88 lines
2.9 KiB
TeX
88 lines
2.9 KiB
TeX
\documentclass[a4paper]{article}
|
|
|
|
\usepackage{csquotes}
|
|
\usepackage[acronym]{glossaries}
|
|
\usepackage[utf8x]{inputenc}
|
|
\usepackage{siunitx}
|
|
|
|
\makeglossaries{}
|
|
\newacronym{cis}{CiS}{Cells in Silico}
|
|
\newacronym{cpm}{CPM}{Cellular Potts Model}
|
|
\newacronym{ecm}{ECM}{Extracellular Matrix}
|
|
\newacronym{mcs}{MCS}{Monte-Carlo Step}
|
|
\newacronym{nastja}{NAStJA}{Neoteric Autonomous Stencil code for Jolly Algorithms}
|
|
|
|
\begin{document}
|
|
|
|
\title{Research Summary}
|
|
\author{Paul Brinkmeier}
|
|
\date{June 2023}
|
|
\maketitle
|
|
|
|
\section{\acrfull{ecm}}
|
|
|
|
For an extensive overview, see \cite{frantz2010}.
|
|
|
|
\begin{itemize}
|
|
\item The \acrshort{ecm} constitutes the non-cellular parts of all tissues.
|
|
\item It consists of:
|
|
\begin{itemize}
|
|
\item Fibrous proteins, most importantly collagen, elastin and fibronectin.
|
|
\item Up to 30\% collagen.
|
|
Forms fibrils and fibers of different sizes which can \enquote{stick together} to make up networks.
|
|
There are a bunch of different collagen types.
|
|
\item Proteoglycans, which fill the interstitial space in the form of a hydrated gel.
|
|
\end{itemize}
|
|
\item Cells move through and remodel their \acrshort{ecm}, which in turn changes their behavior. \\
|
|
$\implies$ \emph{in silico} models need to take this into account.
|
|
\item Different tissues have different \acrshortpl{ecm}.
|
|
\end{itemize}
|
|
|
|
\subsection{Properties of the Extracellular Matrix}
|
|
|
|
Our approach takes a macroscopic view of the \acrshort{ecm}.
|
|
Individual fibrils/fibers should not be modeled.
|
|
Nevertheless we include some microscopic properties.
|
|
|
|
\begin{itemize}
|
|
\item \textbf{Density}
|
|
\item \textbf{Stiffness}: Matrix stiffness has an effect on tumor gowth, e.g. \cite{levental2009}.
|
|
Measured using Young's modulus/elastic modulus which is given in \si{\Pa}.
|
|
\item \textbf{Viscoelasticity}
|
|
\item \textbf{Pore size}
|
|
\end{itemize}
|
|
|
|
\cite{frantz2010} mentions Matrigel™ and collagen type I gels, so we will focus on these.
|
|
|
|
\section{\acrfull{cpm}}
|
|
|
|
\begin{itemize}
|
|
\item The \acrshort{cpm} is a grid-based Monte-Carlo simulation for cells.
|
|
\item Each cell consists of many voxels.
|
|
These voxels contain its cell ID.
|
|
\item In each \acrfull{mcs}, a random voxel copies the cell ID of its neighbor.
|
|
\item The hamiltonian $H$ gives the energy of a generation. It depends on the volume and surface of cells and their reciprocal adhesion.
|
|
\item A \acrshort{mcs} is always accepted if it reduces $H$.
|
|
If it does not reduce $H$, it is accepted probabilistically.
|
|
\end{itemize}
|
|
|
|
\section{\acrshort{nastja} \& \acrshort{cis}}
|
|
|
|
\begin{itemize}
|
|
\item \acrfull{nastja} is a massively parallel stencil code solver based on OpenMPI.
|
|
\item \acrfull{cis} is an implementation of the \acrshort{cpm} in \acrshort{nastja}.
|
|
\end{itemize}
|
|
|
|
\section{The \acrshort{ecm} in the \acrshort{cpm}}
|
|
|
|
\clearpage
|
|
|
|
\section{Glossary}
|
|
|
|
\printglossary[type=\acronymtype]
|
|
|
|
\bibliographystyle{plain}
|
|
\bibliography{references}
|
|
|
|
\end{document}
|