ENH integrate new appendices

tex/thesis.tex

@@ -1558,16 +1558,15 @@ quantified for \gls{stp} protein using the \gls{bca} assay.
 % TODO defend why the microcarriers were saturated with stp
 The effective diffusivity of the microcarriers was determined using a
 pseudo-steady-state model. Each microcarrier was assumed to be a porous sphere
-with a fixed number of `\gls{stp} binding sites' equal to the maximum number of
+with a fixed number of `\gls{stp} binding sites' equal to the number of
-\gls{stp} molecules that could binding to the surface per area (eg, we assumed
+\gls{stp} molecules experimentally determined to bind to the microcarriers.
-the surface was fully covered by \gls{stp}). Because the reaction rate between
+Because the reaction rate between biotin and \gls{stp} was so fast, we assumed
-biotin and \gls{stp} was so fast, we assumed that the interface of free biotin
+that the interface of free biotin shrunk as a function of \gls{stp} bound until
-shrunk as a function of \gls{stp} bound until the center of the microcarriers
+the center of the microcarriers was reached. We also assumed that the pores in
-was reached. We also assumed that the pores in the microcarriers were large
+the microcarriers were large enough that the interactions between the \gls{stp}
-enough that the interactions between the \gls{stp} and surfaces would be small,
+and surfaces would be small, thus the apparent diffusivity could be represented
-thus the apparent diffusivity could be represented as a fraction of the
+as a fraction of the diffusion coefficient of \gls{stp} in water. This model was
-diffusion coefficient of \gls{stp} in water. This model was given by
+given by \cref{eqn:stp_diffision_1,eqn:stp_diffision_2}:
-\cref{eqn:stp_diffision_1,eqn:stp_diffision_2}:
 
 % TODO actually derive these equations, eg state the initial conditions and
 % governing equation
@@ -1598,15 +1597,23 @@ diffusion coefficient of \gls{stp} in water. This model was given by
 The diffusion rate of \gls{stp} was assumed to be
 \SI{6.2e-7}{\cm\squared\per\second}\cite{Kamholz2001}. Since all but $\beta$ was
 known, the experimental data was fit using these equations using
-\inlinecode{ode45} in MATLAB and least squares as the fitting error. These equations were then used analogously to describe the reaction profile of
+\inlinecode{ode45} in MATLAB and least squares as the fitting error. These
+equations were then used analogously to describe the reaction profile of
 \glspl{mab} assuming a diffusion rate of
-\SI{4.8e-7}{\cm\squared\per\second}\cite{Sherwood1992}. These same coefficients
+\SI{4.8e-7}{\cm\squared\per\second}\cite{Sherwood1992}.
+
+These same coefficients
 were used in determining the kinetics of the washing steps, and
 \SI{5.0e-6}{\cm\squared\per\second}\cite{Niether2020} was used as the diffusion
 coefficient for free biotin (which should be the only species left in solution
-after all the \gls{snb} has hydrolyzed). All diffusion coefficients were taken
+after all the \gls{snb} has hydrolyzed).
-to be valid at \gls{rt} and in \gls{di} water, which is a safe assumption given
+
-that our reaction medium was 1X \gls{pbs}.
+All diffusion coefficients were taken to be valid at \gls{rt} and in \gls{di}
+water, which is a safe assumption given that our reaction medium was 1X
+\gls{pbs}.
+
+See \cref{sec:appendix_binding} and \cref{sec:appendix_washing} for the MATLAB
+code (and output in the case of the washing steps) used.
 
 % METHOD add the equation governing the washing steps
 
@@ -4471,7 +4478,7 @@ hosted using \gls{aws} using their proprietary Aurora implementation.
 
 The code is available here: \url{https://github.gatech.edu/ndwarshuis3/mdma}.
 
-\chapter{binding kinetics code}
+\chapter{binding kinetics code}\label{sec:appendix_binding}
 
 The \gls{stp} binding kinetic profile was fit and calculated using the following
 MATLAB code. Note that the \inlinecode{geometry} parameter was varied so as to
@@ -4486,7 +4493,7 @@ reflect the \gls{mab} coating process.
 
 \lstinputlisting{../code/diffusion_mab.m}
 
-\chapter{washing kinetics code}
+\chapter{washing kinetics code}\label{sec:appendix_washing}
 
 The wash steps for the \gls{dms} were modeled using the following code: