Software

I am a developer of the NEURON simulator, used in more than 3,000 published studies, and one of the top ten contributors to its open-source codebase. I am also a major contributor to NetPyNE, which builds network models on top of NEURON.

NEURON reaction-diffusion

Most electrophysiology models treat ion concentrations as fixed. NEURON's reaction-diffusion module (RxD), tracks ions, second messengers and metabolites as they react and diffuse inside cells and through the extracellular space, so that changes in concentration feed back on electrical activity. That is what makes it possible to simulate ischemia and spreading depolarization in detailed neurons and in networks of tens of thousands of cells.

My contributions include:

extracellular reaction-diffusion, using a volume-averaged description of tissue by its free volume fraction and tortuosity (Newton et al., 2018);
3D intracellular simulation, including voxelization of morphologies and its numerical integration (McDougal et al., 2022);
performance: just-in-time compilation, multithreading and parallel simulation across processors (Awile et al., 2022).

Extracellular potassium concentration during a simulated spreading depression wave, with cell locations shown as white points — Extracellular K⁺ 30 s into a spreading depression wave, averaged over 1 mm³ of simulated tissue; white points mark the locations of cells. From Newton, McDougal, Hines & Lytton (2018), *Frontiers in Neuroinformatics*, Fig 1A, CC BY 4.0.

NetPyNE

NetPyNE is an NIH-funded Python package, built on NEURON, for data-driven multiscale models of brain circuits: a model is written in a standard declarative format, and NetPyNE builds, simulates and analyzes the network.

I have contributed to NetPyNE's development and used it in several of my models, including the in vitro and in vivo spreading-depolarization models and the cardiac models.

Models on ModelDB

Code for these models is shared on ModelDB so others can run and build on them.

Dendritic vulnerability to ischemia and spreading depression (Newton et al., 2026)
Network models of potassium-channel downmodulation and seizures (Ho et al., 2025)
Spreading depolarization in brain slices (Kelley et al., 2022)
Efficient 3D reaction-diffusion in neurons (McDougal et al., 2022)
Synaptic specificity in the maintenance phase of plasticity (Huertas et al., 2022)
Extracellular reaction-diffusion in NEURON (Newton et al., 2018)