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A poster describing the Molecular Simulation Design Framework, software tools that are collaboratively developed to support transparent, reproducible, usable, and extensible molecular simulations. &nbsp

Single slide for presentation at NSF CSSI PI meeting in Seattle, WA, February 13-14, 2020Molecular simulation plays an important role in many sub-fields of science and engineering. Systems composed of soft matter are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges since the differences in potential energy between distant configurations are on the same order as the thermal motion, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Furthermore, performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ``bespoke’' fashion. The result is that many soft matter simulations are not reproducible based on the information provided in a publication, and large-scale screening of soft materials systems is a formidable challenge. To address the issues of reproducibility and computational screening capability, we have been developing the Molecular Simulation and Design Framework (MoSDeF) software suite. We also propose a set of principles to render molecular simulations Transparent, Reproducible, Usable by others, and Extensible (TRUE). While it is not required to use MoSDeF to create TRUE simulations, MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in performing molecular simulations, thus enhancing their reproducibility.

Molecular simulation plays an important role in many sub-fields of science and engineering. Systems composed of soft matter are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges since the differences in potential energy between distant configurations are on the same order as the thermal motion, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Furthermore, performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ``bespoke’' fashion. The result is that many soft matter simulations are not reproducible based on the information provided in a publication, and large-scale screening of soft materials systems is a formidable challenge. To address the issues of reproducibility and computational screening capability, we have been developing the Molecular Simulation and Design Framework (MoSDeF) software suite. We also propose a set of principles to render molecular simulations Transparent, Reproducible, Usable by others, and Extensible (TRUE). While it is not required to use MoSDeF to create TRUE simulations, MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in performing molecular simulations, thus enhancing their reproducibility.

Molecular simulation plays an important role in many sub-fields of science and engineering. Systems composed of soft matter are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges since the differences in potential energy between distant configurations are on the same order as the thermal motion, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Furthermore, performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ``bespoke’' fashion. The result is that many soft matter simulations are not reproducible based on the information provided in a publication, and large-scale screening of soft materials systems is a formidable challenge. To address the issues of reproducibility and computational screening capability, we have been developing the Molecular Simulation and Design Framework (MoSDeF) software suite. We also propose a set of principles to render molecular simulations Transparent, Reproducible, Usable by others, and Extensible (TRUE). While it is not required to use MoSDeF to create TRUE simulations, MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in performing molecular simulations, thus enhancing their reproducibility.

Poster that detailed preliminary work related to examining the structure/property relationships in lubricating monolayer films using molecular dynamics and the molecular simulation and design framework (MoSDeF) to perform screening.This poster won first prize at the 2018 Vanderbilt University Data Science Symposium.

This project is focused on developing, deploying and distributing the Integrated Molecular Design Environment for Lubrication Systems (iMoDELS), an open-source simulation and design environment (SDE) that encapsulates the expertise of specialists in first principles, forcefields and molecular simulation related to nanoscale lubrication in a simple web-based interface. The iMoDELS SDE is being developed using model-integrated computing (MIC), a state-of-the-art powerful, well-established, extensible, community-supported, and application-hardened software engineering framework that supports scientific and engineering workflows. Making iMoDELS broadly accessible is motivated by the high cost (over $800B/yr in the US) of friction and wear, which, along with the methodology to overcome them, lubrication, are collectively known as tribology. Tribology involves molecular mechanisms occurring on a nanometer scale, and hence understanding tribological behavior on this scale is critical to developing new technologies for reducing wear due to friction. Deployment of iMoDELS will enable non-computational specialists to be able to evaluate, design and optimize nanoscale lubrication systems, such as hard disk drives, NEMS (nanoelectromechanical systems) and MEMS (microelectromechanical systems), and experiments involving rheological measurements via atomic force microscopes (AFMs) and surface force apparatuses (SFAs).