Ph.D. Dissertation - EN / Bilkent University

Ph.D. Dissertation - EN / Bilkent University

Erol ÖZGÜR, Ph.D.
Post Doctoral Research Associate
Bilkent University
Institute of Materials Science and Nanotechnology
Bilkent Ankara TURKEY
[email protected]
[email protected]
+90 312 290 35 51 (office)
+90 542 634 11 75 (mobile)
Web: http://www.bilkent.edu.tr/~erol
Google Scholar: http://scholar.google.com.tr/citations?hl=en&user=PLKt_XcAAAAJ
EDUCATION
2008-2014
Ph.D., Materials Science and Nanotechnology
Bilkent University, Ankara, TURKEY
Dissertation: Design and Development of Novel Large Scale
Applications in Micro/nanophotonics and Nanobiotechnology
2006-2008
M.S., Biophysics
Ankara University, Ankara, TURKEY
Thesis: Examination of Cooperation of the Elements Taking Part
in Intracellular Calcium Signaling as an Integrated System in
Mammalian Culture Cells
2001-2006
B.S., Molecular Biology and Genetics
Bilkent University, Ankara, TURKEY
RESEARCH
2014-Present
Post Doctoral Research Associate
Nanoscale Devices and Imaging Group
Institute of Materials Science and Nanotechnology
Bilkent University
Skills and Experience
 Photonics: Large scale fabrication of surface tension induced
microresonators
 Plasmonics: Surface Enhanced Raman Spectroscopy (SERS), Surface
Plasmon Resonance (SPR) Biosensors
 Atomic Force Microscopy
 Scanning Near Field Optical Microscopy (SNOM)
2008-2014
Research Assistant,
Nanomaterials and Nanophotonics Laboratory
Institute of Materials Science and Nanotechnology,
Bilkent University
Skills and Experience
 Optics: Optical microresonators, optical biological sensors, nonlinear
optical microcavities, fiber tapering, laser-tissue interactions
 Micro/nanofabrication: Photolithography, deposition (thermal, e-beam,
sputter, PECVD, ALD), chemical and plasma etching
 Nanotechnology: Nanowire alignment on large area substrates,
nanowire optical sensors, template-based nanostructures, nanowire
phase change memory, E-beam lithography, nanoparticle synthesis
 Surface chemistry: Silane and thiol-based surface modification
 Materials Science: Scanning electron microscopy, X-ray photoelectron
spectroscopy, X-ray diffraction, ellipsometry, UV-Vis-IR spectroscopy
 Electronics: Semiconductor parametric analysis, wire bonding, flexible
nanowire based electronic devices
2006-2008
Research Assistant,
Institute of Health Sciences, Biophysics Dept.,
Ankara University
Skills and Experience
 Molecular and Biological Imaging: Confocal microscopy,
microfluorimetry, spectrofluorimetry, fluorescent microscopy, optical
microscopy, fluorescent labeling, radioactive labeling
 Electrophysiology: Measurement of action potentials, patch-clamp
recording
 Mathematical Modeling: Mathematical modeling of calcium signaling,
mathematical modeling of action potentials and single ion channel
dynamics, MATLAB simulations
2001-2006
B.S. Student
Faculty of Science, Molecular Biology and Genetics Dept.,
Bilkent University
Skills and Experience
 Molecular Biology: DNA extraction, electrophoresis, cloning, transient
and stable transfection, protein extraction, Western blot, RNA extraction,
RT-PCR
 Cell culture
 Immunology
 Microbiology
RESEARCH INTERESTS
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Optical microresonators
Optical and plasmonic biosensors
Semiconducting nanowires
Biomedical optics
Lab-on-a-chip technologies
Laser-tissue interactions
Nonlinear optical imaging
Flexible and organic electronics
Mathematical modeling of biological systems
Electrophysiology
Optogenetics
Sustainability science
PUBLICATIONS
In Preparation
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“Mobile plasmonic biosensing within an enhanced detection range using a chirped
diffraction grating”.
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“Mobile plasmonic biosensor fabricated by nanoimprint lithography”.
Submitted
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“Wafer-scale Arrays of Surface Tension Induced Optical Microcavities with
Embedded Fluorescent Nanodiamonds”. E. Ozgur, A. Dana. Advanced Materials,
(2016)
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“Thermally-tunable ultrasensitive infrared absorption spectroscopy platforms
based on thin phase-change films”. G. Bakan, S. Ayas, E. Ozgur, K. Celebi, A. Dana.
Small, (2016)
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“Label-free Optical Biodetection of Pathogen Virulence Factors in Complex Media
Using Microtoroids with Multifunctional Surface Functionality”. P. Toren, E. Ozgur, M.
Bayindir. Biomaterials, (2016)
Published
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“A smartphone based surface plasmon resonance imaging (SPRi) platform for onsite biodetection”. H. Guner, E. Ozgur, G. Kokturk, M. Celik, E. Esen, A. E. Topal, S.
