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Journal of Computational Neuroscience

Springer Science and Business Media LLC

Preprints posted in the last 90 days, ranked by how well they match Journal of Computational Neuroscience's content profile, based on 29 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit.

1
An Analytical Description for Action Potential Thresholds Defined by Concavity Changes

Herrera-Valdez, M. A.

2026-04-24 neuroscience 10.64898/2026.04.21.719992 medRxiv
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A novel mathematical framework to define the threshold of action potentials in excitable cells is presented. Unlike previously applied methods that rely on approximations or specific fixed-point bifurcations, the approach focuses on the geometry of membrane potential trajectories. Specifically, the focus is on the concavity changes during the upstroke of an electrical pulse. These changes in concavity form a curve of inflection points that defines a region in phase space crossed by all the action potentials in the system, and containing no non-action potential trajectories. Such region is called the excitability region and its size can be measured, thus providing a measure for the excitability of a dynamical system, and a way to compare the excitability between systems representing different biological phenotypes and stimulus conditions. The work transforms the traditionally vague physiological concept of excitability into a rigorous analytical description applicable across continuous, single compartment models of electrical excitability.

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Membrane voltage multistability in coupled glial cells

Janjic, P.; Solev, D.; Zhou, M.; Kocarev, L.

2026-05-06 neuroscience 10.64898/2026.05.03.722503 medRxiv
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Growing interest to describe the electrical behavior of glial cells, mainly astrocytes, in intact brain tissue poses more and more challenges to commonly accepted belief they only respond in a linear manner in uptake of the excess of extracellular potassium and maintenance of their network equipotentiality. Their highly conductive mutual interconnections via gap junction (GJ) connections introduce yet another class of nonlinear elements. As more studies report nonlinearities in membrane voltage Vm dependence of both, the membrane and junctional conductances, the need to formulate minimal dynamical models of their transient behavior is getting more acute. Since ODE models of coupled cells, even in simplest 1-d arrays, require simplified descriptions and small set of parameters, rare quantitative studies on glia makes the task even more difficult. This study attempts to qualify a self-coupled cell, or a glial cell coupled to fixed voltage as useful system for detecting the nature of instabilities and transitions coming from coupling. In a novel biophysical model of coupled astrocyte, we introduce nonlinear kinetics of deactivation for large junctional voltages for the first time. We found that N-shaped nonlinearities and corresponding fold structure in the vector field of isolated cell serves as a baseline on top of which coupling nonlinearities enrich the bifurcation picture. Numerical simulations of 1-d array of coupled astrocytes show that coupling increases the propensity of astrocytic Vm to bistability and front propagation. We believe that presented illustrations of possible effects of coupling nonlinearities will motivate neurobiologists to further explore their impact in disease. Significance statementTransient changes in membrane voltage of glial cells may produce significant transient voltage difference between directly coupled cells. Nonlinear steady-state conductance of their interconnection elements, the gap junctions, introduce nonlinear current profiles which are very difficult to measure and quantitate using the available methods due to marked permeability of the junctions and leakiness of glial membrane in general. We propose a minimal model of glial membrane extended with a self-coupled feedback loop, which under realistic simplifying assumptions could serve for qualitative analysis of the impact of coupling, on the stability of resting membrane voltage. Neuronal cells of the brain and spinal cord cannot exist and function without supportive and neuromodulatory functions of the diverse population of glial cells. This applies to virtually all physiological processes on cell level - from cell development, metabolic support, membrane signaling, slow molecular signal transduction, ion homeostasis, neurovascular coupling, myelination, to mention only a few, manifest neuro-glial interaction. Even though all glial cell types are interconnected, the most abundant ones, the astrocytes are massively interconnected by gap junctions to form ordered networks. Electrically, astrocytic networks display membrane voltage equipotentiality, which is considered system-wide resting state for given neuro-glial circuit or unit. With molecular and cellular substrates of glial connectivity being slowly elucidated, network science and dynamical modeling are slowly "invading" that area with many important issues left open. In this study using classical dynamical systems approaches we give indications how nonlinear intercellular coupling between astrocytes affects physiological resting state and its instabilities compared to isolated, uncoupled cell. We strongly believe the suggested minimal model could fill the gap in ODE modeling of neuro-glial circuits, within broadest scope of hypothesis-driven research in cell-level neuroscience.

