 Jun 2013 21:54:44 +0000 (17:54 -0400)]
apparatus/afm.tex: Add range of the 2253E piezo

DAC range (V_dac) * gain (V_piezo / V_dac) * sensitivity (m / V_piezo):

  >>> 20 * 20 * 8.8e-09    # z axis
  3.5199999999999998e-06
  >>> 20 * 20 * 4.16e-09   # x axis
  1.6639999999999999e-06

8 years agohooke: Flesh out discussion of drivers and plugins
W. Trevor King [Thu, 13 Jun 2013 19:16:12 +0000 (15:16 -0400)]
hooke: Flesh out discussion of drivers and plugins

Also add a missing close-paren to history.tex, along with a caveat
footnote that sometimes rewriting is worth it.

8 years agoroot.tex: Don't show the index
W. Trevor King [Thu, 13 Jun 2013 17:49:48 +0000 (13:49 -0400)]
root.tex: Don't show the index

* It's not complete.
* The second column overlaps with the 'Index' chapter title.

8 years agoroot.tex: I'll be submitting this thesis in July, not May
W. Trevor King [Thu, 13 Jun 2013 17:49:19 +0000 (13:49 -0400)]
root.tex: I'll be submitting this thesis in July, not May

Time keeps on slipping...

8 years agoroot.tex: Enable auxilliary blurbs and disable viscosity appendix
W. Trevor King [Thu, 13 Jun 2013 17:18:06 +0000 (13:18 -0400)]
root.tex: Enable auxilliary blurbs and disable viscosity appendix

8 years agosalt/main.tex: Fill in best-fit dx and ku0
W. Trevor King [Thu, 13 Jun 2013 17:09:19 +0000 (13:09 -0400)]
salt/main.tex: Fill in best-fit dx and ku0

Using the numbers from my presentation slides.

8 years agofuture: Fill in conclusions/future chapter
W. Trevor King [Thu, 13 Jun 2013 17:05:57 +0000 (13:05 -0400)]
future: Fill in conclusions/future chapter

8 years agosalt/main.tex: Add fisher-CaCl citation and remove NaCl reference
W. Trevor King [Thu, 13 Jun 2013 15:33:06 +0000 (11:33 -0400)]
salt/main.tex: Add fisher-CaCl citation and remove NaCl reference

I didn't get enough NaCl data to publish something significant :/.

8 years agosalt/main.tex: Add 1TIT-hbond figure based on lu00b
W. Trevor King [Thu, 13 Jun 2013 15:23:11 +0000 (11:23 -0400)]
salt/main.tex: Add 1TIT-hbond figure based on lu00b

8 years agofigures/i27/1TIT.pml: Zoom out a bit to match thesis slides
W. Trevor King [Thu, 13 Jun 2013 03:37:42 +0000 (23:37 -0400)]
figures/i27/1TIT.pml: Zoom out a bit to match thesis slides

8 years agohooke/main.tex: Rework lead-in paragraph to avoid 'uninteresting'
W. Trevor King [Thu, 13 Jun 2013 03:36:31 +0000 (23:36 -0400)]
hooke/main.tex: Rework lead-in paragraph to avoid 'uninteresting'