Publications by James Gonzalo King

Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep

Marwan Muhammad Ahmed Abdellah, Oren Amsalem, Marine Laure Bertschy, Grigori Chevtchenko, Benoît Jean-Albert Coste, Jean-Denis Georges Emile Courcol, András Ecker, Cyrille Pierre Henri Favreau, Adrien Christian Fleury, Michael Emiel Gevaert, Jayakrishnan Harikrishnavilas Raveendran Nair, Joni Henrikki Herttuainen, Sean Lewis Hill, Elisabetta Iavarone, Genrich Ivaska, Anna-Kristin Kaufmann, Samuel Claude Kerrien, James Gonzalo King, Pramod Shivaji Kumbhar, Polina Litvak, Patrycja Lurie, Ioannis Magkanaris, Henry Markram, Vignayanandam Ravindernath Muddapu, Rodrigo de Campos Perin, Fabien Petitjean, Michael Reimann, Nadir Roman Guerrero, Ying Shi, Liviu Soltuzu, Mohameth François Sy, Mustafa Anil Tuncel, Alexander Désiré Ulbrich, Werner Alfons Hilda Van Geit, Matthias Wolf

2023

High synaptic threshold for dendritic NMDA spike generation in human layer 2/3 pyramidal neurons

Suraj Honnuraiah, James Gonzalo King

Neurons receive synaptic input primarily onto their dendrites. While we know much about the electrical properties of dendrites in rodents, we have only just started to describe their properties in the human brain. Here, we investigate the capacity of human dendrites to generate NMDA-receptor-dependent spikes (NMDA spikes). Using dendritic glutamate iontophoresis, as well as local dendritic synaptic stimulation, we find that human layer 2/3 pyramidal neurons can generate dendritic NMDA spikes. The capacity to evoke NMDA spikes in human neurons, however, was significantly reduced compared with that in rodents. Simulations in morphologically realistic and simplified models indicated that human neurons have a higher synaptic threshold for NMDA spike generation primarily due to the wider diameter of their dendrites. In summary, we find reduced NMDA spike generation in human compared with rodent layer 2/3 pyramidal neurons and provide evidence that this is due to the wider diameter of human dendrites.

2022

Modeling and simulation of rat non-barrel somatosensory cortex. Part I: Modeling anatomy

Alexis Arnaudon, Sirio Bolaños Puchet, Benoît Jean-Albert Coste, Jean-Denis Georges Emile Courcol, Thomas Brice Delemontex, Adrien Michel Achille Devresse, Hugo Thabo Dictus, Alexander Dietz, András Ecker, Daniela Egas Santander, Cyrille Pierre Henri Favreau, Gianluca Ficarelli, Michael Emiel Gevaert, Juan Bautista Hernando Vieites, Joni Henrikki Herttuainen, Kathryn Hess Bellwald, James Bryden Isbister, Lida Kanari, Daniel Keller, James Gonzalo King, Pramod Shivaji Kumbhar, Samuel Lieven D. Lapere, Janis Lazovskis, Ran Levi, Huanxiang Lu, Henry Markram, Eilif Benjamin Muller, Nicolas René Jean Ninin, Judit Planas Carbonell, Christoph Pokorny, Srikanth Ramaswamy, Michael Reimann, Juan Luis Riquelme Roman, Armando Romani, Felix Schürmann, Ying Shi, Vishal Sood, Werner Alfons Hilda Van Geit, Liesbeth Maria L Vanherpe, Matthias Wolf

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, hierarchical, interregional structure with a highly specific laminar architecture. The last decade has seen the emergence of extensive new data sets on anatomy and connectivity at the whole brain scale, providing promising new directions for studies of cortical function that take into account the inseparability of whole-brain and microcircuit architectures. Here, we present a data-driven computational model of the anatomy of non-barrel primary somatosensory cortex of juvenile rat, which integrates whole-brain scale data while providing cellular and subcellular specificity. This multiscale integration was achieved by building the morphologically detailed model of cortical circuitry embedded within a volumetric, digital brain atlas. The model consists of 4.2 million morphologically detailed neurons belonging to 60 different morphological types, placed in the nonbarrel subregions of the Paxinos and Watson atlas. They are connected by 13.2 billion synapses determined by axo-dendritic overlap, comprising local connectivity and long-range connectivity defined by topographic mappings between subregions and laminar axonal projection profiles, both parameterized by whole brain data sets. Additionally, we incorporated core- and matrix-type thalamocortical projection systems, associated with sensory and higher-order extrinsic inputs, respectively. An analysis of the modeled synaptic connectivity revealed a highly nonrandom topology with substantial structural differences but also synergy between local and long-range connectivity. Long-range connections featured a more divergent structure with a comparatively small group of neurons serving as hubs to distribute excitation to far away locations. Taken together with analyses at different spatial granularities, these results support the notion that local and interregional connectivity exist on a spectrum of scales, rather than as separate and distinct networks, as is commonly assumed. Finally, we predicted how the emergence of primary sensory cortical maps is constrained by the anatomy of thalamo-cortical projections. A subvolume of the model comprising 211,712 neurons in the front limb, jaw, and dysgranular zone has been made freely and openly available to the community.

