### Abstract

A transport equation for confined structures is used to calculate the ionic currents through various transmembrane proteins. The transport equation is a diffusion-type equation where the concentration of the particles depends on the one-dimensional position in the confined structure and on the local energy. The computational significance of this continuum model is that the (6 + 1)-dimensional Boltzmann equation is reduced to a (2 + 1)-dimensional diffusion-type equation that can be solved with small computational effort so that ionic currents through confined structures can be calculated quickly. The applications here are three channels, namely OprP, Gramicidin A, and KcsA. In each case, the confinement potential is estimated from the known molecular structure of the channel. Then the confinement potentials are used to calculate ionic currents and to study the effect of parameters such as the potential of mean force, the ionic bath concentration, and the applied voltage. The simulated currents are compared with measurements, and very good agreement is found in each case. Finally, virtual potassium channels with selectivity filters of varying length are simulated in order to discuss the optimality of the filter.

Original language | English (US) |
---|---|

Article number | 680 |

Pages (from-to) | 524-532 |

Number of pages | 9 |

Journal | Journal of Computational Electronics |

Volume | 14 |

Issue number | 2 |

DOIs | |

State | Published - Mar 7 2015 |

### Fingerprint

### Keywords

- Boltzmann equation
- Confined structures
- Ionic transport

### ASJC Scopus subject areas

- Electrical and Electronic Engineering
- Atomic and Molecular Physics, and Optics
- Electronic, Optical and Magnetic Materials
- Modeling and Simulation

### Cite this

*Journal of Computational Electronics*,

*14*(2), 524-532. [680]. https://doi.org/10.1007/s10825-015-0680-6

**A transport equation for confined structures applied to the OprP, Gramicidin A, and KcsA channels.** / Khodadadian, Amirreza; Heitzinger, Clemens.

Research output: Contribution to journal › Article

*Journal of Computational Electronics*, vol. 14, no. 2, 680, pp. 524-532. https://doi.org/10.1007/s10825-015-0680-6

}

TY - JOUR

T1 - A transport equation for confined structures applied to the OprP, Gramicidin A, and KcsA channels

AU - Khodadadian, Amirreza

AU - Heitzinger, Clemens

PY - 2015/3/7

Y1 - 2015/3/7

N2 - A transport equation for confined structures is used to calculate the ionic currents through various transmembrane proteins. The transport equation is a diffusion-type equation where the concentration of the particles depends on the one-dimensional position in the confined structure and on the local energy. The computational significance of this continuum model is that the (6 + 1)-dimensional Boltzmann equation is reduced to a (2 + 1)-dimensional diffusion-type equation that can be solved with small computational effort so that ionic currents through confined structures can be calculated quickly. The applications here are three channels, namely OprP, Gramicidin A, and KcsA. In each case, the confinement potential is estimated from the known molecular structure of the channel. Then the confinement potentials are used to calculate ionic currents and to study the effect of parameters such as the potential of mean force, the ionic bath concentration, and the applied voltage. The simulated currents are compared with measurements, and very good agreement is found in each case. Finally, virtual potassium channels with selectivity filters of varying length are simulated in order to discuss the optimality of the filter.

AB - A transport equation for confined structures is used to calculate the ionic currents through various transmembrane proteins. The transport equation is a diffusion-type equation where the concentration of the particles depends on the one-dimensional position in the confined structure and on the local energy. The computational significance of this continuum model is that the (6 + 1)-dimensional Boltzmann equation is reduced to a (2 + 1)-dimensional diffusion-type equation that can be solved with small computational effort so that ionic currents through confined structures can be calculated quickly. The applications here are three channels, namely OprP, Gramicidin A, and KcsA. In each case, the confinement potential is estimated from the known molecular structure of the channel. Then the confinement potentials are used to calculate ionic currents and to study the effect of parameters such as the potential of mean force, the ionic bath concentration, and the applied voltage. The simulated currents are compared with measurements, and very good agreement is found in each case. Finally, virtual potassium channels with selectivity filters of varying length are simulated in order to discuss the optimality of the filter.

KW - Boltzmann equation

KW - Confined structures

KW - Ionic transport

UR - http://www.scopus.com/inward/record.url?scp=84929703714&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84929703714&partnerID=8YFLogxK

U2 - 10.1007/s10825-015-0680-6

DO - 10.1007/s10825-015-0680-6

M3 - Article

AN - SCOPUS:84929703714

VL - 14

SP - 524

EP - 532

JO - Journal of Computational Electronics

JF - Journal of Computational Electronics

SN - 1569-8025

IS - 2

M1 - 680

ER -