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An astro-neural-field model with application to cortical spreading depolarization

Baspinar, E.; Avitabile, D.; Nouveau, C.; Desroches, M.; Campillo, F.; Mantegazza, M.

2026-06-12 neuroscience 10.64898/2026.06.10.731347 medRxiv
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We present a novel astro-neural-field population model with application to migraine-related cortical spreading depolarization. The model is composed of four spatio-temporal state variables: excitatory and inhibitory membrane potentials, astrocytic potassium uptake recruitment, and extracellular potassium concentration. Extending a previous neural field model, we incorporate activity-dependent astrocytic potassium clearance via a nonlinear term coupled to astrocyte dynamics. The astrocyte transfer function, like its neural counterpart, exhibits three regimes governed by extracellular potassium, capturing its effect on clearance. This yields a more comprehensive framework, better fits experimental data, and provides new insights into the mechanisms of cortical spreading depolarization.

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Inter-hemispheric connections modulate splitting in a computational model of the bilateral SCN

Zemlianova, K.; McDaniel, J.; Lander, A. G.; Nwaezeapu, J.; Gutierrez, G. J.

2026-05-05 neuroscience 10.64898/2026.04.30.722022 medRxiv
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The phenomenon of splitting was originally observed in hamsters which, after prolonged exposure to constant light, exhibit two rest/wake cycles within a subjective day. Splitting is a consequence of the left and right suprachiasmatic nuclei (SCN) falling out of synchrony. While it is known that split activity is characterized by an antiphase relationship between the left and right SCN and between the core and shell within each hemisphere, the role of the commissural projections that connect the right and left SCN is not known. In the present study, we investigate the impact of the inter-hemispheric connections on the split and unsplit dynamics of a computational model of the bilateral SCN. Our model has 4 nodes corresponding to each right and left core and shell. We simulated our bilateral model under different lighting conditions and measured its period and the phase relationships among the 4 nodes. To further characterize the dynamics of the system, we performed a bifurcation analysis. We found that the bilateral model automatically splits unless entrained by bright light/dark cycles, or unless it has excitatory inter-hemispheric connections. This suggests that excitatory cross-connections may be important for freerunning behavior. We found that constant light of varying intensities transitions the model between split and unsplit activity only in very limited conditions, but the strength and polarity of the contralateral connections play a much greater role in this dynamical transition. These findings suggest that splitting may involve plasticity of the inter-hemispheric connections of the SCN.

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Awake alpha bursting emerges as the dynamic working state in a lateral geniculate thalamocortical cell model

McGahan, K.; McCarthy, M.; Kopell, N.

