Publications

Peer-Reviewed Articles

1. Contraction response of a polyelectrolyte hydrogel to nonuniformly applied electric fields, E.M. Bahceci and A.Erbaş. Soft Matter ( 2024). DOI: https://doi.org/10.1039/D4SM01000K
2. Heterogenous flexibility contributes to chromosome segregation in the cell nucleus. M. Girard, M.O. de la Cruz, J.F. Marko, and A. Erbaş. Phys. Rev. E (2024).   DOI:https://doi.org/10.1101/2020.12.01.40383
3. Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. A. G. Attar, J. Paturej, E.J. Banigan, and A. Erbaş. Nucleus (2024).   DOI: https://doi.org/10.1080/19491034.2024.2351957
4. A polymer-physics view of peripheral chromatin: de Gennes’ self-similar carpet model.
   O.S Sarıyer & A. Erbaş. Phys. Rev. E (2024) DOI:10.1103/PhysRevE.109.054403
5. Molecular Rheology of Nano-confined Oligomer Melts,
   A. B. Yıldırım, A Erbaş, L Biancofiore. J. Rheology (2024). DOI: https://doi.org/10.1122/8.0000751
6. Structural properties of cyclic polyelectrolytes in a dilute good solvent. A. Grzyb, K. Haydukivska, J.S. Kłos, A. Erbaş, and J Paturej. Macromolecules (2024). DOI: 10.1021/acs.macromol.3c01981
7. Mechanical deformation affects the condensation of counterions in highly swollen polyelectrolyte hydrogels. M. Rafique & A. Erbas, Soft Matter (2023). DOI: 10.1039/D3SM00585B
8. Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization, J. Paturej & A. Erbas, Phys. Biology (2023). DOI: 10.1088/1478-3975/ace750
9. Hydrogel-integrated optical fiber sensors and their applications: A comprehensive review.
   Sadeque et al. J. Materials Chem. C (2023) DOI: 10.1039/D3TC01206A
10. Effect of Charge State on the Equilibrium and Kinetic Properties of Mechanically Interlocked [5]Rotaxane: A Molecular Dynamics Study.
    A. U. Özkan, D. Tuncel & A. Erbaş, J. Phys. Chem. B (2023). DOI: 10.1021/acs.jpcb.2c07645
11. Facilitated Dissociation of Nucleoid Associated Proteins in the Bacterial Confinement (cover issue).
    Z. Koşar, A.G. Attar, and A. Erbaş, Biophysical J., (2022). DOI: 10.1101/2021.03.11.434965
12. Can the Concentration of a Transcription Factor Affect Gene Expression?
    Z. Koşar and A. Erbaş, Frontiers in Soft Matter (2022). DOI: 10.3389/frsfm.2022.914494
13. Interactions Between Densely Grafted Molten Polymer Brushes:  Scaling theories versus molecular simulations. A. Erbaş, Turkish J. Physics (2021). DOI:10.3906/fiz-2010-5
14. Chromophore Amphiphile-Polyelectrolyte Hybrid Hydrogels for Photocatalytic Hydrogen Production.
    H. Sai, A. Erbaş, A. Dannenhoffer, D. Huang, A, Weingarten, Z. A. Pinto, E. Siismets, K. Jang, K. Qu, M. O. de la Cruz, S. I. Stupp, J. Material. Chem. A (2020). DOI: 10.1039/C9TA08974H3
15. How Do DNA-Bound Proteins Leave Their Binding Sites? Role of facilitated dissociation.
    A. Erbaş, J. F. Marko, Current Opinion in Chem. Bio. (2019). DOI: 10.1016/j.cbpa.2019.08.007
16. Rebinding Kinetics of Ligand Particles in Confinement
    A. Erbaş, M. O. de la Cruz, J. F. Marko, Biophysical J. (2019). DOI:10.1016/j.bpj.2019.02.033
17. Effects of Electrostatic Interactions on Ligand Dissociation Kinetics
    A. Erbaş, M. O. de la Cruz, J. F. Marko, Phys. Rev. E (2018) DOI:10.1103/PhysRevE.97.022405
18. Co-Assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion-π Interactions. Z. Yu, A. Erbaş, F. Tantakitti, L. C. Palmer, J. A. Jackman, M. O. de la Cruz, N. Cho, S. I. Stupp, J. Am. Chem. Soc. (2017). DOI:10.1021/jacs.7b02058
19. Facilitated Dissociation of Transcription Factors from Single DNA Binding Sites
    R. I. Kamar, E. J. Banigan, A. Erbaş, R. D. Giuntoli, M. Olvera de la Cruz, R. C. Johnson, J. F. Marko,
    Proc. Natl. Acad. Sci. U.S.A. (2017). DOI:10.1073/pnas.1701884114
20. Ionic Conductivity in Polyelectrolyte Hydrogels, H. Li, A. Erbaş, J. Zwanikken, M. O. de la Cruz, Macromolecules (2016). DOI: 10.1021/acs.macromol.6b01276
21. Interactions between Polyelectrolyte Gel Surfaces, A. Erbaş, M. O. de la Cruz,
    Macromolecules (2016). DOI: 10.1021/acs.macromol.6b01416
22. Morphology-Induced Conductivity in Dry Ionic Liquid,  A. Erbas, M. Olvera de la Cruz,
    Phys. Chem. Chem. Phys.  (2016).  DOI: 10.1039/C5CP07090B
23. Energy Conversion in Polyelectrolyte Hydrogels, A. Erbas, M. Olvera de la Cruz,
    ACS Macro Letters  (2015). DOI:10.1021/acsmacrolett.5b00363 (cover issue),
24. Friction between Ring-Polymer Brushes, A. Erbas, J. Paturej,
    Soft Matter  (2015). DOI: 10.1039/C4SM02818J
25. Detachment of Semiflexible Polymer Chains from a Substrate – a Molecular Dynamics investigation, J. Paturej, A. Erbas, A. Milchev, V.G. Rostiashvili,
    J. Chem. Phys. 141, 22, (2014). DOI: 10.1063/1.4902551
26. Confinement-Dependent Friction in Peptide-Bundles, A. Erbas and R. R. Netz,
    Biophysical J. 104, 6, (2013).  DOI: 10.1016/j.bpj.2013.02.008
27. Viscous Friction of Hydrogen-Bonded Matter, A. Erbas, D. Horinek and R. R. Netz,
    J. Am. Chem. Soc. 134, pp 623 (2012). DOI: 10.1021/ja209454a
28. Viscous Compressible Hydrodynamics at Planes, Spheres, and Cylinders with Finite Surface Slip (cover issue), A. Erbas, R. Podgornik, and R. R. Netz,
    Euro. Phys. E 32, pp 147 (2010). DOI: 10.1140/epje/i2010-10610-7
29. Phase Diagrams and Crossover in Spatially Anisotropic d=3 Ising, XY Magnetic, and Percolation Systems: Exact Renormalization – Group Solutions of Hierarchical Models,
    A. Erbas, A. Tuncer, B. Yücesoy, and A. N. Berker,
    Phys. Rev. E 72, 026129 (2005).  DOI: 10.1103/PhysRevE.72.026129
    

