Journal of Computational Neuroscience最新文献

{"title":"Rhythm generation, robustness, and control in stick insect locomotion: modeling and analysis.","authors":"Zahra Aminzare, Jonathan E Rubin","doi":"10.1007/s10827-025-00913-6","DOIUrl":"https://doi.org/10.1007/s10827-025-00913-6","url":null,"abstract":"<p><p>Stick insect stepping patterns have been studied for insights about locomotor rhythm generation and control, because the underlying neural system is relatively accessible experimentally and produces a variety of rhythmic outputs. Harnessing the experimental identification of effective interactions among neuronal units involved in stick insect stepping pattern generation, previous studies proposed computational models simulating aspects of stick insect locomotor activity. While these models generate diverse stepping patterns and transitions between them, there has not been an in-depth analysis of the mechanisms underlying their dynamics. In this study, we focus on modeling rhythm generation by the neurons associated with the protraction-retraction, levation-depression, and extension-flexion antagonistic muscle pairs of the mesothoracic (middle) leg of stick insects. Our model features a reduced central pattern generator (CPG) circuit for each joint and includes synaptic interactions among the CPGs; we also consider extensions such as the inclusion of motoneuron pools controlled by the CPG components. The resulting network is described by an 18-dimensional system of ordinary differential equations. We use fast-slow decomposition, projection into interacting phase planes, and a heavy reliance on input-dependent nullclines to analyze this model. Specifically, we identify and eludicate dynamic mechanisms capable of generating a stepping rhythm, with a sequence of biologically constrained phase relationships, in a three-joint stick insect limb model. Furthermore, we explain the robustness to parameter changes and tunability of these patterns. In particular, the model allows us to identify possible mechanisms by which neuromodulatory and top-down effects could tune stepping pattern output frequency.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential temporal filtering in the fly optic lobe.","authors":"Alexander Borst","doi":"10.1007/s10827-025-00914-5","DOIUrl":"https://doi.org/10.1007/s10827-025-00914-5","url":null,"abstract":"<p><p>Visual interneurons come in many different flavors, representing luminance changes at one location as ON or OFF signals with different dynamics, ranging from purely sustained to sharply transient responses. While the functional relevance of this representation for subsequent computations like direction-selective motion detection is well understood, the mechanisms by which these differences in dynamics arise are unclear. Here, I study this question in the fly optic lobe. Taking advantage of the known connectome I simulate a network of five adjacent optical columns each comprising 65 different cell types. Each neuron is modeled as an electrically compact single compartment, conductance-based element that receives input from other neurons within its column and from its neighboring columns according to the intra- and inter-columnar connectivity matrix. The sign of the input is determined according to the known transmitter type of the presynaptic neuron and the receptor on the postsynaptic side. In addition, some of the neurons are given voltage-dependent conductances known from the fly transcriptome. As free parameters, each neuron has an input and an output gain, applied to all its input and output synapses, respectively. The parameters are adjusted such that the spatio-temporal receptive field properties of 13 out of the 65 simulated neurons match the experimentally determined ones as closely as possible. Despite the fact that all neurons have identical leak conductance and membrane capacitance, this procedure leads to a surprisingly good fit to the data, where specific neurons respond transiently while others respond in a sustained way to luminance changes. This fit critically depends on the presence of an H-current in some of the first-order interneurons, i.e., lamina cells L1 and L2: turning off the H-current eliminates the transient response nature of many neurons leaving only sustained responses in all of the examined interneurons. I conclude that the diverse dynamic response behavior of the columnar neurons in the fly optic lobe starts in the lamina and is created by their different intrinsic membrane properties. I predict that eliminating the hyperpolarization-activated current by RNAi should strongly affect the dynamics of many medulla neurons and, consequently, also higher-order functions depending on them like direction-selectivity in T4 and T5 neurons.