Mario Dipoppa | École Normale Supérieure (original) (raw)

Papers by Mario Dipoppa

Bulletin of the American Physical Society, 2008

Submitted for the MAR08 Meeting of The American Physical Society Effective One-Dimensional Electr... more Submitted for the MAR08 Meeting of The American Physical Society Effective One-Dimensional Electron-Hole Interaction in SingleWalled Carbon Nanotubes1 JACK DESLIPPE, MARIO DIPOPPA, UC Berkeley and LBNL, DAVID PRENDERGAST, Molecular Foundry, LBNL, RODRIGO CAPAZ, Universidade Federal do Rio de Janeiro, STEVEN LOUIE, UC Berkeley and LBNL — Using the results of ab initio GW-Bethe-Salpeter-Equation (GW-BSE) calculations on the excitonic effects in single-walled carbon nanotubes (SWCNTs), we derive a 1D quantum model for the electron-hole interaction in both semiconducting and metallic SWCNTs. The model includes the important effects of spatial dependent screening and reproduces the exciton binding energies and envelope wave functions of the complete GW-BSE solution of the electron-hole excited states. The inclusion of the spatial dependence in the dielectric function is essential to capture the positioning of the higher exciton states in the spectrum whose calculated energies differ dram...

The spatio-temporal correlation of natural images during fixational eye instability is studied. T... more The spatio-temporal correlation of natural images during fixational eye instability is studied. The statistics of eye movements and static natural images are first analyzed separately and then combined to obtain an analytical formula for the correlation function. Previous work on this subject is presented and important shortcomings are pointed out. A more rigorous and general formula is derived and tested numerically.

Transcriptomics has revealed the exquisite diversity of cortical inhibitory neurons1–7, but it is... more Transcriptomics has revealed the exquisite diversity of cortical inhibitory neurons1–7, but it is not known whether these fine molecular subtypes have correspondingly diverse activity patterns in the living brain. Here, we show that inhibitory subtypes in primary visual cortex (V1) have diverse correlates with brain state, but that this diversity is organized by a single factor: position along their main axis of transcriptomic variation. We combined in vivo 2-photon calcium imaging of mouse V1 with a novel transcriptomic method to identify mRNAs for 72 selected genes in ex vivo slices. We used transcriptomic clusters (t-types)4 to classify inhibitory neurons imaged in layers 1-3 using a three-level hierarchy of 5 Families, 11 Classes, and 35 t-types. Visual responses differed significantly only across Families, but modulation by brain state differed at all three hierarchical levels. Nevertheless, this diversity could be predicted from the first transcriptomic principal component, wh...

Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a ... more Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting in an increased need for computer vision algorithms that extract useful information from video data. Here we introduce a new video analysis tool that combines the output of supervised pose estimation algorithms (e.g. DeepLabCut) with unsupervised dimensionality reduction methods to produce interpretable, low-dimensional representations of behavioral videos that extract more information than pose estimates alone. We demonstrate this tool by extracting interpretable behavioral features from videos of three different head-fixed mouse preparations, as well as a freely moving mouse in an open field arena, and show how these interpretable features can facilitate downstream behavioral and neural analyses. We also show how the behavioral features produced by our model improve...

Context guides perception by influencing the saliency of sensory stimuli. Accordingly, in visual ... more Context guides perception by influencing the saliency of sensory stimuli. Accordingly, in visual cortex, responses to a stimulus are modulated by context, the visual scene surrounding the stimulus. Responses are suppressed when stimulus and surround are similar but not when they differ. The mechanisms that remove suppression when stimulus and surround differ remain unclear. Here we use optical recordings, manipulations, and computational modelling to show that a disinhibitory circuit consisting of vasoactive-intestinal-peptide-expressing (VIP) and somatostatin-expressing (SOM) inhibitory neurons modulates responses in mouse visual cortex depending on the similarity between stimulus and surround. When the stimulus and the surround are similar, VIP neurons are inactive and SOM neurons suppress excitatory neurons. However, when the stimulus and the surround differ, VIP neurons are active, thereby inhibiting SOM neurons and relieving excitatory neurons from suppression. We have identifi...

