(253ay) A General Tool Chain for Screening of Soft Materials

Authors: 
Klein, C., Vanderbilt University
Sallai, J., Vanderbilt University
Jones, T. J., Vanderbilt University
Iacovella, C. R., Vanderbilt University
McCabe, C., Vanderbilt University
Cummings, P. T., Vanderbilt University
We present a set of tools [1] used to generate arbitrary starting configurations for molecular dynamics simulations and enable users to rapidly screen the parameter space of soft materials with a particular focus on systems involving functionalized surfaces. The core tool, mBuild [2], generates starting configurations by minimizing or even eliminating the need to explicitly translate and orient components when building systems - users simply state which components to connect. mBuild supports parameterized structures through generative modeling. This allows for declaratively expressing repetitive structures, e.g. polymer chains, crystal structures, planar or spatial tiling, as well as for parameterizing the affine transformations applied to subcomponents of a composite component. For end users, this minimizes and often eliminates the need to explicitly rotate and translate components when assembling systems. Additionally, the approach enables users to programmatically vary parameters for a family of systems (e.g., polymer chain length) or interchange individual components (e.g., polymer type), while still employing the same general framework. Building upon prior work [2], we demonstrate the utility and flexibility of our tool chain by examining the frictional properties of several families of monolayers. Specifically, we explore the parameter space of alkane and PEG monolayers on both crystalline and amorphous substrates with varying surface patterns. Surface density and patterning of the monomers as well as monomer chain length are trivially tunable via the mBuild python interface that is designed to integrate with the scientific Python stack. As such, this allows the rapid generation of unique input files, which were used as input to perform parameter sweeps of the structural and tribological behavior of the monolayers.

[1] J. Sallai, G. Varga, S. Toth, C.R. Iacovella, C. Klein, C. McCabe, Á. Lédeczi, P.T. Cummings. "Web- and Cloud-based Software Infrastructure for Materials Design." The 14th International Conference on Computational Science (ICCS), Procedia Comput. Sci., 2014, 29, 2034-2044

[2] C. Klein, J. Sallai, T.J. Jones, C.R. Iacovella, C. McCabe, P.T. Cummings. "A hierarchical component based approach to screening properties of soft matter." accepted at Mol. Mod. and Sim.: Applications and Perspectives