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Biophys J. 2010 Mar 17;98(6):959-67. doi: 10.1016/j.bpj.2009.11.034.

Monte Carlo simulation of buffered diffusion into and out of a model synapse.

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  • 1Department of Anesthesiology, Stony Brook University, Stony Brook, New York, USA.


Buffered diffusion occurs when ligands enter or leave a restricted space, such as a chemical synapse, containing a high density of binding sites. This study used Monte Carlo simulations to determine the time and spatial dependences of buffered diffusion without a priori assumptions about kinetics. The synapse was modeled as a box with receptors on one inner face. The exterior was clamped to some ligand concentration and ligands diffused through two sides. Onset and recovery simulations were carried out and the effects of receptor density, ligand properties and synapse geometry were investigated. This study determined equilibration times for binding and the spatial gradient of unliganded receptors. Onset was characterized by a high spatial gradient; equilibration was limited by the time needed for sufficient ligands to enter the synapse. Recovery showed a low spatial gradient with receptor equilibration limited by ligand rebinding. Decreasing ligand association rate or increasing ligand diffusion coefficient reduced the role of buffered diffusion and decreased the spatial gradient. Simulations with irreversible ligands showed larger, persistent spatial gradients. These simulations identify characteristics that can be used to test whether a synaptic process is governed by buffered diffusion. They also indicate that fundamental differences in synapse function may occur with irreversible ligands.

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