2026-06-11 neuroscience 10.64898/2026.06.08.730831 medRxiv
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The awake thalamus is known to be able to filter primary sensory input with and without external modulation. Through the construction and analysis of a novel computational model of a lateral geniculate thalamocortical neuron, we demonstrate how the processing of sensory retinal input is influenced by the underlying thalamic dynamic state. Our model, using only currents verified against expression data from publicly available datasets, is the first to produce five experimentally established distinct dynamic firing regimes. We demonstrate that the thalamocortical cell transitions between these dynamic states in response to glutamatergic signals from the cortex or cholinergic arousal signals coming from the brainstem. We focus on signal processing in the model dynamic states associated with the awake thalamic alpha rhythm where we find that the ability of retinal inputs to generate thalamic spikes is a balance between the timing of retinal spikes, the excitability break imposed by the M-current, and the decay time of the L-type calcium current. Finally, we explore how these two currents help the thalamus process extra-retinal rhythmic inputs, showing the model produces entrainment to slower inhibitory and excitatory rhythms, as well as detailing the importance of nesting faster frequency rhythms within slow cycles for successful thalamic transmission. Our results suggest that the awake alpha rhythm is indirectly causal by acting as a marker for the interaction of these two currents. This biophysically-constrained lateral geniculate thalamocortical cell model generates predictions regarding rhythmic dynamics under different arousal states, thalamic control of retinogeniculate transmission, and the possible impacts neurological disorders, like schizophrenia, have on thalamic processing. Variations of this model could be used to explore the functions of higher order thalamic nuclei, thereby extending its use to investigating more complex cognitive processes. Author summaryThe thalamus generates multiple distinct brain rhythms, processes primary sensory inputs, and modulates its output using feedback signals. Previous computational models of the thalamus have typically focused on a subset of these three thalamic functions without drawing relationships among them. Here we present a novel computational thalamic cell model that unites these thalamic processes. We focus on the awake alpha rhythm, a well known thalamic oscillation, and show that it is a signature of a critical working state that enables the experimentally observed thalamic filtering of retinal signals. Additionally, we find this state is optimal for processing and passing non-sensory rhythmic signals. Our model generates testable predictions about which ionic currents control the transmission of external signals. It highlights the roles of two currents from our model that do not have specified functions in the awake thalamus in previous computational models. The work concludes with hypotheses about why neurological disorders that perturb the thalamus from this alpha rhythm working state lead to significant processing errors locally within the thalamus and globally within the brain.

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A flexible cross-correlation based population model of interaural time difference coding in barn owl's midbrain

Fischer, B. J.; Syeda, R. F.; Pena, J. L.

2026-05-01 neuroscience 10.64898/2026.04.29.721697 medRxiv
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The cross-correlation model has long served as the standard computational framework for describing interaural time difference (ITD) processing in the barn owls auditory system. While successful in explaining initial sinusoidal responses at the site of coincidence detection in the nucleus laminaris, this previous standard model fails to capture the full diversity of ITD tuning observed in the inferior colliculus (IC), where neurons exhibit sharper-than-sinusoidal ITD tuning, nonlinear frequency integration, level-dependent gain control, and interaural level difference (ILD)-dependent modulation of ITD selectivity. Here we present a modified cross-correlation model that addresses these limitations through the addition of parameterized gain control, linear filters with inhibitory surround structure, static nonlinearities, and ILD-dependent modulation of the cross-correlation computation. We show that divisive gain control produces realistic rate-level functions, including non-monotonic responses. Furthermore, inhibitory weights in the linear filter, combined with a threshold or expansive nonlinearity, generate sharper-than-sinusoidal ITD tuning consistent with experimental observations. This model reproduces both linear and nonlinear two-tone frequency integration and demonstrates that independent variation of filter bandwidth and nonlinearity shape accounts for the experimentally observed lack of correlation between side-peak suppression and frequency tuning width across the neuronal population. In addition, ILD-dependent modifications to the model produce shifts in best ITD and reductions in ITD tuning strength, as observed in the lateral shell of the central nucleus of the IC. The model parameters can be efficiently determined using simulation-based inference, enabling generation of realistic neuronal populations. Thus, this flexible, analytically tractable framework provides a foundation for investigating population coding of auditory space in the owls midbrain.

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Mostly-monocular responses and other visual functions in a multiscale network model of Macaque V1

Xiao, Z.-C.; Lin, K. K.; Young, L.-S.

2026-06-24 neuroscience 10.64898/2026.06.19.733440 medRxiv
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Visual signals from the two eyes merge gradually as they pass through the primary visual cortex (V1). Here we use a computational model of Macaque V1 to study the first stage of this integration along the magnocellular pathway, in layer 4C, aiming to infer neuroanatomical origins of binocular response. It is known that neurons in layer 4C are predominantly monocular, though some do exhibit varying degrees of binocularity. We find (1) the emergence of narrow binocular strips along borders of ocular dominance columns (ODC), a finding that aligns with experiments; (2) most consistent with data is when 10 - 30% of interactions near ODC boundaries are cross-columnar; and (3) feedback from layer 6 is largely monocular. These results were obtained through systematic hypothesis testing using a multiscale model that is orders of magnitude faster than its biologically-detailed predecessors. We propose that multiscale modeling can be an effective tool for bridging anatomy and function.

