Extracellular space diffusion modelling identifies distinct functional advantages of archetypical glutamatergic and GABAergic synapse geometries

The brain extracellular space (ECS) is a convoluted compartment of nano- and microscale interconnected ducts. A key step in signaling between neural cells is diffusion of signaling molecules through the ECS, yet, signaling is generally considered solely from the stance of cells and their properties. Where ECS diffusion is addressed, this is commonly done using volume-averaging techniques blind to individual signaling events and ECS geometry. We hypothesized that ECS geometry can shape local diffusion and thereby tune signaling arising from point-sources. To access the scale of individual transmitter release events and synapse geometries, we developed a computational diffusion model, DifFlux , based on super-resolved images of hippocampal ECS in live mouse brain slices and combined this with single molecule Monte Carlo diffusion simulations. Our approach allows us to simulate diffusion of molecules of our choosing in true live ECS geometries. We asked how the ECS shapes local diffusion in dense neuropil and along larger cellular processes in CA1 stratum radiatum . We observed local diffusional anisotropy and directionality imposed by ECS geometry. Further, we identified distinct functional advantages of dendritic spine and somatodendritic synapse ECS geometries, shedding light on the longstanding conundrum of why glutamatergic and GABAergic synapses are so conspicuously morphologically different. Our modelling broadly identifies ECS structure as a direct modulator of extrasynaptic signaling that can operate in parallel to conventional regulation mechanisms.