Ayas, C. Elbuken, Y. Uludag, A. Dana. Sensor. Actuat. B, 239, 571-577 (2017)
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“A review on oligonucleotide based detection with optical microresonators:
strategies and challenges”. P. Toren, E. Ozgur, M. Bayindir. Lab on a Chip, 16, 25722595 (2016)
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“Universal infrared absorption spectroscopy using uniform electromagnetic
enhancement”. S. Ayas, G. Bakan, E. Ozgur, K. Celebi, A. Dana. ACS Photonics, 3,
(3), 337-342 (2016)
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“Real-time and selective detection of single nucleotide DNA mutations using
surface engineered microtoroids". P. Toren, E. Ozgur, M. Bayindir. Analytical
Chemistry, 87 (21), 10920-10926 (2015)
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“Label-free biosensing with high selectivity in complex media using microtoroidal
resonators”. E. Ozgur, P. Toren, O. Aktas, E. Huseyinoglu, M. Bayindir. Scientific
Reports, 5, 13173 (2015)
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“Phosphonate based organosilane modification of a protein resistant and
bioconjugable silica surface”. E. Ozgur, P. Toren, M. Bayindir. J. Mater. Chem. B, 2
(41), 7118-7122 (2014)
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“The interplay between plasma membrane and endoplasmic reticulum Ca 2+
ATPases in agonist-induced temporal Ca2+ dynamics”. F. A. Cicek, E. O. Ozgur, E.
Ozgur, M. Ugur. J. Bioenerg. Biomemb. 46 (6), 503-510 (2014)
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“Polymeric nanocarriers for expected nanomedicine: Current challenges and
future prospects”. B. Daglar, E. Ozgur, M. E. Corman, L. Uzun, G. B. Demirel. RSC
Advances, 4 (89), 48639-48659 (2014)
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“A new route for fabricating on-chip chalcogenide microcavity resonator arrays”.
O. Aktas, E. Ozgur, O. Tobail, M. Kanik, E. Huseyinoglu, M. Bayindir. Advanced Optical
Materials, 2 (7), 618-625 (2014)
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“Impact of mesoporous silica nanoparticle surface functionality on hemolytic
activity, thrombogenicity and non-specific protein adsorption”. A. Yildirim, E. Ozgur, M.
Bayindir. J. Mater. Chem. B, 1 (14), 1909-1920 (2013)
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“Manually assembled macroscopic nanowire image sensor”. E. Ozgur, O. Aktas,
M. Bayindir. Optics & Photonic News, 23, 36 (2012)
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“Macroscopic assembly of indefinitely long and parallel nanowires into large area
photodetection circuitry”. E. Ozgur, O. Aktas, M. Kanik, M. Yaman, M. Bayindir. Nano
Letters, 12 (5), 2483-2487 (2012)
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“Structural coloring in large scale core-shell nanowires”. T. Khudiyev, E. Ozgur,
M. Yaman, M. Bayindir. Nano Letters, 11 (11), 4661-4665 (2011)
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“Arrays of indefinitely-long, uniform nanowires and nanotubes”. M. Yaman, T.
Khudiyev, E. Ozgur, M. Kanik, O. Aktas, E. O. Ozgur, H. Deniz, E. Korkut, M. Bayindir.
Nature Materials, 10 (7), 494-501 (2011)
PRESENTATIONS
Oral
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“Macroscopic nanowire photodetection circuitry”. MRS Fall 2012, Boston, USA,
Nov 30 (2012)
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“Indefinitely long aligned nanowires assembled into a large area photodetection
device”. MRS Fall 2011, Boston, USA, Nov 28 (2011)
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“Macroscopic photoconductive nanowire arrays”. OMN 2011, Istanbul, Turkey,
Aug 10 (2011)
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“Uniform photoconductive nanowire arrays readily assembled into large area
electronics”. NanoTR-VII, Istanbul, Turkey, Jul 1 (2011)
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“Label-free and ultrasensitive microcavity biosensors with high selectivity”.
NanoTR-VII, Istanbul, Turkey, Jul 1 (2011)
Poster
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“Ultrasensitive label-free microcavity biosensors with high selectivity”. OMN 2011,
Istanbul, Turkey, Aug 10 (2011)
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“Emergent semiconductor properties in selenium nanowire arrays fabricated by
direct size reduction technique”. MRS Spring 2011, San Francisco, USA, Apr 27 (2011)
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“Calcium signaling, examined as an integrated system”. 2nd International
Congress on Cell Membranes and Oxidative Stress Focus on Calcium Signaling and
TRP Channels, Isparta, Turkey, Jun 26 (2008)
PATENTS
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“Two distinct homogenous ring-shaped light emission from a single
multimode optical fiber”. A. A. Seymen, E. Ozgur, B. Ortac. (In
preparation)
HONORS and AWARDS
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Ministry of Science, Industry and Technology 2011 Entrepreneurship
Grant
The Scientific and Research Council of Turkey (TUBITAK) National
Scholarship Programme for Ph.D. Students
Bilkent University Graduate Scholarship
The Scientific and Research Council of Turkey (TUBITAK) National
Scholarship Programme for M.S. Students
Bilkent University Full Scholarship for Undergraduate Students
8th rank in 2001 University Entrance Exams