Martin Vögele

TL;DR: In atomistic and coarse-grained molecular dynamics simulations, this work resolves how pneumolysin docks to cholesterol-rich bilayers and how membrane pores form and confirms critical PLY membrane-binding sites identified previously by mutagenesis.

TL;DR: The dependence of single-particle diffusion coefficients on the size and shape of the simulation box in molecular dynamics simulations of fluids and lipid membranes is investigated and it is found that the diffusion coefficients of lipids and a carbon nanotube embedded in a lipid membrane diverge with the logarithm of the box width.

TL;DR: The authors' coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water, which can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

TL;DR: By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, it is shown that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon nanotubes in membranes.

TL;DR: This work develops three-dimensional molecular learning networks for each of these tasks, finding that they consistently improve performance relative to one- and two-dimensional methods.