Biological and synthetic membranes: What can be learned from a coarse-grained description?

Abstract

We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ simple and soft effective potentials, coarse-grained models can provide rather direct insight into collective phenomena in membranes on large time and length scales. We present a summary of recent progress in this rapidly evolving field, and pay special attention to model development and computational techniques. Applications of coarse-grained models to changes of the membrane topology are illustrated with studies of membrane fusion utilizing simulations and self-consistent field theory.

Micellar drug nanocarriers and biomembranes: how do they interact?

“…A validation of the proposed models for assembled chains has 50 been done considering the size and the stability of micelles. In particular, the Pluronic L64 represented by the formula (EO) 13 -(PO) 30 -(EO) 13 has been considered. In Figure 3B, together with a snapshot of simulated system I of core and corona radii obtained in the same conditions.…”

“…This behavior is in agreement with the experimental one reported by Pemboung et al 46 In particular, 1 H-NMR and spin labeled probes results suggest a release of L64 chains inside dodecylphosphocoline (DPC) and DPPC micelles. 30 Simulations snapshots show that chains attach to the lipid bilayer inserting the hydrophobic segment made of PO beads in the hydrophobic portion of the bilayer. In Figure 5C a detail of an inserted L64 chain of system II is depicted.…”

“…[6][7][12][13] Tumor angiogenesis creates the gateway for tumor access of nanosized objects. Matsumura and Maeda described the enhanced 30 permeability and retention (EPR) effect in the 1980s, 14 the "gaps" created by angiogenesis can be much larger (100 nm to 2 µm) than those reported in normal tissues. For this main reason, nanosized drugs tend to accumulate in tumor tissue much more than they do in normal tissues.…”

“…Hybrid models, due to their computational efficiency, are gaining popularity for simulations of several soft matter systems 15 including nanocomposites 29 and biomembranes. [30][31] For example, a solvent-free coarse-grained model for lipid bilayer membranes where nonbonded interactions were treated by a weighted-density functional has been introduced by Hömberg and Müller. 32 Very recently, Sevink et al 33 introduced a hybrid scheme, combining 20 Brownian dynamics (BD) and dynamic density functional theory (DDFT), that is able to model efficiently complete vesicles with molecular detail.…”

“…Particle and field representation of coarse-grained models has been considered in the single chain in mean field (SCMF) method 25 and has been applied to homopolymer and block copolymer systems as reported by Muller et al [34][35] More recently, the Molecular Dynamic (MD) method has been combined with selfconsistent field (SCF) description, which hereafter we call "MD-SCF" approach. In particular, an implementation suitable for the 30 treatment of atomistic force fields and/or specific CG models has been reported and validated. [36][37] The main feature of the MD-SCF approach, is that the evaluation of non-bonded forces and the potential between atoms of different molecules is replaced by the evaluation of a potential 35 dependent on the local density at position r. According to SCF theory, a many body problem like molecular motion in a manymolecule system is reduced to the derivation of a partition function of a single molecule in an external potential V(r).…”