2020
DOI: 10.1021/acs.jpcb.0c09947
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Permeation Rates of Oxygen through a Lipid Bilayer Using Replica Exchange Transition Interface Sampling

Abstract: Several simulations strategies have emerged to predict the permeability of solutes across membranes, which is important for many biological or industrial processes such as drug design. The widespread inhomogeneous solubility-diffusion (ISD) model is based on the Smoluchowski equation and describes permeation as purely diffusive. The counting method, which counts membrane transitions in a long molecular dynamics (MD) trajectory, is free of this diffusive assumption, but it lacks sufficient statistics when the p… Show more

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Cited by 10 publications
(9 citation statements)
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“…45 In recent work, the connection between RETIS and the permeability was derived, 37 and this method can be a valid alternative for the counting method. 46 Another train of thought is the use of biased simulations, where a large variety of free energy is canceled out artificially by adding a bias potential. 20,47,48 The Journal of Chemical Physics ARTICLE scitation.org/journal/jcp…”
Section: Article Scitationorg/journal/jcpmentioning
confidence: 99%
“…45 In recent work, the connection between RETIS and the permeability was derived, 37 and this method can be a valid alternative for the counting method. 46 Another train of thought is the use of biased simulations, where a large variety of free energy is canceled out artificially by adding a bias potential. 20,47,48 The Journal of Chemical Physics ARTICLE scitation.org/journal/jcp…”
Section: Article Scitationorg/journal/jcpmentioning
confidence: 99%
“…PyRETIS, in its different releases, has been shown effective in multiple studies on a rather broad set of topics ranging from chemical reactions, [9][10][11][12] the adoption of a bacterial protein to DNA, 13 thin film breakage, 14,15 the solid-solid transition between the wurtzite and rock salt crystal structures, 16 and the oxygen permeation through membranes. 17 These comprehensive studies have served as a sturdy foundation, guiding the software's development over the past three years.…”
Section: Introductionmentioning
confidence: 99%
“…24 Here, we employ transition interface sampling (TIS), 25 an extension of TPS, that can efficiently compute rate constants for complex systems. [26][27][28] In previous work, we have estimated the homogenous nucleation rate for methane hydrates using TIS. 12 In this work, we apply TIS to the estimation of the nucleation rate of CO 2 hydrate at high pressure and moderate undercooling (or supersaturation).…”
Section: Introductionmentioning
confidence: 99%