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-scale model of neural entrainment by transcranial alternating current stimulation in realistic cortical anatomy.","authors":"Xuelin Huang, Xile Wei, Jiang Wang, Guosheng Yi","doi":"10.1007/s10827-025-00912-7","DOIUrl":"https://doi.org/10.1007/s10827-025-00912-7","url":null,"abstract":"<p><p>Transcranial alternating current stimulation (tACS) enables non-invasive modulation of brain activity, holding promise for cognitive research and clinical applications. However, it remains unclear how the spiking activity of cortical neurons is modulated by specific electric field (E-field) distributions. Here, we use a multi-scale computational framework that integrates an anatomically accurate head model with morphologically realistic neuron models to simulate the responses of layer 5 pyramidal cells (L5 PCs) to the E-fields generated by conventional M1-SO tACS. Neural entrainment is quantified by calculating the phase-locking value (PLV) and preferred phase (PPh). We find that the tACS-induced E-field distributions across the L5 surface of interest (SOI) are heterogeneous, resulting in diverse neural entrainment of L5 PCs due to their sensitivities to the direction and intensity of the E-fields. Both PLV and PPh follow a smooth cosine dependency on the E-field polar angle, with minimal sensitivity to the azimuthal angle. PLV exhibits a positive linear dependence on the E-field intensity. However, PPh either increases or decreases logarithmically with E-field intensity that depends on the E-field direction. Correlation analysis reveals that neural entrainment can be largely explained by the normal component of the E-field or by somatic polarization, especially for E-field directed outward relative to the cortical surface. Moreover, cell morphology plays a crucial role in shaping the diverse neural entrainment to tACS. Although the uniform E-field extracted at the soma provides a good approximation for modeling tACS at the cellular level, the non-uniform E-field distribution should be considered for investigating more accurate cellular mechanisms of tACS. These findings highlight the crucial roles of heterogeneous E-field distributions, cell morphology, and E-field non-uniformity in modulating neuronal spiking activity by tACS in realistic neuroanatomy, deepening our understanding of the cellular mechanism underlying tACS. Our work bridges macroscopic brain stimulation with microscopic neural activity, which benefits the development of brain models and derived clinical applications relying on model-driven brain stimulation with tACS-induced weak E-fields.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Do the receptive fields in the primary visual cortex span a variability over the degree of elongation of the receptive fields?","authors":"Tony Lindeberg","doi":"10.1007/s10827-025-00907-4","DOIUrl":"10.1007/s10827-025-00907-4","url":null,"abstract":"<p><p>This paper presents the results of combining (i) theoretical analysis regarding connections between the orientation selectivity and the elongation of receptive fields for the affine Gaussian derivative model with (ii) biological measurements of orientation selectivity in the primary visual cortex to investigate if (iii) the receptive fields can be regarded as spanning a variability in the degree of elongation. From an in-depth theoretical analysis of idealized models for the receptive fields of simple and complex cells in the primary visual cortex, we established that the orientation selectivity becomes more narrow with increasing elongation of the receptive fields. Combined with previously established biological results, concerning broad vs. sharp orientation tuning of visual neurons in the primary visual cortex, as well as previous experimental results concerning distributions of the resultant of the orientation selectivity curves for simple and complex cells, we show that these results are consistent with the receptive fields spanning a variability over the degree of elongation of the receptive fields. We also show that our principled theoretical model for visual receptive fields leads to qualitatively similar types of deviations from a uniform histogram of the resultant descriptor of the orientation selectivity curves for simple cells, as can be observed in the results from biological experiments. To firmly investigate the validity of the underlying working hypothesis, we finally formulate a set of testable predictions for biological experiments, to characterize the predicted systematic variability in the elongation over the orientation maps in higher mammals, and its relations to the pinwheel structure.