Mehmet Sayar – Curriculum Vitae

Mehmet Sayar
Curriculum Vitae
Personal Information
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Date of birth: March 20, 1973
Place of birth: Eskişehir, Turkey
Country of Citizenship: Republic of Turkey
Languages: Turkish (native), English (fluent), German (beginner)
Education and Academic Career
2005–present Assistant Professor, Department of Mechanical Engineering and Department of
Chemical & Biological Engineering, Koç University, Istanbul, Turkey.
2003–2005 Postdoctoral Research Associate, Max-Planck Institute for Polymer Research,
Mainz, Germany.
Theory Group of Prof. Dr. Kurt Kremer, Project Leader: Dr. Christian Holm
1999–2003 Ph.D., Department of Materials Science and Engineering, Northwestern University,
USA.
Thesis Advisor: Prof. Dr. Samuel I. Stupp
1997–1999 M.S., Department of Materials Science and Engineering, University of Illinois, Urbana/Champaign, USA.
Thesis Advisor: Prof. Dr. Samuel I. Stupp
1996–1997 Research and Teaching Assistant, Polymer Research Center and Department of
Civil Engineering, Boğaziçi University, Istanbul, Turkey..
Research Advisor: Prof. Dr. Ali R. Atılgan
1994–1995 Undergraduate Research Assistant, Department of Civil Engineering, Boğaziçi
University, İstanbul, Turkey.
Research Advisor: Prof. Dr. Ali R. Atılgan
1992–1996 B.S., Department of Civil Engineering, Boğaziçi University, Istanbul, Turkey.
Koç University, Sarıyer, 34450 İstanbul – Turkey
H +90 (212) 3381840 • B msayar@ku.edu.tr
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Awards and Fellowships
2012 TÜBA GEBİP Young Scientist Award.
2004 Marie Curie Intra European Fellowship.
Postdoctoral Research
2001 Nanoscale Science and Engineering Center Graduate Fellow.
Northwestern University
1997 Fulbright Scholarship.
M. Sc. at University of Illinois Urbana Champaign
1996 Honor student.
Boğaziçi University, Faculty of Engineering
1992 Boğaziçi University Alumni Association Award.
Scholarship granted to those students who rank first when entering their departments.
1991 Hacı Ömer Sabancı Foundation Award.
Scholarship granted to those students who rank in the top 1% in the national university
entrance examination
Projects
Submitted TÜBİTAK 1001 Project Proposal , Title: “Aggregation of Polyglutamine Tracts
Sep. 2015 Driven by httN T α-helices”, Position: Principle Investigator.
Budget: 340760 TL
2015-2018 TÜBİTAK 1001 Project (114F348), Title: “Dynamical behavior of helical
biomolecules and the influence of geometrical entanglement on scaling properties”,
Position: Investigator.
Budget: 367002 TL
2013-2016 TÜBİTAK-DFG Joint Research Project (212T184), Title: “Multiscale simulation of environment-induced conformational transitions in peptides: folding, partitioning and aggregation”, Position: Principle Investigator.
Budget: 258452 TL
2012–2014 TÜBİTAK 1001 Project (112T496), Title: “Formation. Structure and Stability
of Nanofibers and Networks Formed by Amphiphilic Peptides”, Position: Principle
Investigator.
Budget: 128120 TL
2011–2012 Max-Planck Society Partner Group Grant, Scientific Collaboration with MaxPlanck Institute for Polymer Research, Position: Principle Investigator.
Extended for one more year after the successfull completion of the second phase of the project.
Budget: 20000 Euro
2009–2012 TÜBİTAK 1001 Project (108T553), Title: “A coarse-grained model of DNA and
the investigation of the equilibrium plasmid structures as a function of temperature”,
Position: Principle Investigator.
Budget: 121780 TL
2009–2011 Max-Planck Society Partner Group Grant, Scientific Collaboration with MaxPlanck Institute for Polymer Research, Position: Principle Investigator.
Extended for two more year after the successfull completion of the second phase of the project.
Budget: 40000 Euro
Koç University, Sarıyer, 34450 İstanbul – Turkey
H +90 (212) 3381840 • B msayar@ku.edu.tr
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2007–2009 TÜBİTAK National Young Scientist Career Development Grant, Title:
“Computational Analysis of Self-Organization of Like-Charged Organic Molecules
into Nanoscale Structures”, Position: Principle Investigator.
Budget: 87500 TL
2006–2009 Max-Planck Society Partner Group Grant, Scientific Collaboration with MaxPlanck Institute for Polymer Research, Position: Investigator.