One of the most fundamental organizational principles of the brain is the separation of excitator... more One of the most fundamental organizational principles of the brain is the separation of excitatory (E) and inhibitory (I) neurons. In addition to their opposing effects on post-synaptic neurons, E and I cells tend to differ in their selectivity and connectivity. Although many such differences have been characterized experimentally, it is not clear why they exist in the first place. We studied this question in an artificial neural network equipped with multiple E and I cell types. We found that a deep convolutional recurrent network trained to perform an object classification task was able to capture salient distinctions between E and I neurons. We explored the necessary conditions for the network to develop distinct selectivity and connectivity across cell types. We found that neurons that project to higher-order areas will have greater stimulus selectivity, regardless of whether they are excitatory or not. Sparser connectivity is required for higher selectivity, but only when the r...

Advances in Cognitive Psychology

working memory, neural oscillations, neural networks, selective gating, persistent activity Worki... more working memory, neural oscillations, neural networks, selective gating, persistent activity Working memory (WM) is a primary cognitive function that corresponds to the ability to update, stably maintain, and manipulate short-term memory (stM) rapidly to perform ongoing cognitive tasks. A prevalent neural substrate of WM coding is persistent neural activity, the property of neurons to remain active after having been activated by a transient sensory stimulus. this persistent activity allows for online maintenance of memory as well as its active manipulation necessary for task performance. WM is tightly capacity limited. therefore, selective gating of sensory and internally generated information is crucial for WM function. While the exact neural substrate of selective gating remains unclear, increasing evidence suggests that it might be controlled by modulating ongoing oscillatory brain activity. here, we review experiments and models that linked selective gating, persistent activity, and brain oscillations, putting them in the more general mechanistic context of WM. We do so by defining several operations necessary for successful WM function and then discussing how such operations may be carried out by mechanisms suggested by computational models. We specifically show how oscillatory mechanisms may provide a rapid and flexible active gating mechanism for WM operations.

SummaryIn the mouse primary visual cortex (V1), sensory responses are shaped by behavioral factor... more SummaryIn the mouse primary visual cortex (V1), sensory responses are shaped by behavioral factors such as locomotion. These factors are thought to control a disinhibitory circuit, whereby interneurons expressing vasoactive intestinal peptide (Vip) inhibit those expressing somatostatin (Sst), disinhibiting pyramidal cells (Pyr). We measured the effect of locomotion on these neurons and on interneurons expressing parvalbumin (Pvalb) in layer 2/3 of mouse V1, and found in-consistencies with the disinhibitory model. In the presence of large stimuli, locomotion increased Sst cell responses without suppressing Vip cells. In the presence of small stimuli, locomotion increased Vip cell responses without suppressing Sst cells. A circuit model could reproduce each cell type’s activity from the measured activity of other cell types, but only if we allowed locomotion to increase feedforward synaptic weights while modulating recurrent weights. These results suggest that locomotion alters cortic...

Cell Reports, 2016

HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Http Www Theses Fr, 2012

La memoire de travail est une fonction cognitive qui correspond a la capacite d’actualiser, de ma... more La memoire de travail est une fonction cognitive qui correspond a la capacite d’actualiser, de maintenir, et de manipuler la memoire a court terme de maniere rapide. Cette capacite etant limitee, un mecanisme que nous appelons le selective gating est necessaire pour filtrer l’information non pertinente et effacer les engrammes obsoletes. Bien que des nombreux modeles aient aborde ce probleme et son lien avec l’activite neuronale persistante et les oscillations neuronales, ils n’ont pas explore le probleme du selective gating. Dans cette these, nous developpons un nouveau paradigme ou oscillations neuronales et correlations permettent de controler de maniere flexible le fonctionnement de la memoire de travail grâce au selective gating. Nous decrivons ici un modele de memoire de travail ou le reseau de memoire a court terme peut etre place en differents regimes de selective gating en fonction de la frequence des oscillations neuronales qui affectent le systeme. De plus nous demontrons que le niveau de correlation de l’activite d'arriere plan est le principal facteur controlant les regimes de selective gating a travers son impact sur la synchronisation des potentiels d’actions dans le reseau de memoire de travail. En effet, la stabilite de l’activite persistante peut etre formellement analysee et decrite par un etat appele splay state. L’analyse du splay state montre que l’activite persistante est desynchronisee et par consequent detruite par des stimulations synchronises. La majorite de ces conclusions theoriques sont en accord avec de nombreuses observations experimentales

