Diffusion processes in biological membranes studied by molecular dynamics simulations and analytical models

Abstract : Various recent experimental and simulation studies show that the lateral diffusion of molecules in biological membranes exhibits anomalies, in the sense that the molecular mean square displacements increase sub-linearily instead of linearly with time. Mathematically, such diffusion processes can be modeled by generalized diffusion equations which involve an additional fractional time derivative compared to the corresponding normal counterpart. The aim of this thesis is to gain some more physical insight into the lateral diffusion processes in biological membranes. For this purpose, molecular dynamics simulations of a lipid POPC bilayer are analyzed by employing concepts from the statistical physics of liquids. The long-time tail of the center-of-mass velocity autocorrelation function, which reflects the diffusional regime of the molecules under consideration, is related to their low-frequency dynamics and to the dynamical structure around each molecule. The latter is studied in terms of the time dependent van Hove pair correlation function for their centers-of-mass. It is in particular demonstrated that the first shell of neighbors of a diffusing lipid molecule decays very slowly with t^(-beta), with 0 < beta < 1. This finding is in agreement with the observation that lipid molecules tend to form collective flow patterns, which has been recently reported by other authors. In order to evaluate the impact of the molecular dynamics force field on the nature of the observed diffusion process, the POPC bilayer was simulated with the OPLS all atom force field and with the coarse-grained MARTINI force field. In the latter, four heavy atoms are combined into one bead. In both cases lateral sub-diffusion with similar exponents is observed, but the diffusional motion obtained with the coarse grained force field is about three times faster and appears also to be faster than in experiments. This result is reflected in the low-fequency dynamics of the POPC molecules and in the dynamical structure of their local environment.
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Slawomir Stachura. Diffusion processes in biological membranes studied by molecular dynamics simulations and analytical models. Chemical Physics [physics.chem-ph]. Université Pierre et Marie Curie - Paris VI, 2014. English. ⟨NNT : 2014PA066239⟩. ⟨tel-01127089⟩

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