Scientific focus of the division:
- Synthesis of functionalized carbon-based materials (graphene, nanodiamonds, nanotubes, amorphous carbon, carbogenic quantum dots etc.) and their applications in biosensing, electrochemistry, water purification etc.
- Theoretical design and synthesis of novel carbon-based materials including graphene derivatives
- Development of hybrid carbogenic structures with embedded nanoparticles (Fe, Fe3O4,Si)
- Combined experimental and theoretical description of interaction of carbon nanostructures with biomacromolecules and their functional components
- Structure and dynamics of biomacromolecules and their functional components, interaction of biomacromolecules with membrane bilayer, enzyme and RNA catalysis, development of new theoretical tools for description of biomacromolecules, nanomaterials and their mutual interactions
- Molecular dynamics simulations of biomacromolecules, force field development and testing (namely for RNA), quantum chemical and hybrid QM/MM calculations, simulation of lipid bilayer penetration, interaction of metals with graphene.
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 Superhydrophobic properties of textile due to impregnation by carbon nanotubes |
Results highlights:
 Granatier J, Lazar P, Otyepka* M, Hobza* P: The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) to Plane-Wave DFT Calculations. J. Chem. Theor. Comput., 7(11), 3743-3755, 2011
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 Ditzler, M.; Otyepka, M.; Sponer, J.; Walter, N. Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Acc. Chem. Res., 2010, 1, 40-47.
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 Georgakilas V, Bourlinos AB, Zboril R, Steriotis TA, Dallas P, Stubos AK, Trapalis Ch. Organic functionalization of graphenes. Chem. Commun., 46(10), 1766-1768, 2010.
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 Riley, K. E.; Pitoňák, M.; Jurečka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories, Chem. Rev. 2010, 110, 5023–5063.
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 Zbořil, R.; Karlický, F.; Bourlinos, A. B.; Steriotis, T. A.; Stubos, A. K.; Georgakilas, V.; Šafářová, K.; Jančík, D.; Trapalis, C.; Otyepka, M. Graphene Fluoride: A Stable Stoichiometric Graphene Derivative and Its Chemical Conversion to Graphene, Small 2010, 6, 2885-2891.
Link
 Bourlinos, A. B.; Georgakilas, V.; Zboril, R.; Steriotis, T. A.; Stubos, A. K. Liquid-Phase Exfoliation of Graphite Towards Solubilized Graphenes, Small 2009, 5, 1841-1845.
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 Bourlinos, A.B.; Stassinopoulos, A.; Anglos, D.; Zboril, R.; Karakassides, M.; Giannelis, E.P., Surface functionalized carbogenic quantum dots, Small 2008, 4, 455-458.
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 Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham III, T. E.; Sponer, J.; Otyepka, M., Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins, J. Chem. Theory and Comput. 2010, 6, 3836-3849.
Link
 Banas, P.; Walter, N.G.; Šponer, J.; Otyepka, M., Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics, J. Phys. Chem. B 2010, 114, 8701-8712.
Link
 Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T.E.; Jurecka, P.: Refinement of the Cornell et al. Nucleic Acids Force Field based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011
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 Pavlova, M.; Klvana, M.; Prokop, Z.; Chaloupkova, R.; Banas, P.; Otyepka, M.; Wade, R. C.; Tsuda, M.; Nagata, Y.; Damborsky, J. Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate, Nature Chem. Biol. 2009, 5, 727-733.
Link
 Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca, J.; Damborsky, J. CAVER: A new tool to explore routes from protein clefts, pockets and cavities, BMC Bioinformatics 2006, 7, 316.
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 Scanning Probe Microscope
 Scanning Electron Microscope
 An obligue (RNA-RNA) interaction identified in reverse kink-turn |
Visiting scientists – Team leaders:
Athanasios B. Bourlinos, Ph.D. (
Home institution: Institute of Materials Science (IMS) of the National Center for Scientific Research “Demokritos”, Greece) Institute of Materials Science (IMS) of the National Center for Scientific Research “Demokritos” is the major National Research Center in Greece. IMS is the succession of the Direction of Physics, one of the historical departments of Demokritos, which was established in year 1961. The combination of high quality scientific personnel and very good infrastructure has contributed to the achievement of excellent scientific work and substantial external funding of the order of 1 MEuro/year. In year 2000 IMS was awarded funds for the establishment of the Center of Excellence for Nanostructured Materials in Greece.
Assoc. Prof. Michael A. Karakassides (
Home institution: University of Ioannina, Department of Materials Science & Engineering, Greece) Biomaterials, Hybrids and Mesoporous Materials Group group (group is led by Assoc. Prof. Michael A. Karakassides) was established in 2001 and currently gathers more than 15 researchers, including post-graduate students. It aims at a variety of topics in inorganic porous and hybrids solids, ceramics and glasses and nanomaterials, either in pure or in composite form. Advance applications, such as, biomaterials, carbon nanotubes, graphene, nanocomposites, and traditional ones, such as clay materials, vitrification and ceramization processing of industrially produced ceramics, water cleaning processing with the aid of hybrid nano-ceramic etc., are both included in the activities of BHMM group. High-importance objectives of the group, are the design and the development of new functional materials, including synthesis and processing optimization and characterization up to commercialization level.
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