Biomedical Engineering Department

 

Assist. Prof. Dr. ERSIN EMRE OREN

Department of Biomedical Engineering
Department of Materials Science and Nanotechnology Engineering
TOBB University of Economics and Technology
Sogutozu Cad. No: 43,
Sogutozu, Ankara, 06560 TURKEY
e-mail: eeoren@etu.edu.tr
phone: +90 (312) 292-4514 (office); +90 (312) 292-4585 (lab)
fax: +90 (312) 292-4091		 Ersin Emre Oren
TÜRKÇE
Bionanodesign Research Highlights

SCIENTIFIC PUBLICATIONS

60 listed: 46 articles, 7 proceedings, 5 meeting abstracts & 2 theses;
As of October 2024;   Science Citation Index: Total # of citations: 1796, h-index: 23
                                Google Scholars: Total # of citations: 2709, h-index: 25; i10-index: 34

Journal Articles (Indexed by SCI)

IJOS IJOS IJOS Soft Matter Advanced Materials MRS Bulletin

  1. J.H. Keeper, J. Seto, E.E. Oren, O.V. Horst, L-H Hung & R. Samudrala. “Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep” Frontiers in Materials, , (2024). doi: 10.3389/fmats.2024.1436379
  2. Z. Aminiranjbar, C. Akin Gultakti, M. N. Alangari, Y. Wang, B. Demir, Z. Koker, A. K. Das, M. P. Anantram, E.E. Oren & J. Hihath. “Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements” ACS Sensors, 9, 2888-2896 (2024). doi:10.1021/acssensors.3c02734
  3. B. Demir, C. Akin Gultaktı, Z. Koker, M. P. Anantram & E.E. Oren. “Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations” ACS J. Phys. Chem. B, 128, 4646-4654 (2024). doi:10.1021/acs.jpcb.4c00445
  4. B. Liu, B. Demir, C. Akin Gultaktı, J. Marrs, Y. Gong, R. Li, E.E. Oren & J. Hihath. “Self-aligning nanojunctions for integrated single-molecule circuits” ACS Nano,18, 4972 (2024). doi:10.1021/acsnano.3c10844
    5. * Cover.
  5. L. Luo, S. Manda, Y. Park, B. Demir, J. Sanchez, M. P. Anantram, E.E. Oren, A. Gopinath & M. Rolandi. “DNA nanopores as artificial membrane channels for bioprotonics” Nature Communications,14, 5364 (2023). doi:10.1038/s41467-023-40870-1
  6. B. Demir, H. Mohammad, M. P. Anantram & E.E. Oren. “DNA - Au (111) interactions and transverse charge transport properties for DNA - based electronic devices” Physical Chemistry Chemical Physics, 25, 16570-16577 (2023). doi:10.1039/D2CP05009A
  7. Y. Wang, B. Demir, H. Mohammad, E.E. Oren & M. P. Anantram. “Computational study of the role of counterions and solvent dielectric in determining the conductance of b-DNA” Physical Review E, 107, 044404 (2023). doi:10.1103/PhysRevE.107.044404
  8. M. Alangari, B. Demir, C. Akin Gultakti, E.E. Oren & J. Hihath. “Mapping DNA Conformations Using Single-Molecule Conductance Measurements” Biomolecules, 13(1), 129 (2023). doi:10.3390/biom13010129
  9. T.O. Ogurtani, A. Celik & E.E. Oren. “Effects of anisotropic surface drift diffusion on the strained heteroepitaxial nanoislands subjected to electromigration stressing” Journal of Applied Physics, 131, 075301 (2022). doi:10.1063/5.0067760
  10. H. Mohammad, B. Demir, C. Akin, B. Luan, J. Hihath, E.E. Oren & M.P. Anantram "Role of intercalation in the electrical properties of nucleic acids for use in molecular electronics"Nanoscale Horizons, 6 (8), 651-660 (2021). doi:10.1039/D1NH00211B
    11. * Cover.
