Biomedical Engineering Department

 

Dr. Öğr. Üyesi ERSİN EMRE ÖREN

Biyomedikal Mühendisliği Bölümü
Malzeme Bilimi ve Nanoteknoloji Mühendisliği Bölümü
TOBB Ekonomi ve Teknoloji Üniversitesi
Söğütözü Cad. No: 43,
Söğütözü, Ankara, 06560 TÜRKİYE
e-posta: eeoren@etu.edu.tr
telefon: +90 (312) 292-4514 (ofis); +90 (312) 292-4585 (lab)
fax: +90 (312) 292-4091		 Ersin Emre Oren
ENGLISH
Bionanodesign Research Highlights

BİLİMSEL YAYIN LİSTESİ

60 tane: 46 makale, 7 basılı bildiri, 5 konferans özeti ve 2 tez;
Ekim 20243 itibarıyla:  Science Citation Index: Total # of citations: 1796, h-index: 23
                                   Google Scholars: Total # of citations: 2709 h-index: 25; i10-index: 34

Uluslararası Hakemli Dergilerde Yayınlanan Makaleler (SCI tarafından taranan)

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. * Kapak.
  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. * Kapak.
  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. * Kapak.
  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). (İç Kapak) doi:10.1039/c2sm06426j
    20. * İç Kapak.
  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 (2011). 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. * Editörler tarafından seçilerek ayrıca Virtual Journal of Nanoscale Science & Technology September 27, 2010'da yayınlanmıştır.
  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. * İç Kapak.
  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). doi:10.1557/mrs2008.103
    34. * Kapak.
  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
Uluslararası bilimsel toplantılarda sunulan ve bildiri kitabında (Proceedings) basılan bildiriler
  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).
Konferans Özetleri
  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. D. Sahin, H. Kahraman, E.E. Oren, C. Tamerler & M. Sarikaya. “Peptide (GEPI)-protein molecular hybrid construction for materials and medical applications – ‘GEPI-based tag application” FEBS Journal, 275, 371-371 (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).
Tezler
  1. E.E. Oren. “Elektrogöçe bağlı boşluk-tanecik sınırı etkileşimlerinin bilgisayar modellemesi ve bambu yapılardaki katot bozulma zamanlarının tahmini” Doktora Tezi, Orta Doğu Teknik Üniversitesi, Ocak 2003.
  2. E.E. Oren. “Ara bağlantı elemanlarının elektrogöç'e bağlı tanecik içi boşluk hareketi ve bilgisayar modellemesi” Yüksek Lisans Tezi, Orta Doğu Teknik Üniversitesi, Eylül 2000.
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