title: Free energy calculation of permeant-membrane interactions using molecular dynamics simulations.
abstract: Nanotoxicology, the science concerned with the safe use of nanotechnology and nanostructure design for biological applications, is a field of research that has recently received great attention, as a result of the rapid growth in nanotechnology. Many nanostructures are of a scale and chemical composition similar to many biomolecular environments, and recent papers have reported evident toxicity of selected nanoparticles. Molecular simulations can help develop a mechanistic understanding of how structural properties affect bioactivity. In this chapter, we describe how to compute the free energy of interactions between cellular membranes and benzene, the main constituent of some toxic carbonaceous particles, with well-tempered metadynamics. This algorithm reconstructs the free energy surface and accelerates rare events in a coarse-grained representation of the system.
authors.affiliation: Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Paolo
authors.initials: P
authors.lastname: Elvati
authors.forename: Angela
authors.initials: A
authors.lastname: Violi
mesh_terms: D001554:Benzene / Q000737:chemistry; D002462:Cell Membrane / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010539:Permeability; D010713:Phosphatidylcholines / Q000737:chemistry; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D010713:Phosphatidylcholines; D001554:Benzene; C028694:1-palmitoyl-2-oleoylphosphatidylcholine