  11. Y. Li, J.M. Artés, B. Demir, S. Gokce, H.M. Mohammad, M. Alangari, M.P. Anantram, E.E. Oren & J. Hihath “Detection and identification of genetic material via single-molecule conductance” Nature Nanotechnology, 13, 1167-1173 (2018). doi:10.1038/s41565-018-0285-x
  12. E. Kayali, E. Mercan, E.E. Oren & G.C. Buke “Few layer graphene synthesis via SiC decomposition at low temperature and low vacuum” Journal of Physics D: Applied Physics, 49, 165301 (2016). doi:10.1088/0022-3727/49/16/165301
  13. H. Yazici, M.B. O'Neill, T. Kacar, B.R. Wilson, E.E. Oren, M. Sarikaya & C. Tamerler “Engineered chimeric peptides as antimicrobial surface coating agents towards infection-free implants” ACS Applied Materials & Interfaces, 8 (8), 5070-5081 (2016). doi:10.1021/acsami.5b03697
  14. H. Erdogan, E. Babur, M. Yilmaz, E. Candas, M. Goerdesel, Y. Dede, E.E. Oren, G. Demirel, M. Ozturk & G. Demirel “Morphological versatility in self-assembly of Val-Ala and Ala-Val dipeptides” Langmuir, 31, 7337-7345 (2015). doi:10.1021/acs.langmuir.5b01406
  15. T.O. Ogurtani, A. Celik & E.E. Oren. “Stranski-Krastanow islanding initiated on the stochastic rough surfaces of the epitaxially strained thin films” Journal of Applied Physics, 115, 224307 (2014). doi:10.1063/1.4883295
  16. H. Yazıcı, H. Fong, B. Wilson, E.E. Oren, F.A. Amos, H. Zhang, K.S. Evans, M.L. Snead, M. Sarikaya & C. Tamerler. “Biological response on a titanium implant-grade surface functionalized with modular peptides” Acta Biomaterialia, 9, 5341-5352 (2013). doi:10.1016/j.actbio.2012.11.004
  17. M. Gungormus, E.E. Oren, J.A. Horst, H. Fong, M. Hnilova, M.J. Somerman, M.L. Snead, R. Samudrala, C. Tamerler & M. Sarikaya. “Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides” International Journal of Oral Science, 4, 69-77 (2012). doi:10.1038/ijos.2012.40
    18. * Cover.
  18. S. Cetinel, S. Dincer, A. Cebeci, E.E. Oren, J.D. Whitaker, D.T. Schwartz, N.G. Karaguler, M. Sarikaya & C. Tamerler. “Peptides to bridge biological-platinum materials interface” Bioinspired, Biomimetic and Nanobiomaterials, 1, 143-153 (2012). doi:10.1680/bbn.12.00008
  19. M. Hnilova, C.R. So, E.E. Oren, B.R. Wilson, T. Kacar, C. Tamerler & M. Sarikaya. “Peptide-directed co-assembly of nanoprobes on multimaterial patterned solid surfaces” Soft Matter, 8, 4327-4334 (2012). doi:10.1039/c2sm06426j
    20. * Back Cover.