Preprints (available on public repositories)

1. Multi-exponential DNA Residence Behaviors of Transcription Factors Under The Discrete Affinity Model Z Kosar, A Erbas @bioRxiv, 2023.09. 21.558872

2. Phase Behavior and Dissociation Kinetics of Lamins in a Polymer Model of Progeria, Hadiya A. Hameed, J. Paturej, A. Erbas @bioRxiv, 2024

   Book Chapters

1. The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation Rates by Surface Plasmon Resonance (SPR) and Benchmarking Performance Metrics. Computational Methods for Estimating the Kinetic Parameters of Biological Systems, Pages 237-253, Humana, New York, NY

• A. Goktug Attar, MSc Thesis. 3D genome organization and nuclear morphology (Adv: Aykut Erbas).
• Muzaffar Rafique, MSc Thesis. Mechanical deformation of polyelectrolyte hydrogels (Adv: Aykut Erbas).
• Darya Karimpour, MSc Thesis.  Molecular Dynamics Simulations of surface-grafted co-polymers. (Adv: Aykut Erbas).
• Ata Utku Özkan, MSc Thesis.  Molecular Dynamics Simulations Study of [5]Rotaxane  in Bulk and at Interfaces. (Adv: Aykut Erbas). Abstract: English.
• Zafer Koşar, MSc Thesis. Protein-DNA dissociation kinetics and chromosome organization in a model bacterial confinement (Adv: Aykut Erbas). Abstract: English.
• Aykut Erbaş, PhD Thesis. Friction of Soft Matter at  the  Nano-Scale  (Adv:Roland R. Netz). Abstract: English, German, Turkish
• Aykut Erbaş, MSc Thesis. Two Statistical Physics Problems: Phase Diagram Calculation of Spatially Anisotropic, Surfaced d= 3 Layered Systems by Renormalization-Group Theory and Vehicle-Route Optimization with Traffic Factors for Migros Home Delivery System by Simulated Annealing  (Adv: A. Nihat Berker). Abstract: English, Turkish
• Aykut Erbaş, BSc Thesis. Heat Capacity of Hierarchical Ising Lattices   (Adv: A. Nihat Berker). Abstract: English, Turkish

Journal covers