Choosing a type of a sample material
Data processing
Characteristic length Liquid environment or vacuum environment? Computation time Finishing the solver selection

SPM simulator: choosing a type of a sample material

In this page, we choose a type of a sample material that is examined in the SPM experiment.
Please choose the one from the following three types:
(1)high polymers and soft matters
(2)organic compounds
(3)surfaces of crystals of metals, semiconductors, and non-organic compounds
If you want to process digital images obtained by the SPM experiments and do not want to perform numerical simulations, please choose an item of "Digital processing of SPM images" at the end of this page.

If you have decided an experimental method such as AFM, STM, and so on, please click here. Otherwise, please read the following contents.

Which type of a sample material do you use in an experiment?

A type of a sample material

A method for an experiment

A characteristic length of measurements


High polymers and soft matters

AFM (Atomic Force Microscope)


DNA, proteins, collagen, anti-angiogenic peptides, rubber, materials with viscosity and surface tension, organic materials on the HOPG plate

Organic compounds

AFM (Atomic Force Microscope)


pentacene, pentacenequinone, octane, carbon nanotubes, fullerene, graphite, graphene sheets, porphyrin, butadiene, dichlorobenzene, phthalocyanine, polyacetylene, calcite, and other small molecules

Surfaces of crystals of metals, semiconductors, and non-organic compounds

AFM (Atomic Force Microscope),
STM (Scanning Tunneling Microscope),
STS (Scanning Tunneling Spectroscopy),
KPFM (Kelvin Probe Force Microscopy)


Si(111)DAS7x7, Si(001)-3x1:H, Si(001)-c(4x2), a bismuth atom on Ag(111), RuO2(110), TiO2(110), Au(001), metallic catalysts, mica

If you are not interested in the approach for classifying types of sample materials shown above and you want to process digital images obtained by SPM experiments, please visit the following page.

Digital processing of SPM images

You can process images obtained with SPM experiments and numerical simulations in a digital manner as you like.
You can use basic digital image processing tools, for example, the Fourier transformation, adjustment of contrast, edge detection, and noise reduction.
We prepare a tool for estimating a shape of the tip from experimental data of SPM.
We prepare a function to correct digital images obtained with SPM experiments using technologies of neural network learning.

The above experimental image is provided by Professor Hiroyuki Hirayama, Nano-Quantum Physics at Surfaces and Interfaces, Department of Materials and Engineering, Tokyo Institute of Technology.

If you cannot find a material that you want to examine from the above list, or if you cannot find a digital processing tool that you want to apply to your image data in this page, 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.