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NAST Seminar December, 9, 2011‏

DNA aptamers – novel receptors in biosensors

Prof.  Tibor Hianik

Comenius University Bratislava

venerdì 9 dicembre 2011 ore 12:00

Aula U. M. Grassano

Facoltà di Scienze Matematiche, Fisiche e Naturali

Dipartimento di Fisica

Università degli Studi di Roma “Tor Vergata”

 

Abstract:
The talk will deal with the following topics:

Structure and properties of DNA aptamers. Aptamer engneering, preparation of
nanostructured surfaces and aptamer immobilization. Electrochemical and
acoustical methods of aptamer-ligand detection. Examples of biosensors for
detection thrombin, prions, and ochratoxin.

 

Biographical:

Professor Tibor Hianik is head of the Laboratory of Biophysics of Comenius
University Bratislava.

He is chair of the Master and PhD program in Biophysics at CUB. Prof. T.
Hianik supervised 16 PhD students and more than 30 diploma works.

A substantial area of his research is focussed on the development of
biosensors based on DNA aptamers and antibodies.

He has authored 135 papers in International Journals, two monographs, six
chapters in books and serves as associate editor of the International
Journal Bioelectrochemistry (Elsevier) and editor of the International
Journal of General Physiology and Biophysics (SAS). He also served as a
guest editor of special issue of Electroanalysis (Wiley) focused on
electrochemical aptasensors.

He is member of the Council of Bioelectrochemical Society, member of
commission C6 on Biological Physics of IUPAP and president of the Slovak
Biophysical Society.

 

Comment 

Prof. Olivia Pulci

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Contact details

 

Office:  Physics Department,
Università di Roma “Tor Vergata”
Via della Ricerca Scientifica 1
00133 Roma, Italy

Tel: +39 0672594548
Fax: +39 062023507

Send an E-Mail

 

Current Professional Position

Associate Professor in Condensed Matter at the Faculty of Science of The University of Rome Tor Vergata

 

Research Experience

Olivia Pulci is a computational theoretical physicist, received a Laurea Cum Laude at the University  “La Sapienza” (Rome) in 1992, and the PhD degree at the University of Rome Tor Vergata  in 1996.

She is presently associate professor in Condensed Matter at Department of Physics – Faculty of Science – at the University of Rome Tor Vergata.

In the years 1997-2000 she worked   at the Friedrich Schiller Universitaet (Jena, Germany), at the Ecole Polytechnique (Palaiseau, France) and the the Fritz Haber Institute of the Max Plank Gesellschaft (Berlin).

Since 2003 OP teaches  “Theory of Solid State Physics” for the Laurea Specialistica in Material Science.

Since 2007 OP is beamline responsible scientist at the European Theoretical Spectroscopy

Facility (ETSF,  www.etsf.eu) for the Optical Beamline.

 

Expertise

  • Surfaces:

Ground state properties: equilibrium geometry, determination of relaxation and reconstruction, study of the relative stability of surfaces under different growth conditions. Electronic band structure and optical properties of surfaces. Effect of steps.

  • Nanocrystals, nanodots:

Absorption and emission spectra of silicon nanocrystals, free standing and embed-ded.

  • Towards systems of biological interest:

study of water, and formamide in water; optical spectra within QM/MM+MBPT of indole in water solution; study of the photoisomerization of rhodopsin; optical properties of Flavin

  • Functionalizing graphene and other 2-D systems:

study of graphene, silicene and polygermine with adsorbates.

  • Cultural heritage: understanding the yellowing of ancient paper through the study of possible oxidation processes in cellulose

keywords: Ab-initio calculations, computational physics, Density Functional Theory (DFT), Time-Dependent DFT (TDDFT), Many-Body Perturbation Theory, ground state properties, electronic band structure calculations, optical absorption spectra, Reflectance Anisotropy, Surface Differential Reflectivity, GW approximation, excitonic effects (BSE).

