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 234bf989c090b309c3fa5f85ab5e40aa8e10815f..57da52223b6914cea8bb528165bd8eac229e7115 100644 (file)
--- 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 3671a81182297ccfda51f1c4d79b16523a3af9f5..1fca0139c74a43d5d276c0b28d6b709c995653a6 100644 (file)
--- 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 064efcba50a532a8b72080c4f49a7b27e7821b2f..cc2a4e66868ab4706b9d2ea7690079c05cc78da5 100644 (file)
--- 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 ec0050341f056bd85b786123a370ac17847a87fd..fa872bea008d776ac5f935071ca761099fed15fd 100644 (file)
--- 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