The geometrical mutual AFM simulator: GeoAFM

In this page, we introduce to you a simulation mode of the GeoAFM, a simulation mode for obtaining the shape of the tip from the sample surface data and the observed AFM image.
We link items representing various examples of calculations with the GeoAFM to other web pages below.
Following these links and jumping into the other web pages, you can obtain a movie file and documents that explain how to use the software.
Using a sophisticated Graphical User Interface, you can freely edit the project file, in which various input parameters for the calculation are described.
If you want to prepare structural data of the sample material by yourself, please refer to the web page, "how to prepare structural data of the sample materials".
Using these contents in an effective manner, you can learn how to use the GeoAFM.

[A simulation mode for obtaining the shape of the tip from the sample surface data and the observed AFM image]

You can estimate the shape of the tip from the sample surface data and the observed AFM image.
This simulation mode examines measurements of the contact AFM.
Thus, this simulation mode examines the case where the tip on the cantilever is in contact with the surface of the sample and it scans the whole surface of the sample.

Examples: please choose an example that helps you to perform your task from the following list:

A simulation of the shape of the tip from the observed AFM image for a Glycoprotein (1clg) on HOPG (Highly Oriented Pyrolytic Graphite) with a broken double tip and data of the sample material's molecular structure

A simulation of the shape of the tip from the observed AFM image for a GroEL (chaperonin) with a broken double tip and data of the sample material's molecular structure (The chaperonin is a basket-shaped polymer of 140 angstrom width, 140 angstrome depth and 200 angstrom height.)

A simulation of the shape of the tip from the observed AFM image for Si(111)-(7x7)DAS structure and data of the crystal structure

[How to prepare structural data of sample materials]
To perform the above simulations, you have to prepare structural data of sample materials.
Structural data of various proteins are provided as a pdf file format from the Protein Data Bank http://www.rcsb.org/pdb/home/home.do.
Using these structural data, you can perform simulations with ease.
We describe details of the structural data of the tips and the samples in this web page.
If you cannot find a proper structural data from the Protein Data Bank or if you do not know how to prepare the structural data of the sample material, pleasee contact us by e-mail at the bottom of this web page.

Documents

• We describe examples of simulations for obtaining the shape of the tip from the data of the surface of the sample and the observed AFM image with the GeoAFM in the tutorial.
• We describe details of how to set parameters of the simulation mode for obtaining the shape of the tip from the data of the surface of the sample and the observed AFM image with GeoAFM in the reference manual.
• We explain details of technical issues about obtaining the shape of the tip from the data of the surface of the sample and the observed AFM image with the GeoAFM on page 49, page 51, and page 52 in the guidebook.

If you cannot find an example that you want to perform from the above list, please contact us by e-mail.
When you send an e-mail to us, a string of characters is put into a subject of the e-mail automatically.
This string tells us at which stage of the simulation you have a trouble.

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