Please upload PDFs of papers you would like to discuss.

To upload papers go to Manage Wiki (to the left) and click on the Files icon. Upload your PDF and copy the tag code it gives you for your paper. This tag code should appear at the top of the page in a green box.
The tag code should look like: [[ file:name of file.pdf ]]
Hit the EDIT tab at the top right of this page and paste the tag code onto this page and your PDF will appear for all to download. Please include the title of the paper.


A Hybrid model for 3D Simulations of Sprouting Angiogenesis

Shapes and the origin of life: orvie2008_Dou.p5.pdf

Folded Leaf Shape: Leaf_Shape_PO.pdf

A method for a mid-scale analysis of loop patterns: Perna_PRE1.pdf
Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation:

An auxin-driven polarized transport model for phyllotaxis: J├Ânsson et al PNAS 2006.pdf

Developmental patterning by mechanical signals in Arabidopsis: Hamant et al Science 2008.pdf

Supplement to Developmental patterning by mechanical signals...: Hamant et al Science 2008 Suppl.pdf

Discrete shells, Grinspun et al. 2003 :
Triangular springs for modeling nonlinear membranes, Delingette 2008 :
A level set approach for computing solutions to incompressible two-phase flow, Sussman et al. 1994:

Turning a plant tissue into a living cell froth through isotropic growth, Corson et al. 2009

Modeling cell rheology with the Subcellular Element Model:
Stochastic process semantic for dynamical grammars:
In silico leaf venation networks : growth and reorganisation driven by mechanical forces

Self-similar structures near boundaries in strained systems

Mechanical Forces of Fission Yeast Growth , SI

Computational Morphodynamics: a modeling framework to understand plant growth; submitted to Annual Review of Plant Biology

A variational level set approach to multiphase motion,
A multiphase level set framework for image segmentation using the Mumford and Shah model,

Papers on Notch Signaling:
Alex Small and David Sprinzak suggest discussing the first 2 papers in the afternoon on Thursday or Friday of next week (September 3 or 4).
1) Review article from the Gerhardt group:
2) Recent experimental paper from the Gerhardt group:
3) Modeling paper from the Gerhardt group:
4) Modeling paper from Popel group:
5) Another experimental paper: See also the commentary:

Suggestion for journal club
Modeling embryogenesis and cancer: an approach based on an equilibrium between the
autostabilization of stochastic gene expression and the interdependence of cells for proliferation . Suggested by Arezki Boudaoud.