2022

STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale

Omar Awile, Tristan Mathieu Carel, Giacomo Castiglioni, Alessandro Cattabiani, Weiliang Chen, Baudouin Paul Michel Maria Joseph Del Marmol, Iain Hepburn, James Gonzalo King, Christos Kotsalos, Pramod Shivaji Kumbhar, Samuel Marie A Melchior

Recent advances in computational neuroscience have demonstrated the usefulness and importance of stochastic, spatial reaction-diffusion simulations. However, ever increasing model complexity renders traditional serial solvers, as well as naive parallel implementations, inadequate. This paper introduces a new generation of the STochastic Engine for Pathway Simulation (STEPS) project (), denominated STEPS 4.0, and its core components which have been designed for improved scalability, performance, and memory efficiency. STEPS 4.0 aims to enable novel scientific studies of macroscopic systems such as whole cells while capturing their nanoscale details. This class of models is out of reach for serial solvers due to the vast quantity of computation in such detailed models, and also out of reach for naive parallel solvers due to the large memory footprint. Based on a distributed mesh solution, we introduce a new parallel stochastic reaction-diffusion solver and a deterministic membrane potential solver in STEPS 4.0. The distributed mesh, together with improved data layout and algorithm designs, significantly reduces the memory footprint of parallel simulations in STEPS 4.0. This enables massively parallel simulations on modern HPC clusters and overcomes the limitations of the previous parallel STEPS implementation. Current and future improvements to the solver are not sustainable without following proper software engineering principles. For this reason, we also give an overview of how the STEPS codebase and the development environment have been updated to follow modern software development practices. We benchmark performance improvement and memory footprint on three published models with different complexities, from a simple spatial stochastic reaction-diffusion model, to a more complex one that is coupled to a deterministic membrane potential solver to simulate the calcium burst activity of a Purkinje neuron. Simulation results of these models suggest that the new solution dramatically reduces the per-core memory consumption by more than a factor of 30, while maintaining similar or better performance and scalability.

FRONTIERS MEDIA SA2022

An Optimizing Multi-platform Source-to-source Compiler Framework for the NEURON MODeling Language

Omar Awile, Jorge Blanco Alonso, Michael Lee Hines, Liam Roger George Keegan, James Gonzalo King, Pramod Shivaji Kumbhar, Felix Schürmann

Domain-specific languages (DSLs) play an increasingly important role in the generation of high performing software. They allow the user to exploit domain knowledge for the generation of more efficient code on target architectures. Here, we describe a new code generation framework (NMODL) for an existing DSL in the NEURON framework, a widely used software for massively parallel simulation of biophysically detailed brain tissue models. Existing NMODL DSL transpilers lack either essential features to generate optimized code or capability to parse the diversity of existing models in the user community. Our NMODL framework has been tested against a large number of previously published user models and offers high-level domain-specific optimizations and symbolic algebraic simplifications before target code generation. NMODL implements multiple SIMD and SPMD targets optimized for modern hardware. When comparing NMODL-generated kernels with NEURON we observe a speedup of up to 20 × , resulting in overall speedups of two different production simulations by ∼7× . When compared to SIMD optimized kernels that heavily relied on auto-vectorization by the compiler still a speedup of up to ∼2× is observed.

Springer2020

Dense Computer Replica of Cortical Microcircuits Unravels Cellular Underpinnings of Auditory Surprise Response

Oren Amsalem, James Gonzalo King, Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, Idan Segev

The nervous system is notorious for its strong response evoked by a surprising sensory input, but the biophysical and anatomical underpinnings of this phenomenon are only partially understood. Here we utilized in-silico experiments of a biologically-detailed model of a neocortical microcircuit to study stimulus specific adaptation (SSA) in the auditory cortex, whereby the neuronal response adapts significantly for a repeated (“expected”) tone but not for a rare (“surprise”) tone. SSA experiments were mimicked by stimulating tonotopically-mapped thalamo-cortical afferents projecting to the microcircuit; the activity of these afferents was modeled based on our in-vivo recordings from individual thalamic neurons. The modeled microcircuit expressed naturally many experimentally-observed properties of SSA, suggesting that SSA is a general property of neocortical microcircuits. By systematically modulating circuit parameters, we found that key features of SSA depended on synergistic effects of synaptic depression, spike frequency adaptation and recurrent network connectivity. The relative contribution of each of these mechanisms in shaping SSA was explored, additional SSA-related experimental results were explained and new experiments for further studying SSA were suggested.