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"397-417"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A solvable neural circuit model revealing the dynamical principle of non-optimal temporal weighting in perceptual decision making.","authors":"Xuewen Shen, Fangting Li, Bin Min","doi":"10.1007/s10827-025-00910-9","DOIUrl":"10.1007/s10827-025-00910-9","url":null,"abstract":"<p><p>Understanding the mechanism of accumulating evidence over time in deliberate decision-making is crucial for both humans and animals. While numerous models have been proposed over the past few decades to characterize the temporal weighting of evidence, the dynamical principle governing the neural circuits in decision making remain elusive. In this study, we proposed a solvable rank-1 neural circuit model to address this problem. We first derived an analytical expression for integration kernel, a key quantity describing how sensory evidence at different time points is weighted with respect to the final decision. Based on this expression, we illustrated that how the dynamics introduced in the auxiliary space-namely, a subspace orthogonal to the decision variable-modulates the flow fields of decision variable through a gain modulation mechanism, resulting in a variety of integration kernel types, including not only monotonic ones (recency and primacy) but also non-monotonic ones (convex and concave). Furthermore, we quantitatively validated that integration kernel shapes can be understood from dynamical landscapes and non-monotonic temporal weighting reflects topological transitions in the landscape. Additionally, we showed that training on networks with non-optimal weighting leads to convergence toward optimal weighting. Finally, we demonstrate that rank-1 connectivity induces symmetric competition to generate pitchfork bifurcation. In summary, we present a solvable neural circuit model that unifies diverse types of temporal weighting, providing an intriguing link between non-monotonic integration kernel structure and topological transitions of dynamical landscape.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"441-458"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling characteristics of neuronal firing in the thalamocortical network of connections in control and parkinsonian primates.","authors":"Carly Ferrell, Qile Jiang, Margaret Olivia Leu, Thomas Wichmann, Michael Caiola","doi":"10.1007/s10827-025-00909-2","DOIUrl":"10.1007/s10827-025-00909-2","url":null,"abstract":"<p><p>According to current anatomical models, motor cortical areas, the basal ganglia, and the ventral motor thalamus form partially closed (re-entrant) loop structures. The normal patterning of neuronal activity within this network regulates aspects of movement planning and execution, while abnormal firing patterns can contribute to movement impairments, such as those seen in Parkinson's disease. Most previous research on such firing pattern abnormalities has focused on parkinsonism-associated changes in the basal ganglia, demonstrating, among other abnormalities, prominent changes in firing rates, as well as the emergence of synchronized beta-band oscillatory burst patterns. In contrast, abnormalities of neuronal activity in the thalamus and cortex are less explored. However, recent studies have shown both changes in thalamocortical connectivity and anatomical changes in corticothalamic terminals in Parkinson's disease. To explore these changes, we created a computational framework to model the effects of changes in thalamocortical connections as they may occur when an individual transitions from the healthy to the parkinsonian state. A 5-dimensional average neuronal firing rate model was fitted to replicate neuronal firing rate information recorded in healthy and parkinsonian primates. The study focused on the effects of (1) changes in synaptic weights of the reciprocal projections between cortical neurons and thalamic principal neurons, and (2) changes in synaptic weights of the cortical projection to thalamic interneurons. We found that it is possible to force the system to change from a healthy to a parkinsonian state, including the emergent oscillatory activity, by only adjusting these two sets of synaptic weights. Thus, this study demonstrates that small changes in the afferent and efferent connections of thalamic neurons could contribute to the emergence of network-wide firing patterns that are characteristic for the parkinsonian state.