Carbon nanostructures, biomacromolecules and simulations

 About the group:

Graphene and its derivatives (fluorographene, graphene oxide) belong to extensively studied compounds within the framework of our research. The research includes the development of novel methods for the functionalization and chemical modification of graphene and its derivatives. We benefit from a tight connection between both theoretical and experimental approaches. Other research directions include explorations of fluorescent carbon quantum dots and their application for cell imaging, along with the study of porous carbon nanostructures for environmental and catalytic applications. The group develops theoretical methods and tools for the study of biomacromolecules and nanomaterials. The focus is on the structure and dynamics of biomacromolecules and their functional components, on the interaction of biomacromolecules with membrane bilayers, on enzyme and RNA catalysis.







Results highlights:

P. Trouillas, J. C. Sancho-García, V. De Freitas, J. Gierschner, M. Otyepka, O. Dangles: Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment,CHEMICAL REVIEWS vol. 116, iss. 9, pp. 4937-4982, 2016.
DOI: 10.1021/acs.chemrev.5b00507
M. H. Kolář, P. Hobza: Computer Modeling of Halogen Bonds and Other σ-Hole Interactions, CHEMICAL REVIEWS vol. 116, iss. 9, pp. 5155-5187, 2016.
DOI: 10.1021/acs.chemrev.5b00560
M. Dubecký, L. Mitas, P. Jurečka: Noncovalent Interactions by Quantum Monte Carlo, CHEMICAL REVIEWS vol. 116, iss. 9, pp. 5188-5215, 2016.
DOI: 10.1021/acs.chemrev.5b00577
cover-11-05-2016-14-34-58
X. Chia, A. Adriano, P. Lazar, Z. Sofer, J. Luxa, M. Pumera: Layered Platinum Dichalcogenides (PtS 2 , PtSe 2 , and PtTe 2 ) Electrocatalysis: Monotonic Dependence on the Chalcogen Size , ADV. FUNCT. MATER.,  2016.
DOI: 10.1002/adfm.201505402
C. C. Givelet, P. I. Dron, J. Wen, T. F. Magnera, M. Zamadar, K. Čépe, H. Fujiwara, Y. Shi, M. R. Tuchband, N. Clark, R. Zboril, J. Michl: Challenges in the Structure Determination of Self-Assembled Metallacages. What Do Cage Cavities Contain, Solvent or Internal Vapor Bubbles?, J. AM. CHEM. SOC., ASAP, 2016.
DOI: 10.1021/jacs.5b12050
V. Georgakilas, A. Demeslis, E. Ntararas, A. Kouloumpis, K. Dimos, D. Gournis, M. Kocman, M. Otyepka, R. Zbořil: Hydrophilic Nanotube Supported Graphene-Water Dispersible Carbon Superstructure with Excellent Conductivity, ADVANCED FUNCTIONAL MATERIALS vol. 25, iss. 10, pp. 1481-1487, 2015.
DOI: 10.1002/adfm.201403801
V. Urbanová, K. Holá, A. B. Bourlinos, K. Čépe, A. Ambrosi, A. H. Loo, M. Pumera, F. Karlický, M. Otyepka, R. Zbořil: Thiofluorographene-Hydrophilic Graphene Derivative with Semiconducting and Genosensing Properties, ADV. MATER., vol. 27, iss. 14, pp. 2305-2310, 2015.
DOI: 10.1002/adma.201500094
K. Hola, Y. Zhang, Y. Wang, E. P. Giannelis, R. Zboril, A. L. Rogach: Carbon dots—Emerging light emitters for bioimaging, cancer therapy and optoelectronics, NANO TODAY 9, 5, (2014).
DOI: 10.1016/j.nantod.2014.09.004
