Research focused on new materials is conceived as an independent whole that consists of physical and chemical laboratories. They are responsible for primary research in nano-technologies, properties of the technological basis for developing nano-structures, metering and diagnostics and application. The common thread between individual activities is the creation of mathematic-physical models, both in primary and applied research, and the application of supercomputer approaches for effectively solving these models:

  • Developing nano-particle carriers that will target transport medicine to a specific place in the human body
  • Developing new materials for the construction and engineering industries; for example, self-cleaning paint
  • Research of magnetic properties of holograms with the aim to improve their protective function
  • Research of nano-structures with plasma waves for sensors

RP4's project results to download:

This tool performes automatized calculation of interaction, cohesion, or adhesion energies between user defined parts of geometry optimized structures, or structures extracted from dynamics trajectories. Especially automatized treatment of large number of extracted structures significantly facilitates the analysis of simulation results. Tool may be utilized for analysis of long molecular dynamics trajectories needed for reliable study of interaction.

This set of scripts for MATLAB environment was created as a tool for determining the structural compatibility of two atomic planes (i.e. hkl planes, where hkl are Miller indices of given plane) of crystalline materials. Inputs include the coordinates of atoms in given planes, relevant distances between two atoms and size (area) of planes. Outputs are (a) visualization of overlap of two given atomic planes, (b) visualization of pairs of atoms in which the distance between atoms is equal or shorter than given relevant dostance, and (c) number of these atomic pairs. Input files containing the atomic coordinates can be created manually but the tool also allows you to calculate the coordinates of atoms in the plane rotated by a specific angle (together with automatic creation of input file with the newly calculated coordinates). Further, using this tool it is possible to determine the dependence of number of overlapping atoms on angle by which one atomic plane is rotated relative to the second one.

This tool is useful in study of nanocomposite structures containing crystalline components (nanoparticles on substrate, thin films on substrate, epitaxial growth).

This pack contains two m-files (mol_frag.m, MPRGP.m) for MATLAB environment and one illustration of input file (sample.txt).
Based on the results of elemental analysis of given real sample this tool is able to calculate the ratio of molecules or molecular fragments present in the sample. Also the charges (if we are dealing with ions) are taken into account. Software is useful in cases where it is necessary to determine the amount of impurities – especially the residues after preparation process. Direct determination of the ratio of molecules or their fragments is significantly helpful during the preparation of molecular models that are the most similar to real models but it can be also helpful for the interpretation of experimenatl data obtained from elemental analysis.


Head of the research programme
  • Jaromír Pištora


Deputy head of research programme
  • Gražyna Simha Martynková
Research programme secretary
  • Jaroslav Vlček



IT4Innovations Newsletter Q1/2020
IT4Innovations Newsletter Q1/2020
The warranty support for Anselm from the supplier is to end on May 18, 2020
On May 18, it will be seven years since our first supercomputer Anselm was fully […]
Press Release: Field of HPC possible to study at a unique doctoral school
Press Release: Field of HPC possible to study at a unique doctoral school
Press Release: Czech supercomputers ready to combat coronavirus
Czech supercomputers ready to combat coronavirus
Preferential offer to use IT4Innovations computational resources related to COVID-19
Dear users of IT4Innovations computational resources, In the light of the current events regarding the […]
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