[HTML][HTML] Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex

SA Neymotin, RA McDougal, AS Bulanova, M Zeki… - Neuroscience, 2016 - Elsevier
Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms,
without attention to the complex array of molecular events that also control cell excitability …

Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics

M Abdellah, A Foni, E Zisis, NR Guerrero… - …, 2021 - academic.oup.com
Motivation Astrocytes, the most abundant glial cells in the mammalian brain, have an
instrumental role in developing neuronal circuits. They contribute to the physical structuring …

Multitarget multiscale simulation for pharmacological treatment of dystonia in motor cortex

SA Neymotin, S Dura-Bernal, P Lakatos… - Frontiers in …, 2016 - frontiersin.org
A large number of physiomic pathologies can produce hyperexcitability in cortex. Depending
on severity, cortical hyperexcitability may manifest clinically as a hyperkinetic movement …

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

M Abdellah, JJG Cantero, NR Guerrero… - Briefings in …, 2023 - academic.oup.com
Ultraliser is a neuroscience-specific software framework capable of creating accurate and
biologically realistic 3D models of complex neuroscientific structures at intracellular (eg …

Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model

SA Neymotin, RA McDougal, MA Sherif, CP Fall… - Neural …, 2015 - direct.mit.edu
Calcium () waves provide a complement to neuronal electrical signaling, forming a key part
of a neuron's second messenger system. We developed a reaction-diffusion model of an …

Generating neuron geometries for detailed three-dimensional simulations using anamorph

K Mörschel, M Breit, G Queisser - Neuroinformatics, 2017 - Springer
Generating realistic and complex computational domains for numerical simulations is often a
challenging task. In neuroscientific research, more and more one-dimensional morphology …

3D-printer visualization of neuron models

RA McDougal, GM Shepherd - Frontiers in neuroinformatics, 2015 - frontiersin.org
Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal
diversity, researchers have three-dimensionally traced tens of thousands of neurons; many …

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling

M Abdellah, A Foni, JJG Cantero… - Briefings in …, 2024 - academic.oup.com
Understanding the intracellular dynamics of brain cells entails performing three-dimensional
molecular simulations incorporating ultrastructural models that can capture cellular …

Modeling neurons in 3d at the nanoscale

W Chen, I Hepburn, A Martyushev… - … Modelling of the Brain …, 2022 - Springer
For decades, neurons have been modeled by methods developed by early pioneers in the
field such as Rall, Hodgkin and Huxley, as cable-like morphological structures with voltage …

Robust quasi-uniform surface meshing of neuronal morphology using line skeleton-based progressive convolution approximation

X Zhu, X Liu, S Liu, Y Shen, L You… - Frontiers in …, 2022 - frontiersin.org
Creating high-quality polygonal meshes which represent the membrane surface of neurons
for both visualization and numerical simulation purposes is an important yet nontrivial task …