Simbios Talk by Victor Pinks II, Marmion Academy, July 8, 2009

Title: "The Computational Microscope" - Integrating Molecular Dynamics Simulations into Laboratory Exercises with OpenMM Zephyr

We have begun development of interactive chemistry, biology and physics experimentation ‘in-silico’ at Marmion Academy. Our goals are to make this system accessible to science students to perform three dimensional ‘live’ modeling of chemical systems fundamental to physics, chemistry and biochemistry. Live simulations are not ‘movies’ of molecular motion. They are ‘actual computer experiments’ which have become the foundation of new research in academic, industry and governmental efforts to speed up the discovery process for new drugs, materials and nanotechnology (for starters).

We believe these tools are also useful for teaching purposes. Studies show that combining the visual channel with traditional hands-on laboratory experimentation accelerates the amalgamation of conceptual understanding of the chemical physics phenomena underlying laboratory observation. Interactive molecular dynamics allows students to see observables like temperature, pressure, freezing, boiling and osmosis at the atomic level. It is at this level that many chemical concepts are fundamentally similar and can be simplified by live modeling for students to assimilate using their natural abilities.

Our ultimate goal is to develop a curriculum that is both simple yet high impact. In this talk, I will describe our efforts using OpenMM Zephyr to build this curriculum. Our initial focus will be on the fundamental effects of 1) anharmonicity plus modeling of forces combined with 2) differences of chemical structure on the overall macroscopic behavior of measureable quantities such as the colligative properties of solutions, freezing, melting, partial pressures, and the self-organization of various phases of matter. This will subsequently be extended to explicit water, nano-materials and large molecule systems (including proteins) that can be instructional and easily integrated into an AP laboratory curriculum.

Dr. Victor Pinks II is the Technology Director and Science Department Chairman at Marmion Academy in Aurora, Illinois. He is a computational scientist formally mentored by chemical physicist Robert S. Wilson (Northern Illinois University) who saw molecular dynamics (MD) simulations as a means to test various spectral lineshape theories. The Wilson Group specialized in algorithm and molecular dynamics engine authoring methods. A strong theoretical background combined with MD algorithm development/engine authoring/coding plus traditional graduate training have been significant in guiding his work to integrate computer simulations into real laboratory exercises. Dr. Pinks continues independent research to bridge real world experiments with model world simulations through the development of his feedback mechanism for MD that allows ‘realism convergence’ of force functions through parameter optimization of both theoretically transparent and opaque models.