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Flying over Atoms


Jack Markham
Laconia High School, Rosendale, WI 54974

Flying over Atoms is a CD-ROM for Mac OS and Windows that provides tools for teaching about atoms and solid surfaces in an introductory chemistry course. Flying over Atoms introduces and stimulates interest in atomic surfaces and current methods for imaging at the atomic scale.

Flying over Atoms uses Scanning Tunneling Microscope (STM) data and the software program Vistapro, published by Rom Tech, Inc. (not provided) to allow students to create QuickTime movies of atomic landscapes. Several sample movies created using Vistapro by the author and his students at Laconia High School are provided on the CD as well as an introduction to scanning tunneling microscopy, a lesson plan, and STM images and data files.

Flying over Atoms is one of JCE Software's most interesting and unusual publications. It represents a partnership between a dedicated high school teacher and a team of research scientists that should be an inspiration to teachers and researchers alike.

The original submission of data files for Vistapro and a few introductory images blossomed into an exciting collection of information, images, and movies that allows students to experience surfaces at the atomic level, even without Vistapro.

Reviewer Comments

Our reviewers (experienced computer-oriented chemistry educators) had this to say about Flying over Atoms:

I would very much like to see this program published. I believe it is a very creative application of Vistapro.
My high school students were very curious about each picture.
Probably lots of us have been using STM images in our introductory classes to make the existence of atoms more believable to skeptical students. The animations present in this submission make the images much more interesting--the motion adding to the 3-D perception. I think it's also nice that the STM data were obtained from an honest-to-goodness researcher--almost pioneer--in the STM field.
I have to say this is one of the most interesting and innovative submissions to JCE Software I've seen in a long time. Bravo to the author.

How to Use Flying over Atoms

Flying over Atoms is appropriate for use in introductory chemistry classes. Instructors can use the images and introduction as lecture aids when introducing solids and surfaces. The materials are also appropriate for independent use by individual students or groups of students. The images and movies will allow students to explore many aspects of solid surfaces. If they have access to Vistapro, students can explore the surfaces on their own, finding and identifying interesting surface features.

Students need guidance as they use the materials in Flying over Atoms. The instructor should become familiar with STM by using the materials in Flying over Atoms and then present an explanation to students. It is the author's experience that high school students will not sit down with materials like Flying over Atoms and go through all the reference materials independently. The materials must be presented to them in an interesting and thought provoking way. Then, they will enthusiastically explore the STM images, Vistapro atomic landscapes, and make movies. The lesson plan on the CD will help in developing such a presentation.

Development History

Vistapro is a three-dimensional graphic editor that creates topographical maps based on Digital Elevation Model (DEM) data from the United States Geological Survey. The user can edit and enhance the landscape in numerous ways, and explore it at ground level or from the air. Vistapro has been used in geology, earth science, and astronomy courses to allow students to visualize and explore distant areas of the earth, the surface of the moon, and planets where data are available.

The author became familiar with Vistapro when he used the data for Mars included on the Vistapro CD with his physics students. He wondered if the elevation data from a scanning tunneling microscope could be used with Vistapro. A data translation utility made this possible. The resulting data files, images, and movies evolved into the Flying over Atoms CD.

Hardware and Software Requirements

Hardware and software requirements for Flying over Atoms are listed in Table 1. In addition, Adobe Acrobat Reader is required to read the documentation.

Table 1. Hardware and software requirements.
Computer CPU RAM Drives Graphics System Software Included Software Not Included
Mac OS Compatible 68030 or Power Mac > 16 MB 2 x CD-ROM
Hard disk
Color monitor > 256 colors System 7 or higher QuickTime
Acrobat Reader
WWW Browser
Windows Compatible 80386 or higher > 12 MB 2 x CD-ROM
Hard disk
Color monitor > 256 colors Windows 95
Windows 3.x
Acrobat Reader
WWW Browser


Bob Hamers of the University of Wisconsin-Madison Department of Chemistry was very helpful to the author during the development of Flying over Atoms. Members of his research group including Harry Chen, Ernie Frank, and Steve Higgins contributed STM data and images. The introduction to STM included in Flying over Atoms was written by Ernie Frank.

