Publications by Pramod Shivaji Kumbhar

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

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

Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome

James Gonzalo King, Eilif Benjamin Muller, Michael Reimann, Marwan Muhammad Ahmed Abdellah, Giuseppe Chindemi, Pramod Shivaji Kumbhar, András Ecker, Daniela Egas Santander, Ioannis Magkanaris, Sirio Bolaños Puchet, Jorge Blanco Alonso, James Bryden Isbister

Synaptic plasticity underlies the brain’s ability to learn and adapt. While experiments in brain slices have revealed mechanisms and protocols for the induction of plasticity between pairs of neurons, how these synaptic changes are coordinated in biologica ...

2024

Modeling and simulation of neocortical micro- and mesocircuitry. Part II: Physiology and experimentation

Henry Markram, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Alexis Arnaudon, Eilif Benjamin Muller, Daniel Keller, Michael Reimann, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Giuseppe Chindemi, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Armando Romani, Christian Andreas Rössert, Judit Planas Carbonell, Genrich Ivaska, András Ecker, Daniela Egas Santander, Natali Barros Zulaica, Alexander Dietz, Omar Awile, Samuel Lieven D. Lapere, Matthias Wolf, Sirio Bolaños Puchet, Thomas Brice Delemontex, Jorge Blanco Alonso, Mustafa Anil Tuncel, Tanguy Pierre Louis Damart, Maria Reva, James Bryden Isbister, Darshan Mandge, Weina Ji, Aleksandra Zuzanna Teska, Polina Litvak, Gianluca Ficarelli, Joni Henrikki Herttuainen, ,

Community-based reconstruction and simulation of a full-scale model of region CA1 of rat hippocampus

Henry Markram, Felix Schürmann, James Gonzalo King, Srikanth Ramaswamy, Juan Bautista Hernando Vieites, Alexis Arnaudon, Eilif Benjamin Muller, Michael Reimann, Huanxiang Lu, Ying Shi, Marwan Muhammad Ahmed Abdellah, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Lida Kanari, Juan Luis Riquelme Roman, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Liesbeth Maria L Vanherpe, Armando Romani, Cyrille Pierre Henri Favreau, Michele Migliore, Mohameth François Sy, Szabolcs Kali, Judit Planas Carbonell, Genrich Ivaska, Sàra Sàray, Carmen Alina Lupascu, Rosanna Migliore, Audrey Mercer, András Ecker, Alberto Antonietti, Cristina Colangelo, Anna-Kristin Kaufmann, Julian Martin Budd, Elisabetta Giacalone, Thomas Brice Delemontex, Davide Bella, Fabien Petitjean, , , , ,

MOD2IR: High-Performance Code Generation for a Biophysically Detailed Neuronal Simulation DSL

Felix Schürmann, Pramod Shivaji Kumbhar, Snehal Pramod Kumbhar, Omar Awile, Ioannis Magkanaris

Advances in computational capabilities and large volumes of experimental data have established computer simulations of brain tissue models as an important pillar in modern neuroscience. Alongside, a variety of domain specific languages (DSLs) have been dev ...

ACM2023

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

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

2023

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

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

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 imp ...

FRONTIERS MEDIA SA2022

Modernizing the NEURON Simulator for Sustainability, Portability, and Performance

Felix Schürmann, James Gonzalo King, Pramod Shivaji Kumbhar, Omar Awile, Ioannis Magkanaris

The need for reproducible, credible, multiscale biological modeling has led to the development of standardized simulation platforms, such as the widely-used NEURON environment for computational neuroscience. Developing and maintaining NEURON over several d ...

2022

A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex

Henry Markram, Vincent Delattre, Rodrigo de Campos Perin, James Gonzalo King, Eilif Benjamin Muller, Marwan Muhammad Ahmed Abdellah, Werner Alfons Hilda Van Geit, Giuseppe Chindemi, Aurélien Tristan Jaquier, Pramod Shivaji Kumbhar, Christian Andreas Rössert, András Ecker, Mustafa Anil Tuncel

Pyramidal cells (PCs) form the backbone of the layered structure of the neocortex, and plasticity of their synapses is thought to underlie learning in the brain. However, such long-term synaptic changes have been experimentally characterized between only a ...

Nature Portfolio2022

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

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

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 c ...

Springer2020

An efficient analytical reduction of detailed nonlinear neuron models

Felix Schürmann, Idan Segev, Guy Eyal, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Oren Amsalem

Detailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these ...

Nature Research2020

CoreNEURON : An Optimized Compute Engine for the NEURON Simulator

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

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 ...

2019

Code Generation in Computational Neuroscience: A Review of Tools and Techniques

Romain Brette, Michael Lee Hines, Pramod Shivaji Kumbhar

Advances in experimental techniques and computational power allowing researchers to gather anatomical and electrophysiological data at unprecedented levels of detail have fostered the development of increasingly complex models in computational neuroscience ...

2018

Leveraging a Cluster-Booster Architecture for Brain-Scale Simulations

Felix Schürmann, James Gonzalo King, Michael Lee Hines, Aleksandr Ovcharenko, Pramod Shivaji Kumbhar

The European Dynamical Exascale Entry Platform (DEEP) is an example of a new type of heterogeneous supercomputing architecture that include both a standard multicore-based "Cluster" used to run less scalable parts of an application, and an Intel MIC-based ...

Springer Int Publishing Ag2016

Reconstruction and Simulation of Neocortical Microcircuitry

Nenad Buncic, Jean-Vincent Le Bé, Selim Arsever, Henry Markram, Gilad Silberberg, Sébastien Lasserre, Vincent Delattre, Raphael Dumusc, Rodrigo de Campos Perin, Imad Riachi, Thomas Berger, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Michael Lee Hines, Sean Lewis Hill, Juan Bautista Hernando Vieites, Georges Khazen, Shruti Muralidhar, Anastasia Ailamaki, Eilif Benjamin Muller, Farhan Tauheed, Jean Pierre Ghobril, Julie Meystre, Daniel Keller, Idan Segev, Michael Reimann, Thomas Heinis, John Richard Walker, Martin Telefont, Yun Wang, Ying Shi, Joseph William Graham, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Jean-Denis Georges Emile Courcol, Ahmet Bilgili, Werner Alfons Hilda Van Geit, Athanassia Chalimourda, , , , , , , , , , , , , , , , , , , , , , , , , , , ,

Rebasing I/O for Scientific Computing: Leveraging Storage Class Memory in an IBM BlueGene/Q Supercomputer

Felix Schürmann, Alessandro Curioni, Fabien Jonathan Delalondre, John Anthony Biddiscombe, Miguel Angel Gila Arrondo, Davide Tacchella, Peter Morjan, Robert Germain, Blake Fitch, Pramod Shivaji Kumbhar, Bernard Metzler, Lars Schneidenbach

Storage class memory is receiving increasing attention for use in HPC systems for the acceleration of intensive IO operations. We report a particular instance using SLC FLASH memory integrated with an IBM BlueGene/Q supercomputer at scale (Blue Gene Active ...

Springer2014