  20. O. Akyildiz, E.E. Oren & T.O. Ogurtani. “Grain boundary grooving in bi-crystal thin films induced by surface drift-diffusion driven by capillary forces and applied uniaxial-tensile stresses” Philosophical Magazine, 92, 804-829 (2012). doi:10.1080/14786435.2011.634850
  21. M. Hnilova, D. Khatayevich, A. Carlson, E.E. Oren, C. Gresswell, S. Zheng, F. Ohuchi, M. Sarikaya & C. Tamerler. “Single-Step Fabrication of Patterned Gold Film Array by an Engineered Multi-Functional Peptide” Journal of Colloid and Interface Science, 365, 97-102 (2012). doi:10.1016/j.jcis.2011.09.006
  22. O. Akyildiz, E.E. Oren & T.O. Ogurtani. “Mesoscopic nonequilibrium thermodynamics treatment of the grain boundary thermal grooving induced by the anisotropic surface drift diffusion” Journal of Materials Science, 46, 6054-6064 (2011). doi:10.1007/s10853-011-5567-8
  23. E.E. Oren, R. Notman, I.W. Kim, J.S. Evans, T.R. Walsh, R. Samudrala, C. Tamerler & M. Sarikaya. “Probing the molecular mechanisms of quartz-binding peptides” Langmuir, 26, 11003-11009 (2010). doi:10.1021/la100049s
  24. T.O. Ogurtani, A. Celik & E.E. Oren. “Generic role of the anisotropic surface free energy on the morphological evolution in a strained-heteroepitaxial solid droplet on rigid substrates” Journal of Applied Physics, 108, 103516 (2010). doi:10.1063/1.3512970
  25. R. Notman, E.E. Oren, C. Tamerler, M. Sarikaya, R. Samudrala & T. R. Walsh. “Solution studies of strong and weak quartz-binding peptides using replica exchange molecular dynamics” Biomacromolecules, 11, 3266-3274 (2010). doi:10.1021/bm100646z
  26. T.O. Ogurtani, A. Celik & E.E. Oren. “Morphological evolution in a strained-heteroepitaxial solid droplet on a rigid substrate: Dynamical simulations” Journal of Applied Physics, 108, 063527 (2010). doi:10.1063/1.3483937
    27. * Editorially chosen to appear in the Virtual Journal of Nanoscale Science & Technology September 27, 2010.
  27. A. Dezieck, O. Acton, K. Leong, E.E. Oren, H. Ma, C. Tamerler, M. Sarikaya & A.K.-Y. Jen. “Threshold voltage control in organic thin film transistors with dielectric layer modified by a genetically engineered polypeptide” Applied Physics Letters, 97, 013307(2010). doi:10.1063/1.3459978
  28. C. Tamerler, D. Khatayevich, M. Gungormus, T. Kacar, E.E. Oren, M. Hnilova & M. Sarikaya. “Molecular biomimetics: Gepi-based biological routes to technology” Biopolymers: Peptide Science, 94, 78-94 (2010). doi:10.1002/bip.21368
  29. C.R. So, J.L. Kulp, E.E. Oren, H. Zareie, C. Tamerler, J.S. Evans & M. Sarikaya. “Molecular recognition and supramolecular self-assembly of a genetically engineered gold binding peptide on Au{111}” ACS Nano, 3, 1525-1531 (2009). doi:10.1021/nn900171s
  30. T. Kacar, J. Ray, M. Gungormus, E.E. Oren, C. Tamerler & M. Sarikaya. “Quartz binding peptides used as linkers for making multi-(bio)functional micro-patterned systems” Advanced Materials, 21, 295-299 (2009). doi:10.1002/adma.200801877
    31. * Front inside cover.
  31. M. Hnilova, E.E. Oren, U.O.S. Seker, B. Wilson, S. Collino, J.S. Evans, C. Tamerler & M. Sarikaya. “Effect of molecular conformations on adsorption behavior of gold binding peptides” Langmuir, 24, 12440-12445(2008). doi:10.1021/la801468c
  32. T.O. Ogurtani, O. Akyildiz & E.E. Oren. “Morphological evolution of tilted grain-boundary thermal grooving by surface diffusion in bicrystal thin solid films having strong anisotropic surface Gibbs free energy” Journal of Applied Physics, 104, 013518 (2008). doi:10.1063/1.2952520
  33. J.S. Evans, R. Samudrala, T. Walsh, E.E. Oren & C. Tamerler. “The molecular design of inorganic-binding polypeptides” MRS Bulletin, 33, (5) 514-518 (2008). (Cover designed by EEO) doi:10.1557/mrs2008.103
    34. * Cover.
