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Matthias Jeschke

last modified 2010-11-11 18:09


Title of PhD thesis:
Efficient Non-spatial and Spatial Simulation of Biochemical Reaction Networks

Defended: 


10/19/2010
Reviewers: 
Adelinde M. Uhrmacher, University of Rostock, Rostock, Germany


Kevin Burrage, University of Oxford, UK


Koichi Takahashi, RIKEN Institute, Japan


Synopsis

Reaction networks describe interactions between (molecular) species and their proper function is crucial for all living beings. Analyzing them in vitro is often aggravated by the spatial and temporal scale of the system: the size of species can range from nanometers to micrometers, some networks may fire in only a few nanoseconds while others require days to finish. As an alternative to real-world experiments, the system of interest (here: the reaction networks) can be abstracted to a model, which is then taken as the input for an experiment in silico --- a simulation.

This dissertation is focused on algorithms for performing non-spatial and spatial stochastic simulations of reaction networks and on the exploration of improved or alternative approaches. A central topic is the evaluation and a subsequent comparison of algorithm performance in terms of execution speed and accuracy. A thorough discussion on the intricacies of a such an evaluation is followed by two large-scale studies which demonstrate the application of the elaborated concepts.

The second part of this work takes up the idea of temporal leap methods, extends it to the spatial realm, and introduces a variant for a parallel execution. Subjected to a theoretical and practical performance analysis, (parallel) spatial \tauleaping shows a strong dependence to both algorithm and model parameters, e.g. the particle distribution.

Finally, the realization of a multi-algorithm simulation is explored by introducing inter-rules that forge a link between the synchronized execution of subsidiary algorithms. A simple notation for the description of discrete-event simulations is extended to allow the representation of moving individuals that can interact with particles in a discretized volume. Despite being qualitative only, several example models and experiments show the feasibility of this approach.

Important publications

  • Matthias Jeschke and Adelinde M. Uhrmacher (2008): Multi-resolution Spatial Simulation For Molecular Crowding - In: Proceedings of the Winter Simulation Conference, ed. by S.J. Mason, R.R. Hill, L. Moench, O. Rose.
  • Matthias Jeschke and Roland Ewald (2008): Large-Scale Design Space Exploration of SSA - In: Computational Methods in Systems Biology, vol. Volume 5307/2008, pp. 211-230, Springer Berlin / Heidelberg. Lecture Notes in Computer Science.
  • Matthias Jeschke, Roland Ewald, Alfred Park, Richard Fujimoto and Adelinde M. Uhrmacher (2008): Parallel and Distributed Spatial Simulation of Chemical Reactions - In: Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS 2008), pp. 51 - 59.
  • Matthias Jeschke, Roland Ewald and Adelinde M. Uhrmacher (2011): Exploring the Performance of Spatial Stochastic Simulation Algorithms - Journal of Computational Physics, 230(7):2562-2574.

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