Who: Dr. György Hantal, Computational Physics Group, Faculty of Physics, University of Vienna
Place: Donostia International Physics Center
Date: Friday, 4 May 2018, 12:00
Molecular interfaces play an important role in many technological and biological processes, such as adsorption or heterogeneous (enzyme) catalysis. Thanks to recent methodological and computational developments, molecular simulations have become an essential tool in understanding the mechanism of such processes. Major difficulties in the analysis of fluid interfaces are their dynamic nature and the presence of capillary waves (technically a correlated thermal noise due to the motion of particles), which smear the real, intrinsic structure of fluid interfaces making not only their shape but also their constituting atoms change over time.
In this talk, I will discuss three, conceptually different, so called intrinsic analyzing techniques applicable to either macroscopically flat or arbitrarily shaped interfaces.[1-3] Such techniques allow one to decouple capillary waves from the true, intrinsic structure of the interface and/or tell which particles reside at a given instance in the simulation at the interface ? be it that of a two-phase liquid system or that of a biomolecule. In the second part of this talk, I will present, through examples, a new computational tool, the Pytim software package, a flexible, easily extendable python framework for interface analyses. Pytim enables the user to analyze trajectory file formats of popular simulation packages such as Gromacs, Charmm, Namd, Lammps, or Amber using just a couple of scripting lines.
 E. Chacón, P. Tarazona, Intrinsic profiles beyond the capillary wave theory: a Monte Carlo study, Phys. Rev. Lett. 91 (16) (2003) 166103.
 L. B. Pártay, G. Hantal, P. Jedlovszky, A. Vincze, G. Horvai, A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid?vapor interface of water, J. Comput. Chem. 29 (6) (2008) 945?956.
 A. P. Willard, D. Chandler, Instantaneous liquid interfaces, J. Phys. Chem. B 114 (5) (2010) 1954?1958.
 M. Sega, G. Hantal, B. Fábián, P. Jedlovszky, Pytim: a python package for the interfacial analysis of molecular simulations, submitted to J. Comput. Chem.