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Excluded volume effects in on- and off-lattice reaction-diffusion models.
Lina Meinecke1, Markus Eriksson2
1Department of Information Technology, Uppsala University, Uppsala, Sweden. lina.meinecke@it.uu.se.
IET Systems Biology
|May 7, 2017
Summary
Cellular automata models offer efficient approximations for reaction-diffusion systems with crowding. However, their accuracy decreases significantly at higher crowder densities due to grid artifacts.
Area of Science:
- Computational biology
- Biophysics
- Mathematical modeling
Background:
- Reaction-diffusion systems are crucial in cellular processes.
- Excluded volume effects from crowding impact these systems.
- Microscopic simulations are computationally intensive in crowded environments.
Purpose of the Study:
- To evaluate the accuracy of on-lattice cellular automata models for simulating reaction-diffusion systems with crowding.
- To compare on-lattice and off-lattice Brownian dynamics simulations in crowded environments.
Main Methods:
- Investigated on-lattice cellular automata models.
- Compared with off-lattice Brownian dynamics simulations.
- Analyzed diffusion and reaction rates under varying crowder densities and molecular sizes.
Main Results:
- Off-lattice models show more severe diffusion slowdown due to random obstacle distribution.
- On-lattice models exhibit grid artifacts that increase with crowder density.
- Reaction rates in crowded environments are sensitive to grid structure and molecular size.
Conclusions:
- On-lattice cellular automata models provide accurate approximations for reaction-diffusion systems only at low crowder densities.
- Realistic modeling of molecular sizes is important for excluded volume effects.
- Computational efficiency of on-lattice models is limited by accuracy at high crowder densities.
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