John Hinkley, author of Vistapro, wrote a translation utility that allowed translation of RAW STM data into the DEM format that Vistapro requires.

The students of Laconia High School, past and present, helped test and work the bugs out of Flying over Atoms. QuickTime movies created by some of these students are included in Flying over Atoms.


Vistapro is a product of Rom Tech, Inc., 2000 Cabot Blvd., Suite 110, Langhorne, PA 19047; phone: 1-215-750-6606; WWW: http://www.romt.com/. Versions are available for Mac OS, Windows, and DOS. Vistapro can be ordered from the publisher for $69.95, and is also available from many retail software vendors.

What's included on the Flying over Atoms CD?

The contents of Flying over atoms are divided into several categories. In addition to a Read Me text file and a Welcome file at the root level of the Flying over Atoms CD-ROM, you will find the following folders or directories, with content described below.

INSTALL contains installation files for Mac OS and Windows computers.

DOCS contains documentation in Adobe Acrobat (*.PDF) format.

HTML contains HTML pages that allow you to access the images, movies, and data included in Flying over Atoms.

SURFACES contains QuickTime movies, still images, and data files for each surface.

The STM files provided in this Flying over Atoms package are in a format that allows them to be imported into either the Macintosh version or the PC version of Vistapro. Choose Open as DEM in Vistapro. Once the file has been opened, save it as a DEM file. Use this DEM file for subsequent image manipulation.

STM Data files

7001Ag.DEM is a Ag(111) surface imaged at 120 Kelvin. The size of the image is 1600 angstroms x 1600 angstroms. The triangular shape is due to the thermal contraction of two different layers, Si(111) as substrate and Ag(111). These straight lines correspond to some unique crystallographic orientation. You are looking at a topographic view. Each step has vertical height of 2.5 angstroms. Individual atoms are not resolved due to the sea of electrons characteristic of a metal. The RAW data file is 1000 angstroms on a side.

Silver Bunching After Chlorine Gas Exposure
034Ag.DEM is an example of silver step bunching. Upon exposure to chlorine gas, the steps on a silver surface, which were more or less randomly spatially distributed across the surface, bunch together into larger arrays of steps. Image size is 4000 angstroms x 4000 angstroms.

Clean Si 001 Empty State
7085Si.DEM is a clean Si(001) surface that was imaged at sample positive bias of +2.0 V. In other words, the microscope was probing the empty states. This can be linked to the concept of pi* orbitals such as in the carbon-carbon double bond. In that case, one would see a node between the two species in the bond. There are also some defects on the surface that show up as holes and protrusions. The RAW data file is 293 angstroms on a side.

Clean Si 001 Filled State
7084Si.DEM is a clean Si(001) surface that was imaged at a negative sample bias. In other words, the microscope was probing the filled states.

Si with 3% B
1081BSi.DEM is a Si(001) surface exposed to boron. The sample bias voltage is -2.0 V, so filled states are being imaged and the change in surface structure caused by boron adsorption can be seen by comparing this image to the clean filled state image. In addition, you find a zigzag pattern, which is also clean Si dimers except these are the "buckled" dimers (asymmetric dimers). Other somewhat disordered regions are due to the boron species. Complex boron substitution mechanisms result in something called c(4x4) surface reconstruction, which shows as a diamond shaped structure. You need a good topographic view to see this diamond shape. 3-D is not the best way to view it. The RAW data file is 234 angstroms on a side.

Low Coverage Bithiophene
3043bith.DEM is a Ag surface with a small amount of 2,2'-bithiophene adsorbed on the surface. The bithiophene molecules appear as elongated "hot-dog" shaped features on the surface. STM shows the molecules bond only at the edges of steps on the surface. The orientation of individual bithiophene molecules is also resolved and they align with the long molecular axis parallel to the step edge direction. Image size is 250 angstroms x 250 angstroms.

Copyright © 1998 Division of Chemical Education Inc. of the American Chemical Society.
All rights reserved.
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