Titulo Estágio
Develop a multilevel model to study Cell Potts Models based upon Artificial Chemistries
Área Tecnológica
Sistemas Evol. e Comp.
Local do Estágio
CISUC/ECOS
Enquadramento
Cellular
Potts Models (CPM) have shown themselves to be a very good tool to represent
individual cells, and tissues produced by many different cells [1]. Artificial
Chemistries (AC) are equally good in representing the chemical relations inside
a cell [2].
[1]:
A. F. M. Marée, V. A. Grieneisen, and P. Hogeweg.The Cellular Potts Model and
biophysical properties of cells, tissues and morphogenesis. In A. R. A.
Anderson, M. A. J. Chaplain, and K. A. Rejniak, editors, Single-Cell-Based
Models in Biology and Medicine, pages 107-136. Birkhäuser Verlag, Basel (2007).
[2]:
Peter Dittrich, Pietro Speroni di Fenizio (2007) Chemical Organization Theory,
Bull. Math. Biol., 69(4):1199-1231, 2007
Objetivo
You
should link the two kind of models by producing a multilevel system where each
cell is modeled with a CPM, and the internal dynamic inside each cell is
modeled with an AC. From the AC inside a cell the parameters for the CPM should
be extracted. As well as when will the cell reproduce. A similar result was
reached in 2000 by Hogeweg using Cell Potts models with boolean networks
embedded in the cells [3]. Yet in last 10 years not much work has extended
those results. By switching from boolean networks to artificial Chemistries you
should first reproduce the existing results, and then start to extend them.
Artificial Chemistries have been thoroughly studied, and we know by now how to
represent the evolution over AC. Integrating this evolution with a cell based
model would provide the kind of extension that can push the field into new
topics.
Note
that this work, at this stage, does not aim to represent reality as it is
(which would require an analysis far beyond the scope of a master thesis), but
to show the model to be realistic, and powerful enough to represent reality.
Note that if the student will then decide to follow up the work with a PhD
thesis, it should probably not be a problem.
[3]
P. Hogeweg: Evolving Mechanisms of Morphogenesis: on the Interplay between
Differential Adhesion and Cell Differentiation: J. theor. Biol. (2000) 203,
317}333 doi:10.1006/jtbi.2000.1087
Plano de Trabalhos - Semestre 1
Phase
1 - Revision of literature and State of the Art.
Phase
2 – Program a simple model for Cell Potts Models and for AC
Phase
3 - Integrate the two programs, by linking the parameters in the CPM to the
values in the AC.
Phase
4 - Elaboration of a proposal for the dissertation.
Plano de Trabalhos - Semestre 2
Phase
5 - Test the Cell Potts Models, and reproduce Hogeweg results.
Phase
6 - Extend the results by integrating the work with Organization Theory
analysis of evolution in Artificial Chemistries
Phase
7 - Writing the Dissertation.
Phase
8 - Writing a scientific article.
Condições
This
is not an easy work, and it will require a student with creative spark, ability
to follow his intuition, ability to program in C, C++ and possibly even in
Python (to integrate with existing programs). Knowledge of Artificial
Chemistries, Cell Potts Models, and Chemical Organization Theory is not
necessary when starting, but an ability to learn and apply what learned is
fundamental.
Orientador
Pietro Speroni di Fenizio e Luis Paquete
speroni@dei.uc.pt 📩