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The interplay between detection and localization in human vision

Coupette, F.; Brainard, D. H.; Smithson, H. E.; Read, D. J.

2026-07-10 neuroscience 10.64898/2026.07.06.736811 medRxiv
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Fixational eye movements (FEMs) comprise the involuntary small scale eye motion conducted during fixation on a stationary stimulus. As a consequence, the visual information can be spread across multiple photoreceptors reducing the local signal-to-noise ratio. Yet, the signals transmitted by individual photoreceptors adapt to constant stimulation so that an entirely still scene would eventually fade from view. Because FEMs convert a stationary stimulus in the world to a temporally varying one on the retina, they can act to prevent this stimulus fading. Thus, FEMs can be understood as a sampling protocol than needs to be adjusted to the underlying processing circuitry. We analyse the impact of FEMs on the rate of information acquisition at the level of the retina for two common tasks of the human eye that typically go hand in hand: detection and localization. Here, we build a simple analytical model of visual perception, i.e. we subject a continuous receptor array to a stimulus moving across the retina as a consequence of FEMs with receptor excitations depending on past stimulation through a linear response function. Using Bayesian inference we quantify both the probability of detection and the accuracy of localization as a function of parameters controlling eye movements and stimulus. We find that localization of a stimulus is equivalent to the detection of the stimulus gradient. This allows us to discern optimal properties of eye movements for the respective tasks and provides a link between two typical psychophysical observables: detection thresholds and Vernier acuity. Our analysis suggests that typical human FEMs tend to facilitate localization at the expense of detection. Simply put, if you can see a stimulus you also know where it is. Finally, we propose a variety of experimental protocols to investigate the interplay between FEMs, detection, and localization with the potential of inferring intrinsic properties of an individuals visual system.

9
Geometric Kinematics of Human Eyes

Turski, J.

2026-05-10 neuroscience 10.64898/2026.04.10.716809 medRxiv
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In previous studies by the author on binocular vision with the asymmetric eye (AE), which models a healthy human eye with misaligned optical components, the results were primarily presented in the Rodrigues vector (RV) framework and supported by simulations and 3D visualizations in GeoGebras dynamic geometry environment. In this paper, the novel geometric kinematics of the human eye, that is, the eye with misaligned optics, and simplified assumptions about the eye rotations (the eyes translational movements are disregarded), are developed within the framework of rigid-body rotations. The originality of the analysis lies in a precise geometric decomposition of a full rotation of the eyes posture into a torsion-free rotation (the geodesic part) and a torsional rotation (the non-geodesic extension of the geodesic part). This decomposition is extended to the corresponding decomposition of the angular velocity. A novel derivation of the eyes angular velocity from the RV formulation of the eye kinematics is proposed.

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Modelling individual ampullary afferents in two species of gymnotiform fish using simulation-based inference

Mayer, S.; Benda, J.; Grewe, J.

2026-06-30 neuroscience 10.64898/2026.06.24.734418 medRxiv
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Ampullary electroreceptors are widespread across aquatic vertebrates. The purpose of sensing exogeneous electric fields is conserved across species but the implementations differ and the encoding mechanisms remain incompletely understood. We compared baseline and stimulus-driven response properties of ampullary electroreceptor afferents in the weakly electric fish Apteronotus leptorhynchus and Eigenmannia virescens. We find that their activity is well captured by an extended leaky integrate-and-fire model that generalizes across both species. The model shares similarities to a previous model of the tuberous electroreceptor afferents but further incorporates a low-pass pre-filtering and additional noise sources to reproduce the observed spectral response characteristics. The low-pass is essential to shape stimulus encoding in the high-frequency range. Accurate prediction of low-frequency stimulus encoding further requires two distinct noise sources: stimulus-independent white current noise and activity-dependent noise in the adaptation current, which is shaped by the adaptation time constant to yield effective pink noise dynamics. Using simulation-based inference, we trained a neural network to map model parameters to neuronal response features. This approach enables the generation of heterogeneous, biologically plausible model populations that may serve as a realistic input layer for studying neuronal processing on the next level. With this, we provide a unified and mechanistic model of ampullary electroreceptor encoding in these species and possibly beyond.