J. Fanfrlík, A. Přáda, Z. Padělková, A. Pecina, J. Macháček, M. Lepšík, J. Holub, A. Růžička, D. Hnyk and P. Hobza: "The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics", ANGEW. CHEM. INT. ED., vol. 53, iss. 38, pp. 10139-10142, 2014.
DOI: 10.1002/anie.201405901
P. Lazar, C. K. Chua, K. Holá, R. Zbořil, M. Otyepka, M. Pumera: Dichlorocarbene-Functionalized Fluorographene: Synthesis and Reaction Mechanism, SMALL, 2015.
DOI: 10.1002/smll.201500364
J. Sponer, P. Banáš, P. Jurecka, M. Zgarbova, P. Kührová, M. Havrila, M. Krepl, P. Stadlbauer and M. Otyepka: "Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.", J. PHYS. CHEM. LETT., vol. 5, iss. 10, pp. 1771-1782, 2014.
DOI: 10.1021/jz500557y
P. Lazar, E. Otyepková, P. Banáš, A. Fargašová, K. Šafářová, L. Lapčík, J. Pechoušek, R. Zbořil and M. Otyepka: "The nature of high surface energy sites in graphene and graphite", CARBON, vol. 73, pp. 448-453, 2014.
DOI: 10.1016/j.carbon.2014.03.010
K. Hola, A. Bourlinos, O. Kozak, K. Berka, K. Siskova, M. Havrdova, J. Tucek, K. Safarova, M. Otyepka, E. Giannelis and R. Zboril: "Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO− induced red-shift emission", CARBON, vol. 70, pp. 279-286, 2014.
DOI: 10.1016/j.carbon.2014.01.008
X. Chia, A. Ambrosi, M. Otyepka, R. Zbořil and M. Pumera: "Fluorographites (CFx)n Exhibit Improved Heterogeneous Electron-Transfer Rates with Increasing Level of Fluorination: Towards the Sensing of Biomolecules ", CHEMISTRY - A EUROPEAN JOURNAL, vol. 20, iss. 22, pp. 6665-6671, 2014.
DOI: 10.1002/chem.201402132
M. Paloncýová, G. Fabre, R. H. DeVane, P. Trouillas, K. Berka and M. Otyepka: "Benchmarking of Force Fields for Molecule–Membrane Interactions",J. CHEM. THEORY COMPUT., 10 (9), pp. 4143-4151, 2014.
DOI: 10.1021/ct500419b
M. Paloncýová, R. H. DeVane, B. P. Murch, K. Berka and M. Otyepka: "Rationalization of Reduced Penetration of Drugs through Ceramide Gel Phase Membrane", LANGMUIR, 30 (46), pp 13942–13948, 2014.
DOI: 10.1021/la503289v
ancac3_v007i002.indd
Lazar, P; Zhang, S; Safarova, K; Li, Q; Froning, JP; Granatier, J; Hobza, P; Zboril, R; Besenbacher, F; Dong, MD; Otyepka, M: “Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions”, ACS NANO, 7 (2), 1646-1651, 2013.
DOI: 10.1021/nn305608a
F. Karlický, K. K. R. Datta, M. Otyepka and R. Zbořil: "Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives" ACS NANO, 7 (8), pp 6434–6464, 2013.
DOI: 10.1021/nn4024027
Lazar, P; Karlicky, F; Jurecka, P; Kocman, M; Otyepkova, E; Safarova, K; Otyepka, M; "Adsorption of Small Organic Molecules on Graphene", J. AM. CHEM. SOC., 135 (16), 6372-6377, 2013.
DOI: 10.1021/ja403162r
Vasilios Georgakilas, Michal Otyepka, Athanasios B. Bourlinos, Vimlesh Chandra, Namdong Kim, K. Christian Kemp, Pavel Hobza, Radek Zboril, and Kwang S. Kim: Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications CHEMICAL REVIEWS, 112 (11), 6156-6214, 2012.
DOI: 10.1021/cr3000412



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.