  34. E.E. Oren, C. Tamerler, D. Sahin, M. Hnilova, U.O.S. Seker, M. Sarikaya & R. Samudrala. “A novel knowledge-based approach to design inorganic-binding peptides” Bioinformatics, 23, (21), 2816-2822 (2007). doi:10.1093/bioinformatics/btm436
  35. T.O. Ogurtani, A. Celik & E.E. Oren. “Morphological evolution of edge-hillocks on single crystal films having anisotropic drift-diffusion under the capillary and electromigration forces” Thin Solid Films, 515 (5), 2974-2983 (2007). doi:10.1016/j.tsf.2006.08.020
  36. U.O.S. Seker, B. Wilson, S. Dincer, I.W. Kim, E.E. Oren, J.S. Evans, C. Tamerler, & M. Sarikaya. “Adsorption behavior of linear and cyclic genetically engineered platinum binding peptides” Langmuir, 23, 7895-7900 (2007). doi:10.1021/la700446g
  37. C. Tamerler, M. Duman, E.E. Oren, M. Gungormus, X. Xiong, B.A. Parviz & M. Sarikaya. “Materials specificity and directed assembly of a gold binding peptide” Small, 2 (11), 1372-1378 (2006). doi:10.1002/smll.200600070
  38. C. Tamerler, E.E. Oren, M. Duman, E. Venkatasubramanian & M. Sarikaya. “Adsorption kinetics of an engineered gold binding peptide by surface plasmon resonance spectroscopy and a quartz crystal microbalance” Langmuir, 22, 7712-7718 (2006). doi:10.1021/la0606897
  39. E.E. Oren, C. Tamerler & M. Sarikaya. “Metal recognition of septapeptides via polypod molecular architecture” Nano Letters, 5 (3), 415-419 (2005). doi:10.1021/nl048425x
  40. T.O. Ogurtani & E.E. Oren. “Irreversible thermodynamics of triple junctions during the intergranular void motion under the electromigration forces” International Journal of Solids and Structures, 42 (13), 3918-3952 (2005). doi:10.1016/j.ijsolstr.2004.11.013
  41. T.O. Ogurtani & E.E. Oren. “Electromigration-induced void grain-boundary interactions: the mean time to failure for copper interconnects with bamboo and near-bamboo structures” Journal of Applied Physics, 96 (12), 7246-7253 (2004). doi:10.1063/1.1815389
  42. A. Kalkanli & E.E. Oren. “Effect of spraying rate on microstructure of spray deposited Al-Fe-V-Si alloy” Powder Metallurgy, 46 (4), 324-328 (2003). doi:10.1179/003258903225008571
  43. T.O. Ogurtani, M.R. Gungor & E.E. Oren. “Simulation of dislocation damping spectra associated with the collective motion of point defects and kink chain subjected to the bulk segregation” Journal of Applied Physics, 91 (4), 1860-1870 (2002). doi:10.1063/1.1429769
  44. T.O. Ogurtani & E.E. Oren. “Computer simulation of void growth dynamics under the action of electromigration and capillary forces in narrow thin interconnects” Journal of Applied Physics, 90 (3), 1564-1572 (2001). doi:10.1063/1.1382835
  45. E.E. Oren & A.C. Tas. “Hydrothermal synthesis of pure & Dy doped BaTiO3 powders at 90 °C” Metallurgical and Materials Transactions B, 30, 1089-93 (1999). doi:10.1007/s11663-999-0115-5
  46. E.E. Oren, E. Taspinar & A.C. Tas. “Preparation of lead zirconate (PbZrO3) by homogeneous precipitation and calcinations” Journal of American Ceramic Society, 80 (10), 2714-2716 (1997). doi:10.1111/j.1151-2916.1997.tb03181.x
Proceedings
  1. R. Samudrala, E.E. Oren, C. Cheng, J. Horst, B. Bernard, M. Gungormus, M. Hnilova, H. Fong, C. Tamerler & M. Sarikaya. “Knowledge-based design of inorganic-binding peptides” The FNANO08 Conference Proceedings, 75-80 (2008).