60000 Euro
Graduate Students
2005-2007 Özge (Engin) Şensoy, M.S. degree in CMSE, co-advised with Prof. Burak Erman,
continued her education as a Ph.D. student in my group.
2007-2011 Dr. Özge (Engin) Şensoy, Ph.D. degree in CMSE, worked as a postdoctoral
research associate at Weill Cornell Medical College. Currently a full time faculty
member as Assistant Professor at Medipol University, Istanbul, Turkey.
2009-2014 Dr. Cahit Dalgıçdir, Ph.D. degree in CMSE, currently a postdoctoral research
associate at Konstanz University, Germany.
2011-2013 Murat Öztürk, M.S. degree in CMSE, co-advised with Asst. Prof.
Kabakçıoğlu, Currently a PhD. candidate at Indiana University, USA.
Alkan
2012-2014 Deniz Aydın, M.S. degree in CHBI, co-advised with Prof. Burak Erman, currently a
PhD. candidate at EPFL, Switzerland.
2012-2015 Ayşegül Turupçu, M.S. degree in CHBI, co-advised with Prof. Burak Erman,
currently a PhD. candidate at University of Natural Resources and Life Sciences
Vienna, Austria.
2013-2015 Farhad Ramezanghorbani, M.S. degree in CMSE, currently a PhD. candidate at
University of Florida, USA.
2010-to date Beytullah Özgür, Ph.D candidate in CMSE.
2015-to date Doğancan Özturan, Ph.D. candidate in BMSE.
Citations
Google Scholar
Citation Indices
Citations
h-index
i10-index
Web of Knowledge
All
372
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15
Since 2010
192
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Sum of Times Cited
Sum of Times Cited without self-citations
Citing Articles
Citing Articles without self-citations
Average Citations per Item
h-index
Koç University, Sarıyer, 34450 İstanbul – Turkey
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Manuscripts Submitted and in Preparation
[1] Aydin, D., Gul, A., Erman, B., & Sayar, M. A comparative molecular dynamics study
of HLA-B*51 and HLA-B*52: Implications for the pathogenic role of HLA-B*51 in
Behçet’s Disease. (Submitted).
[2] Dalgicdir, C. & Sayar, M. Conformation and Aggregation of LK Peptide in Bulk
Water and at the Air/Water Interface. J. Phys. Chem. B (Submitted).
[3] Beytullah, O. & Sayar, M. Network Formation in ABA Triblock Peptides: A Coarse
Grained MD Analysis. (In preparation).
[4] Beytullah, O. & Sayar, M. Aggregation of Polyglutamine Tracts Driven by httNT
alpha-helices. (In preparation).
[5] Dalgicdir, C. & Sayar, M. Application of Iterative Boltzmann Method to Phase
Separating Binary Mixtures. (In preparation).
[6] Dalgicdir, C., Globisch, C., Peter, C., & Sayar, M. A Transferrable Coarse Grained
Model For EALA Peptide. (In preparation).
[7] Ozgur, B. & Sayar, M. Coarse Grained Modeling of ABA Triblock Peptides. (In
preparation).
[8] Ozturk, M., Sayar, M., & Kabakcioglu, A. Supercoiling Behavior of DNA under
Torsional Stress. (In preparation).
[9] Ramezanghorbani, F., Dalgicdir, C., & Sayar, M. How to represent environment driven
coconformation transitions in peptides? (In preparation).
[10] Turupcu, A., Erman, B., & Sayar, M. Molecular Dynamics Simulation of IL-1 Receptor
Superfamily Members. (In preparation).
Publications
[1] Dalgicdir, C., Globisch, C., Peter, C., & Sayar, M. Tipping the Scale from Disorder
to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and
Molecular Interfaces. PLoS Comput Biol 11, e1004328 (2015).
[2] Bakota, E. L., Sensoy, O., Ozgur, B., Sayar, M., & Hartgerink, J. D. Self-Assembling
Multidomain Peptide Fibers with Aromatic Cores. Biomacromolecules 14, 1370–1378
(2013).
[3] Dalgicdir, C., Sensoy, O., Peter, C., & Sayar, M. A transferable coarse-grained model
for diphenylalanine: How to represent an environment driven conformational transition.
J. Chem. Phys. 139, 234115 (2013).
[4] Engin, O. & Sayar, M. Adsorption, Folding and Packing of an Amphiphilic Peptide at
the Air/Water Interface. J. Phys. Chem. B 116 (7), 2198–2207 (2012).
