MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations

The MDANSE softwareMolecular Dynamics Analysis of Neutron Scattering Experimentsis presented. It is an interactive application for postprocessing molecular dynamics (MD) simulations. Given the widespread use of MD simulations in material and biomolecular sciences to get a better insight for experimental techniques such as thermal neutron scattering (TNS), the development of MDANSE has focused on providing a user-friendly, interactive, graphical user interface for analyzing many trajectories in the same session and running several analyses simultaneously independently of the interface. This first version of MDANSE already proposes a broad range of analyses, and the application has been designed to facilitate the introduction of new analyses in the framework. All this makes MDANSE a valuable tool for extracting useful information from trajectories resulting from a wide range of MD codes

Structure and Dynamics of Ionic Micelles: MD Simulation and Neutron Scattering Study

Fully atomistic molecular dynamics (MD) simulations have been carried out on sodium dodecyl sulfate (SDS), an anionic micelle, and three cationic (C_<i>n</i>TAB; <i>n</i> = 12, 14, 16) micelles, investigating the effects of size, the form of the headgroup, and chain length. They have been used to analyze neutron scattering data. MD simulations confirm the dynamical model of global motion of the whole micelle, segmental motion (headgroup and alkyl chain), and fast torsional motion associated with the surfactants that is used to analyze the experimental data. It is found that the solvent surrounding the headgroups results in their significant mobility, which exceeds that of the tails on the nanosecond time scale. The middle of the chain is found to be least mobile, consolidating the micellar configuration. This dynamical feature is similar for all the ionic micelles investigated and therefore independent of headgroup form and charge and chain length. Diffusion constants for global and segmental motion of the different micelles are consistent with experimentally obtained values as well as known structural features. This work provides a more realistic model of micelle dynamics and offers new insight into the strongly fluctuating surface of micelles which is important in understanding micelle dispersion and related functionality, like drug delivery