Molecular Dynamics Movies

The movies below (click on the blue links) were done in our research group using the LAMMPS (or Tinker) programs and visualized with the VMD program. 


1) Hydrated Na-Fluorohectorite

The simulation was done with the ClayFF force field (pbc, NPT, 300 K and 1 atm, 4165 atoms). The amount of water was varied to reproduce the experimental inter-lamellar space: d_exp = 12.4 A, d_theo = 12.39 A. For more info, see Langmuir 32 (2016) 10582-10588.


2) Nanoparticle-Ceramics 

The simulation was done with the EAM (nanoparticle) and Tersoff (ceramics) force fields, and using a Lennard Jones potential to describe the ceramics-nanoparticle interaction. We used pbc in two dimensions, NPT, 300 K and 1 atm (6872 atoms). The final density, radial distribution functions (RDF) and approximate structure match the experimental data. For more info, see Phys. Chem. Chem. Phys. 18 (2016) 31966-31972.


3) Nanoparticles 

The simulated annealing technique may be used to find low energy minima of nanoparticles. Here, we carried out a Molecular Dynamics simulation using the LAMMPS program (NVT, EAM, vacuum) to find a minimum-energy structure (= truncated octahedron) of Pd1289. This was one of many simulations used in the investigation published at Angew. Chem. Int. Ed. 51 (2012) 11473-11477.

4) Localized Atomic Mobility 

The concept of short-time scale localized atomic mobility was used to investigate the stability of different regions and layers of transition-metal nanoparticles. The simulation shown was done using the LAMMPS program (NVT, EAM, vacuum) to visualize how corner, edge and face atoms of different layers melt (the last three layers are shown). This mobility was combined with a quantum Density-of-States calculation to qualitatively discuss localized catalytic activities at those atomic regions. For more information, see J. Phys. Chem. C 118 (2014) 21647-21654.

5) Supramolecular Columns 

This simulation shows how stable are supramolecular columns formed by cyclohexane-trisamides. The Molecular Dynamics was carried out with TINKER (pbc, MMFF94). Different views of the system are shown: top view (up, left), side view emphasizing the hydrogen bonds (blue lines, up, right), and side and top view of the central column (down, left). For more information about supramolecular columns, see Chem. Eur. J. 19 (2013) 1647-1657. For information about supramolecular columns with transition metal complexes, see Chem. Eur. J. 22 (2016) 17681-17689. 

Cover page 

“Proton activity inside the channels of zeolite L”, R.Q. Albuquerque, G. Calzaferri,  Chem. Eur. J. 13 (2007) 8939.

VIP paper 

“Photoactive hybrid nanomaterial for targeting, labeling and killing antibiotic resistant bacteria”, C.A. Strassert, M. Otter, R.Q. Albuquerque, A. Höne, Y. Vida, B. Mayer, L. De Cola, Angew. Chem. Int. Ed. 48 (2009) 7928.

Pictorial view of the multifunctional nanomaterial used to target, label, and photoinactivate antibiotic-resistant bacteria. The zeolite L nanocrystal is loaded with the DXP emitter (green ellipsoid), and its surface is functionalized with a phthalocyanine derivative (red ellipsoid) and with amino groups (blue circles), where the latter provide noncovalent binding of the hybrid nanomaterial to the bacterial surface. On the right, a schematic view of the connection of the functional groups to the zeolite L framework is shown.


International Press

Paper (Angew. Chem. Int. Ed. 48 (2009) 7928) cited in the research highlights of a journal of the Nature group.