CellMath:
Mathematics and Computation for the Systems Biology of Cells
This project is financed by the Netherlands Organisation for Scientific Research
(NWO), research program "Computational Life Sciences".
Granted proposal
[
ps-file |
pdf-file]
Aim
The aim of the project is to develop, implement, and validate
mathematical and computational techniques for the
systems biology of the cell.
Biologists and mathematicians together will formulate
realistic mathematical models of metabolic and regulatory
networks including intrinsic spatial non-homogeneity.
Depending on the cellular phenomenon considered,
models and methods of appropriate temporal and spatial scales
will be developed and can then be applied:
models in the form of ordinary differential equations
and methods for system reduction;
multi-adaptive computational methods for
partial differential equations (PDEs) for moderate spatial and temporal
variability within a cell or an organelle;
particle models describing the interaction
of individual molecules and computational methods
for the evaluation of the dynamic behavior; and methods for integration
of these different approaches into a single simulation.
The planned outcome of the project are computational and mathematical
algorithms, implemented in auto-adaptive computational models, and simulation
results for the functioning of living cells.
Research focus
- system reduction techniques
for ordinary differential equations (ODEs) of the type
that arises in chemical networks (simplification and modularization in
the chemical `dimension')
- particle-based methods for modelling of features with
high spatial variability or low number of molecules
- multi-adaptive numerical methods for the efficient solving
of reaction-diffusion PDEs with varying spatial and temporal scales,
and space dependent chemical schemes
- methods that allow 1-3 to be integrated into a single simulation,
in order to take advantage of simplification and modularization wherever and
whenever possible
Subprojects
- VU/IMBW and CWI/MAS2.3: Focus on 1 and 4
- UvA/SCS:
Focus on 2 and 4
- CWI/MAS1.1:
Focus on 3 and 4
