diff --git a/doc/research/figures/sherman2015-table1.png b/doc/research/figures/sherman2015-table1.png new file mode 100644 index 0000000..339b058 Binary files /dev/null and b/doc/research/figures/sherman2015-table1.png differ diff --git a/doc/research/references.bib b/doc/research/references.bib index 34b1f1e..97001ce 100644 --- a/doc/research/references.bib +++ b/doc/research/references.bib @@ -1,3 +1,77 @@ +@article{chaudhuri2020, + abstract = {Substantial research over the past two decades has established that extracellular matrix (ECM) elasticity, or stiffness, affects fundamental cellular processes, including spreading, growth, proliferation, migration, differentiation and organoid formation. Linearly elastic polyacrylamide hydrogels and polydimethylsiloxane (PDMS) elastomers coated with ECM proteins are widely used to assess the role of stiffness, and results from such experiments are often assumed to reproduce the effect of the mechanical environment experienced by cells in vivo. However, tissues and ECMs are not linearly elastic materials—they exhibit far more complex mechanical behaviours, including viscoelasticity (a time-dependent response to loading or deformation), as well as mechanical plasticity and nonlinear elasticity. Here we review the complex mechanical behaviours of tissues and ECMs, discuss the effect of ECM viscoelasticity on cells, and describe the potential use of viscoelastic biomaterials in regenerative medicine. Recent work has revealed that matrix viscoelasticity regulates these same fundamental cell processes, and can promote behaviours that are not observed with elastic hydrogels in both two- and three-dimensional culture microenvironments. These findings have provided insights into cell–matrix interactions and how these interactions differentially modulate mechano-sensitive molecular pathways in cells. Moreover, these results suggest design guidelines for the next generation of biomaterials, with the goal of matching tissue and ECM mechanics for in vitro tissue models and applications in regenerative medicine. This Review explores the role of viscoelasticity of tissues and extracellular matrices in cell–matrix interactions and mechanotransduction and the potential utility of viscoelastic biomaterials in regenerative medicine.}, + author = {Ovijit Chaudhuri and Justin Cooper-White and Paul A. Janmey and David J. Mooney and Vivek B. Shenoy}, + doi = {10.1038/s41586-020-2612-2}, + issn = {1476-4687}, + issue = {7822}, + journal = {Nature 2020 584:7822}, + keywords = {Humanities and Social Sciences,Science,multidisciplinary}, + month = {8}, + pages = {535-546}, + pmid = {32848221}, + publisher = {Nature Publishing Group}, + title = {Effects of extracellular matrix viscoelasticity on cellular behaviour}, + volume = {584}, + url = {https://www.nature.com/articles/s41586-020-2612-2}, + year = {2020}, +} +@article{sheu2001, + abstract = {The influence of glutaraldehyde as a crosslinking agent to increase the strength of collagen matrices for cell culture was examined in this study. Collagen solutions of 1% were treated with different concentrations (0-0.2%) of glutaraldehyde for 24h. The viscoelasticity of the resulting collagen gel solution was measured using dynamic mechanical analysis (DMA), which demonstrated that all collagen gel solutions examined followed the same model pattern. The creep compliance model of Voigt-Kelvin satisfactorily described the change of viscoelasticity expressed by these collagen gel solutions. These crosslinked collagen gel solutions were freeze-dried to form a matrix with a thickness of about 0.2-0.3mm. The break modulus of these collagen matrices measured by DMA revealed that the higher the degree of crosslinking, the higher the break modulus. The compatibility of fibroblasts isolated from nude mouse skin with these collagen matrices was found to be acceptable at a cell density of 3×105cells/cm2 with no contraction, even when using a concentration of glutaraldehyde of up to 0.2%. Copyright © 2001 Elsevier Science Ltd.