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Hill-Based Reformulation of the Hodgkin-Huxley Model for Interpretable Neuronal Excitability

Saab, B.; Fahs, J.; Daou, A.

2026-06-10 neuroscience 10.64898/2026.06.06.730614 medRxiv
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Conductance-based models of neuronal excitability depend critically on the mathematical form used to describe voltage-dependent ion channel gating. The classical Hodgkin-Huxley (HH) formalism employs empirically derived rate expressions fitted to squid giant axon data that are not readily transferable across cell types or interpretable in terms of measurable gating properties. Here we introduce a Hill-based reformulation of the HH model in which steady-state sodium and potassium activation curves and the sodium inactivation rate are recast using Hill-type sigmoidal functions, a biologically motivated family widely used to describe cooperative and saturating processes in enzyme kinetics, gene regulation, and receptor binding. Systematic benchmarking against four compact sigmoid alternatives demonstrates that Hill functions provide superior fits to the original HH-derived gating data across all three targets. The resulting hybrid model reproduced canonical spike waveforms and frequency-current behavior, preserving the broad input-output organization of the original model. Importantly, the reformulation linked specific gating parameters to firing regimes and spike features, revealing how shifts in activation, inactivation, and steepness can systematically reshape excitability phenotypes. By making the relationship between channel kinetics and neuronal output more transparent, this framework provides an interpretable route for adapting conductance-based models to cell-specific excitability and channel-dependent changes in neural function.

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A unified law for inhibitory control in active dendrites

HE, Y.; Huang, B.; Du, K.; Huang, T.; He, G.; Poirazi, P.

2026-05-19 neuroscience 10.64898/2026.05.15.725398 medRxiv
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Neuronal computation depends on the balance between excitation and inhibition, yet how this balance is implemented across the dendritic tree remains unclear. Classical views predict that inhibition should be most effective near the soma or along the path from excitation to output, but many interneuron subtypes preferentially target remote dendritic compartments. This apparent paradox is sharpened by active dendrites, where local NMDA spikes, calcium plateaus and backpropagating action potentials can make distal branches powerful contributors to somatic firing. Here we develop an analytical framework that extracts general principles of inhibition from biophysically detailed multi-compartment simulations. By reformulating the implicit voltage update of detailed neuron models as a matrix recursion, we derive exact voltage sensitivities to inhibitory synaptic perturbations. This leads to a unified {Phi}-a law: the somatic impact of inhibition factorizes into a global dendritic susceptibility term and a local synaptic perturbation term. Using this law to map inhibitory leverage and identify optimal inhibitory interventions, we show that active dendritic excitation can shift inhibitory hot zones from perisomatic regions toward distal or intermediate compartments. Across neocortical, hippocampal and striatal neuron models, the same response law explains convergent inhibitory strategies despite distinct cellular mechanisms. Our framework turns detailed numerical simulation into analytical theory, providing a general principle for how diverse dendritic inhibition controls active neurons.

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A continuum of asynchronous states in cerebral cortex networks, and how they determine responsiveness

Bassat, M.; Tesler, F.; Destexhe, A.

2026-05-09 neuroscience 10.64898/2026.05.06.723408 medRxiv
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The awake brain is known to display asynchronous (AS) states during periods of attention and arousal, but the responsiveness properties of such states remain unclear. Here, we investigate this question using computational models of spiking networks of excitatory and inhibitory neurons, mimicking recurrently-connected networks in layer 2/3 of the cerebral cortex. The networks can generate a continuum of AS states, but with different responsiveness characteristics. By using a mean-field model to infer the dynamic properties of the system, we find that there are two families of AS states, which we call "underdamped" (UD) and "overdamped" (OD). Responsiveness is maximised at the transition between OD and UD states, which identifies a "working point" that may present advantageous computational properties.

