Neurotransmitter Diffusion Across Synapse (1)

Описание: The animation demonstrates how neurotransmitters diffuse across the synaptic cleft. Starting from high concentration the presynaptic membrane, the concentration profile gradually spreads outward in all directions, forming a smooth diffusion of neurotransmitters across the cleft. The height of the surface represents concentration magnitude, allowing us to visualize how diffusion flattens the initial peak over time.

I've explored two version of this animation, one with a a sharp Gaussian peak and one with a wave-like concentration profile. The former is more representative of biophysical neurotransmitter diffusion, as the peak of neurotransmitter concentration represents the impulse
release of a neuron.

I've also explored a random-walk approach. Each particle undergoes random Brownian motion, gradually spreading across the synaptic cleft. As they reach the postsynaptic membrane, their color changes to represent receptor binding, after which they stop moving and disappear.

Additionally, I have created an advanced version of the simulation based off realistic neurotransmitter diffusion dynamics in full 3D cylindrical geometry (radial and vertical directions). This model captures both the radial spreading across the 400 nm active zone and vertical diffusion through the 20 nm synaptic cleft, showing how concentration gradients evolve at different depths from the presynaptic to postsynaptic membrane. The three-panel visualization reveals cross-sectional heat maps, 3D concentration surfaces, and depth-dependent radial profiles, providing comprehensive insight into the spatiotemporal evolution of neurotransmitter concentration during chemical synaptic transmission. The diffusion equation used is credited to researchers at UCSD, and is based off their work here: https://isn.ucsd.edu/courses/beng221/...

This animation was created for the EPS 109 course "Computer simulations with Jupyter notebooks" at the University of California, Berkeley: https://militzer.berkeley.edu/EPS109. It offers a general introduction to computer simulations for all science majors. Participants will use the Jupyter notebooks to perform calculations, design 3D graphics, and build on existing computer programs. No prior programming experience is required. The course teaches fundamental skills for scientists and helps students with future homework. It covers data processing techniques as well standard simulations methods including Monte Carlo and molecular dynamics. The algorithms are illustrated with a variety of applications in earth and planetary science as well as astronomy.