From individuals to emergence

Stromatolite reef (Hamelin Pool, Australia)

Simulated growth of a stromatolite

This project is financed by the Portuguese Fundcao para a Ciencia e a Tecnologia (FCT).

Abstract

Computational modelling of individual cells is an emerging field in
computational science with great potential. Until recently many biological
models were quite abstract compared to the cells which compose the real
system. At the highest level of abstraction, individual cells are not
represented at all but are modelled instead as a continuous mass which may
flow and diffuse. These models are applied to larger systems such as
tissues and tumours where the macroscopic behaviour can be well described
analytically.


These models are useful but their abstractness can pose a problem. It
is quite difficult to incorporate all but the most simple features of cells
into analytical models and this is due to the fact that it is not always
clear how individual cell behaviours translate into macroscopic effects.
So even if the genetic regulation of a cell is understood there is no general
means for translating this knowledge into behaviour at scales larger than a
single cell. To build this bridge we opt to model individual cells whose
characteristics are well under stood and. if possible, linked to a genetic
control. By simulating a system of virtual cells we can observe how a change
at the cellular level may effect the emergent patterns of the system. And
since cells interact locally, these simulations are computationally simple
with linear computation time in the number of cells.


We have adopted two biological systems to model. The first is a blastula
(a primitive aggregate of cells resulting from the division of a
fertilized egg) and the process of gastrulation under which blastocells
under go major shape changes and migrations resulting in the more complex
gastrula. We are modelling this system at the cell level using a cortical
model for the individual cells, i.e. a model in which the cell membrane is
the essential feature. Chemotaxis and adhesion are other features of the model.


The second system are stromatolites. Stromatolites are laminated and
lithified structures built principally though the actions of cyanobacteria.
Layers are accreted to stromatolites by cyanobacteria which, when covered by
sediment, glide to escape burial cementing the sediment in place in the
process. They are an excellent example of emergent morphogenesis from a
microscopic system. Furthermore they are of great importance in the
history of the Earth as they are the oldest known sign of life on Earth;
stromatolite fossils that are roughly ~3.5 billion years old have been found.

The Research Team