Marc Rosner

Convent of the Sacred Heart, Upper School

Mentor: Dr. Anthony Nicholls

Funding and Support: Charles Edison Fund and Columbia University Summer Research Fellowship Program for Science Teachers

        August 1995

Molecular Modeling with Computers

Who: 8th Grade Physical Science
Where: Upper School Macintosh Laboratory
When: Fall Chemistry Unit
Why: To foster student appreciation for-and understanding of-the way scientists use computers to model molecules.


1. My research was driven by the theory that computer-based molecular modeling is useful in understanding the surface morphology, electrostatic potential, and reaction mechanisms of biological macromolecules. A practical problem associated with my work was crossing boundaries between different computer platforms.

2. Scientists have already firmly established the structure and function of many biological macromolecules. As all computer simulations are idealized representations of the real world, a certain purity of assumption places limitations on the power of the software to mimic reality. [Content Standard Unifying Concepts- Evidence, models, and explanations] The situation giving rise to this type of research is a virtual information explosion in structural biology, emanating from the discovery and confirmation of amino acid sequences in proteins; and in the need for scientists to represent and communicate their findings; and in the need for paradigms and tools to drive additional research.

3. In exploring this question, I conducted extensive molecular modeling on a Silicon Graphics Indigo 2, using GRASP software. I translated images via different media, including Kodak ColorEase prints and transparencies; software files in various operating systems; analog video; and quicktime movies. The biggest obstacle I encountered was finding a direct interface between the SGI and video. Other media translations worked well.

4. I learned a lot about specific biological macromolecules: their structure, function, and reactivity. I also discovered a great deal about computers, software, networks, and multimedia.

5. Further experiments could address the "fit" of molecules when they interact; by performing calculations of distance and charge in reaction complexes, we have the potential to identify rules and boundaries governing biochemical reactions.

6. I can make this research more concrete for my students by showing them images and videos of the molecules I studied, and leading them in basic molecular simulations of their own. [Teaching Standard E- Model skills of scientific inquiry] We will use RasMol and a color printer. Prior understanding which will act as a vehicle for intellectual growth includes basic biology, chemistry, physics, and computing. For instance, students have learned that amino acids are the building block of proteins; DNA encodes genetic instructions; enzymes speed up biochemical reactions with a "lock-and-key" style mechanism. In other words, they bring with them facts, theories, skills, and conceptions from their course work. Of course they also bring much from their own lives, their families, media, etc. And surely they bring misconceptions and simplification which we can potentially challenge together.

7. I think the simple molecular modeling will work well in my eighth grade physical science course; and the electrostatic interactions of proteins are appropriate for study in junior and senior physics and biology. Our art department is also developing a video editing course at upper levels, and I am offering consultation in Macintosh computers and quick-time movies.


1. Seat students, take attendance.

2. Demonstrate RasMac: opening files; moving and rotating structures; changing display options and colour schemes; exporting and printing images. [Teaching Standard D- Make science tools accessible]

3. Lead students in conducting above skills, practicing with aspirin and DNA. [Content Standard A- Use technology/mathematics to improve investigations]

4. Question and answers (worksheet or discussion): [Teaching Standard D- Orchestrate scientific discourse]

Which display options and color schemes would you choose to...
...identify the atoms in a molecule
...analyze the bonding and structure of a molecule
...guess how the molecule would interact with another molecule
...create a diagram for a research article or art for a magazine cover.
Content Standard E- Understandings about science/technology]

5. Printing.

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