Communication: Consistent picture of lateral subdiffusion in lipid bilayers: Molecular dynamics simulation and exact results

Abstract

This communication presents a molecular dynamics simulation study of a bilayer consisting of 128 dioleoyl-sn-glycero-3-phosphocholine molecules, which focusses on the center-of-mass diffusion of the lipid molecules parallel to the membrane plane. The analysis of the simulation results is performed within the framework of the generalized Langevin equation and leads to a consistent picture of subdiffusion. The mean square displacement of the lipid molecules evolves as ∝ tα, with α between 0.5 and 0.6, and the fractional diffusion coefficient is close to the experimental value for a similar system obtained by fluorescence correlation spectroscopy. We show that the long-time tails of the lateral velocity autocorrelation function and the associated memory function agree well with exact results which have been recently derived by asymptotic analysis [G. Kneller, J. Chem. Phys. 134, 224106 (2011)10.1063/1.3598483]. In this context, we define characteristic time scales for these two quantities.

Communication: Probing anomalous diffusion in frequency space

“…In the following this will be illustrated with MD trajectories from an earlier simulation study of a lipid POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) bilayer, whose molecules exhibit lateral subdiffusion. 11 Similar results have been found for other types of lipid bilayers, using MD simulations [12][13][14] and experimental techniques. 15,16 For our study we use two simulation models (for details we refer to Ref.…”

“…WDFT but completely absent for the MEE. Here, the log-log plot reveals, in contrast, some certainly unphysical oscillations in the very low frequency region of the DOS, which can be attributed to "all-pole" form (12). Table I resumes the results for the parameters α and D α .…”

“…4 the continuous lines represent interpolations of the discrete Fourier spectrum and in Fig. 5 function (12). In both figures the dots represent the sampled values which have been used for the fit of relation (5).…”

“…12 For the atomic resolution model one observes for both spectral estimation methods a deviation of g(ω) towards a constant, as ω approaches zero. This indicates the onset of an apparent normal diffusion due to increasing statistical errors in the MSD with increasing lag time.…”

Diffusion of tagged particles in a crowded medium

“…This lively debate is reflected by conflicting experimental reports in the literature concerning the role of complex environmental factors in the mobility of biomolecules in the cytoplasm and extra-cellular matrix. Some authors maintain that crowding merely slows down transport by reducing in a complex fashion the diffusion coefficient but does not alter the MSD exponent [5,[16][17][18], while others [6,[19][20][21] contend the identification of crowding in the cytoplasm with anomalous (typically sub-diffusive) transport [22][23][24], a feature observed in lateral diffusion in cellular membranes [25][26][27]. In this case one would have ∆R 2 ∝ t α with α < 1 (sub-diffusion) or ∆R 2 ∝ t α with α > 1 (super-diffusion).…”