Invited Talks and lectures

  1. XVIII Meeting of Theoretical Solid State Physics, Fai della Paganella (Trento), 30 March 1999 (invited).
  2. 17th Heimbach Meeting, Isola Polvese, Italy 29 September -3 October 2003 (2 invited lectures)
  3. EPIOPTIC-8 School, Erice 20th-26th July 2004 (2 Invited Lectures, 4 hours)
  4. Deutsche Physikalische Gesellschaft Spring Meeting 2005: Invited Talk (8 March 2005 Berlin, Germany)
  5. Invited talk at the EPS 2006 Meeting (DPG, Dresden, Germany, 27-31March 2006)  “Ab-initio calculations of excitations at surfaces”
  6. Invited Lecture at EPIOPTICS-9 (38th school, Erice 20-26 July 2006), ‘The optical properties of surfaces: ab-initio calculations within two-particle schemes’
  7. Invited talk at the 11th Nanoquanta Workshop on Electronic Excita-tions: ‘A decade of applications of the Bethe-Salpeter Equation’, 19-22 September 2006 Houffalize (Belgium). Title of the talk: Electronic and Optical properties of Surfaces: ab-initio calculations within MBPT and TDDFT approaches
  8. Invitation to give a talk at the APS March meeting (March 2007) (I could not travel for health reasons)
  9. Invited talk at the conference SIMBIOMA ‘Progress in ab initio mod-elling of biomolecules : towards computational spectroscopy’, Rome 2-4 April 2007
  10. Invited talk at the ‘PhD school for Nano and Bio Technologies’, 21-31 May 2007, Rome Tor Vergata. Title of the Talk: ‘Ab-initio calculations of optical properties of Silicon nanocrystals’
  11. Invited talk at the International workshop on computational physics and Materials ‘Progress in Computational Electronic Structure Theory’ Bonn 10-12 January 2008 ‘ Optical spectrum of water: many-body per-turbation theory meets molecular dynamics’
  12. Invited talk at the russian-italian mini-workshop 14 March 2008 Castel Gandolfo, Rome ‘Ab-initio calculations of Silicon nanocrystals’
  13. Two Invited Lectures at EPIOPTICS-X school (Erice 20-27 June 2008)
  14. Invited talk at the conference School of Nanophotonic and Photovoltaics Ab initio theory and calculation of the optical properties of nanostruc-tures Santiago de Cuba 7-14 January 2009
  15. Invited talk at the NAST-ISM(CNR) meeting Rome (Italy) (22 June 2009) ‘Theoretical Approaches to the Ab-initio study of complex systems’
  16. Invited talk at ICFSI-12 Weimar (Germany) 5-10 July 2009
  17. Invited talk at OSI-8 Ischia (Italy) 6-11 September 2009
  18. Invited talk at ICCMSE 2009 Rhodes (Crete, Greece) 29-September- 4 October 2009
  19. Invited talk at the conference ‘PhysCompTech’ Natal, Brasil 1-5 March 2010
  20. Invited talk at the international School on optical properties of surfaces EPIOTICS-XI (Erice July 2010)
  21. Invitation to ECOSS27 (29 August- 3 September 2010) (could not attend for family reasons)
  22. Invited talk at the international conference NANO 2010 (Rome La Sapienza 13-17 September 2010)
  23. Invited talk at the 2nd International School on Nanophotonics and Pho-tovoltaic, Tsakhadzor, Armenia (16-22 September 2010)
  24. Invited talk at ICSFS15 (Beijing, China 5-10 October 2010)
  25. Invited talk at the first meeting of the Mediterranean Institute of Fun- damental Physics (MIFP) Marino, ROME 16-19 March 2011
  26. Invitation to give a talk at CECAM July 2011 Lausanne
  27. Invited talk at the School of Nanophotonics Maratea (September2011)

 

Peer Review:

OP served as:

  1. Referee of international journals (Phys. Rev. Lett., Physical Review B, Thin Solid Films, Physica Status Solidi, Superlattices and Microstructures, The Journal of Physical Chemistry, Appl. Phys. Lett.).
  2. 2007-2009: Member of the evaluation panel for CINECA-INFM supercomputer projects
  3. 2010: evaluator of proposals to the CEA-Eurotalents projects
  4. since 2011: Reviewer for CINECA ISCRA projects

  

Organization of conferences:

