From 07644e1724c093c345259051edaf814673f9b4b3 Mon Sep 17 00:00:00 2001
From: ndwarshuis <ndwar@yavin4.ch>
Date: Tue, 27 Jul 2021 17:42:11 -0400
Subject: [PATCH] ADD reaction kinetics results paragraphs

---
 tex/thesis.tex | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/tex/thesis.tex b/tex/thesis.tex
index e0b4aee..9c55557 100644
--- a/tex/thesis.tex
+++ b/tex/thesis.tex
@@ -96,6 +96,7 @@
 \newacronym{tmb}{TMB}{3,3',5,5'-Tetramethylbenzidine}
 \newacronym{gvhd}{GVHD}{graft-vs-host disease}
 \newacronym{bcma}{BCMA}{B-cell maturation antigen}
+\newacronym{di}{DI}{deionized}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % SI units for uber nerds
@@ -951,6 +952,8 @@ transferred to another 96 well plate wherein expansion continued.
 % METHOD snb decay curve generation and analysis (including the equation used to
 % fit the data)
 
+% METHOD add reaction kinetics diffusion mathy stuff
+
 \subsection{Luminex Analysis}
 
 Luminex was performed using a \product{ProcartaPlex kit}{\thermo}{custom} for
@@ -1148,7 +1151,38 @@ higher, further showing that the decay of \gls{snb} is not a concern.
   \label{fig:dms_flowchart}
 \end{figure*}
 
-% RESULT add paragraph explaining the reaction kinetics stuff
+We also investigated the reaction kinetics of all three coating steps.
+
+To quantify the reaction kinetics of the biotin binding step, we reacted
+multiple batches of microcarriers at \gls{rt} with
+\gls{20}{\mg\of{\carrier}\per\ml} with \gls{snb} in parallel and sacrificially
+analyzed each at varying timepoints using the \gls{haba} assay. This was
+performed at two different concentrations. We observed that for either
+concentration, the reaction was over in \SIrange{20}{30}{\minute}
+(\cref{fig:dms_biotin_rxn_mass}). Furthermore, when put in terms of fraction of
+input \gls{snb}, we observed that the curves are almost identical
+(\cref{fig:dms_biotin_rxn_frac}). Given this, the reaction step for biotin
+attached was set to \gls{30}{\minute}.
+
+% TODO these numbers might be totally incorrect
+Next, we quantified the amount of \gls{stp} reacted with the surface of the
+biotin-coated microcarriers. Different batches of biotin-coated \glspl{dms} were
+coated with \SI{40}{\ug\per\ml} \gls{stp} and sampled at various timepoints
+using the \gls{bca} assay to indirectly quantify the amount of attached
+\gls{stp} mass. We found this reaction took \SI{45}{\minute}
+(\cref{fig:dms_stp_per_time}).
+
+% TODO find real numbers for this
+Finally, we used the reaction data from the \gls{stp} binding curve to estimate
+the \gls{mab} binding curve. Assuming a quasi-steady-state paradigm, we
+estimated that the diffusion rate coefficient for the microcarriers was
+{\#}{diffusion rate}. Using this diffusion rate and the maximum mass of
+\glspl{mab} bound the microcarriers (\cref{fig:mab_coating}), we estimated that
+the \gls{mab} reaction should proceed in {\#}{mab curve}.
+
+% TODO add additional paragraph about how this diffusion coefficient was used to
+% estimate the wash step times.
+
 \begin{figure*}[ht!]
   \begingroup