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Updated: May 18, 2026

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates

A Method for Determination and Simulation of Permeability and Diffusion in a 3D Tissue Model in a Membrane Insert System for Multi-well Plates

Published on: February 23, 2018

Calculating diffusion and permeability coefficients with the oscillating forward-reverse method.

Bryan W Holland¹, Chris G Gray, Bruno Tomberli

¹Department of Physics and Biophysical Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1. bryan.holland@ucalgary.ca

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|October 4, 2012

Summary

This summary is machine-generated.

A new steering protocol improves molecular dynamics simulations for calculating water diffusion and potential of mean force across lipid bilayers. This method provides accurate, detailed insights into water transport through dipalmitoylphosphatidylcholine membranes.

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Area of Science:

Computational Chemistry
Biophysics
Materials Science

Background:

The forward-reverse (FR) method is used to determine potential of mean force w(z) and position-dependent diffusion coefficient D(z).
The oscillating FR (OFR) method showed inconsistencies in D(z) calculations.
Accurate simulation of molecular transport across membranes is crucial for understanding biological and material processes.

Purpose of the Study:

To develop and apply a new steering protocol to the OFR method for accurate determination of D(z) and improved convergence of w(z).
To investigate water permeation through a dipalmitoylphosphatidylcholine (DPPC) bilayer.
To determine the permeability coefficient (P) for H2O in DPPC.

Main Methods:

Development of a novel steering protocol for molecular dynamics simulations.
Application of the enhanced OFR method to simulate water diffusion and potential of mean force across a DPPC bilayer.
Calculation of bulk diffusion coefficient, spatial diffusion profiles, and permeability coefficients.

Main Results:

The bulk diffusion coefficient for water at 350 K was determined to be (6.03±0.16)×10⁻⁵ cm²/s.
A potential of mean force barrier of wmax/(kBT)=8.4 was observed for water in the DPPC bilayer.
Diffusion constant varied significantly within the bilayer, peaking in the core and minimizing in the head-group region.

Conclusions:

The new steering protocol accurately determines D(z) and w(z) for water in DPPC bilayers with greater convergence.
The study provides detailed spatial information on water transport across membranes.
Permeability coefficients for H2O in DPPC were calculated at different temperatures, offering valuable data for membrane transport studies.