Modeling of Complex Systems

Subgroup leader:
Prof. Dr. Beata Ziaja-Motyka


The Modeling of Complex Systems subgroup explores how the unique properties of X-ray free-electron laser radiation may be employed to characterize and modify extended atomic or molecular assemblies and solids. Among our research interests are:

1. Radiation-Induced Changes in Complex Systems.

The X-ray flashes from a free-electron laser will enable novel 3D insight into the nanoworld and thus shed light on future technological applications. The theoretical goal is to investigate ultrafast transformations in solids induced by intense radiation, such as changes of optical and magnetic properties of materials, and formation of defects.

Example: Nonthermal phase transition in semiconductors induced by a femtosecond XUV laser pulse.

The illustration of the graphitization process in diamond induced by the ultrashort XUV laser pulse. Six snapshots of atomic positions in the supercell for the case of the energy deposition of 0.95 eV per atom recorded at different times (0 fs, 20 fs, 40 fs, 60 fs, 80 fs and 100 fs). The position of the maximum of the Gaussian-shaped laser pulse is at 30 fs. The figure was prepared with help of VESTA 3 plotting software.

Thermal and nonthermal melting of silicon under femtosecond x-ray irradiation. For silicon under a femtosecond x-ray irradiation, the non-adiabatic energy exchange triggers a phase transition into low-density liquid (LDL) phase above the threshold of ~0.6 eV per atom in terms of the absorbed dose. This semi-metallic state is characterized by a closed band gap, with the local order present in atomic structure. At higher doses above 0.9 eV/atom, silicon melts into high-density liquid (HDL) phase with amorphous atomic arrangement. The modeled phase transition occurs within 300-500 fs, in a good agreement with the timescales observed in experiments. The transition into high-density liquid phase proceeds as a result of the interplay between nonthermal and thermal effects. Neglecting electron-phonon coupling results in a significant overestimation of the phase transition threshold, which then is ~2 eV/atom.

Selected references:

N. Medvedev, H. O. Jeschke and B. Ziaja,
"Nonthermal phase transitions in semiconductors induced by a femtosecond XUV laser pulse",
New J. Phys. 15 (2013) 015016 ;

J. Gaudin et al.,
"Photon energy dependence of graphitization threshold for diamond irradiated with an intense XUV FEL pulse",
Phys. Rev. B 88 (2013) 060101;

N. Medvedev, H. O. Jeschke, B. Ziaja,
"Nonthermal graphitization of diamond induced by a femtosecond X-ray laser pulse",
Phys. Rev. B 88 (2013) 224304

N. Medvedev, Z. Li, B. Ziaja , " Thermal and nonthermal melting of silicon under femtosecond x-ray irradiation " , Phys. Rev. B 91 (2015) 054113

2. Diffraction Imaging Techniques.

Using the X-ray flashes from a free-electron laser, scientists can uncover the atomic structure of biomolecules, cell constituents, and viruses. This provides the basis for future medical breakthroughs. Research by the theory group is focused on novel techniques to retrieve static and dynamic information on the structure of the imaged objects at atomic resolution.

Example: Coherent diffraction imaging of a biomolecule



(a) Atomic arrangement of a three-phosphoglycerate kinase molecule (pdb:2YBE). A study molecule, chosen for the Single Particles, Clusters and Biomolecules (SPB) Instrument - experiment modeling project at the European XFEL. (b) Visualization of the 3D simulated diffraction data from a three-phosphoglycerate kinase molecule (pdb:2YBE). Here: ideal case, without radiation damage.

Selected references:
A. P. Mancuso et al.,
"CONCEPTUAL DESIGN REPORT Scientific Instrument Single Particles, Clusters, and Biomolecules (SPB)",
XFEL.EU TR-2011-007, January 2012.

B. Ziaja, Z. Jurek, N. Medvedev, V. Saxena, S. K. Son, R. Santra,
"Towards realistic simulations of macromolecules irradiated under the conditions of coherent diffraction imaging with an X-ray Free-Electron Laser" ,
Photonics 2 (2015) 256

3. Properties of Laser-Created Plasmas.

With an X-ray free-electron laser, plasmas can be created that are as hot as the interiors of giant planets. It will be possible to follow the evolution of dense plasmas in time. The theoretical research of our group concentrates on the properties of plasmas far from equilibrium, and on the high-field regime that leads to the creation of new states of matter.

Example: Effect of screening by external charges on the atomic orbitals.

K-shell thresholds for aluminum as a function of the charge state calculated with the two-step HFS model. The experimental data are taken from Ciricosta et al., PRL 109 (2012) 065002. Unscreened HFS refers to calculations for isolated ions.


S. K. Son, R. Thiele, Z. Jurek, B. Ziaja and R. Santra,
"Quantum-mechanical calculation of ionization potential lowering in dense plasmas", PRX 4 (2014) 031004.

Example: Nanoplasma formation by high intensity hard x-rays.

Electron emission spectra from hard x-ray irradiated Xe clusters.

Nanoplasma formation from Ar and Xe clusters irradiated by intense x-ray pulses was investigated with our modeling tool, XMDYN, and compared to the experimental data obtained at the XFEL facility SACLA. We found that in this wavelength regime nanoplasma formation is a highly indirect process. In Ar clusters it is predominantly triggered by secondary electrons rather than by photo- or Auger electrons. It is formed already during the x-ray pulse but the following thermal electron emission lasts long after the pulse is finished. The simulation of xenon clusters (Z=54) was the first demonstration of a novel methodological development connecting the codes XMDYN and XATOM on-the-fly. This enables high-accuracy modeling of systems containing deep-shell ionized heavy atoms.


T. Tachibana et al., " Nanoplasma formation by high intensity hard x-rays " , Sci. Rep. 5 (2015) 10977