}, + author = {Ming Thau Sheu and Ju Chun Huang and Geng Chang Yeh and Hsiu O. Ho}, + doi = {10.1016/S0142-9612(00)00315-X}, + issn = {0142-9612}, + issue = {13}, + journal = {Biomaterials}, + keywords = {Collagen,Dynamic mechanical analysis,Glutaraldehyde,Viscoelasticity}, + month = {7}, + pages = {1713-1719}, + pmid = {11396874}, + publisher = {Elsevier}, + title = {Characterization of collagen gel solutions and collagen matrices for cell culture}, + volume = {22}, + year = {2001}, +} +@report{slater2017, + author = {Katie Slater and Jeff Partridge and Himabindu Nandivada}, + title = {Tuning the Elastic Moduli of Corning ® Matrigel ® and Collagen I 3D Matrices by Varying the Protein Concentration Application Note}, + url = {https://www.corning.com/ catalog/cls/documents/application-notes/CLS-AC-AN-449.pdf}, + year = {2017}, +} +@article{aisenbrey2020, + abstract = {Matrigel, a basement-membrane matrix extracted from Engelbreth–Holm–Swarm mouse sarcomas, has been used for more than four decades for a myriad of cell-culture applications. However, Matrigel is limited in its applicability to cellular biology, therapeutic-cell manufacturing and drug discovery, owing to its complex, ill-defined and variable composition. Variations in the mechanical and biochemical properties within a single batch of Matrigel — and between batches — have led to uncertainty in cell-culture experiments and a lack of reproducibility. Moreover, Matrigel is not conducive to physical or biochemical manipulation, making it difficult to fine-tune the matrix to promote intended cell behaviours and achieve specific biological outcomes. Recent advances in synthetic scaffolds have led to the development of xenogenic-free, chemically defined, highly tunable and reproducible alternatives. In this Review, we assess the applications of Matrigel in cell culture, regenerative medicine and organoid assembly, detailing the limitations of Matrigel and highlighting synthetic-scaffold alternatives that have shown equivalent or superior results. Additionally, we discuss the hurdles that are limiting a full transition from Matrigel to synthetic scaffolds and provide a brief perspective on the future directions of synthetic scaffolds for cell-culture applications.}, + author = {Elizabeth A. Aisenbrey and William L. Murphy}, + doi = {10.1038/S41578-020-0199-8}, + issn = {20588437}, + issue = {7}, + journal = {Nature reviews. Materials}, + month = {7}, + pages = {539}, + pmid = {32953138}, + publisher = {NIH Public Access}, + title = {Synthetic alternatives to Matrigel}, + volume = {5}, + url = {/pmc/articles/PMC7500703/ /pmc/articles/PMC7500703/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7500703/}, + year = {2020}, +} +@article{puxkandl2002, + abstract = {Collagen type I is the most abundant structural protein in tendon, skin and bone, and largely determines the mechanical behaviour of these connective tissues. To obtain a better understanding of th...}, + author = {R. Puxkandl and I. Zizak and O. Paris and J. Keckes and W. Tesch and S. Bernstorff and P. Purslow and P. Fratzl}, + doi = {10.1098/RSTB.2001.1033}, + issn = {09628436}, + issue = {1418}, + journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences}, + keywords = {Xray,collagen,mechanical properties,synchrotron,viscolelastic}, + month = {2}, + pages = {191-197}, + pmid = {11911776}, + publisher = { + The Royal Society + }, + title = {Viscoelastic properties of collagen: synchrotron radiation investigations and structural model}, + volume = {357}, + url = {https://royalsocietypublishing.org/doi/10.1098/rstb.2001.1033}, + year = {2002}, +} @article{giraud1998, abstract = {In this letter, we show that an eleven-velocity two-dimensional lattice Boltzmann model using several relaxation times obeys a Jeffreys viscoelastic constitutive law with full isotropic behavior. The connection between the free parameters of the model and the Jeffreys transport coefficients is made with the help of a modified Chapman-Enskog expansion taking into account large relaxation time effects. Numerical simulation of a pulsed Couette flow is performed leading to an excellent agreement with predictions.