2020

CoreNEURON : An Optimized Compute Engine for the NEURON Simulator

Jérémy Pierre Benoit Fouriaux, Michael Lee Hines, James Gonzalo King, Pramod Shivaji Kumbhar, Aleksandr Ovcharenko, Felix Schürmann

The NEURON simulator has been developed over the past three decades and is widely used by neuroscientists to model the electrical activity of neuronal networks. Large network simulation projects using NEURON have supercomputer allocations that individually measure in the millions of core hours. Supercomputer centers are transitioning to next generation architectures and the work accomplished per core hour for these simulations could be improved by an order of magnitude if NEURON was able to better utilize those new hardware capabilities. In order to adapt NEURON to evolving computer architectures, the compute engine of the NEURON simulator has been extracted and has been optimized as a library called CoreNEURON. This paper presents the design, implementation, and optimizations of CoreNEURON. We describe how CoreNEURON can be used as a library with NEURON and then compare performance of different network models on multiple architectures including IBM BlueGene/Q, Intel Skylake, Intel MIC and NVIDIA GPU. We show how CoreNEURON can simulate existing NEURON network models with 4-7x less memory usage and 2-7x less execution time while maintaining binary result compatibility with NEURON.

2019

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Typical responses of cortical neurons to identical sensory stimuli appear highly variable. It has thus been proposed that the cortex primarily uses a rate code. However, other studies have argued for spike-time coding under certain conditions. The potential role of spike-time coding is directly limited by the internally generated variability of cortical circuits, which remains largely unexplored. Here, we quantify this internally generated variability using a biophysical model of rat neocortical microcircuitry with biologically realistic noise sources. We find that stochastic neurotransmitter release is a critical component of internally generated variability, causing rapidly diverging, chaotic recurrent network dynamics. Surprisingly, the same non-linear recurrent network dynamics can transiently overcome the chaos in response to weak feed-forward thalamocortical inputs, and support reliable spike times with millisecond precision. Our model shows that the noisy and chaotic network dynamics of recurrent cortical microcircuitry are compatible with stimulus-evoked, millisecond spike-time reliability, resolving a long-standing debate.

2019

Simplification of neural network models

Csaba Erö, Wulfram Gerstner, Marc-Oliver Gewaltig, James Gonzalo King, Henry Markram, Eilif Benjamin Muller, Christian Antonio Pozzorini, Christian Andreas Rössert, Idan Segev, Willem Anna Mark Wybo

The simplification of neural network models is described. For example, a method for simplifying a neural network model includes providing the neural network model to be simplified, defining a first temporal filter for the conveyance of input from a neuron to an other spatially-extended neuron along the arborized projection, defining a second temporal filter for the conveyance of input from yet another neuron to the spatially-extended neuron along the arborized projection, replacing, in the neural network model, the first, spatially-extended neuron with a first, spatially-constrained neuron and the arborized projection with a first connection extending between the first, spatially-constrained neuron and the second neuron, wherein the first connection filters input from the second neuron in accordance with the first temporal filter and a second connection extending between the first spatially-constrained neuron and the third neuron.

2018

Automated point-neuron simplification of data-driven microcircuit models

Giuseppe Chindemi, Wulfram Gerstner, Marc-Oliver Gewaltig, James Gonzalo King, Henry Markram, Eilif Benjamin Muller, Taylor Howard Newton, Max Christian Nolte, Christian Antonio Pozzorini, Srikanth Ramaswamy, Michael Reimann, Christian Andreas Rössert, Idan Segev, Willem Anna Mark Wybo

A method is presented for the reduction of morphologically detailed microcircuit models to a point-neuron representation without human intervention. The simplification occurs in a modular workflow, in the neighborhood of a user specified network activity state for the reference model, the "operating point". First, synapses are moved to the soma, correcting for dendritic filtering by low-pass filtering the delivered synaptic current. Filter parameters are computed numerically and independently for inhibitory and excitatory input using a Green's function approach. Next, point-neuron models for each neuron in the microcircuit are fit to their respective morphologically detailed counterparts. Here, generalized integrate-and-fire point neuron models are used, leveraging a recently published fitting toolbox. The fits are constrained by currents and voltages computed in the morphologically detailed partner neurons with soma corrected synapses at three depolarizations about the user specified operating point. The result is a simplified circuit which is well constrained by the reference circuit, and can be continuously updated as the latter iteratively integrates new data. The modularity of the approach makes it applicable also for other point-neuron and synapse models. The approach is demonstrated on a recently reported reconstruction of a neocortical microcircuit around an in vivo-like working point. The resulting simplified network model is benchmarked to the reference morphologically detailed microcircuit model for a range of simulated network protocols. The simplified network is found to be slightly more sub-critical than the reference, with otherwise good agreement for both quantitative and qualitative validations. Changes since version 1: filter fitting approach replaced by a new method to directly extract the filters using a Green's functions approach. Methods Section 2.1, Results Section 3.1 and Figures 1, 2, 4, 5 have been updated to reflect these changes. Discussion has been updated to incorporate the new findings

2016