Modeling Stochastic Diffusion of Acetylcholine(ACh) at neuromuscular junction using MCell4
Session Number
3
Advisor(s)
Dr. Ashwin Mohan, PhD, SYNAPSE Lab @ IMSA
Location
A119
Discipline
Medical and Health Sciences
Start Date
15-4-2026 2:15 AM
End Date
15-4-2026 3:00 AM
Abstract
Acetylcholine (ACh) is a neurotransmitter that neuronal synapses use to trigger muscle movement. When this diffusion malfunctions, it can contribute to diseases like myasthenia gravis and Alzheimer’s disease. Studying acetylcholine at the molecular level in laboratories is costly and difficult because its diffusion occurs at extremely small spatial scales and within microseconds, requiring specialized imaging technology and highly controlled experimental conditions. Previous studies showed simulations can accurately reproduce ACh diffusion across nerve–muscle connections, and these tools have improved over time. However, reliably modeling individual molecules remains challenging, and many studies lack visual tools for exploring results. This study addresses that gap by combining MCell4 with CellBlender. Our model centers on the stochastic diffusion of ACh and the receptors it binds to as a starting point. Our model shows Brownian motion of the ACh molecules using the Monte Carlo simulation in MCell. CellBlender is used as a 3D visualizer that allows us to view scaled molecules at miniscule levels. The model is able to record reactions, and create data plots with MatPlotLib using .dat files created by MCell. Our model offers an accessible and adaptable framework for examining neurotransmitter behavior, which could be used for other chemical signaling systems in the body.
Modeling Stochastic Diffusion of Acetylcholine(ACh) at neuromuscular junction using MCell4
A119
Acetylcholine (ACh) is a neurotransmitter that neuronal synapses use to trigger muscle movement. When this diffusion malfunctions, it can contribute to diseases like myasthenia gravis and Alzheimer’s disease. Studying acetylcholine at the molecular level in laboratories is costly and difficult because its diffusion occurs at extremely small spatial scales and within microseconds, requiring specialized imaging technology and highly controlled experimental conditions. Previous studies showed simulations can accurately reproduce ACh diffusion across nerve–muscle connections, and these tools have improved over time. However, reliably modeling individual molecules remains challenging, and many studies lack visual tools for exploring results. This study addresses that gap by combining MCell4 with CellBlender. Our model centers on the stochastic diffusion of ACh and the receptors it binds to as a starting point. Our model shows Brownian motion of the ACh molecules using the Monte Carlo simulation in MCell. CellBlender is used as a 3D visualizer that allows us to view scaled molecules at miniscule levels. The model is able to record reactions, and create data plots with MatPlotLib using .dat files created by MCell. Our model offers an accessible and adaptable framework for examining neurotransmitter behavior, which could be used for other chemical signaling systems in the body.