[5] Engin, O., Villa, A., Peter, C., & Sayar, M. A Challenge for Peptide Coarse Graining:
Transferability of Fragment-Based Model. Macromol. Theory Simul. 20, 451–465
(2011).
[6] Engin, O., Villa, A., Sayar, M., & Hess, B. Driving Forces for Adsorption of Amphiphilic
Peptides to Air-Water Interface. J. Phys. Chem. B 114, 11093–11101 (2010).
Koç University, Sarıyer, 34450 İstanbul – Turkey
H +90 (212) 3381840 • B msayar@ku.edu.tr
Í home.ku.edu.tr/∼msayar
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[7] Sayar, M. & Holm, C. Equilibrium Polyelectrolyte Bundles with Different Multivalent
Counterion Concentrations. Phys. Rev. E 82, 031901 (2010).
[8] Sayar, M., Bavsaroglu, B., & Kabakcioglu, A. Twist-writhe partitioning in a coarsegrained DNA minicircle model. Phys. Rev. E 81, 04916 (2010).
[9] Engin, O., Sayar, M., & Erman, B. The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of
unfolded peptides. Phys. Biol. 6, 016001 (2009).
[10] Engin, O. & Sayar, M. In Hansman, U. H. E., Meinke, J., Mohanty, S., Nadler,
W., & Zimmermann, O. (eds.), From Computational Biophysics to Systems Biology
(CBSB08), Proceedings of the NIC Workshop 2008, vol. 40 (2008).
[11] Emanuel, M., Mohrbach, H., Sayar, M., Schiessel, H., & Kulic, I. M. Buckling of stiff
polymers: Influence of thermal fluctuations. Phys. Rev. E 76, 1703–1707 (2007).
[12] Hess, B., Sayar, M., & Holm, C. Stability of Hydrophobically Modified Poly(pphenylene)sulfonate Bundles as Observed by Molecular Dynamics Simulation. Macromolecules 40, 1703 (2007).
[13] Sayar, M. & Holm, C. Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium. Europhys. Lett. 77, 16001 (2007).
[14] Sayar, M. & Stupp, S. I. Assembly of 1D Supramolecular Objects: From Monomers to
Networks. Pyhs. Rev. E 72, 011803 (2005).
[15] Limbach, H. J., Sayar, M., & Holm, C. Polyelectrolyte Bundles. J. Phys. Condens.
Matter 16, 2135–2144 (2004).
[16] Lecommandoux, S., Klok, H. A., Sayar, M., & Stupp, S. I. Synthesis and selforganization of rod-dendron and dendron-rod-dendron molecules. J. Phys. A, Poly.
Chem. 41, 3501–3518 (2003).
[17] Sayar, M., de la Cruz, M. O., & Stupp, S. I. Polar Order in Nanostructured Organic
Materials. Europhys. Lett. 61, 334–340 (2003).
[18] Sayar, M. & Stupp, S. I. Self-organization of rod-coil molecules into nanoaggregates:
A coarse grained model. Macromolecules 34, 7135–7139 (2001).
[19] Sayar, M., Solis, F. J., de la Cruz, M. O., & Stupp, S. I. Competing interactions
among supramolecular structures on surfaces. Macromolecules 33, 7226–7228 (2000).
[20] Stupp, S. I., et al. Self-assembly of organic nano-objects into functional materials.
MRS Bull. 25, 42–48 (2000).
[21] Alparslan, A. K., Sayar, M., & Atilgan, A. R. State-space prediction model for chaotic
time series. Phys. Rev. E 58, 2640–2643 (1998).
[22] Demirel, M. C., Sayar, M., & Atilgan, A. R. Statistical mechanics of Fermi-Pasta-Ulam
chains with the canonical ensemble. Phys. Rev. E 55, 3727–3730 (1997).
[23] Sayar, M., Demirel, M. C., & Atilgan, A. R. Dynamics of disordered structures: Effect
of non-linearity on the localization. J. Sound Vibr. 205, 372–379 (1997).
