Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro
IntroductionComputational models are valuable tools for understanding and studying a wide range of characteristics and mechanisms of the brain. Furthermore, they can also be exploited to explore biological neural networks from neuronal cultures. However, few of the current in silico approaches consi...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Neuroinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fninf.2025.1549916/full |
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| author | Rachele Fabbri Rachele Fabbri Ermes Botte Ermes Botte Ermes Botte Arti Ahluwalia Arti Ahluwalia Arti Ahluwalia Chiara Magliaro Chiara Magliaro Chiara Magliaro |
| author_facet | Rachele Fabbri Rachele Fabbri Ermes Botte Ermes Botte Ermes Botte Arti Ahluwalia Arti Ahluwalia Arti Ahluwalia Chiara Magliaro Chiara Magliaro Chiara Magliaro |
| author_sort | Rachele Fabbri |
| collection | DOAJ |
| description | IntroductionComputational models are valuable tools for understanding and studying a wide range of characteristics and mechanisms of the brain. Furthermore, they can also be exploited to explore biological neural networks from neuronal cultures. However, few of the current in silico approaches consider the energetic demand of neurons to sustain their electrophysiological functions, specifically their well-known oxygen-dependent firing.MethodsIn this work, we introduce Digitoids, a computational platform which integrates a Hodgkin-Huxley-like model to describe the time-dependent oscillations of the neuronal membrane potential with oxygen dynamics in the culture environment. In Digitoids, neurons are connected to each other according to Small-World topologies observed in cell cultures, and oxygen consumption by cells is modeled as limited by diffusion through the culture medium. The oxygen consumed is used to fuel their basal metabolism and the activity of Na+-K+-ATP membrane pumps, thus it modulates neuronal firing.ResultsOur simulations show that the characteristics of neuronal firing predicted throughout the network are related to oxygen availability. In addition, the average firing rate predicted by Digitoids is statistically similar to that measured in neuronal networks in vitro, further proving the relevance of this platform.DicussionDigitoids paves the way for a new generation of in silico models of neuronal networks, establishing the oxygen dependence of electrophysiological dynamics as a fundamental requirement to improve their physiological relevance. |
| format | Article |
| id | doaj-art-dc1c10b51b964e8baaada00bd87a08aa |
| institution | Matheson Library |
| issn | 1662-5196 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj-art-dc1c10b51b964e8baaada00bd87a08aa2025-07-01T05:28:09ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962025-07-011910.3389/fninf.2025.15499161549916Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitroRachele Fabbri0Rachele Fabbri1Ermes Botte2Ermes Botte3Ermes Botte4Arti Ahluwalia5Arti Ahluwalia6Arti Ahluwalia7Chiara Magliaro8Chiara Magliaro9Chiara Magliaro10Research Center “E. Piaggio”, University of Pisa, Pisa, ItalyDepartment of Information Engineering (DII), University of Pisa, Pisa, ItalyResearch Center “E. Piaggio”, University of Pisa, Pisa, ItalyDepartment of Information Engineering (DII), University of Pisa, Pisa, ItalyInteruniversity Center for the Promotion of 3R Principles in Teaching and Research (Centro 3R), Pisa, ItalyResearch Center “E. Piaggio”, University of Pisa, Pisa, ItalyDepartment of Information Engineering (DII), University of Pisa, Pisa, ItalyInteruniversity Center for the Promotion of 3R Principles in Teaching and Research (Centro 3R), Pisa, ItalyResearch Center “E. Piaggio”, University of Pisa, Pisa, ItalyDepartment of Information Engineering (DII), University of Pisa, Pisa, ItalyInteruniversity Center for the Promotion of 3R Principles in Teaching and Research (Centro 3R), Pisa, ItalyIntroductionComputational models are valuable tools for understanding and studying a wide range of characteristics and mechanisms of the brain. Furthermore, they can also be exploited to explore biological neural networks from neuronal cultures. However, few of the current in silico approaches consider the energetic demand of neurons to sustain their electrophysiological functions, specifically their well-known oxygen-dependent firing.MethodsIn this work, we introduce Digitoids, a computational platform which integrates a Hodgkin-Huxley-like model to describe the time-dependent oscillations of the neuronal membrane potential with oxygen dynamics in the culture environment. In Digitoids, neurons are connected to each other according to Small-World topologies observed in cell cultures, and oxygen consumption by cells is modeled as limited by diffusion through the culture medium. The oxygen consumed is used to fuel their basal metabolism and the activity of Na+-K+-ATP membrane pumps, thus it modulates neuronal firing.ResultsOur simulations show that the characteristics of neuronal firing predicted throughout the network are related to oxygen availability. In addition, the average firing rate predicted by Digitoids is statistically similar to that measured in neuronal networks in vitro, further proving the relevance of this platform.DicussionDigitoids paves the way for a new generation of in silico models of neuronal networks, establishing the oxygen dependence of electrophysiological dynamics as a fundamental requirement to improve their physiological relevance.https://www.frontiersin.org/articles/10.3389/fninf.2025.1549916/fullin silico modelingneuron firingoxygen metabolismin vitro neuronal networkdigitalized neuronal network |
| spellingShingle | Rachele Fabbri Rachele Fabbri Ermes Botte Ermes Botte Ermes Botte Arti Ahluwalia Arti Ahluwalia Arti Ahluwalia Chiara Magliaro Chiara Magliaro Chiara Magliaro Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro Frontiers in Neuroinformatics in silico modeling neuron firing oxygen metabolism in vitro neuronal network digitalized neuronal network |
| title | Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro |
| title_full | Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro |
| title_fullStr | Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro |
| title_full_unstemmed | Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro |
| title_short | Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons in vitro |
| title_sort | digitoids a novel computational platform for mimicking oxygen dependent firing of neurons in vitro |
| topic | in silico modeling neuron firing oxygen metabolism in vitro neuronal network digitalized neuronal network |
| url | https://www.frontiersin.org/articles/10.3389/fninf.2025.1549916/full |
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