Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits

Scaffolds and patterned substrates are among the most successful strategies to dictate the connectivity between neurons in culture. Here, we used numerical simulations to investigate the capacity of physical obstacles placed on a flat substrate to shape structural connectivity, and in turn collectiv...

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Main Authors: Adriaan-Alexander Ludl, Jordi Soriano
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-08-01
Series:Frontiers in Computational Neuroscience
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fncom.2020.00077/full
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spelling doaj-60cd876b21894103ab21823e216b65ff2020-11-25T03:55:13ZengFrontiers Media S.A.Frontiers in Computational Neuroscience1662-51882020-08-011410.3389/fncom.2020.00077557191Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal CircuitsAdriaan-Alexander Ludl0Adriaan-Alexander Ludl1Adriaan-Alexander Ludl2Jordi Soriano3Jordi Soriano4Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, NorwayDepartament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, SpainUniversitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, SpainDepartament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, SpainUniversitat de Barcelona Institute of Complex Systems (UBICS), Barcelona, SpainScaffolds and patterned substrates are among the most successful strategies to dictate the connectivity between neurons in culture. Here, we used numerical simulations to investigate the capacity of physical obstacles placed on a flat substrate to shape structural connectivity, and in turn collective dynamics and effective connectivity, in biologically-realistic neuronal networks. We considered μ-sized obstacles placed in mm-sized networks. Three main obstacle shapes were explored, namely crosses, circles and triangles of isosceles profile. They occupied either a small area fraction of the substrate or populated it entirely in a periodic manner. From the point of view of structure, all obstacles promoted short length-scale connections, shifted the in- and out-degree distributions toward lower values, and increased the modularity of the networks. The capacity of obstacles to shape distinct structural traits depended on their density and the ratio between axonal length and substrate diameter. For high densities, different features were triggered depending on obstacle shape, with crosses trapping axons in their vicinity and triangles funneling axons along the reverse direction of their tip. From the point of view of dynamics, obstacles reduced the capacity of networks to spontaneously activate, with triangles in turn strongly dictating the direction of activity propagation. Effective connectivity networks, inferred using transfer entropy, exhibited distinct modular traits, indicating that the presence of obstacles facilitated the formation of local effective microcircuits. Our study illustrates the potential of physical constraints to shape structural blueprints and remodel collective activity, and may guide investigations aimed at mimicking organizational traits of biological neuronal circuits.https://www.frontiersin.org/article/10.3389/fncom.2020.00077/fullnetwork formationsimulationspatterned networksstructural connectivityeffective connectivitynetwork bursts
collection DOAJ
language English
format Article
sources DOAJ
author Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Jordi Soriano
Jordi Soriano
spellingShingle Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Jordi Soriano
Jordi Soriano
Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
Frontiers in Computational Neuroscience
network formation
simulations
patterned networks
structural connectivity
effective connectivity
network bursts
author_facet Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Adriaan-Alexander Ludl
Jordi Soriano
Jordi Soriano
author_sort Adriaan-Alexander Ludl
title Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
title_short Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
title_full Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
title_fullStr Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
title_full_unstemmed Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits
title_sort impact of physical obstacles on the structural and effective connectivity of in silico neuronal circuits
publisher Frontiers Media S.A.
series Frontiers in Computational Neuroscience
issn 1662-5188
publishDate 2020-08-01
description Scaffolds and patterned substrates are among the most successful strategies to dictate the connectivity between neurons in culture. Here, we used numerical simulations to investigate the capacity of physical obstacles placed on a flat substrate to shape structural connectivity, and in turn collective dynamics and effective connectivity, in biologically-realistic neuronal networks. We considered μ-sized obstacles placed in mm-sized networks. Three main obstacle shapes were explored, namely crosses, circles and triangles of isosceles profile. They occupied either a small area fraction of the substrate or populated it entirely in a periodic manner. From the point of view of structure, all obstacles promoted short length-scale connections, shifted the in- and out-degree distributions toward lower values, and increased the modularity of the networks. The capacity of obstacles to shape distinct structural traits depended on their density and the ratio between axonal length and substrate diameter. For high densities, different features were triggered depending on obstacle shape, with crosses trapping axons in their vicinity and triangles funneling axons along the reverse direction of their tip. From the point of view of dynamics, obstacles reduced the capacity of networks to spontaneously activate, with triangles in turn strongly dictating the direction of activity propagation. Effective connectivity networks, inferred using transfer entropy, exhibited distinct modular traits, indicating that the presence of obstacles facilitated the formation of local effective microcircuits. Our study illustrates the potential of physical constraints to shape structural blueprints and remodel collective activity, and may guide investigations aimed at mimicking organizational traits of biological neuronal circuits.
topic network formation
simulations
patterned networks
structural connectivity
effective connectivity
network bursts
url https://www.frontiersin.org/article/10.3389/fncom.2020.00077/full
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