### 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 language | English |
---|---|

Pages (from-to) | 100-112 |

Number of pages | 13 |

Journal | Journal of Molecular Liquids |

Volume | 189 |

DOIs | |

Publication status | Published - Jan 2014 |

### Fingerprint

### 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

**Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst-Planck equation.** / Boda, D.; Kovács, Róbert; Gillespie, Dirk; Kristóf, T.

Research output: Contribution to journal › Article

*Journal of Molecular Liquids*, vol. 189, pp. 100-112. https://doi.org/10.1016/j.molliq.2013.03.015

}

TY - JOUR

T1 - Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst-Planck equation

AU - Boda, D.

AU - Kovács, Róbert

AU - Gillespie, Dirk

AU - Kristóf, T.

PY - 2014/1

Y1 - 2014/1

N2 - 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.

AB - 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.

KW - Ion channel

KW - Monte Carlo

KW - Nernst-Planck

KW - Transport

UR - http://www.scopus.com/inward/record.url?scp=84890560255&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84890560255&partnerID=8YFLogxK

U2 - 10.1016/j.molliq.2013.03.015

DO - 10.1016/j.molliq.2013.03.015

M3 - Article

AN - SCOPUS:84890560255

VL - 189

SP - 100

EP - 112

JO - Journal of Molecular Liquids

JF - Journal of Molecular Liquids

SN - 0167-7322

ER -