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.

Abstract: Microscopic structure of a fully hydrated di-palmytoil-phosphatidyl-choline lipid bilayer mem- brane in the liquid-crystalline phase has been analyzed with all-atom molecular dynamics sim- ulations based on the recently parameterized CHARMM36 force field. Within the membrane a single molecule of the alpha-aminoacid tryptophan (precursor of important neurotransmitters such as serotonin and melatonin) has been embedded and his structure and binding sites have been explored. In addition, properties such as radial distribution functions, energy and pressure profiles and the potentials of mean force of water-tryptophan and lipid-tryptophan have been evaluated. It has been observed that tryptophan tends to be close to the lipid headgroups but that it can be fully hydrated during short time intervals of the order of 1 ns. This would indicate that hydrophobic forces as well as the attraction of tryptophan to polar sites of the lipids play a significant role in the definition of the structure and binding states of tryptophan.