  • Organizer and Member of the Scientific and Advisory Board of the conference “Ab initio Theoretical Approaches to the Electronic Structure and Optical Spectra of Materials”, CECAM, Lyon, September 2002.
  • Organizer and Member of the Scientific and Advisory Board of the conference “Ab initio Electron-Excitations Theory: Towards systems of Biological Interest”, DIPC, S. Sebastian, Spain, 21-24 September 2003.
  • Organizer and Member of the Scientific and Advisory Board of the conference “Theory and Modeling of Electronic Excitations in Nanoscience“, Acquafredda di Maratea, Italy, 19-23 September 2004
  • Organizer and Coordinator of the section “Ab-initio approaches to excited states and transport” of the MMD (Matter, Materials and Devices) workshop (INFM-meeting 2005, Genova, June 22-25 2005)
  • Organizer and Member of the Scientific and Advisory Board of the conference GW2005: 40 Years of the GW Approximation for the Electronic Self Energy: Achievements and Challenges Physikszentrum Bad Honnef, Germany 12-15 September 2005
  • Member of the International Advisory and Programme Committee of ICFSI-12 (Weimer 2009)
  • Member of the Program Committee of PLMCN10, Cuernavaca, Mexico, 11-16 of April, 2010
  • Member of the International Advisory Board and Programme Committee for the 13th International Conference on the Formation of Semiconductor Interfaces (ICFSI-13) Prague, Czech Republic, July 3-8 2011
  • Local committee member for NANOSEA 2012 S. Margherita di Pula 2012
  • Member of the International Programme Committee of OECSE13 (Rome 2013) 

 

Scientific coordination:

  • Since 2004 Scientifc Coordinator of the section ‘Surfaces and Interfaces’ (IT7) for the NoE (Network of Excellence) European Project ‘NANOQUANTA: Nanoscale Quantum Simulations’
  • Since 2005: Member of the Nanoquanta scientific committee for the organization of the European Theoretical Spectroscopy Facility (ETSF)
  • Since 2007: Member of the scientific committee of NaST (Laboratorio d’Ateneo) Rome Tor Vergata
  • Since 2007: Research Team Leader in the European Theoretical Spectroscopy Facility (ETSF: http://www.etsf.eu) core node of Rome Tor Vergata
  • Since 2008: Optical Beamline reference scientist for the European Theoretical Spectroscopy Facility
  • Since November 2010: Coordinator of the IRSES European Project “New Century of Superconductivity: Ideas, Materials, Technologies” (SIMTECH), project n. 246937
  • Since March 2010: Member of ‘Collegio dei Docenti’ of Tor Vergata University for the PhD in Physics 

 

Recent (selected) Publications:

  • A. Mosca Conte, L. Guidoni, R. Del Sole, and Olivia Pulci, Photo-isomerization of the Protonated Schiff Base Minimal Model: a theoretical investigation by quantum Many-Body and TDDFT methods (Chem. Phys. Lett) (accepted)
  • E. Cannuccia, O. Pulci, R. Del Sole, M. Cascella, Optical properties of flavin mononucleotide: a QM/MM study of protein environment effects  Chemical Physics 389 (2011) 35–38
  • R. Guerra, M. Marsili, O. Pulci, and S. Ossicini Local field effects in silicon nanocrystals Phys. Rev. B 84, 075342 (2011)
  • G. Bussetti, et al. Coexistence of Negatively and Positively Buckled Isomers on n+-Doped Si(111)-2×1 Phys. Rev. Lett. 106, 067601 (2011)
  • M. Schwitters, D. S. Martin, P. Unsworth, T. Farrell, J. E. Butler, M. Marsili, O. Pulci, and P.Weightman The contribution of steps to the optical properties of vicinal Diamond (100):H surfaces Phys. Rev. B 83, 085402 (2011)
  • O. Pulci, A. Marini, M. Palummo, and R. Del Sole, Test of long-range exchange-correlation kernels of TDDFT at surfaces: application to Si(111)2x1, Phys. Rev. B 82, 205319 (2010) (selected as Editor’s suggestion)
  • Stefano Ossicini, Michele Amato, Roberto Guerra, Maurizia Palummo, and Olivia Pulci, Silicon and Germanium Nanostructures for Photovoltaic Applications: Ab-Initio Results, Nanoscale Research Letters 5, 16371649 (2010)
  • M. Marsili, O. Pulci, The fascinating physics of carbon surfaces: first-principles study of hydrogen on C(001), C(111), and graphene, invited Review paper in Journ. of Phys. D 43, 374016 (2010)
  • Paola Gori, Munise Rakel, Christoph Cobet, Wolfgang Richter, Norbert Esser, Axel Ho®mann, Rodolfo Del Sole, Antonio Cricenti, and Olivia Pulci, Optical spectra of ZnO in the far UV: First Principle Calculations and Ellip-sometric measurements, Phys. Rev. B 81, 125207 (2010)
  • Adriano Mosca Conte, Emiliano Ippoliti, Rodolfo Del Sole, Paolo Carloni, Olivia Pulci Many-Body meets QM/MM: Application to indole in water solution accepted Phys. Stat. Sol. b) Volume 247, Issue 8, August 2010, Pages: 19201924
  • E. Degoli, R. Guerra, M. Marsili, O. Pulci, and S. Ossicini, Local-fields and disorder effects in free-standing and embedded Si nanocrystallites accepted Phys. Stat. Sol. (b) Volume 247, Issue 8, August 2010, Pages: 21132117
  • O. Pulci, P. Gori, M. Marsili, V. Garbuio, A. P. Seitsonen, F. Bechstedt, A. Cricenti, and R. Del Sole, Ab initio calculations of electronic and optical properties of group IV 2-dimensional materials, Phys. Stat. Sol. (a) 207, 291 (2010)
  • O. Pulci, E. Degoli, F. Iori, M. Marsili, M. Palummo, R. Del Sole, S. Ossicini, Electronic and optical properties of Si and Ge nanocrystals: an ab-initio study, Superlattices and Microstructures 47, 178 (2010)
  • Silicon Nanocrystallites in SiO2 Matrix: The Role of Disorder and Size R. Guerra, I. Marri, R. Magri, L. Martin-Samos, O. Pulci, E. Degoli, and S. Ossicini, Phys. Rev. B 79, 155320 (2009)
  • M. Marsili, O. Pulci, M. Palummo, P.L. Silvestrelli, and R. Del Sole, Electronic and optical properties of acetylene and ethylene on Si(001), “Su-perlattices and Microstructures” 46, 240 (2009)
  • O. Pulci, V. Garbuio, R. Del Sole, Optical and electron energy loss spectra of liquid water: an ab-initio study paper in the book Synchrotron Radiation and Nanostructures, in honour of Paolo Perfetti, World Scientific, Ed. Cri-centi, Margaritondo, pag. 90 (2009)
  • Ab-initio study of Ethylene on Si(001), M. Marsili, O. Pulci,R. Del Sole proceedings of the school EPIOPTICS-10, Erice 2008 World Scientific, ed. A. Cricenti
  • First-principles calculations and bias-dependent STM measurements at the alpha-Sn/Ge(111) surface: A clear indication for the 1U2D configuration P. Gori, F. Ronci, S. Colonna, A. Cricenti, O. Pulci, G. Le Lay, European Physics Letters 85, 66001 (2009)
  • Optical Properties of Silicon Nanocrystallites in SiO2 Matrix: Crystalline vs. Amorphous Case, R. Guerra, I. Marri, R. Magri, L. Martin-Samos, O. Pulci, E. Degoli, and S. Ossicini “Superlattices and Microstructures” 46, 246 (2009)
  • Tight Binding calculations of quasiparticle wavefunctions for C(111)2x1 M. Marsili, O. Pulci, F. Bechstedt, and R. Del Sole Phys. Rev. B 78, 205414 (2008)
