The Loverde laboratory utilizes all-atomistic (AA) and coarse-grained molecular dynamics (CG-MD) simulations, in combination with advanced sampling techniques, to investigate soft and biological materials for biomedicine. We are interested in molecular self-assembly, interactions of polymeric and model cellular membranes with hydrophobic drugs, and development of multi-scale models for biopolymers. We have a strong interest in the development of collaborations with both experimental and theoretical/computational groups.
Poly(ethylene glycol) (PEG) and various zwitterionic species are now used routinely as components in soft biomaterials. The study of mixtures composed of PEGylated-lipids with zwitterionic lipids provides an excellent opportunity to understand molecular interactions in such systems. To this end, we examine the liposome/bicelle/micelle phase behavior of such mixture in bulk solution and as monolayers at the air-water interface, utilizing a CG-MD approach rooted in experimental parameters that inform the nature of the short-range interactions. At lower PEG concentrations we find self-assembly of the PEGylated lipid into a liposome coexisting with a mixture of smaller bicelles (see below). Examination of large individual bicelles (1000 lipids) at increasing concentrations of PEG indicates that the degree of PEG de-mixing towards the outer radius of the bicelle is correlated with the overall concentration of PEG in the bicelle (not shown here). The CG-MD approach should be a useful complement to experimental studies designed to probe solute (drug) interactions with such membrane systems.
Furthermore, we are now in the process of the development of CG-MD force-fields for a number of hydrophobic drugs, peptide-based amphiphilic molecules, and polymers/bio-polymers. Please contact us if you are interested in visiting or getting involved.
Fig. 100 ns simulation of a 2 Mol % mixed PEGlipid and DMPC system forming a mixture of bicelles and a liposome. These simulations were run utilizing LAMMPS with a combination of CPU's and GPU's. Collaboration with Wataru Shinoda.
Why do a PhD rotation with the Loverde laboratory?
Fig. A. An initial AA simulation of 10 mol% paclitaxel (in red) in a POPC bilayer (transparent blue). B. Water within 5 Angstroms of the POPC bilayer is shown in blue. C. A top view of the paclitaxel - bilayer system illustrating the random dispersion in the membrane. After 10 ns simulation, there is evidence of local aggregations and fluctuations of water in the outer hydrophobic zone of the bilayer, but this will be increasingly evident with simulations for lonter time-scales. The membrane patch is 100 Angstroms by 100 Angstroms.
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