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From eye anatomy to navigation: a biologically accurate model of bees polarisation vision

Kolyfetis, G.; Gkanias, E.; Aliyam Veetil Zynudheen, A. A.; Jie, V. W.; Galizia, C. G.; Baird, E.; Webb, B.; Foster, J.

2026-06-03 neuroscience 10.64898/2026.06.01.729196 medRxiv
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Skylight polarisation patterns provide a critical navigational cue for many insects. Bees perceive these patterns through specialised ommatidia in the dorsal rim area of their compound eyes, enabling them to estimate the suns direction and navigate between food sources and the hive. Although polarisation-based navigation has been extensively studied behaviourally, computational models that link DRA anatomy with navigational performance are lacking. Here, we simulate polarisation vision in honeybees (Apis mellifera) and bumblebees (Bombus terrestris) using real sky polarisation images to capture biologically relevant skylight properties. Our biologically grounded simulation incorporates species-specific DRA anatomy, including ommatidial optical axis directions, photoreceptor receptive fields, and microvillar orientations. We evaluate navigational accuracy and consistency across sun elevations under two distinct, potentially complementary navigational models: the matched filter, which requires scanning across body orientations to identify the solar axis, and the vector-sum model, which generates instantaneous sun azimuth estimates from a single body orientation, making it independent of active scanning. Matched filter errors in estimating solar axis are below 5{degrees} across most sun elevations and in both species. Absolute errors in the vector-sum model are lower for honeybees than bumblebees (median [~]10{degrees} and [~]30{degrees}, respectively), reflecting differences in DRA anatomy, particularly viewing direction and microvillar arrangement. Both models allow stable course control across most sun elevations in both species, yet the matched filter, being limited to solar axis alignment, only enables positive or negative phototaxis. Overall, this work provides a mechanistic and comparative framework based on realistic DRA anatomy to study polarisation-based navigation, generating testable predictions for insect navigation under natural sky conditions. Author SummaryMany insects, including bees, navigate with the help of skylight polarisation patterns which hold information about the suns position even when it is not visible. Bees detect these patterns through the dorsal rim area (DRA) of their complex eyes. How differences in DRA anatomy between bee species translate into differences in navigational ability has remained unclear. Here, we built a biologically realistic simulation of polarisation vision in honeybees and bumblebees. We used real sky images to examine what polarisation information is available to each species. We then tested two models of sun position estimation based on the polarisation pattern: one that requires the bee to actively scan the sky, and one that generates an instantaneous estimate from a single body orientation. In both species, both models show that accurate sun position estimation and stable navigation are possible using just polarisation information under a wide range of sun elevations. Differences in navigational performance between honeybees and bumblebees arise because the two DRAs look at different parts of the sky. Our results provide a robust framework for understanding how DRA anatomy shapes polarisation-based navigation in bees.

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Using Disinhibition versus Direct Control in a Spiking Neural Model of Dopamine-Driven Reinforcement Learning

Sautto, R.; Cuperlier, N.; Manos, T.; Belkaid, M.

2026-05-26 neuroscience 10.64898/2026.05.22.727086 medRxiv
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Dopaminergic signalling is central to value learning and decision making. It has been observed that multiple pathways with different patterns of connectivity project to midbrain dopaminergic neurons, some involving direct excitatory projections while others involve disinhibition. However, the respective contributions of these patterns to dopamine control, and their computational and functional advantages remain unclear. In the current work we simulate and evaluate two fully spiking neural models of dopaminergic control, based either solely on disinhibition, or solely on direct inhibitory and excitatory projections. We compare these models in terms of their engineering properties, their resulting spiking profiles, and their ability to successfully acquire representations of expected value in a 3-armed bandit task. We find that both models are able to operate at an asynchronous-irregular firing regime, but that the firing profile of the direct integration model is less resilient to disruption and more sensitive to incoming signals. In addition, the disinhibition model performs better in the learning task. We conclude that while the direct model is more parsimonious, disinhibition-based control remains advantageous in the operational context. Our results have implications for the study of decision-making brain circuits as well as for the design of brain-inspired systems.