Koç University, Sarıyer, 34450 İstanbul – Turkey
H +90 (212) 3381840 • B msayar@ku.edu.tr
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Invited Talks
Mar. 2004 Title: “Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?”, Host:
Prof. Monica Olvera de la Cruz, Materials Science Dept. , Northwestern University
Mar. 2004 Title: “Polyelectrolyte Bundles”, Host: Prof. Canan Atılgan, Sabanci University,
Istanbul, Turkey
Dec. 2004 Title: “Self Organization of Organic Molecules into Nanostructured Materials”, Host:
Irsadi Aksun, Koc University College of Engineering, Istanbul, Turkey
Sep. 2006 Title: “Aggregation of Polyelectrolyte Chains into Finite Size Aggregates”, Host:
Gerhard Wegner, MPIP, Mainz/Germany
Nov. 2010 Title: “Structure and Thermodynamics of Biopolymers”, Host: Prof. Monica Olvera
de la Cruz, Northwestern University
Feb. 2011 Title: “Biopolymers as Building Blocks for Novel Materials”, Prof. Tülay Tulun, ITU,
Istanbul
Feb. 2012 Title: “Peptide Based Materials: Assembly, Structure and Thermodynamic Properties”,
Host: Dr. Christian Holm, University of Stuttgart
Mar. 2012 Title: “Biopolimerler & Kendiliğinden Organizasyon: Oyunun Kurallarn Öğrenmek”,
Genç Kimyacılar Derneği, Istanbul
Jun. 2013 Adsorption and Assembly of Peptides at a Hydrophobic/Hydrophilic Interface: Environment driven conformational change, Host: Dr. Christine Peter, MaxPlanck Institute
for Polymer Research, Mainz, Germany
Sep. 2013 Title: “Adsorption and Assembly of Peptides at the Hydrophobic/Hydrophilic Interface:
Environment driven conformational change”, Host: Dr. Mustafa Güler, UNAM, Bilkent,
Ankara
Dec. 2013 Title: “Adsorption and Assembly of Peptides at the Hydrophobic/Hydrophilic Interface:
Environment driven conformational change”, Department of Chemistry, Boğaziçi
University
Conferences
Nov. 2004 Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?, Mehmet Sayar,
Juelich Soft Matter Days, Kerkrade, NL
Mar. 2005 Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?, Mehmet Sayar,
Hans J. Limbach, Christian Holm, American Physical Society March Meeting, Los
Angeles, USA
Apr. 2005 Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?, Mehmet Sayar,
Christian Holm, WE Heraus Seminar, Bad Honnef, Netherlands
May. 2005 Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium, Mehmet Sayar,
Christian Holm, Gordon Conference, Il Ciocco, Italy
Oct. 2006 Model Polyelectrolyte Systems with Hierarchical Self Asembly: Importance of Counterion Valency, Mehmet Sayar, Berk Hess, Christian Holm, Active Biomimetic Materials,
Badhonnef/Germany
Jul. 2006 Polyelectrolyte Bundles, Mehmet Sayar, İstanbul İstatistik Fizik Günleri, Istanbul,
Turkey
May. 2007 Aggregation of Like Charged Polyelectrolytes, Mehmet Sayar, Christian Holm, GRC
Conference on Chemistry of Supramolecules & Assemblies, Il Ciocco, Italy
Koç University, Sarıyer, 34450 İstanbul – Turkey
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Jun. 2008 Understanding Bubble Formation and Dynamics in DNA, M. Sayar, B. Avsaroglu, A.
Kabakcioglu, Polyelectrolytes 2008, Coimbra, Portugal
Mar. 2009 Supercoil Formation During DNA Melting, Mehmet Sayar, Barış Avşaroğlu, Alkan
Kabakçıoğlu, American Physical Society March 2009 Meeting, Pittsburgh, USA
Sep. 2010 Twist writhe partitioning in a coarse grained DNA minicircle model, Sayar, M. and
Bavsaroglu, B. and Kabakcioglu, A., Novel Simulation Approaches to Soft Matter
Systems, Dresden, Germany
Jun. 2010 Driving Force for Adsorption of Amphiphilic Peptides to Air/Water Interface, Engin
O., Villa A., Hess B. and Sayar M., Multiscale Molecular Modelling 2010, Edinburgh,
UK
Mar. 2011 Twist/Writhe Partitioning in DNA Minicircles , Mehmet Sayar & Alkan Kabakcioglu,
Biophysical Society, Baltimore, USA
Jun. 2011 Self Assembly of Amphiphilic Peptides into One dimensional Objects , Özge Engin,