Proceedings of the National Academy of Sciences, 2013

Frontiers in Neuroscience, 2010

Frontiers in Computational Neuroscience, 2013

Working memory (WM) requires selective information gating, active information maintenance, and ra... more Working memory (WM) requires selective information gating, active information maintenance, and rapid active updating. Hence performing a WM task needs rapid and controlled transitions between neural persistent activity and the resting state. We propose that changes in correlations in neural activity provides a mechanism for the required WM operations. As a proof of principle, we implement sustained activity and WM in recurrently coupled spiking networks with neurons receiving excitatory random background activity where background correlations are induced by a common noise source. We first characterize how the level of background correlations controls the stability of the persistent state. With sufficiently high correlations, the sustained state becomes practically unstable, so it cannot be initiated by a transient stimulus. We exploit this in WM models implementing the delay match to sample task by modulating flexibly in time the correlation level at different phases of the task. The modulation sets the network in different working regimes: more prompt to gate in a signal or clear the memory. We examine how the correlations affect the ability of the network to perform the task when distractors are present. We show that in a winner-take-all version of the model, where two populations cross-inhibit, correlations make the distractor blocking robust. In a version of the mode where no cross inhibition is present, we show that appropriate modulation of correlation levels is sufficient to also block the distractor access while leaving the relevant memory trace in tact. The findings presented in this manuscript can form the basis for a new paradigm about how correlations are flexibly controlled by the cortical circuits to execute WM operations.

The emergence and stability of splay states is studied in fully coupled finite networks of N exci... more The emergence and stability of splay states is studied in fully coupled finite networks of N excitable quadratic integrate-and-fire neurons, connected via synapses modeled as pulses of finite amplitude and duration. For such synapses, by introducing two distinct types of synaptic events (pulse emission and termination), we were able to write down an exact event-driven map for the system and to evaluate the splay state solutions. For M overlapping post synaptic potentials the linear stability analysis of the splay state should take in account, besides the actual values of the membrane potentials, also the firing times associated to the M previous pulse emissions. As a matter of fact, it was possible, by introducing M complementary variables, to rephrase the evolution of the network as an event-driven map and to derive an analytic expression for the Floquet spectrum. We find that, independently of M , the splay state is marginally stable with N − 2 neutral directions. Furthermore, we have identified a family of periodic solutions surrounding the splay state and sharing the same neutral stability directions. In the limit of δ-pulses, it is still possible to derive an eventdriven formulation for the dynamics, however the number of neutrally stable directions, associated to the splay state, becomes N. Finally, we prove a link between the results for our system and a previous theory [Watanabe and Strogatz, Physica D, 74 (1994), pp. 197-253] developed for networks of phase oscillators with sinusoidal coupling.

Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast... more Two-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p: a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.

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Nano letters, Jan 1, 2009

The optical response of single-walled carbon nanotubes is dominated by exciton states with unusua... more The optical response of single-walled carbon nanotubes is dominated by exciton states with unusually large binding energies. We show that screening in semiconducting tubes enhances rather than reduces the electron-hole interaction for separations larger than the tube diameter. This "antiscreening" region deepens the relative energy level of the higher exciton states yielding unconventional excitation spectra. The effect explains the discrepancy in the current experimentally extrapolated exciton binding energies (deduced using conventional model spectra) and those obtained from ab initio calculations on isolated tubes.