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Hindmarsh-Rose neuronal network with spike-timing-dependent plasticity demonstrates coordinated reset neuromodulation

Sharafi, S.; Gilmer, J.; Al Borno, M.; Uchida, T. K.

2026-06-01 neuroscience 10.64898/2026.05.27.728228 medRxiv
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Computational models of brain structures impacted by Parkinsons disease are useful for exploring potential therapies. We use the Hindmarsh-Rose neuronal model to simulate synchronized activity in the subthalamic nucleus, capturing key features of the pathological rhythms observed in Parkinsons disease using a relatively small network of 100 neurons. Our model incorporates unidirectional excitatory chemical synapses whose strengths evolve according to a spike-timing-dependent plasticity (STDP) rule. To account for inputs from unmodelled neurons, both uniformly distributed white noise and Poisson noise were explored. White noise produced a single stable state of synchronized neuronal activity whereas Poisson noise resulted in two stable states, one synchronized and one desynchronized. We applied coordinated reset stimulation with a rapidly varying sequence (RVS CR) to examine its ability to reduce neuronal synchrony. The neuronal population was divided into subpopulations representing distinct physical sites of stimulation, as in deep brain stimulation therapy, and phase-shifted stimuli were delivered to each subpopulation in a random sequence. We explored how stimulation frequency and the number of stimulation sites affect the efficacy of RVS CR at desynchronizing the network. We demonstrate that RVS CR efficacy is sensitive to the depression-to-potentiation ratio in the STDP rule, which may be an important parameter to tune when reconciling simulations with experimental data. Numerical simulation of neuronal networks is constrained by computational resources when models demand large networks. This work proposes a model that demonstrates similar utility with a relatively small network, enabling researchers to study pathological neuronal activity and treatments more efficiently.

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Vesicular acidification modulates the synaptic current: a hybrid diffusion reaction model analysis

Bar-on, R.; Greger, I. H.; Holcman, D.

2026-04-28 neuroscience 10.64898/2026.04.23.720425 medRxiv
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Glutamate synaptic vesicles co-release protons, producing a brief acidification of the synaptic cleft that could modulate AMPA receptor (AMPARs) operation. To evaluate the extent of receptor acidification, we develop a diffusion-reaction model that couples vesicle-evoked proton and glutamate transients to AMPAR dynamics. Our simulations reveal that the rapid diffusion of protons and glutamate within the flat-cylindrical synaptic cleft leads to a mixture of protonated, singly glutamate-bound and doubly glutamate-bound AMPARs. We studied four postsynaptic AMPAR distributions - uniform disk, sub-disk, Gaussian cluster, and point-like cluster - and showed a [~] 50% increase in the number of acidified receptors when AMPARs are clustered on the postsynaptic cleft compared to a uniform arrangement. We further explored the impact of pH revealing that at acidic conditions (pH [~] 5), approximately 80-90% of open receptors are non-acidified, whereas under strongly acidic conditions (pH [~] 3), about 80-90% of open receptors exist in the protonated form. Finally, we explored how acidification modulates AMPARs during paired-pulse stimulation, a measure of short-term synaptic depression. While the presence of protons does not markedly alter the overall trends, acidified receptor states reduce the occupancies of their neutral counterparts by roughly 10-15%, indicating a mild redistribution toward protonated receptor conformations. To conclude, our model suggests that AMPAR protonation can influence the synaptic current, and we predict that this effect is determined primarily by the dissociation kinetics of glutamate and protons from AMPAR.

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Meta-learning leading to homeostatic plasticity stabilizes synaptic weights together with predictable activity levels

Woergoetter, F.; Moeller, K.; Tamosiunaite, M.

