Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation
Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availabili...
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description | Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here. |
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A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. 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This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Linaro D, Storace M, Giugliano M (2011) Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation. 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A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here.</description><subject>Biological transport, Active</subject><subject>Brain</subject><subject>Calculus</subject><subject>Channel gating</subject><subject>Computational Biology/Computational Neuroscience</subject><subject>Computational neuroscience</subject><subject>Computer Simulation</subject><subject>Data processing</subject><subject>Diffusion</subject><subject>Excitability</subject><subject>Gene expression</subject><subject>Genetic aspects</subject><subject>Ion Channel Gating - physiology</subject><subject>Ion channels</subject><subject>Ion Channels - physiology</subject><subject>Ion currents</subject><subject>Kinetics</subject><subject>Ligands</subject><subject>Markov Chains</subject><subject>Mathematical models</subject><subject>Membrane Potentials - physiology</subject><subject>Methods</subject><subject>Models, Neurological</subject><subject>Nervous system</subject><subject>Neurons</subject><subject>Neurons - metabolism</subject><subject>Neuroscience/Theoretical Neuroscience</subject><subject>Noise</subject><subject>Ordinary differential equations</subject><subject>Physiological aspects</subject><subject>Population density</subject><subject>Potassium currents</subject><subject>Properties</subject><subject>Sodium</subject><subject>Statistical analysis</subject><subject>Statistics</subject><subject>Stochastic models</subject><subject>Stochasticity</subject><subject>Studies</subject><subject>Synapses</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>DOA</sourceid><recordid>eNqVkktv1DAQxyMEoqXwDRDkBhx28SOOkwvSquKxUgUSj7M1scdbL4m9tRPUfnuc7rbqXpDQHGyNf_Of8cwUxUtKlpRL-n4bpuihX-5055aUEEoJe1ScUiH4QnLRPH5wPymepbQlJF_b-mlxwmjFsgY7LX6vtJ4ijFiCN6WFNJbJDVMPowu-DLbUl-A99qUPLmHpfKmDN5MewWtcdJDQlEMwM4BTDD6V3U1pnLVTmgVgt4vh2g23cs-LJxb6hC8O51nx69PHn-dfFhffPq_PVxcLXXM5LjoGVZNL5QRoK4gwjGmopamM5I3UbUWobequ4ygkFYzVsjNYa8M4NGAF8LPi9V5314ekDn1KivJsDSVNnYn1njABtmoXc4HxRgVw6tYR4kZBHJ3uUbXcgGmRiZbpqrMaKiotBVIjQY5Nl7U-HLJN3YBGox8j9Eeixy_eXapN-KM4EZzTKgu8OQjEcDVhGtXgksa-B49hSqoRDWvaPLhMvv0nSQmVbW4Klxld7tEN5E84b0POrbMZHFweIVqX_SsmeM1ky-aAd0cBmRnxetzAlJJa__j-H-zXY7baszqGlCLa-85QouZFvhuQmhdZHRY5h7162NX7oLvN5X8BSpzxDA</recordid><startdate>20110301</startdate><enddate>20110301</enddate><creator>Linaro, Daniele</creator><creator>Storace, Marco</creator><creator>Giugliano, Michele</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISN</scope><scope>ISR</scope><scope>7TK</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20110301</creationdate><title>Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation</title><author>Linaro, Daniele ; Storace, Marco ; Giugliano, Michele</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c637t-b2a4803530a19505d22ca67d4d7387c9401f86bb3e57152267bde6cd23a8af5a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Biological transport, Active</topic><topic>Brain</topic><topic>Calculus</topic><topic>Channel gating</topic><topic>Computational Biology/Computational Neuroscience</topic><topic>Computational neuroscience</topic><topic>Computer Simulation</topic><topic>Data processing</topic><topic>Diffusion</topic><topic>Excitability</topic><topic>Gene expression</topic><topic>Genetic aspects</topic><topic>Ion Channel Gating - physiology</topic><topic>Ion channels</topic><topic>Ion Channels - physiology</topic><topic>Ion currents</topic><topic>Kinetics</topic><topic>Ligands</topic><topic>Markov Chains</topic><topic>Mathematical models</topic><topic>Membrane Potentials - physiology</topic><topic>Methods</topic><topic>Models, Neurological</topic><topic>Nervous system</topic><topic>Neurons</topic><topic>Neurons - metabolism</topic><topic>Neuroscience/Theoretical Neuroscience</topic><topic>Noise</topic><topic>Ordinary differential equations</topic><topic>Physiological aspects</topic><topic>Population density</topic><topic>Potassium currents</topic><topic>Properties</topic><topic>Sodium</topic><topic>Statistical analysis</topic><topic>Statistics</topic><topic>Stochastic models</topic><topic>Stochasticity</topic><topic>Studies</topic><topic>Synapses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Linaro, Daniele</creatorcontrib><creatorcontrib>Storace, Marco</creatorcontrib><creatorcontrib>Giugliano, Michele</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>Neurosciences Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Linaro, Daniele</au><au>Storace, Marco</au><au>Giugliano, Michele</au><au>Graham, Lyle J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2011-03-01</date><risdate>2011</risdate><volume>7</volume><issue>3</issue><spage>e1001102</spage><epage>e1001102</epage><pages>e1001102-e1001102</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored. A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerical methods. In fact, exact techniques employ the microscopic simulation of the random opening and closing of individual ion channels, usually based on Markov models, whose computational loads are prohibitive for next generation massive computer models of the brain. In this work, we operatively define a procedure for translating any Markov model describing voltage- or ligand-gated membrane ion-conductances into an effective stochastic version, whose computer simulation is efficient, without compromising accuracy. Our approximation is based on an improved Langevin-like approach, which employs stochastic differential equations and no Montecarlo methods. As opposed to an earlier proposal recently debated in the literature, our approximation reproduces accurately the statistical properties of the exact microscopic simulations, under a variety of conditions, from spontaneous to evoked response features. In addition, our method is not restricted to the Hodgkin-Huxley sodium and potassium currents and is general for a variety of voltage- and ligand-gated ion currents. As a by-product, the analysis of the properties emerging in exact Markov schemes by standard probability calculus enables us for the first time to analytically identify the sources of inaccuracy of the previous proposal, while providing solid ground for its modification and improvement we present here.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>21423712</pmid><doi>10.1371/journal.pcbi.1001102</doi><oa>free_for_read</oa></addata></record> |
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subjects | Biological transport, Active Brain Calculus Channel gating Computational Biology/Computational Neuroscience Computational neuroscience Computer Simulation Data processing Diffusion Excitability Gene expression Genetic aspects Ion Channel Gating - physiology Ion channels Ion Channels - physiology Ion currents Kinetics Ligands Markov Chains Mathematical models Membrane Potentials - physiology Methods Models, Neurological Nervous system Neurons Neurons - metabolism Neuroscience/Theoretical Neuroscience Noise Ordinary differential equations Physiological aspects Population density Potassium currents Properties Sodium Statistical analysis Statistics Stochastic models Stochasticity Studies Synapses |
title | Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation |
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