Computational Modelling Group

Dr. Daniel Mason MChem

University of Southampton
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Research project:

Multiscale Modelling of Cellular Calcium Signalling

This project involved computational modelling of the cell. Despite being small in size, cellular systems are highly complex and the processes that contribute to this complexity operate on a number of scales. These scales are separated by vast spatio-temporal magnitudes.

Computational simulations traditionally tackle systems at a single scale, however simulating an entire cell using the most detailed of methods is not possible. The approach taken in this project was to simulate the processes occurring over several scales, and pass information between them.

In this way, processes occurring at the smallest scales may impart an effect on the largest, and vice versa. This approach is known as multiscale modelling, and may be applied to many other problems in computational simulation.

The final model links molecular and ionic diffusion, ion channel gating, cellular energetics, and organelle interactions. Together, these provide detailed information on whole-cell dynamics that support experimental hypotheses, and provide insight to the mechanisms that may occur during the onset of a disease state.

A former PhD student of Prof J.W.Essex and Prof. H. Fangohr.

Research Interests

Life sciences simulation: Bioinformatics, Biomathematics, Biomolecular simulations, Systems biology

Physical Systems and Engineering simulation: Diffusion

Algorithms and computational methods: Agents, Cellular automata, Finite differences, Finite elements, Multi-core, Multi-scale

Visualisation and data handling methods: Data Management

Visualisation and data handling software: Pylab, VMD, VTK

Software Engineering Tools: Mercurial

Programming languages and libraries: Python

Computational platforms: Linux, Windows

Transdisciplinary tags: Complex Systems, Computer Science, HPC, Quantitative Biology, Scientific Computing, Software Engineering, Visualisation

Working with...

Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)



Multiscale Heirarchy