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"419-439"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simplified model of NMDA-receptor-mediated dynamics in leaky integrate-and-fire neurons.","authors":"Jan-Eirik Welle Skaar, Nicolai Haug, Hans Ekkehard Plesser","doi":"10.1007/s10827-025-00911-8","DOIUrl":"10.1007/s10827-025-00911-8","url":null,"abstract":"<p><p>A model for NMDA-receptor-mediated synaptic currents in leaky integrate-and-fire neurons, first proposed by Wang (J Neurosci, 1999), has been widely studied in computational neuroscience. The model features a fast rise in the NMDA conductance upon spikes in a pre-synaptic neuron followed by a slow decay. In a general implementation of this model which allows for arbitrary network connectivity and delay distributions, the summed NMDA current from all neurons in a pre-synaptic population cannot be simulated in aggregated form. Simulating each synapse separately is prohibitively slow for all but small networks, which has largely limited the use of the model to fully connected networks with identical delays, for which an efficient simulation scheme exists. We propose an approximation to the original model that can be efficiently simulated for arbitrary network connectivity and delay distributions. Our results demonstrate that the approximation incurs minimal error and preserves network dynamics. We further use the approximate model to explore binary decision making in sparsely coupled networks.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"475-487"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12417261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An attention-based fuzzy CNN-LTSM network for visual object recognition from fMRI images.","authors":"Tangsen Huang, Xiangdong Yin, Ensong Jiang","doi":"10.1007/s10827-025-00905-6","DOIUrl":"10.1007/s10827-025-00905-6","url":null,"abstract":"","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"459-473"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144785977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating computational neuroscience into Africa's academic curriculum: Challenges, opportunities, and strategic implementation.","authors":"Ibeachu P Chinagorom, Peter Oseghale Ohue","doi":"10.1007/s10827-025-00906-5","DOIUrl":"10.1007/s10827-025-00906-5","url":null,"abstract":"<p><p>Computational Neuroscience (CN) is an interdisciplinary field that combines neuroscience, mathematics, artificial intelligence, theoretical models and experimental data to understand how the brain works. It unravels the intricacies of the nervous system contributing significantly to cognitive science, neuroengineering and machine learning. CN importance in artificial intelligence and medical research remains underrepresented in Africa's academic landscape. This paper explores the current state of CN in Africa, the challenges hindering its integration, the emerging opportunities, and the evidence-based strategies for curriculum implementation. Capacity building, interdisciplinary collaboration, open science, theoretical neuroscience, development of local capacity, and leveraging international partnerships are emphasized.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"393-395"},"PeriodicalIF":2.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling traveling calcium waves in cellular structures.","authors":"Patrick A Shoemaker, Bo M B Bekkouche","doi":"10.1007/s10827-025-00898-2","DOIUrl":"10.1007/s10827-025-00898-2","url":null,"abstract":"<p><p>We report a parametric simulation study of traveling calcium waves in two classes of cellular structures: dendrite-like processes and an idealized cell body. It is motivated by the hypothesis that calcium waves may participate in spatiotemporal sensory processing; accordingly, its objective is to elucidate the dependence of traveling wave characteristics (e.g., propagation speed and amplitude) on various anatomical and physiological parameters. The models include representations of inositol trisphosphate and ryanodine receptors (which mediate transient calcium entry into the cytoplasm from the endoplasmic reticulum), as well as other entities involved in calcium transport or reactions. These support traveling cytoplasmic calcium waves, which are fully regenerative for significant ranges of model parameters. We also observe Hopf bifurcations between stable and unstable regimes, the latter being characterized by periodic calcium spikes. Traveling waves are possible in unstable processes during phases with sufficiently high calcium levels in the endoplasmic reticulum. Damped and abortive waves are observed for some parameter values. When both receptor types are present and functional, we find wave speeds on the order of 100 to several hundred micrometers per second and cytosolic calcium transients with amplitudes of tens of micromolar; when ryanodine receptors are absent, these values are on the order of tens of micrometers per second and 1-6 micromolar. Even with significantly downgraded channel conductance, ryanodine receptors can significantly impact wave speeds and amplitudes. Receptor areal densities and the diffusion coefficient for cytoplasmic calcium are the parameters to which wave characteristics are most sensitive.</p>","PeriodicalId":54857,"journal":{"name":"Journal of Computational Neuroscience","volume":" ","pages":"219-245"},"PeriodicalIF":1.5,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}