Atomistic simulations of biologically realistic transmembrane potential gradients

Jonathan N. Sachs, Paul S. Crozier, Thomas B Woolf

Research output: Contribution to journalArticle

Abstract

We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson's equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity.

Original languageEnglish (US)
Article number5
Pages (from-to)10847-10851
Number of pages5
JournalThe Journal of Chemical Physics
Volume121
Issue number22
DOIs
StatePublished - Dec 8 2004

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potential gradients
Dimyristoylphosphatidylcholine
Atoms
Saline water
periodic variations
Charge distribution
Poisson equation
Integral equations
Molecular dynamics
simulation
Ions
cells
charge distribution
atoms
integral equations
baths
resources
Computer simulation
derivation
molecular dynamics

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Atomistic simulations of biologically realistic transmembrane potential gradients. / Sachs, Jonathan N.; Crozier, Paul S.; Woolf, Thomas B.

In: The Journal of Chemical Physics, Vol. 121, No. 22, 5, 08.12.2004, p. 10847-10851.

Research output: Contribution to journalArticle

Sachs, Jonathan N. ; Crozier, Paul S. ; Woolf, Thomas B. / Atomistic simulations of biologically realistic transmembrane potential gradients. In: The Journal of Chemical Physics. 2004 ; Vol. 121, No. 22. pp. 10847-10851.
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