Home Page About CC-ATOMS Proposal Work Description - proposal

Proposal Contents: Summary Introduction Need Goals Research Activities

CHEMICAL BONDS

We expect to be able to designate certain bonds in complex molecules as chemically active, set the valence of certain atoms, and allow users to determine for each possible reaction the energy gained or lost in the reaction as well as the activation energy. This functionality will be added to our molecular dynamics simulators. This capacity should facilitate student explorations of exothermic and endothermic reactions, explosions, chemical equilibria, reaction constants, reaction pathways, reaction rates, catalysis, the effects of solvents, precipitation, and many other important chemical phenomena.

Three Dimensions
Chemistry and biology applications depend on three dimensional calculations and visualizations. Understanding chirality, conformation, reaction site specificity, catalysts, secondary and tertiary structures, and crystals will all require three-dimensional representations. We will extend MW3D to incorporate simulators and a DAEs for calculating and displaying three dimensional molecular dynamics and chemical bonds. This will be built on our MW3D to better harness the stunning power of 3D graphics, build up highly interactive and integrated simulators that resemble their MW2D counterpart, and establish connections to vast materials and biomolecule databases on the Internet.

Large Biological Systems
To explore the steric ligand-receptor interactions at active sites, we will experiment with ways of reducing the number of degrees of freedom using approaches that are used in the research literature. This can be done by a coarse-grained approach, for instance, constructing larger molecules from meso-scale objects. Another approach is to compute molecular dynamics or energy minimization for optimal binding for only the particles contained inside a small sphere around the reaction site (the active zone). All other parts of the solvent and molecule are ignored and their effect is approximated using an effective field approach. Meanwhile, the molecular images of this peripheral zone are rendered using more economical approaches such as a wire frame mode to provide a graphical background of the whole system. Despite the fact that a considerable scientific accuracy is traded off for the interactivity and performance required by education, this approach combines some scientific value and a great deal of educational value. Therefore, it can be regarded as an "educational solution" for complex simulations.
To understand the conformation of large polarized molecules and how they might fit together to accomplish a biological process, such as molecular recognition, we will develop an energy hypersurface hopping algorithm that includes a fast energy minimization algorithm and compensation for temperature effect. The proposed algorithm is based on an algorithm we developed in MW2D. Further improvements will focus on making it suitable to biomolecular systems and being able to reach the target in the tremendous phase space with less time steps. Equipped with such an algorithm, a carefully designed virtual experiment could be used to help students understand the way a ligand binds to a receptor site or how the secondary and tertiary structure of a large protein is influenced by the shape and charges of its constituent amino acids.

Light
To be able to address topics such as photonics and spectroscopy, we need to be able to model photon interactions with electronic and vibrational states of ensembles of atoms and molecules. Light will be represented as photon particles that can interact with atoms and molecules. Excited electronic and vibrational states will have to be added to the system as well as rules for emitting and absorbing photons. We will not attempt an exact model, but one sufficient to conserve energy while illustrating energy-dependent absorption and emission, coherence, fluorescence, and various photochemical effects.

Twelve units will be developed using WISE, Pedagogica, and one of the Molecular Workbench models, MW2D or MW3D.

Identify collaborators. The materials will be developed in collaboration with faculty at collaborating two-year colleges and curriculum experts. These will include long-time collaborators at the Springfield (MA) Technical Community College (STCC) and others throughout the US recruited through the Center for Occupational Research and Development (CORD) and their Community College Presidents Council. We will identify at least ten faculty from these colleges who will assist us in the materials development and testing process.
Choose topics. With our faculty collaborators, we will identify two concepts in each of biology, chemistry, and physics that are typically taught in technical education and could be illustrated with atomic-scale models. For each of the six concepts, we will develop two or more different applications which some technical students are likely to encounter in their specialty areas, giving a total of at least twelve topics. For example, one concept might be osmosis and applications might to dialysis, recovery through reverse osmosis , and water treatment . Topics will be chosen that could be used in either a core science course or a specialty technical course.
Identify learning goals. Using a "backwards design" approach (Wiggins & McTighe, 1998), we will begin curriculum development by specifying the learning goals for each topic and the evidence we will use to determine whether students achieve these goals. These goals and evaluation criteria will be vetted with collaborating faculty.
Develop hypermodels. For each topic, we will script a series of models in Pedagogica­hypermodels­that support guided exploration of the ideas behind each of the learning goals. We will design embedded assessments that can gather the evidence on student performance that we identified in the previous step.
Develop projects. We will develop twelve complete WISE projects that are based on the hypermodels for each of the topics. Additional student assessment derived from the learning goals will be built into the WISE projects.
Field test. We will make the projects widely available to educators at any level who are willing to provide us with evaluation data. To ensure quality implementations, we will identify at least ten pilot field test sites where two-year college faculty will be provided with assistance in implementing and adapting the projects. No site is likely to use all twelve projects, but we will ensure that each of the projects is tested at multiple sites.
Timetable
This will be a two-year project scheduled to start in the fall of 2002. The model and software development will be completed in the first year as well as the integration of hypermodels with WISE.

Also during the first year, collaborating faculty will be identified, and the twelve pilot topics and required hypermodels defined.

The second year will focus on developing and testing the curriculum materials.

The hypermodels and WISE projects will be developed in the fall of 2003 and tested in classes over the winter and spring of 2003-4.

Student performance data and the implementation studies will be analyzed in the spring and summer of 2004. Testing, debugging, and documentation of the Molecular Workbench software will continue in the seco

This material is based upon work supported by the National Science Foundation under Grant No. EIA-0219345. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.