Biophysical models articles within Nature Communications

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  • Article
    | Open Access

    “Visual performance might vary during natural behaviour such as walking. Here, the authors use wireless virtual reality to show that oscillations in performance on a visual detection task were systematically linked to the phase of the stride cycle.”

    • Matthew J. Davidson
    • , Frans A. J. Verstraten
    •  & David Alais

  • Article
    | Open Access

    The neural mechanisms that give rise to aperiodic EEG signals remains unclear. Here the authors characterize EEG signals generated by neural processes other than brain rhythms, demonstrating that certain drugs alter EEG signals in ways that confound traditional interpretation.

    • Niklas Brake
    • , Flavie Duc
    •  & Gilles Plourde

  • Article
    | Open Access

    Dopamine release occurs in spatiotemporal waves. Here the authors propose that dopamine waves arise locally in the striatum, and provide evidence for striatal acetylcholine waves.

    • Lior Matityahu
    • , Naomi Gilin
    •  & Joshua A. Goldberg

  • Article
    | Open Access

    How neurophysiological dynamics are organized across the cortex and their relationship with cortical micro-architecture is not well understood. Here, the authors find the dominant axis of neurophysiological dynamics reflects characteristics of the power spectrum and the linear correlation structure of the signal, and that spatial variation in neurophysiological dynamics is colocalized with multiple micro-architectural features.

    • Golia Shafiei
    • , Ben D. Fulcher
    •  & Bratislav Misic

  • Article
    | Open Access

    High computational cost severely limit the applications of biophysically detailed multi-compartment models. Here, the authors present DeepDendrite, a GPU-optimized tool that drastically accelerates detailed neuron simulations for neuroscience and AI, enabling exploration of intricate neuronal processes and dendritic learning mechanisms in these fields.

    • Yichen Zhang
    • , Gan He
    •  & Tiejun Huang

  • Article
    | Open Access

    Disruption to the brain’s oxygen supply triggers pathological dynamics and brain injuries. Here, the authors develop a model of coupled metabolic-neuronal activity that generates burst suppression patterns similar to those of infants after birth asphyxia.

    • Shrey Dutta
    • , Kartik K. Iyer
    •  & James A. Roberts

  • Article
    | Open Access

    The brain has been proposed to operate near a critical transition between order and disorder, controlled by a balance between inhibition and excitation. Here, the authors show that individual variability in long-range synchronization between brain regions can be explained by an individual’s proximity to this phase transition.

    • Marco Fuscà
    • , Felix Siebenhühner
    •  & Satu Palva

  • Article
    | Open Access

    Better understanding of a trade-off between the speed and accuracy of decision-making is relevant for mapping biological intelligence to machines. The authors introduce a brain-inspired learning algorithm to uncover dependencies in individual fMRI networks with features of neural activity and predict inter-individual differences in decision-making.

    • Michael Schirner
    • , Gustavo Deco
    •  & Petra Ritter

  • Article
    | Open Access

    The study of learning algorithms in the neocortex requires comprehensive knowledge of synaptic plasticity between its diverse cell types, which is currently lacking. Chindemi et al. describe a modeling approach to fill these gaps in experimental literature, and predict the features of synaptic plasticity in vivo.

    • Giuseppe Chindemi
    • , Marwan Abdellah
    •  & Eilif B. Muller

  • Article
    | Open Access

    Associations have been established between brain folding and white matter connectivity. Here the authors show that axon elongation, in response to mechanical stresses during cortical expansion and folding, may be sufficient to induce tissue remodeling consistent with white matter organization.

    • Kara E. Garcia
    • , Xiaojie Wang
    •  & Christopher D. Kroenke

  • Article
    | Open Access

    Voltage-sensitive dye imaging (VSDI) is a powerful technique for measuring membrane potential dynamics of neurons but the effective resolution is limited. Here, the authors developed an in silico model of VSDI to probe activity in a biologically detailed reconstruction of rodent neocortical microcircuits.

    • Taylor H. Newton
    • , Michael W. Reimann
    •  & Henry Markram

  • Article
    | Open Access

    Structures of mu-opioid receptor (mOR) in complex with morphine derivatives have been determined; but the structural basis of mOR activation by fentanyl-like synthetic opioids remains unclear. Here, authors use state-of-the-art simulation techniques and discover a secondary binding mode which is only accessible when the conserved His297 adopts a neutral HID tautomer state.

    • Quynh N. Vo
    • , Paween Mahinthichaichan
    •  & Christopher R. Ellis

  • Article
    | Open Access

    A principle of neuroanatomy, namely diffuse connectivity, is modeled using a large-scale network of corticothalamic neural masses. We demonstrate that increases in diffuse coupling transition the system through a quasi-critical regime, which coincides with known signatures of complex adaptive brain dynamics, and model fits to human imaging data orient task states to higher levels of diffusivity, consistent with the influence of arousal systems.

