Choosing a type of a sample material Data processing

Characteristic length

Liquid environment or vacuum environment?

Computation time

Finishing the solver selection

SPM simulator: high polymers and soft matters (011b)

In this page, we recommend you FemAFM as a solver that simulates AFM images of high polymers and soft matters under micron scale in air environment about 30 minutes.

In this page, we suppose that the sample material is a high polymer or a soft matter. However, we can apply a method discussed here to organic compounds, metals, semiconductors, and non-organic compounds, as well.

We recommend you the following simulator:

FemAFM: the finite element method AFM simulator Advantages of the FemAFM are as follows: Describing the tip and the sample as continuous masses, the FemAFM performs simulations. Regarding tips and samples as continuous masses made of a single material and assuming the van der Waals force between the tip and the sample, the FemAFM solves equations of continuum mechanics for elastic bodies numerically and examines deformation of the tip and the sample. Considering adhesion between the tip and the sample material due to the viscoelasticity, the FemAFM can calculate the AFM force curve.

To perform the above simulation, you need to prepare structural data of the sample material.
Protein Data Bank http://www.rcsb.org/pdb/home/home.do provides you with structural data of various proteins as files with pdb format.
Using these structural data, you can carry out simulations with ease.

If you cannot find a simulation that you want to perform from the above list or if you do not know how to prepare structural data of your sample material, 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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