A Spatial Extension to the π Calculus
Electronic Notes in Theoretical Computer Science (ENTCS)
Combining micro and macro-modeling in DEVS for computational biology
Proceedings of the 39th conference on Winter simulation: 40 years! The best is yet to come
Parallel and Distributed Spatial Simulation of Chemical Reactions
Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation
Stochastic simulation of biological systems with dynamical compartment structure
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Regenerative systems: challenges and opportunities for modeling, simulation, and visualization
Proceedings of the Fourth International ICST Conference on Performance Evaluation Methodologies and Tools
DEVS-based design of spatial simulations of biological systems
Winter Simulation Conference
Multi-model traffic microsimulations
Winter Simulation Conference
Adapting rule-based model descriptions for simulating in continuous and hybrid space
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
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Spatial phenomena attract increasingly interest in computational biology. Molecular crowding, i.e. a dense population of macromolecules, is known to have a significant impact on the kinetics of molecules. However, an in-detail inspection of cell behavior in time and space is extremely costly. To balance between cost and accuracy, multi-resolution approaches offer one solution. Particularly, a combination of individual and lattice-population based algorithms promise an adequate treatment of phenomena like macromolecular crowding. In realizing such an approach, central questions are how to specify and synchronize the interaction between population and individual spatial level, and to decide what is best treated at a specific level, respectively. Based on an algorithm which combines the Next Subvolume Method and a simple, individual-based spatial approach, we will present possible answers to these questions, and will discuss first experimental results.