    • Eli J. Müller
    • , Brandon R. Munn
    •  & James M. Shine

  • Article
    | Open Access

    Theta oscillations have been implicated in hippocampal processing but mechanisms constraining phase timing of specific cell types are unknown. Here, the authors combine single-cell and multisite recordings with evolutionary computational models to evaluate mechanisms of phase preference of deep and superficial CA1 pyramidal cells.

    • Andrea Navas-Olive
    • , Manuel Valero
    •  & Liset M. de la Prida

  • Article
    | Open Access

    Neurons compute by integrating synaptic inputs across their dendritic arbor. Here, the authors show that distinct cell-types of mouse retinal ganglion cells that receive similar excitatory inputs have different biophysical mechanisms of input integration to generate their unique response tuning.

    • Yanli Ran
    • , Ziwei Huang
    •  & Thomas Euler

  • Article
    | Open Access

    The formation of functional synaptic clusters (FSCs) and their impact on somatic membrane potential (sVm) in vivo are poorly understood. Here, the authors develop a computational approach to show that FSCs have to form via local rather than global plasticity and be moderately large to impact sVm.

    • Balázs B. Ujfalussy
    •  & Judit K. Makara

  • Article
    | Open Access

    Realistic simulations of neurons and neural networks are key for understanding neural computations. Here the authors describe Neuron_Reduce, an analytic approach to simplify neurons receiving thousands of synapses and accelerate their simulations by 40–250 folds, while preserving voltage dynamics and dendritic computations.

    • Oren Amsalem
    • , Guy Eyal
    •  & Idan Segev

  • Article
    | Open Access

    In vivo laser ablation of dendrites in single L2/3 pyramidal neurons reveals that neuronal orientation tuning in V1 is robust to loss of dendritic input. Orientation tuning functions remain unchanged following apical dendrite ablation and change only slightly upon loss of two primary basal dendrites.

    • Jiyoung Park
    • , Athanasia Papoutsi
    •  & Stelios M. Smirnakis

  • Article
    | Open Access

    Whether cortical neurons can fire reliable spikes amid cellular noise and chaotic network dynamics remains debated. Here the authors simulate a detailed neocortical microcircuit model and show that noisy and chaotic cortical network dynamics are compatible with stimulus-evoked, millisecond spike-time reliability.

    • Max Nolte
    • , Michael W. Reimann
    •  & Eilif B. Muller

  • Article
    | Open Access

    Recent experimental work has revealed non-linear dendritic integration in interneurons. Here, the authors show, through detailed biophysical modeling, that fast spiking interneurons are better described with a 2-stage artificial neural network model calling into question the use of point neuron models.

    • Alexandra Tzilivaki
    • , George Kastellakis
    •  & Panayiota Poirazi

  • Article
    | Open Access

    Transcranial alternating current stimulation (TACS) of the brain is widely used in neuroscience, but the electric fields produced when multiple stimulation electrodes are used are not well understood. Here, the authors directly record electric fields in primate brains during multi-electrode TACS.

    • Ivan Alekseichuk
    • , Arnaud Y. Falchier
    •  & Alexander Opitz

  • Article
    | Open Access

    Sensory systems produce stable stimulus representations despite constant changes across multiple stimulus dimensions. Here, the authors reveal dynamic neural coding mechanisms by testing how coding of one dimension (orientation) changes with adaptations to other dimensions (luminance and contrast).

    • Masoud Ghodrati
    • , Elizabeth Zavitz
    •  & Nicholas S. C. Price

  • Article
    | Open Access

    Astrocytes have gained increasing attention for their roles in regulating neural circuits via neurotransmitter uptake, K + buffering, and ability to signal via Ca2 + transients. Here, the authors develop a computational modelling environment for astrocytes, akin to the NEURON environment, called ASTRO.

    • Leonid P. Savtchenko
    • , Lucie Bard
    •  & Dmitri A. Rusakov

  • Article
    | Open Access

    Neocortical circuits exhibit diverse cell types that can be difficult to build into computational models. Here the authors employ a genetic algorithm-based parameter optimization to generate multi-compartment Hodgkin-Huxley models for diverse cell types in the Allen Cell Types Database.

    • Nathan W. Gouwens
    • , Jim Berg
    •  & Anton Arkhipov

  • Article
    | Open Access

    The transport dynamics of messenger ribonucleoproteins in neurons is crucial to our neuronal functions, but the detail remains elusive. Song et al. show that they are transported along the dendrites in alternating run and rest phases with their own random sojourn times, following an aging Lévy walk.

    • Minho S. Song
    • , Hyungseok C. Moon
    •  & Hye Yoon Park

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