}, author = {L. Giraud and D. D'Humières and P. Lallemand}, diff --git a/doc/research/research.pdf b/doc/research/research.pdf index 0b59933..c5ccf62 100644 Binary files a/doc/research/research.pdf and b/doc/research/research.pdf differ diff --git a/doc/research/research.tex b/doc/research/research.tex index aa76cf4..530d3b2 100644 --- a/doc/research/research.tex +++ b/doc/research/research.tex @@ -1,7 +1,9 @@ \documentclass[a4paper]{article} +\usepackage{caption} \usepackage{csquotes} \usepackage[acronym]{glossaries} +\usepackage{hyperref} \usepackage[utf8x]{inputenc} \usepackage{siunitx} \usepackage{todonotes} @@ -55,8 +57,6 @@ Nevertheless we include some microscopic properties. \item \textbf{Density} \end{itemize} -\cite{frantz2010} mentions Matrigel™ and collagen type I gels, so we will focus on these. - \subsection{Viscoelasticity} \todo{What is viscoelasticity? Show some graphs and \enquote{oral} explanation} @@ -65,7 +65,7 @@ Generally modeled using differential equations involving the elastic modulus $E$ \cite{roylance2001} mentions these constitutive models: \begin{itemize} - \item Maxwell: A Viscous flow on the long timescale, but additional elastic resistance to fast deformations (e.g. silly putty, warm tar). + \item Maxwell: Viscous flow on the long timescale, but additional elastic resistance to fast deformations (e.g. silly putty, warm tar). Does not describe creep or recovery. \item Kelvin-Voigt: Does not describe stress relaxation. \item Zener/Standard linear solid: Models creep and stress relexation. @@ -75,7 +75,32 @@ The Lethersich and Jeffreys models are models for viscoelasticity that specifica \subsection{Rheology and Materials Science of the \acrshort{ecm}} -E.g. \cite{sherman2015, gautieri2013} +\cite{frantz2010} mentions Matrigel and collagen type I gels, so we will focus on these. + +Great review with great figures: \cite{chaudhuri2020}. + +\begin{itemize} + \item \cite{sherman2015} lists the elastic modulus of collagen structures at different scales, see \autoref{fig:sherman2015-table1}. + \item \cite{puxkandl2002} defines a model for the viscoelasticity of collagen. + \todo{expand, give actual values} + \item \cite{slater2017} discusses properties of Corning® Matrigel®. + \begin{itemize} + \item Lists elastic moduli for different concentrations and mixtures involving collagen type I around $10^1$ to $10^3$ \si{\pascal}. + \todo{This seems very low; investigate sources} + \item This paper shows the viscuous component in the graphs but doesn't really go into it. + \end{itemize} + \item \cite{aisenbrey2020} discusses alternatives to Corning® Matrigel®. + \item \cite{sheu2001} experimentally investigate the elastic and viscous moduli of collagen gels. + They find that the Kelvin-Voigt model can be used to model their viscoelastic behavior. +\end{itemize} + +\begin{figure}[h] + \includegraphics[width=\textwidth]{figures/sherman2015-table1} + \caption{Comparison of Young's modulus of collagen at multiple hierarchical levels. From \cite{sherman2015}.}. + \label{fig:sherman2015-table1} +\end{figure} + +Since viscoelastic behavior is inherently time-dependent, it will be a challenge to choose a sensible time step resolution for the model. \section{\acrfull{cpm}} @@ -107,6 +132,8 @@ E.g. \cite{sherman2015, gautieri2013} \item Discretisation in space makes it possible to calculate \acrshort{lbm} time steps using stencil codes. \item Extensive literature exists including implementation details, e.g. \cite{krueger2017} \item Can be used to model viscoelasticity, e.g. \cite{giraud1998, malaspinas2010, ispolatov2002} + \item Probably not that simple to model matrix porosity. + \todo{Elaborate} \end{itemize} \section{\acrshort{ecm} Models in the \acrshort{cpm}}