The CIMS project is creating instructional materials that, while designed for use
in discipline-specific courses, aid students in drawing connections between disciplines such
as chemistry, biology and materials science. The scope is molecular science, including both
the study of how molecular structure and motion lead to emergent macroscopic properties, and
the synthesis/engineering of structures with desirable properties. The disciplines share these
goals of molecular science and, although the focus and details may differ, recurring patterns
appear in the explanatory frameworks and tools employed in each of the disciplines. The materials
make these recurring patterns explicit for students, such that they can integrate the ideas
across disciplines and construct a coherent and robust base of molecular science knowledge.
Tutorials
Reaction energy profiles Diagrams that show free energy along a reaction coordinate are used throughout science
to discuss thermally-activated processes such as chemical reactions, diffusion of particles on
surfaces, and protein folding. This is a complete and tested tutorial on the meaning of
"reaction coordinate" and "free energy", and how to use these diagrams
to predict the effects of temperature on chemical processes.
Particulate Level Visualizations
The following are links to some particulate level visualizations. Please contact us if you would
like to help evaluate curricular materials built around these simulations.
Inelastic collisions
Solid materials have a wide range of values for physical properties like electrical conductivity, thermal
conductivity, hardness, etc. Often, properties that are easily macroscopically observable arise from the
nature of the bonds between the atoms making up the materials.
In this exercise, bouncing balls composed of atoms held together by harmonic springs are used to show transfer
of energy into the internal degrees of freedom (i.e. heat) during an elastic collision.
Osmotic pressure
When a balloon is filled to near bursting with SF6 is left
in air, it will often burst after a period of time. This is because the smaller
N2 molecules diffuses into the balloon while the
larger SF6 molecules remains trapped inside.
This is an example of osmotic pressure. This simulation shows this process at the atomic level.
Brownian motion
Particulate level simulations that show only solute particles are convenient, since they
focus student attention on the molecules of most interest. However, such solute molecules
move in a Brownian manner. This simulation helps students show solutes moving in a solvent,
and allows the solvent to be made invisible. Comparison of this with Brown dynamics prepares
students for later simulations that do not include solvent explicitly and instead use
Brownian dynamics.
Chemical Potential- Staircase Demonstration
As we look for connection points across disciplines, we are increasingly drawn to chemical
potential as the connection point. This simulation shows particles thermally distributed on a
staircase. A linear increase in energy leads to an exponential decrease in particle concentration.
This sets up a key aspect of chemical potential, i.e. that the chemical potential has a
contribution that goes as log([concentration]).
The above are constructed with a general simulation engine implemented in Adobe Flash.
This engine supports:
- Weak interactions via Lennard-Jones potentials - Covalent interactions via harmonic springs - Ballistic (i.e. gas phase) dynamics - Brownian dynamics - Walls with specific temperatures - Semi-permeable membranes - User-specifiable reactions (i.e. formation and breaking of covalent bonds) - Construction of user interfaces via Adobe Flex, which makes creating an interface
accessible to those with little programming experience
We are looking for educators interested in testing simulations and associate curricula,
or helping build additional simulations. For more information and access to
unreleased simulations and additional curriculum materials, please