Beytullah Özgür and Mehmet Sayar, NanoTr, Istanbul, Turkey
Mar. 2012 Understanding Formation and Structure of Peptide Nanofivers via Steered MD Simulations, Ozge Engin, Beytullah Ozgur, Mehmet Sayar, Biophysical Society, Sandiego,
USA
Jun. 2012 One Coarse Grained DNA Model for all: From Single Strand to Double Helix, Murat
Ozturk, Alkan Kabakcioglu, Mehmet Sayar, Istatistik Fizik Günleri, İstanbul, Turkey
Jun. 2012 Fiber Formation via Multi Domain Peptides: Effect of Aliphatic to Aromatic Residue
Substitution, Beytullah Ozgur, Ozge Engin, Mehmet Sayar, Istatistik Fizik Günleri,
İstanbul, Turkey
Jun. 2012 Self assembly at the Interface: Conformational Transition in Peptides , Cahit Dalgicdir
& Mehmet Sayar, İstatistik Fizik Günleri, İstanbul, Turkey
Jun. 2012 Self assembly at the Interface: Conformational Transition in Peptides , Cahit Dalgicdir
& Mehmet Sayar, NanoTR VIII, Ankara, Turkey
Jun. 2012 One Coarse Grained DNA Model for all: From Single Strand to Double Helix , Murat
Özturk, Alkan Kabakçıoğlu & Mehmet Sayar, NanoTR VIII, Ankara, Turkey
Oct. 2012 Biopolymers as Building Blocks for Novel Materials: Computational Modeling of Self
assembling materials, Mehmet Sayar, 10th Chemical Physics Congress, Ankara, Turkey
Nov. 2012 Self Assembly of Biomolecules at the air/water interface, Mehmet Sayar, MACAN
Workshop, Sabanci University, İstanbul, Turkey
Mar. 2013 Self Assembly of Peptides at the Air/Water Interface, Mehmet Sayar, American
Physical Society March Meeting, 3 , 2013, Baltimore, USA (2012)
Sep. 2013 Adsorption, Folding, and Packing of an Amphiphilic Peptide at the Air/Water Interface,
Ozge Sensoy and Mehmet Sayar, Workshop on ’Protein Dynamics: From Water
Hydration to Crowding Effects’, Freiburg, Germany
Sep. 2013 Self assembly of an Amphiphilic Peptide: A Multi Scale Approach, Beytullah Ozgur,
Ozge Sensoy, and Mehmet Sayar, Workshop on ’Protein Dynamics: From Water
Hydration to Crowding Effects’, Freiburg, Germany
Sep. 2013 Ozge Sensoy, and Mehmet Sayar, Workshop on ’Protein Dynamics: From Water
Hydration to Crowding Effects’, Freiburg, Germany
Nov. 2013 Peptit Bazlı Moleküllerin Hidrofobik/Hidrofilik Arayüzeylerde Davnanışı: Çevresel
Etkiler Altında Konformasyon Değişimleri, Mehmet Sayar, TÜBA GEBİP Konya
Meeting, Konya, Turkey
Koç University, Sarıyer, 34450 İstanbul – Turkey
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Nov. 2014 Peptit Moleküllerinin Makroskopik ve Moleküler Arayüzeylerde Katlanması , Mehmet
Sayar, TÜBA GEBİP Afyon Meeting, Afyon, Turkey
Teaching Activities
MECH 202 Engineering Materials
MECH 407 Finite Element Analysis
/MECH 507
MECH 590 Seminar in Mechanical Engineering
CHBI 438 Intermolecular and Surface Forces
/MASE 538
CHBI 405 Polymer Engineering
/MECH 423
/CHBI 505
ENGR
ENGR
MATH
MATH
CMSE
200
201
203
201
501
Probability and Statistical Methods for Engineers
Statistics for Engineers
Multivariable Calculus
Statistics
Introduction to Computational Science and Engineering
Conference and Workshop Organization
Jun. 2008 ITAP Conference on Bioinformatics and statistical physics of biopolymers, Organizers:
Alkan Kabakçıoğlu, Mehmet Sayar, Tuğrul Hakioğlu, Marmaris, Turkey
Sep. 2009 Theory and Simulation of Organic and Biological Systems, Organizers: Kurt Kremer,
Denis Andrienko, Mehmet Sayar, KU, Istanbul
Jan. 2012 A Short Course on Computational Methods for Life-Sciences and Nano-technology,
Organizers: Seda Keskin, Mehmet Sayar, KU, Istanbul
University Service
2006-2007
2005-2008
2010-2012
2010-2014
2014-to date
Editor for Kule Journal
Mechanical Engineering Graduate Coordinator
Materials Science and Engineering Graduate Coordinator
Freshman Advisor
CHBI Summer Training Coordinator
Koç University, Sarıyer, 34450 İstanbul – Turkey
H +90 (212) 3381840 • B msayar@ku.edu.tr
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