Group members

NameTitleE-mailPhone
Banáš Paveldoc.,Mgr.,Ph.D.pavel.banas@upol.cz+420 585 63 4769
Bares HugoPh.D.hugo.bares@upol.cz+420 585 63 4339
Bazgier VáclavIng., Mgr.vaclav.bazgier@upol.cz+420 585 63 4769
Berka Kareldoc.,RNDr.,Ph.D.karel.berka@upol.cz+420 585 63 4769
Blahová Prudilová BarboraMgr.barbora.prudilova@upol.cz
Bourlinos AthanasiosMgr.,Ph.D.bourlinos@ims.demokritos.gr
Cahlík AlešIng.ales.cahlik@upol.cz
Čépe KláraMgr.,Ph.D.klara.cepe@upol.cz+420 585 63 1429
Chronopoulos DimitriosPh.D.dimitrios.chronopoulos@upol.cz+420 585 63 4391
Chutora TarasMgr.taras.chutora@upol.cz+420 585 63 4487
De La Torre BrunoPh.D.bruno.de@upol.cz+420 585 63 4472
Edalatmanesh ShayanMgr.shayan.edalatmanesh@upol.cz
Hellerstedt JohnPh.D.johnjack.hellerstedt@upol.cz
Jakubec Petr Mgr., Ph.D.jakubepe@prfnw.upol.cz+420 585 63 4428
Janáček DominikMgr.dominik.janacek@upol.cz+420 585 63 1429
Jelínek PavelIng., Ph.D.pavel.jelinek@upol.cz
Jurečka Petrdoc., RNDr., Ph.D.petr.jurecka@upol.cz+420 585 63 4760
Kalytchuk SergiiPh.D.sergii.kalytchuk@upol.cz+420 585 63 4391
Karlický FrantišekMgr.,Ph.D.frantisek.karlicky@upol.cz+420 585 63 4767
Kührová PetraMgr., Ph.D.petra.kuhrova@upol.cz+420 585 63 4766
Lapčík ĽubomírProf.,Ing.,CSc.lubomir.lapcik@upol.cz+420 585 63 4420
Lazar PetrMgr.,Ph.D.petr.lazar@upol.cz+420 585 63 4767
Manna DebashreePh.D.debashree.manna@upol.cz
Medveď Miroslavdoc., RNDr., Ph.D.miroslav.medved@upol.cz
Moro Lagares MaríaPh.D.maria.moro@upol.cz
Nachtigallová DanaRNDr., Ph.D.dana.nachtigallova@upol.cz
Namvari MinaPh.D.mina.namvari@upol.cz+420 585 63 4384
Navrátilová Veronika Mgr.veronika.navratilova@upol.cz+420 585 63 4423
Otyepka MichalProf., RNDr.Ph.D.michal.otyepka@upol.cz+420 585 63 4764
Otyepková Eva RNDr., Ph.D.eva.otyepkova@upol.cz+420 585 63 4425
Paloncýová MarkétaMgr.marketa.paloncyova@upol.cz+420 585 63 4423
Pérez Reyes Maria CeciliaMgr.mariacecilia.perezreyes@upol.cz+420 585 63 1429
Polách JiříRNDr., Ph.D.jiri.polach@upol.cz
Potsi GeorgiaPh.D.georgia.potsi@upol.cz+420 585 63 4383
Pumera MartinRNDr., Ph.D.martin.pumera@gmail.com
Pykal Martin Mgr.martin.pykal@upol.cz+420 585 63 4423
Rogatch Andreidoc.,Ph.D.andrey.rogach@cityu.edu.hk
Sambhare Susmit BalkrishnaPh.D.susmitbalkrishna.sambhare@upol.cz
Sarmah AmritPh.D.amrit.sarmah@upol.cz
Sedlák RóbertRNDr. Ph.D.robert.sedlak@upol.cz
Sen DipayanPh.D.dipayan.sen@upol.cz
Slavíčková Karlakarla.slavickova@upol.cz+420 585 63 4425
Šponer JiříProf. RNDr. DrSc.jiri.sponer@upol.cz
Stadlbauer PetrMgr.petr.stadlbauer@upol.cz
Stráská JanaMgr.jana.straska@upol.cz+420 585 63 1429
Švec MartinMgr., Ph.d.martin.svec@upol.cz
Tomanec OndřejIng.ondrej.tomanec@upol.cz+420 585 63 1429
Trouillas Patrick Ph.D.patrick.trouillas@upol.cz
Vermisoglou EleniPh.D.eleni.vermisoglou@upol.cz+420 585 63 4473
Vlček JakubMgr.jakub.vlcek@upol.cz+420 585 63 4386
Zgarbová MarieMgr., Ph.D.marie.zgarbova@upol.cz+420 585 63 4766