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Multiscale reaction-diffusion simulations with Smoldyn.

Robinson M, Andrews SS, Erban R - Bioinformatics (2015)

Bottom Line: This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains.Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.

View Article: PubMed Central - PubMed

Affiliation: Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and.

No MeSH data available.


(a) Multiscale Smoldyn simulation of yeast signalling between haploid Saccharomyces cerevisiae of opposite mating types (MATa and MATα; Andrews et al., 2010). The centre region contains a detailed off-lattice model of several MATa and MATα cells, which is coupled to a coarse on-lattice model to describe the diffusion and interaction of a pheromone (α-factor) and a pheromone-degrading protease (Bar1) within the surrounding environment. (b) Speed-up versus lattice spacing h that can be achieved by using the on-lattice model for the bulk of the domain (speed-up equals 1 for a purely off-lattice simulation). The simulation domain is a 100 × 100 × 100 μm cube with an absorbing boundary. The gradient of bound α-factor across the central cell (a measure of simulation accuracy) did not vary with h over the range considered, and the mean was within 1% of that obtained from the purely off-lattice simulation
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btv149-F1: (a) Multiscale Smoldyn simulation of yeast signalling between haploid Saccharomyces cerevisiae of opposite mating types (MATa and MATα; Andrews et al., 2010). The centre region contains a detailed off-lattice model of several MATa and MATα cells, which is coupled to a coarse on-lattice model to describe the diffusion and interaction of a pheromone (α-factor) and a pheromone-degrading protease (Bar1) within the surrounding environment. (b) Speed-up versus lattice spacing h that can be achieved by using the on-lattice model for the bulk of the domain (speed-up equals 1 for a purely off-lattice simulation). The simulation domain is a 100 × 100 × 100 μm cube with an absorbing boundary. The gradient of bound α-factor across the central cell (a measure of simulation accuracy) did not vary with h over the range considered, and the mean was within 1% of that obtained from the purely off-lattice simulation

Mentions: Supplementary Information: Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1.


Multiscale reaction-diffusion simulations with Smoldyn.

Robinson M, Andrews SS, Erban R - Bioinformatics (2015)

(a) Multiscale Smoldyn simulation of yeast signalling between haploid Saccharomyces cerevisiae of opposite mating types (MATa and MATα; Andrews et al., 2010). The centre region contains a detailed off-lattice model of several MATa and MATα cells, which is coupled to a coarse on-lattice model to describe the diffusion and interaction of a pheromone (α-factor) and a pheromone-degrading protease (Bar1) within the surrounding environment. (b) Speed-up versus lattice spacing h that can be achieved by using the on-lattice model for the bulk of the domain (speed-up equals 1 for a purely off-lattice simulation). The simulation domain is a 100 × 100 × 100 μm cube with an absorbing boundary. The gradient of bound α-factor across the central cell (a measure of simulation accuracy) did not vary with h over the range considered, and the mean was within 1% of that obtained from the purely off-lattice simulation
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495299&req=5

btv149-F1: (a) Multiscale Smoldyn simulation of yeast signalling between haploid Saccharomyces cerevisiae of opposite mating types (MATa and MATα; Andrews et al., 2010). The centre region contains a detailed off-lattice model of several MATa and MATα cells, which is coupled to a coarse on-lattice model to describe the diffusion and interaction of a pheromone (α-factor) and a pheromone-degrading protease (Bar1) within the surrounding environment. (b) Speed-up versus lattice spacing h that can be achieved by using the on-lattice model for the bulk of the domain (speed-up equals 1 for a purely off-lattice simulation). The simulation domain is a 100 × 100 × 100 μm cube with an absorbing boundary. The gradient of bound α-factor across the central cell (a measure of simulation accuracy) did not vary with h over the range considered, and the mean was within 1% of that obtained from the purely off-lattice simulation
Mentions: Supplementary Information: Supplementary data are available at Bioinformatics online and include additional details on model specification and modelling of surfaces, as well as the Smoldyn configuration file used to generate Figure 1.

Bottom Line: This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains.Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.

View Article: PubMed Central - PubMed

Affiliation: Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and.

No MeSH data available.