Publications

31) Ozgur, B., & Sayar, M.
Representation of the conformational ensemble of peptides in coarse grained simulations
The Journal of Chemical Physics 153 (5) , 054108 (2020)
https://doi.org/10.1063/5.0012391

30) Ozgur, B., & Dalgicdir, C., & Sayar, M.
Correction to 'Conformation and Aggregation of LKa14 Peptide in Bulk Water and at the Air/Water Interface'
The Journal of Physical Chemistry B 123 (10) , 2463-2465 (2019)
https://doi.org/10.1021/acs.jpcb.9b01566

29) Ramezanghorbani, F. & Dalgicdir, D., & Sayar, M.
A multi-state coarse grained modeling approach for an intrinsically disordered peptide
The Journal of Chemical Physics 147 (9), 094103 (2017)
https://doi.org/10.1063/1.5001087

28) Ozgur, B., & Sayar, M.
Assembly of Huntingtin headpiece into alpha-helical bundles
Biointerphases 12 (2) , 02D413 (2017)
http://avs.scitation.org/doi/abs/10.1116/1.4984009

27) Ozgur, B., & Sayar, M.
Role of Hydrophobic/Aromatic Residues on the Stability of Double-Wall Beta-Sheet Structures Formed by a Triblock Peptide
J. Phys. Chem. B 121 (16) , 4115-4128 (2017)
http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b00650

26) Ozgur, B., & Sayar, M.
Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation
J. Phys. Chem. B 120 (39) , 10243-10257 (2016)
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.6b07545

25) Dalgicdir, C., Globisch, C. Sayar, M. & Peter, C.
Representing environment-induced helix-coil transitions in a coarse grained peptide model
EPJ-ST 225 (8-9), 1463-1481 (2016)
http://link.springer.com/article/10.1140/epjst/e2016-60147-8

24) Dalgicdir, C., & Sayar, M.
Conformation and Aggregation of LKalpha14 Peptide in Bulk Water and at the Air/Water Interface
J. Phys. Chem. B 119, 15164-15175 (2015)
http://pubs.acs.org/doi/10.1021/acs.jpcb.5b08871

23) 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)
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004328

22) 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)
http://pubs.acs.org/doi/full/10.1021/bm4000019

21) 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)
http://scitation.aip.org/content/aip/journal/jcp/139/23/10.1063/1.4848675

20) Engin, O. & Sayar M.
Adsorption, Folding and Packing of an Amphiphilic Peptide at the Air/Water Interface.
The Journal of Physical Chemistry. B 116, 2198--2207 (2012)
http://dx.doi.org/10.1021/jp206327y

19) Engin, O., Villa, A., Peter, C., & Sayar M.
A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models.
Macromolecular Theory And Simulations 20, 451-465 (2011)
http://onlinelibrary.wiley.com/doi/10.1002/mats.201100005/abstract

18) Sayar M., Bavsaroglu, B. & Kabakcioglu, A.
Twist-writhe partitioning in a coarse-grained DNA minicircle model.
Phys. Rev. E 81, 041916 (2010)
http://pre.aps.org/abstract/PRE/v81/i4/e041916

17) Engin, O. Villa, A.,Sayar M. & Hess, B.
Driving Forces for Adsorption of Amphiphilic Peptides to Air-Water Interface.
J. Phys. Chem. B 114, 011093-11101 (2010)
http://pubs.acs.org/doi/abs/10.1021/jp1024922

16) Sayar M. & Holm C.
Equilibrium Polyelectrolyte Bundles with Different Multivalent Counterion Concentrations
Phys. Rev. E 82, 031901 (2010)
http://pre.aps.org/abstract/PRE/v82/i3/e031901

15) Engin O., Sayar M. & Burak, E.
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)

14) Engin, O. & Sayar, M.
Investigation of Structure of Amphipathic Peptides in Different Environments via Replica Exchange Molecular Dynamics Simulations
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 40, 205-208 (2008)

13) Emanuel, M.; Mohrbach, H.; Sayar, M.; Schiessel, H. & Kulic, I. M.
Buckling of stiff polymers: Influence of thermal fluctuations
Phys. Rev. E 76,1703 (2007)

12) Hess B., Sayar M. & Holm, C.
Stability of Hydrophobically Modified Poly(p-phenylene)sulfonate Bundles as Observed by Molecular Dynamics Simulation
Macromolecules 40, 1703 (2007)

11) Sayar M. & Holm, C.
Finite Size Polyelectrolyte Bundles at Thermodynamic Equilibrium
Europhys. Lett. 77, 16001 (2007)

10) Sayar M. & Stupp S. I.
Assembly of 1D Supramolecular Objects: From Monomers to Networks
Phys. Rev. E 72, 011803 (2005)

9) Limbach H. J., Sayar M., & Holm C.
Polyelectrolyte Bundles
J. Phys. Condens. Matter 16, 2135-2144 (2004).

8) Lecommandoux S., Klok H. A., Sayar M., Stupp S. I.
Synthesis and self-organization of rod-dendron and dendron-rod-dendron molecules
J. Phys. A, Poly. Chem. 41, 3501-3518 (2003).

7) Sayar M., de la Cruz M. O., & Stupp S. I.
Polar Order in Nanostructured Organic Materials
Europhys. Lett. 61, 334-340 (2003).

6) Sayar M. & Stupp S. I.
Self-organization of rod-coil molecules into nanoaggregates: A coarse grained model.
Macromolecules 34, 7135-7139 (2001).

5) 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).

4) Stupp S. I., Pralle M. U., Tew, G. N., Li, L. M.,Sayar M. and Zubarev E. R.
Self-assembly of organic nano-objects into functional materials.
MRS Bull. 25, 42048 (2000).

3) Alparslan A. K., Sayar M., & Atilgan A. R.
State-space prediction model for chaotic time series.
Phys. Rev. E 58, 2640-2643 (1998).

2) 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).

1) 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).