About the group

    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.  We are interested in molecular self-assembly, interactions of polymeric and model cellular membranes with hydrophobic drugs, and development of multi-scale models for polymers/biopolymers.  We have a strong interest in the development of collaborations with both experimental and theoretical/computational groups.  Furthermore, we are now in the process of the development of CG-MD and/or mesoscopic (DPD, BD) 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.

"Probing the Structure of PEGylated-lipid Assemblies by Coarse-grained Molecular Dynamics," Wataru Shinoda, D. E. Discher, M. L. Klein, S. M. Loverde, Soft Matter, 9, 11549-11556 (2013).


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.

“Molecular Modeling of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Membranes,” Myungshim Kang and Sharon M. Loverde, Journal of Physical Chemistry B, in press.

Why do a PhD rotation with the Loverde laboratory?
  • Rotation students will be exposed to either coarse-grained or all-atomistic molecular dynamics utilizing either LAMMPS or NAMD.
  • Rotation students will learn how to set-up, run, and analyze molecular dynamics simulations.
  • Rotation students will learn how to utilize the local cluster, Doppio, and also the CUNY High Performance Computing Center.

Interested grad students please email to inquire about applying to the CUNY Graduate Center programs in Chemistry, Biochemistry, or Physics.  In order to apply for the CUNY PhD programs you should apply on line: