Partitioning into phosphatidylcholine-cholesterol membranes: liposome measurements, coarse-grained simulations, and implications for bioaccumulation.

Membrane-water partitioning is an important physical property for the assessment of bioaccumulation and environmental impact. Here, we advance simulation methodology for predicting the partitioning of small molecules into lipid membranes and compare the computational predictions to experimental measurements in liposomes. As a step towards high-throughput screening, we present an automated mapping and parametrization procedure to produce coarse-grained models compatible with the Martini 3 force field.

Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane-Water Partitioning.

With a view to high-throughput simulations, we present an automated system for mapping and parameterizing organic molecules for use with the coarse-grained Martini force field. The method scales to larger molecules and a broader chemical space than existing schemes. The core of the mapping process is a graph-based analysis of the molecule's bonding network, which has the advantages of being fast, general, and preserving symmetry.

Self-assembly and mesophase formation in a non-ionic chromonic liquid crystal: insights from bottom-up and top-down coarse-grained simulation models.

New coarse-grained models are introduced for a non-ionic chromonic molecule, TP6EO2M, in aqueous solution. The multiscale coarse-graining (MS-CG) approach is used, in the form of hybrid force matching (HFM), to produce a bottom-up CG model that demonstrates self-assembly in water and the formation of a chromonic stack. However, the high strength of binding in stacks is found to limit the transferability of the HFM model at higher concentrations.

Assessing the transferability of common top-down and bottom-up coarse-grained molecular models for molecular mixtures.

The performance of three methods for developing new coarse-grained models for molecular simulation is critically assessed. Two bottom-up approaches are employed: iterative Boltzmann inversion (IBI) and the multiscale coarse-graining method (MS-CG), using an atomistic n-octane-benzene reference system. Results are compared to a top-down coarse-graining approach employing the SAFT-γ Mie equation of state.