BbioRxiv7 Nov 2025

From Atoms to Neuronal Spikes: A Multi-Scale Simulation Framework

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Abstract

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A multi-scale simulation framework links atomistic ion‑channel changes to neuronal spikes, revealing disease‑linked AMPAR variants and membrane composition strongly affect excitability.

What’s new

i.Developed a multi-scale simulation approach coupling molecular dynamics with neuronal simulations
ii.Demonstrated that disease-associated AMPAR variants can significantly impact neuronal excitability
iii.Implemented bidirectional coupling between Monte Carlo ion‑channel gating simulations and Arbor neuron models
iv.Included effects of lipid membrane composition and temperature on membrane potential

How they did it

Molecular dynamics simulations were used to predict current and conductance changes of AMPAR variants, and these parameters were fed into detailed cortical pyramidal neuron models using the Arbor framework. In a second example, coarse‑grained Monte Carlo gating simulations of voltage‑gated K+ and Na+ channels were coupled bidirectionally with Arbor, allowing feedback between channel states and membrane potential.

What they found

Molecular dynamics predicted altered current and conductance for disease‑associated AMPAR variants
Arbor simulations indicated these variants may significantly affect neuronal excitability
Bidirectional coupling showed ion‑channel states and membrane potential influence each other
Simulations revealed lipid membrane composition and temperature have significant impacts on excitability

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