2026-06-22 neuroscience 10.64898/2026.06.16.732795 medRxiv
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Stabilizing synaptic plasticity together with the neurons activity has remained a central challenge in theoretical neuroscience since the introduction of Hebbian learning principles. Classical Hebbian learning rules typically lead to unbounded synaptic growth, motivating the development of stabilization mechanisms such as normalization methods, BCM-type learning, synaptic scaling and others. While these approaches can prevent divergence, they can also exhibit different limitations e.g. resulting in too-sparse synaptic configurations or leading to poor scalability with increasing network size. A recently introduced meta-plasticity mechanism, termed annealed linear learning (ALL), dynamically reduces the learning rate as neuronal output increases, thereby preserving stable and interpretable fixed-point behavior of the output. However, the original formulation leads to an irreversible decay of the learning rate, preventing adaptation to changing environmental conditions. To address this, in the present study, we balance learning rate reduction at large outputs with recovery at small outputs and in addition introduce forgetting that gradually reduces synaptic weights. These extensions allow the system to discard outdated representations and adapt to novel input conditions. Analytical investigations demonstrate that the favorable output fixed-point properties of the original ALL framework are preserved under the extended rule. Furthermore, simulations with an artificial agent show that the proposed mechanism enables robust and fast re-learning and adaptation in changing environments.

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Polysynaptic signal propagation in networked neural masses

Madan Mohan, V.; Roberts, J. A.; Pathak, A.; Harris, A. M.; Seguin, C.; Zalesky, A.

2026-05-04 neuroscience 10.64898/2026.04.29.721638 medRxiv
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The routing of information across the brains structural network is central to its wide range of functional capabilities. However, the mechanisms underlying information routing in complex brain networks, particularly between regions that do not share a direct anatomical connection, remain poorly understood. Neural mass models (NMMs), a computational modelling framework capable of capturing complex neural dynamics across scales, can potentially be used to study the dynamical and network bases of these vital polysynaptic routing processes. In this study, we investigate polysynaptic signalling in three widely used NMMs, obeying Ornstein-Uhlenbeck, Stuart-Landau, and Jansen-Rit dynamics, by tracking the propagation of a discrete, focal, high-amplitude perturbation across the underlying network. We find that polysynaptic propagation emerges in all tested NMMs when configured within dynamical regimes that effectively enhance the persistence of perturbations. We also find distinct parameter domains that maximise signal propagation to directly connected regions and to those separated from the source by at least two hops. Finally, we benchmark in silico stimulus propagation in the brain network against an empirical dataset of direct electrical stimulation trials, to explore the relative capabilities of the NMMs in capturing signal propagation to connected versus unconnected regions. This analysis highlights the significance of dynamical repertoire in capturing stimulus propagation outcomes. Overall, this study provides insights into how dynamical and network features shape signal propagation over complex brain networks.

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Gap junctional coupling of molecular layer interneurons enables transient NMDA driven synchronization

Koch, N. A.; Khadra, A.

2026-05-29 neuroscience 10.64898/2026.05.28.728326 medRxiv
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Molecular layer interneurons (MLIs) play a crucial role in modulating the output of the cerebellar cortex through their inhibition of Purkinje cells. MLIs also inhibit other MLIs synaptically and are coupled electrically through gap junctions. While synchronization of MLIs has been observed, comprehensive understanding of the role of gap junctional coupling in shaping MLI network activity is lacking. Dendro-dendritic gap junctional coupling in MLIs involves propagation of signals to and from the dendritic gap junction location which can lead to neural synchronization. However, how this is regulated by the intrinsic electrical properties of MLIs, including dendritic properties, is poorly understood. In this study, we apply conductance-based computational modelling to examine the effect of dendritic filtering on gap junctional coupling in pairs of ball-and-stick MLI models, demonstrating that gap junctional properties, rather than the active dendritic properties of MLIs, primarily dictate gap junction-driven synchronization. By systematically reducing the ball-and-stick model to a one-compartment MLI model, we additionally investigate the role of MLI gap junctional coupling in mediating MLI network synchrony. Our results reveal that transient AMPA input drives brief network-wide synchronization, whereas NMDA-mediated elevated firing enables gap junction-dependent oscillatory synchronization that is further enhanced by MLI-MLI inhibition in a positive feedback loop, producing pronounced peaks of network coactivity resembling sensory-evoked MLI activity observed in vivo. These findings provide important insights into network dynamics of MLIs and how gap junctions shape their activity, with broader implications for other neural networks that rely on gap junctional coupling.