Publications

2026

NEURONpyxl: Fast, flexible, Python-integrated simulation of biophysical neural networks with complex plastic synapses

Abstract

NEURON has been widely used as an empirically-based simulation tool, especially for multi-compartment conductance-based neuronal modeling. We created a Python tool called NEURONpyxl that reads parameters from a spreadsheet to construct full neural networks, making it easier to create complex models in the NEURON simulation environment, incorporating short-term forms of plasticity such as depression or facilitation. Test simulations from well-understood networks were created in NEURONpyxl, and were observed to be numerically similar to simulations of the same network in another neural simulator, the Simulator for Neural Networks and Action Potentials (SNNAP), which has previously been used to model conductance-based networks that include complex synaptic connections and multiple forms of synaptic plasticity. We then used NEURONpyxl to conduct a parameter grid search to optimize conductances in a previously developed network model of Aplysia feeding behavior. We located parameter values that generated simulated motor patterns with durations of protraction and retraction that matched biological feeding behavior under different mechanical loads. NEURONpyxl simplifies building and simulating complex neural networks with different forms of synaptic plasticity, and locating physiologically relevant parameter values.

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• Accompanying Dataset

Citation

Dickman, U., Thomas, P. J., Chiel, H. J., Byrne, J. H., and Neveu, C. L., (2026). Fast, flexible, Python-integrated simulation of biophysical neural networks with complex plastic synapses, Frontiers in Computational Neuroscience. Accepted.

@article{Dickman-2026-FCNS,
author   = {Dickman, Uri and Thomas, Peter J. and Chiel, Hillel J.
            and Byrne, John H. and Neveu, Curtis L.},
year    = {2026},
title   = {NEURONpyxl: Fast, flexible, Python-integrated simulation
          of biophysical neural networks with complex plastic synapses},
journal = {Frontiers in Computational Neuroscience},
notes   = {Accepted}

2025

Thermal characterization of suspended fine wires across continuum to free-molecular gas regimes using the $3\omega$ method

Abstract

The $3\omega$ method is widely used to measure the thermal conductivity and the specific heat of wires and thin films. These measurements are typically performed under high vacuum conditions, which justify the use of heat-transfer models that exclude thermal losses to a surrounding fluid. Here, we study the effect of thermal conduction from a joule-heated wire to a surrounding gas on pressure-dependent $3\omega$ measurements, and show how a one-dimensional (1D) heat-transfer model may be used to reliably determine the wire’s thermal properties. We derive a full analytical solution of the 1D heat transfer equation with finite heat-transfer coefficient $h$ and validate it experimentally using a 16-$\mu$⁢m diameter platinum wire in air across pressures from $10^{-5}$ to $10^3$ mbar. We introduce a model for heat transfer between the wire and the surrounding gas based on kinetic gas theory that accurately describes the data across continuum to free-molecular gas regimes, with ℎ varying from near-zero in high vacuum to approximately $700$ W/(m2 K) at atmospheric pressure. We show that use of a validated $h(p)$ model allows extracting both thermal conductivity $\kappa$ and volumetric heat capacity $\rho c_p$, whereas volumetric heat capacity can be extracted even without invoking a specific $h(p)$ model. Our approach facilitates the characterization of fine wires with moderate to low thermal conductivities and may enable accurate thermal measurements of suspended wires with diameters on the nanometer scale.

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Citation

Peng, C., Ginzburg, J., Dickman, U., Bair, J., & Kuehne, M. (2025). Thermal characterization of suspended fine wires across continuum to free-molecular gas regimes using the $3\omega$ method. Physical Review Applied, 24, 064060.

@article{Peng-2025-PRA,
  title = {Thermal characterization of suspended fine wires
           across continuum to free-molecular gas regimes using the
           3\ensuremath{\omega} method},
  author = {Peng, Chuyue and Ginzburg, Joshua and Dickman, Uri and
            Bair, Jacob and Kuehne, Matthias},
  journal = {Phys. Rev. Appl.},
  volume = {24},
  issue = {6},
  pages = {064060},
  numpages = {13},
  year = {2025},
  month = {Dec},
  publisher = {American Physical Society},
  doi = {10.1103/72dg-6d56},
  url = {https://link.aps.org/doi/10.1103/72dg-6d56}
}