(683f) Quantifying Nanostructure within Molecular Simulations Using Geometry-Based Criteria

Authors: 
Greenfield, M. L., University of Rhode Island
Joodaki, F., University of Rhode Island
Molecular simulations have the potential to track the detailed positions and orientations of molecules over time or within a statistical mechanical ensemble. That wealth of information creates a corresponding challenge of inferring well-sampled physics from the underlying correlations and dynamics, particularly within multicomponent systems in which each molecule brings its own level of complexity. Our group has been revamping geometric analysis methods based on Delaunay and Voronoi tessellation so they yield measures of local microstructure within systems of heterogeneous composition. These tools aid with interpreting intermolecular packing and organization beyond the extent that can be attained using a radial distribution function. The tessellation process divides a simulation cell into a unique set of tetrahedra and polyhedra that fill the box. The shape and the physical extent of a microstructure domain are identified by neighboring polyhedra that share common features. In multicomponent simulations that represent a bitumen-water system, as an example, connected tetrahedra that are each defined by locations of 4, 3, or even 2 atoms of water molecules map the location of a water droplet. The geometric analysis method allows the average droplet volume and spatial extent to be sampled along a simulation trajectory. Tetrahedra with 2 atoms each from water and from bitumen define the interface, enabling direct calculation of its fluctuating shape. In a simulation of a bitumen that is modified by a "biobinder", the geometric analysis quantifies domains of different chemical classes within the bulk system as well as the partial molar volume of each molecule type in a highly multicomponent system. Existing capabilities to identify nanoscale voids within molecular simulation systems are being used to quantify sorption sites and diffusion paths within modified bitumen systems