Stochastic shielding and edge importance for Markov chains with timescale separation.
Nerve cells produce electrical impulses ("spikes") through the coordinated opening and closing of ion channels. Markov processes with voltage-dependent transition rates capture the stochasticity of spike generation at the cost of complex, time-consuming simulations. Schmandt and Galán intr...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-06-01
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| Series: | PLoS Computational Biology |
| Online Access: | http://europepmc.org/articles/PMC6023243?pdf=render |
| _version_ | 1818155337291661312 |
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| author | Deena R Schmidt Roberto F Galán Peter J Thomas |
| author_facet | Deena R Schmidt Roberto F Galán Peter J Thomas |
| author_sort | Deena R Schmidt |
| collection | DOAJ |
| description | Nerve cells produce electrical impulses ("spikes") through the coordinated opening and closing of ion channels. Markov processes with voltage-dependent transition rates capture the stochasticity of spike generation at the cost of complex, time-consuming simulations. Schmandt and Galán introduced a novel method, based on the stochastic shielding approximation, as a fast, accurate method for generating approximate sample paths with excellent first and second moment agreement to exact stochastic simulations. We previously analyzed the mathematical basis for the method's remarkable accuracy, and showed that for models with a Gaussian noise approximation, the stationary variance of the occupancy at each vertex in the ion channel state graph could be written as a sum of distinct contributions from each edge in the graph. We extend this analysis to arbitrary discrete population models with first-order kinetics. The resulting decomposition allows us to rank the "importance" of each edge's contribution to the variance of the current under stationary conditions. In most cases, transitions between open (conducting) and closed (non-conducting) states make the greatest contributions to the variance, but there are exceptions. In a 5-state model of the nicotinic acetylcholine receptor, at low agonist concentration, a pair of "hidden" transitions (between two closed states) makes a greater contribution to the variance than any of the open-closed transitions. We exhaustively investigate this "edge importance reversal" phenomenon in simplified 3-state models, and obtain an exact formula for the contribution of each edge to the variance of the open state. Two conditions contribute to reversals: the opening rate should be faster than all other rates in the system, and the closed state leading to the opening rate should be sparsely occupied. When edge importance reversal occurs, current fluctuations are dominated by a slow noise component arising from the hidden transitions. |
| first_indexed | 2024-12-11T14:40:48Z |
| format | Article |
| id | doaj.art-67c51e536464458ab79b37b60081ebe1 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-11T14:40:48Z |
| publishDate | 2018-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-67c51e536464458ab79b37b60081ebe12022-12-22T01:01:56ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582018-06-01146e100620610.1371/journal.pcbi.1006206Stochastic shielding and edge importance for Markov chains with timescale separation.Deena R SchmidtRoberto F GalánPeter J ThomasNerve cells produce electrical impulses ("spikes") through the coordinated opening and closing of ion channels. Markov processes with voltage-dependent transition rates capture the stochasticity of spike generation at the cost of complex, time-consuming simulations. Schmandt and Galán introduced a novel method, based on the stochastic shielding approximation, as a fast, accurate method for generating approximate sample paths with excellent first and second moment agreement to exact stochastic simulations. We previously analyzed the mathematical basis for the method's remarkable accuracy, and showed that for models with a Gaussian noise approximation, the stationary variance of the occupancy at each vertex in the ion channel state graph could be written as a sum of distinct contributions from each edge in the graph. We extend this analysis to arbitrary discrete population models with first-order kinetics. The resulting decomposition allows us to rank the "importance" of each edge's contribution to the variance of the current under stationary conditions. In most cases, transitions between open (conducting) and closed (non-conducting) states make the greatest contributions to the variance, but there are exceptions. In a 5-state model of the nicotinic acetylcholine receptor, at low agonist concentration, a pair of "hidden" transitions (between two closed states) makes a greater contribution to the variance than any of the open-closed transitions. We exhaustively investigate this "edge importance reversal" phenomenon in simplified 3-state models, and obtain an exact formula for the contribution of each edge to the variance of the open state. Two conditions contribute to reversals: the opening rate should be faster than all other rates in the system, and the closed state leading to the opening rate should be sparsely occupied. When edge importance reversal occurs, current fluctuations are dominated by a slow noise component arising from the hidden transitions.http://europepmc.org/articles/PMC6023243?pdf=render |
| spellingShingle | Deena R Schmidt Roberto F Galán Peter J Thomas Stochastic shielding and edge importance for Markov chains with timescale separation. PLoS Computational Biology |
| title | Stochastic shielding and edge importance for Markov chains with timescale separation. |
| title_full | Stochastic shielding and edge importance for Markov chains with timescale separation. |
| title_fullStr | Stochastic shielding and edge importance for Markov chains with timescale separation. |
| title_full_unstemmed | Stochastic shielding and edge importance for Markov chains with timescale separation. |
| title_short | Stochastic shielding and edge importance for Markov chains with timescale separation. |
| title_sort | stochastic shielding and edge importance for markov chains with timescale separation |
| url | http://europepmc.org/articles/PMC6023243?pdf=render |
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