  • Ab-initio calculation of luminescence and optical gain properties in silicon nanostructures Elena Degoli, Roberto Guerra, Federico Iori, Rita Magri, Ivan Marri, Olivia Pulci, Olmes Bisi, and Stefano Ossicini in special volume “The oretical Spectroscopy”, CR de Physique de l’Academie des Sciences, Elsevier doi:10.1016/j.crhy.2008.09.003 C. R. Physique 10 (2009) 575586
  • Many-Body Theory meets QM/MM: application to indole in water solution A. Mosca Conte, E. Ippoliti, R. Del Sole, P. Carloni, O. Pulci J. Chem. Theory Comput., 5, 1822 (2009)
  • Excited state properties of Liquid Water, V. Garbuio, M. Cascella, O. Pulci, invited topical Review Article at J. Phys.: Condens. Matter 21, 033101 (2009)
  • Ab-initio absorption spectra of 3-tert-butylcyclohexene Katalin Gaal-Nagy, Olivia Pulci, and Giovanni Onida, in the special volume “Theoretical Spectroscopy”, CR de Physique de l’Academie des Sciences, Elsevier doi:10.1016/j.crhy.2008.08.002 C. R. Physique 10 (2009) 491503
  • Codoping goes Nano: Structural and Optical properties of Boron and Phosphorus codoped Silicon Nanocrystals, R. Magri, F. Iori, E. Degoli, O. Pulci, S. Ossicini, AIP Conf. Proc. 963, 359 (2007)
  • Role of Surface passivation and doping in silicon nanocrystals, R. Magri, E. Degoli, F. Iori, E. Luppi, O. Pulci, S. Ossicini, G. Cantele, F. Trani, D. Ninno, Journal of Computational Methods in Science and Engineering, 7, 219-232 (2007)
  • Quantum mechanical calculations of electronic and optical properties of surfaces Cecilia Noguez and Olivia Pulci, ‘Quantum Mechanical Calculations of Electronic and Optical Properties of Semiconductor Surfaces’, chap. 12 in the book ‘Quantum Chemical Calculations of Surfaces and Interfaces of Materials’, ISBN: 1-58883-138-8, American Scientific Publishers, Vladimir A. Basiuk and Piero Ugliengo Eds., Pages: 217-248 (2009)
  • Adsorption of small hydrocarbon molecules on Silicon surfaces: ethylene on Si(001) M. Marsili, N. Witkowski, O. Pulci, O. Pluchery, P. L. Silvestrelli, R. Del Sole, Y. Borensztein, Phys. Rev. B 77, 125337 (2008)
  • Ab-initio optical spectra of complex system E. Cannuccia,O. Pulci, M. Palummo, V. Garbuio, R. Del Sole, Phys. Stat. Solidi C 5 2543 (2008)
  • Engineering Silicon Nanocrystals: E®ect of Codoping with Boron and Phosphorus F. Iori, E. Degoli, R. Magri, I. Marri, G. Cantele, D. Ninno, F. Trani, O. Pulci, S. Ossicini, Phys. Rev. B 76, 085302 (2007)
  • M. Marsili, V. Garbuio, M. Bruno, O. Pulci M. Palummo, E. Degoli, E. Luppi, R. Del Sole Excited state properties calculations: from 0 to 3 dimensional systems proceedings of the school EPIOPTICS-9, Erice 2006 p.41 World Scientific, ed. A. Cricenti
  • E. Luppi, F. Iori, R. Magri, O. Pulci, S. Ossicini, E. Degoli, V. Olevano, Excitons in Silicon Nanocrystallites: the Nature of Luminescence Phys. Rev. B 75, 033303 (2007)
  • M. Palummo, M. Bruno, O. Pulci, E. Luppi, E. Degoli, S. Ossicini, R. Del Sole Ab-initio electronic and optical properties of low dimensional systems: from single particle to many-body approaches Surf. Sci. 601 (13), p.2696-2701, Jul 2007
  • M. Marsili, O. Pulci, F. Fuchs, F. Bechstedt, R. Del Sole, Many body effects in the electronic and optical properties of the (111) surface of diamond. Surf. Sci. 601 (18), p.4097-4101, Sep 2007
  • P. Gori, O. Pulci, S. Colonna, F. Ronci, A. Cricenti Structure and phase transitions of the Sn/Ge(111) surface Surf. Sci. 601 (18), p.4381-4385, Sep 2007
  • M. Palummo, O. Pulci, A. Marini, L. Reining, R. Del sole Many-body e®ects on the EEL spectrum of the C(100) surface Phys. Rev. B 74, 235431 (2006)
  • S. Ossicini et al., First Principle Study of Silicon Nanocrystals: Structural and Electronic Properties, Absorption, Emission and Doping, Journal of Nanoscience and Nanotechnology 8, 479- 492 (2008)
  • S. Ossicini, E. Degoli, F. Iori, O. Pulci, G. Cantele, R. Magri, O. Bisi, F. Trani, D. Ninno, Doping in Silicon Nanocrystals, Surf. Sci. 601, 2724 (2007)
  • V. Garbuio, M. Cascella, L. Reining, R. Del Sole, and O. Pulci, Ab-initio calculations of Many-Body effects in liquids: the electronic excitations of water, Phys. Rev. Lett. 97, 137402 (2006)
  • O. Pulci, M. Marsili, P. Gori, M. Palummo, R. Del Sole, A. Cricenti, F. Bechstedt, Geometry and electronic band structure of surfaces: the case of Ge(111):Sn and C(111) Appl. Phys. A 85, 361 (2006)
  • P. Gori, O. Pulci, and A. Cricenti, Surface structure and energy bands of 1/3ML Sn/Ge(111), Jpn. J. Appl. Phys., 45, 2140 (2006)

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