Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst-Planck equation

D. Boda, Róbert Kovács, Dirk Gillespie, T. Kristóf

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

We have recently introduced the Local Equilibrium Monte Carlo (LEMC) technique (Boda, Gillespie, J. Chem. Theor. Comput. 8 (2012) 824-829) in which a non-equilibrium system is divided into small volume elements and separate Grand Canonical Monte Carlo simulations are performed for each using a local intensive parameter, which, as soon as local equilibrium is assumed, can be identified with the local electrochemical potential. The simulation provides the concentration profiles of the steady-state diffuse system, where ions are transported through a membrane from one bulk compartment to the other. The dynamics of the ions is described with the Nernst-Planck (NP) transport equation. The NP equation is coupled to the LEMC simulations via an iteration procedure that ensures that conservation of mass (the continuity equation) is satisfied. We apply the method to a simple calcium channel model and demonstrate its efficiency. The computer experiments are inspired by real electrophysiological experiments for the Ryanodine Receptor calcium channel. The diffusion coefficients in the channel are fitted to results of Dynamic Monte Carlo simulations.

Original languageEnglish
Pages (from-to)100-112
Number of pages13
JournalJournal of Molecular Liquids
Volume189
DOIs
Publication statusPublished - Jan 2014

Fingerprint

Calcium Channels
calcium
Calcium
Ions
Ryanodine Receptor Calcium Release Channel
simulation
Conservation
continuity equation
compartments
Experiments
iteration
Membranes
conservation
ions
diffusion coefficient
membranes
Monte Carlo simulation
profiles

Keywords

  • Ion channel
  • Monte Carlo
  • Nernst-Planck
  • Transport

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Condensed Matter Physics
  • Atomic and Molecular Physics, and Optics
  • Electronic, Optical and Magnetic Materials
  • Materials Chemistry

Cite this

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abstract = "We have recently introduced the Local Equilibrium Monte Carlo (LEMC) technique (Boda, Gillespie, J. Chem. Theor. Comput. 8 (2012) 824-829) in which a non-equilibrium system is divided into small volume elements and separate Grand Canonical Monte Carlo simulations are performed for each using a local intensive parameter, which, as soon as local equilibrium is assumed, can be identified with the local electrochemical potential. The simulation provides the concentration profiles of the steady-state diffuse system, where ions are transported through a membrane from one bulk compartment to the other. The dynamics of the ions is described with the Nernst-Planck (NP) transport equation. The NP equation is coupled to the LEMC simulations via an iteration procedure that ensures that conservation of mass (the continuity equation) is satisfied. We apply the method to a simple calcium channel model and demonstrate its efficiency. The computer experiments are inspired by real electrophysiological experiments for the Ryanodine Receptor calcium channel. The diffusion coefficients in the channel are fitted to results of Dynamic Monte Carlo simulations.",
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AU - Kovács, Róbert

AU - Gillespie, Dirk

AU - Kristóf, T.

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