Molecular Workbench

Definition

The term Molecular Workbench has three distinct uses. It refers to an open source molecular dynamics engine developed for use in education, to a lesson authoring system that creates student learning activities based on the engine, and to a series of NSF-funded projects at the Concord Consortium which produced the software. A searchable database of Molecular Workbench learning activites contains over 200 entries that are freely available under the Creative Commons non-commercial license.

“The Molecular Workbench (MW) software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and 3D, it provides a simulation platform for teaching and learning science through atomic-scale reasoning. Many important concepts in physics, chemistry and biology that are otherwise too abstract to understand can be visualized with dynamical and interactive simulations.” ( Molecular Workbench retrieved 19:06, 21 July 2006 (MEST). )

The MW engine includes several unusual capabilities that make it useful in explaining and exploring chemical reactions, self-assembly in biological and nano-science systems, and light-matter interactions. The authoring environment supports the creation of simplified user interfaces, a variety of outputs, html text, and student assessments. 3D molecular visualizations can be placed on a MW page and then navigated to explore the shape and interactions in a complex molecule. Basic authoring is WYSIWYG based on a word-processor, but there is also a complete scripting capacity for more sophisticated applications.

See also: microworlds, simulation, visualization, authoring environment.

“MW is based on rigorous molecular dynamics calculations. Its simulation capacities and scientific accuracy are endorsed by calibrating simulations that self-prove scores of scientific laws. Scientists and engineers will find it useful in analyzing physical and chemical processes with simple, abstract models. Such models can be used to prove a concept, design a thought experiment, or serve as a prototype computational model before commiting to more concrete but usually time-consuming calculations involving considerable efforts. MW's revolutionary user interface enables users to quickly build a computational model, set up a simulation and immediately see the results while the simulation unfolds directly on the screen. Furthermore, when a simulation is saved, all the parameters, scripts, annotations and records also get saved in a format that can be loaded back in exactly the same original WYSIWYG form. You are absolutely freed from the burden of having to maintain numerous parameter-result sets in a traditional bookkeeping style.” ( Molecular Workbench retrieved 19:06, 21 July 2006 (MEST). )

System

Molecular Workbench is a special browser for opening model and simulation-based activities

The system runs under Java.

Versions:

• Java Web Start
• Stand-alone

Links

Molecular Workbench homepage (including downlowds)