MiW: A domain specific modeling environment for complex molecular systems

https://doi.org/10.1016/j.procs.2017.05.114Get rights and content
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Abstract

Interest in simulation based screening of soft materials for desired chemical and physical properties has grown in recent years, which promises a reduced time to discovery and significantly lower costs than experimentation. While programmatically generating simulator inputs is fairly straightforward for crystals or small molecules, this is still challenging for complex (connected) molecular systems in general, and soft materials in particular. To tackle this challenge, this work presents a domain specific modeling environment that (1) features a domain specific modeling language (DSML), capable of describing classes of molecular systems in a hierarchical, component based model, with a rich set of composition operators, and support for parameterizable systems though generative modeling; (2) a browser-based, intuitive graphical user interface; (3) support for online collaboration, sharing of components, support for version control with history and branching; and (4) an interpreter to visualize components and molecular systems, and to generate output understood by major molecular dynamics (MD) simulator tools. The paper includes a case study demonstrating the use of the modeling environment to build a generative model of a parameterizable nanostructure, to feed input to a simulation based screening workflow of nanolubrication materials.

Keywords

domain specific languages
component modeling
generative modeling
molecular dynamics

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