diff --git a/tex/references.bib b/tex/references.bib index 9b50b1f..14f6cfa 100644 --- a/tex/references.bib +++ b/tex/references.bib @@ -1167,6 +1167,19 @@ CONCLUSIONS: We developed a simplified, semi-closed system for the initial selec publisher = {Public Library of Science ({PLoS})}, } +@Article{Sherwood1992, + author = {Jill K. Sherwood and Richard B. Dause and W. Mark Saltzman}, + journal = {Nature Biotechnology}, + title = {Controlled Antibody Delivery Systems}, + year = {1992}, + month = {nov}, + number = {11}, + pages = {1446--1449}, + volume = {10}, + doi = {10.1038/nbt1192-1446}, + publisher = {Springer Science and Business Media {LLC}}, +} + @Comment{jabref-meta: databaseType:bibtex;} @Comment{jabref-meta: grouping: diff --git a/tex/thesis.tex b/tex/thesis.tex index 5acdb9e..ba1e9fc 100644 --- a/tex/thesis.tex +++ b/tex/thesis.tex @@ -975,7 +975,63 @@ at \SI{260}{\nm} were taken every minute for \SI{2}{\hour}. \subsection{reaction kinetics quantification} -% METHOD add reaction kinetics diffusion mathy stuff +The diffusion of \gls{stp} into biotin-coated microcarriers was determined +experimentally. \SI{40}{\ug\per\ml} \gls{stp} was added to multiple batches of +biotin-coated microcarriers, and supernatents were taken at fixed intervals and +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 +\gls{stp} molecules that could binding to the surface per area (eg, we assumed +the surface was fully covered by \gls{stp}). Because the reaction rate between +biotin and \gls{stp} was so fast, we assumed that the interface of free biotin +shrunk as a function of \gls{stp} bound until the center of the microcarriers +was reached. We also assumed that the pores in the microcarriers were large +enough that the interactions between the \gls{stp} and surfaces would be small, +thus the apparent diffusivity could be represented as a fraction of the +diffusion coefficient of \gls{stp} in water. This model was given by +\cref{eqn:stp_diffision_1,eqn:stp_diffision_2}: + +% TODO actually derive these equations, eg state the initial conditions and +% governing equation +\begin{equation} + \label{eqn:stp_diffision_1} + \frac{dr}{dt} = \frac{-D_{app}C}{Br(1-r/R)} +\end{equation} + +\begin{equation} + \label{eqn:stp_diffision_2} + \frac{dC}{dt} = \frac{-4 \pi n D_{app} C}{V(1/r-1/R)} +\end{equation} + +\noindent where +\begin{itemize}[label={}] +\item $D_{app}$ is the apparent diffusion rate which is equal to $D_{STP}\beta$ +\item $D_{STP}$ the diffusion rate of \gls{stp} in water +\item $\beta$ a fractional parameter representing the tortuousity and void + fraction of the microcarriers. +\item $r$ is the interfatial radius of the unbound biotin within a microcarrier +\item $t$ is the reaction time +\item $C$ is the concentration of \gls{stp} in the bulk solution +\item $V$ is the volume of the bulk medium +\item $R$ is the average radius of the microcarriers +\item $n$ is the number of microcarriers in the reaction volume +\end{itemize} + +% TODO cite the diffusion rate of stp +The diffusion rate of \gls{stp} was assumed to be +\SI{3.89e-7}{\cm\squared\per\second} {\#}{diffusion rate citation}. 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. + +% TODO this diffusion rate isn't actually reflected in the code +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}. + +% METHOD add the equation governing the washing steps \subsection{Luminex Analysis}