Deniz Sezer

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E-Mail
dsezersabanciunivedu
Phone
(216) 483 9881
Personal Web
Title
Faculty Member
Jobs
Faculty Member
Education
Ph.D. Physics, Cornell University, 2008; 
M.S. Physics, Bogazici University, 2000; 
B.S. Electrical Engineering & Physics, Bogazici University, 1998.
Areas of Interest
Computational Molecular Biophysics: atomically-detailed characterization of drug permeation through lipid bilayer.
Theoretical Physical Chemistry: molecular dynamics simulations for magnetic resonance spectroscopy.
Publications
  • Article
    Sezer, Deniz and Oruç, Tuğçe (2017) "Protonation kinetics compromise liposomal fluorescence assay of membrane permeation", Journal of Physical Chemistry B, Vol.121, No.20, 5218-5227 (SCI)
    Oruç, Tuğçe and Küçük, Sami Emre and Sezer, Deniz (2016) "Lipid bilayer permeation of aliphatic amine and carboxylic acid drugs: rates of insertion, translocation and dissociation from MD simulations", Physical Chemistry Chemical Physics, Vol.18, No.35, 24511-24525 (SCI)
    Halbmair, Karin and Seikowski, Jan and Tkach, Igor and Höbartner, Claudia and Sezer, Deniz and Bennati, Marina (2016) "High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides", Chemical Science, Vol.7, No.5, 3172-3180 (SCI)
    Küçük, Sami Emre and Sezer, Deniz (2016) "Multiscale computational modeling of C-13 DNP in liquids", Physical Chemistry Chemical Physics, Vol.18, No.14, 9353-9357 (SCI)
    Prisner, Thomas and Denysenkov, Vasyl and Sezer, Deniz (2016) "Liquid state DNP at high magnetic fields: instrumentation, experimental results and atomistic modelling by molecular dynamics simulations", Journal of Magnetic Resonance, Vol.264, 68-77 (SCI)
    Küçük, Sami Emre and Biktagirov, Timur and Sezer, Deniz (2015) "Carbon and proton overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone", Physical Chemistry Chemical Physics, Vol.17, No.38, 24874-24884 (SCI)
    Küçük, Sami Emre and Neugebauer, Petr and Prisner, Thomas F. and Sezer, Deniz (2015) "Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO", Physical Chemistry Chemical Physics, Vol.17, No.9, 6618-6628 (SCI)
    Sezer, Deniz (2013) "Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations", Physical Chemistry Chemical Physics, Vol.15, No.2, 526-540 (SCI)
    Sezer, Deniz and Sigurdsson, Snorri Th. (2011) "Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories", Physical Chemistry Chemical Physics, Vol.13, No.28, 12785-12797 (SCI)
  • Book Section / Chapter
    Sezer, Deniz and Roux, Benoit, "Markov state and diffusive stochastic models in electron spin resonance", An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Bowman, Gregory R. and Pande, Vijay S. and Noe, Frank (eds.), Dordrecht: Springer Science+Business Media, January 2014, 115-138
  • Before SU Publications
    • Vasyl P. Denysenkov,  Mark J. Prandolini,  Marat Gafurov, Deniz Sezer, Burkhard Endeward, and Thomas Prisner. Liquid state DNP using a 260 GHz high power gyrotron.  Physical Chemistry Chemical Physics12(22): 5786-5790 (2010). 
    • Ivan Krstic, Olga Frolow, Deniz Sezer, Burkhard Endeward, Juila E. Weigand, Beatrix Suess, Jaochim W. Engels, and Thomas F. Prisner. PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure. Journal of the American Chemical Society, 132(5): 1454-1455 (2010). 
    • Deniz Sezer, Marat Gafurov, Mark J. Prandolini, Vasyl P. Denysenkov, and Thomas F. Prisner. Dynamic nuclear polarization of water by a nitroxide radical: Rigorous treatment of the electron spin saturation and comparison with experiments at 9.2 Tesla. Physical Chemistry Chemical Physics, 11(31): 6638-6653 (2009). 
    • Deniz Sezer,  Mark J. Prandolini and Thomas F. Prisner. Dynamic nuclear polarization coupling factors calculated from molecular dynamics simulations of a nitroxide radical in water. Physical Chemistry Chemical Physics, 11(31): 6626-6637 (2009). 
    • Deniz Sezer, Jack H. Freed and Benoit Roux. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. Journal of the American Chemical Society, 131(7): 2597-2605 (2009).
    • Deniz Sezer, Jack H. Freed and Benoit Roux. Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories. The Journal of Physical Chemistry B, 112(35): 11014-11027 (2008).
    • Deniz Sezer, Jack H. Freed and Benoit Roux. Parametrization, molecular dynamics simulation and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix. The Journal of Physical Chemistry B, 112(18): 5755-5767 (2008).
    • Deniz Sezer}, Jack H. Freed and Benoit Roux. Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories. The Journal of Chemical Physics, 128(16): 165106, pages 16 (2008). 
    • Albert C. Pan, Deniz Sezer and Benoit Roux. Finding transition pathways using the string method with swarms of trajectories. The Journal of Physical Chemistry B, 112(11): 3432-3440 (2008).