Calculating diffusion and permeability coefficients with the oscillating forward-reverse method. 2012

Bryan W Holland, and Chris G Gray, and Bruno Tomberli
Department of Physics and Biophysical Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada N1G 2W1. bryan.holland@ucalgary.ca

The forward-reverse or FR method is an efficient bidirectional work method for determining the potential of mean force w(z) and also supposedly gives in principle the position-dependent diffusion coefficient D(z). Results from a variation called the OFR (oscillating FR) method suggest inconsistencies in the D(z) values when calculated as prescribed by the FR method. A new steering protocol has thus been developed and applied to the OFR method for the accurate determination of D(z) and also provides greater convergence for w(z) in molecular dynamics simulations. The bulk diffusion coefficient for water was found to be (6.03±0.16)×10(-5) cm2/s at 350 K with system size dependence within the statistical error bars. Using this steering protocol, D(z) and w(z) for water permeating a dipalmitoylphosphatidylcholine (DPPC) bilayer were determined. The potential of mean force is shown to have a barrier of peak height, wmax/(kBT)=8.4, with a width of about 10 Å on either side from the membrane center. The diffusion constant is shown to be highest in the core region of the membrane [peak value ∼(8.0±0.8)×10(-5) cm2/s], lowest in the head-group region [minimum value ∼(2.0±0.3)×10(-5) cm2/s], and to tend toward the bulk value as the water molecule leaves the membrane. The permeability coefficient P for H2O in DPPC was determined using the simulated D(z) and w(z) to give values of (0.129±0.075) cm/s at 323 K and (0.141±0.043) cm/s at 350 K. The results show more spatial detail than results presented in previous work while reducing the computational and user effort.

UI MeSH Term Description Entries
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D009991 Oscillometry The measurement of frequency or oscillation changes. Oscillometries
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D004058 Diffusion The tendency of a gas or solute to pass from a point of higher pressure or concentration to a point of lower pressure or concentration and to distribute itself throughout the available space. Diffusion, especially FACILITATED DIFFUSION, is a major mechanism of BIOLOGICAL TRANSPORT. Diffusions
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm

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