From: W. Trevor King <wking@tremily.us>
Date: Thu, 25 Apr 2013 19:33:29 +0000 (-0400)
Subject: Replace '\cite{...}' with '\citep{...}'
X-Git-Tag: v1.0~282
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=8b7e84b4545e3f9f32eadf6a0d6ee5c6527ab823;p=thesis.git

Replace '\cite{...}' with '\citep{...}'

This way we get the configured natbib formatting.
---

diff --git a/src/apparatus/afm.tex b/src/apparatus/afm.tex
index 234bf98..57da522 100644
--- a/src/apparatus/afm.tex
+++ b/src/apparatus/afm.tex
@@ -10,9 +10,9 @@ transitions in DNA\citep{florin95,rief99} and
 polysaccharides\citep{rief97a}.
 
 An AFM\index{AFM} uses a sharp tip integrated at the end of a
-cantilever to interact with the sample\cite{binnig86}.  Cantilever
+cantilever to interact with the sample\citep{binnig86}.  Cantilever
 bending is measured by a laser reflected off the cantilever and
-incident on a position sensitive photodetector\cite{meyer88}
+incident on a position sensitive photodetector\citep{meyer88}
 (\cref{fig:afm-schematic}).  When the bending force constant of the
 cantilever is known\citep{levy02}, the force applied to the sample can
 be calculated using Hooke's law (\cref{eq:sawsim:hooke}).
diff --git a/src/apparatus/polymer-synthesis.tex b/src/apparatus/polymer-synthesis.tex
index 3671a81..1fca013 100644
--- a/src/apparatus/polymer-synthesis.tex
+++ b/src/apparatus/polymer-synthesis.tex
@@ -61,7 +61,7 @@ for the target protein, inserting the plasmid in a bacteria, waiting
 while the bacteria produce your protein, and then purifying your
 proteins from the resulting culture.  In this case,
 \citet{carrion-vazquez99b} extracted messenger RNA coding for titin
-from human cardiac tissue\cite{rief97a}, and used reverse
+from human cardiac tissue\citep{rief97a}, and used reverse
 transcriptase to generate a complementary DNA (cDNA) library from
 human cardiac muscle messenger RNA.  This cDNA is then amplified using
 the polymerase chain reaction (PCR), with special primers that allow
@@ -106,7 +106,7 @@ The octamer is then purified from the culture using immobilized metal
 ion affinity chromatography (IMAC), where the His-tagged end of the
 octamer covalently bonds to a metal ion that is bound to the column
 media (e.g. Ni-NTA\index{Ni-NTA} coated
-beads)\cite{carrion-vazquez00,bartels03,ma10}.  Once the rest of the
+beads)\citep{carrion-vazquez00,bartels03,ma10}.  Once the rest of the
 broth has been washed out of the chromatography column, the octamer is
 eluted via either another molecule which competes for the metal
 ions\citep{ma10} or by changing the pH so the octamer is less
diff --git a/src/apparatus/sample-preparation.tex b/src/apparatus/sample-preparation.tex
index 064efcb..cc2a4e6 100644
--- a/src/apparatus/sample-preparation.tex
+++ b/src/apparatus/sample-preparation.tex
@@ -35,5 +35,5 @@ EGTA\citep{kellermayer03},
 Ni-NTA\citep{schmidt02,itoh04,sakaki05,berkemeier11}, or silanized
 glass\citep{sundberg03,ma10}.  Some groups have also functionalized
 the cantilever tips, with Ni-NTA being the most
-popular\cite{schmitt00}.
+popular\citep{schmitt00}.
 \nomenclature{EGTA}{Ethylene glycol tetraacetic acid}
diff --git a/src/sawsim/methods.tex b/src/sawsim/methods.tex
index ec00503..fa872be 100644
--- a/src/sawsim/methods.tex
+++ b/src/sawsim/methods.tex
@@ -188,9 +188,9 @@ As an alternative to modeling the folded domains explicitly or
 ignoring them completely, another approach is to subtract the
 end-to-end length of the folded protein from the contour length of the
 unfolded protein to create an effective contour length for the
-unfolding\cite{carrion-vazquez99b}.  This effectivly models the folded
-domains as WLCs with the same persistence length as the unfolded
-domains.
+unfolding\citep{carrion-vazquez99b}.  This effectivly models the
+folded domains as WLCs with the same persistence length as the
+unfolded domains.
 
 %The chain of $N_f$ folded domains is modeled as a string, free to
 %assume any extension up to some fixed contour length $L_f=N_fL_{f1}$
@@ -254,7 +254,7 @@ Langevin function\citep{hatfield99}.
 
 More exotic models such as elastic WLCs\citep{janshoff00,puchner08},
 elastic FJCs\citep{fisher99a,janshoff00}, and freely rotating
-chains\cite{puchner08} (FRCs) have also been used to model DNA and
+chains\citep{puchner08} (FRCs) have also been used to model DNA and
 polysaccharides, but are rarely used to model the relatively short and
 inextensible synthetic proteins used in force spectroscopy.
 \nomenclature{FRC}{Freely-rotating chain (like the FJC, except that