  2. T.O. Ogurtani, M.R. Gungor & E.E. Oren. “Interactive computer simulation of dislocation damping spectra associated with the coupled motion of geometric kinks and point defects subjected to the bulk segregation phenomenon” Solid State Phenomena, 89, 141-190 (2003).
  3. E.E. Oren & T.O. Ogurtani. “Void intergranular motion under the action of electromigration forces in thin film interconnects with bamboo structure” MRS Symp. Proc., 695, 209-215 (2002).
  4. E.E. Oren & T.O. Ogurtani. “The effect of initial void configuration on the morphological evolution under the action of normalized electron wind forces” MRS Symp. Proc., 714E, L9.2.1-L9.2.6 (2001).
  5. T.O. Ogurtani & E.E. Oren, “A computer simulation of void dynamics under the action of electromigration and capillary forces in narrow thin interconnects” Advanced Metallization Conference, 16, 483-487 (2000).
  6. E.E. Oren & A.C. Tas. “Hydrothermal synthesis of pure and Dy:BaTiO3 powders at 90°C, the sintering behavior and microstructures of Dy:BaTiO3 powders heated on Ti-strips” Dielectric Ceramic Materials: Ceramic Transactions (Wiley-Am. Ceram. Soc.), 100, 95-104 (1999).
  7. E.E. Oren & A.C. Tas. “Preparation of piezoelectric lead zirconate titanate (PbZr0.52Ti0.48O3) powders by homogeneous precipitation and calcinations” Dielectric Ceramic Materials: Ceramic Transactions (Wiley-Am. Ceram. Soc.), 100, 105-114 (1999).
Meeting Abstracts
  1. M. Gungormus, H. Fong, E.E. Oren, C. Tamerler, M. Somerman & M. Sarikaya. “Cementum-analogs using hydroxyapatite binding peptides: Toward periodontal regeneration” Abstracts of Papers of the American Chemical Society, 237, 25-NANO (2009).
  2. R. Samudrala, E.E. Oren, C. Tamerler & M. Sarikaya. “In silico design of solid binding peptides as molecular building blocks in technology and medicine ” Abstracts of Papers of the American Chemical Society, 237, 32-NANO (2009).
  3. T. Kacar, J. Ray, M. Gungormus, E.E. Oren, C. Tamerler & M. Sarikaya. “Quartz binding peptides as molecular linkers for co-assembling nanoentities on multifunctional micropatterned substrates ” Abstracts of Papers of the American Chemical Society, 237, 13-NANO (2009).
  4. A. Sert, N.G. Karaguler, D. Sahin, E.E. Oren, M. Sarikaya & C. Tamerler. “Construction and expression of a bi-functional peptide by using genetic engineering methods for bionanotechnologies” FEBS Journal, 275, 372-372 (2008).
  5. A. Sert, N.G. Karaguler, D. Sahin, E.E. Oren, M. Sarikaya & C. Tamerler. “Construction and expression of a bi-functional peptide by using genetic engineering methods for bionanotechnologies” FEBS Journal, 275, 372-372 (2008).
Theses
  1. E.E. Oren. “Computer simulation of electromigration induced void – grain boundary interactions with a special reference to the prediction of cathode failure times in bamboo structures” Ph. D. Thesis, Middle East Technical University, January 2003.
  2. E.E. Oren. “Electromigration – induced transgranular void motion in interconnects with special reference to computer simulation” M. Sc. Thesis, Middle East Technical University, September 2000.
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Address: Sogutozu Cad. No: 43, Sogutozu, Ankara, 06560 TURKEY /// Phone: +90 (312) 292-4514 Fax: +90 (312) 292-4091 eeoren@etu.edu.tr