Computational Issues in Modeling Ion Transport in Biological Channels

Self-Consistent Particle-Based Simulations

S. Aboud, Marco Saraniti, R. Eisenberg

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

In this work, a self-consistent Langevin dynamics simulator will be presented, and computational issues unique to the simulation of charge transport through ion channels will be addressed. The simulation approach is divided into two parts; the first is the development of an efficient model to account for the charge transport in bulk electrolyte solutions, while the second is the accurate representation of the channel protein and lipid structure. A cavity is made in the interior of a phospholipid bilayer and an ion channel is inserted, where the atomic coordinates of the protein are obtained from experimental work. The electrostatic potential felt by a potassium ion along the center of the channel is then calculated and comparisons are made between two types of potassium channels, KcsA and MthK.

Original languageEnglish (US)
Pages (from-to)239-243
Number of pages5
JournalJournal of Computational Electronics
Volume2
Issue number2-4
DOIs
StatePublished - Dec 1 2003

Fingerprint

Ion Transport
Charge Transport
Ion Channels
Charge transfer
Potassium Channels
Ions
Protein
Langevin Dynamics
Phospholipids
Potassium
Electrolyte
Lipids
Modeling
Electrostatics
Electrolytes
proteins
Proteins
ions
Cavity
Simulation

Keywords

  • ion channels
  • KcsA
  • Langevin dynamics
  • lipid bilayer
  • MthK
  • nonequilibrium ionic transport

ASJC Scopus subject areas

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

Cite this

Computational Issues in Modeling Ion Transport in Biological Channels : Self-Consistent Particle-Based Simulations. / Aboud, S.; Saraniti, Marco; Eisenberg, R.

In: Journal of Computational Electronics, Vol. 2, No. 2-4, 01.12.2003, p. 239-243.

Research output: Contribution to journalArticle

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