Description:Microscopic simulation of biological matter
Abstract:Microscopic simulations of soft condensed matter systems of relevant biological interest.<br>
The DL_POLY free package for the fully atomistic molecular dynamics simulation of macromolecular systems is used to investigate the interaction between lipid membranes and antibiotic peptides, focusing in particular on the ability of the peptide to open a pore on the membrane surface. These studies complement a corresponding neutron spectroscopy experimental investigation.
The interaction among two lysozyme proteins along several preferential directions is investigated in the framework of the steered molecular dynamics technique by means of the widely used GROMACS package for molecular simulations. This study aims in particular on a precise characterization of the surface contacts among two facing proteins, with relevant implications for the crystallization processes in biological matter.
<br><br><b>Software requirements</b>: The free package GROMACS (www.gromacs.org) and DL_POLY (www.cse.scitech.ac.uk/ccg/software/DL_POLY), for the molecular dynamics simulations; ForTran and C compilers.^