Materials Science & Engineering

Ersin Emre Oren

Research Associate
Mehmet Sarikaya Research Group

Office:  237 Wilcox
Tel:  (206) 616-6643
Fax: (206) 543-3100
E-mail: eeoren@u.washington.edu 

Curriculum Vitae

Research Interests

Molecular Dynamic Studies of GEPI* - Inorganic Interactions, their conformation and binding properties.

*GEPI: Genetically Engineered Proteins for Inorganics.
  

EDUCATION

Sep 2000 - Jan 2003
Ph. D. in Materials and Metallurgical Engineering,
Middle East Technical University, Ankara, Turkey
Thesis title: Computer simulation of electromigration-induced void – grain boundary interactions with a special reference to the prediction of cathode failure times in bamboo structures.
Research Adviser: Prof. Dr. Tarik Omer Ogurtani

Sep 1997 - Sep 2000
M. Sc. in Materials and Metallurgical Engineering,
Middle East Technical University, Ankara, Turkey
Thesis title: Electromigration – induced transgranular void motion in interconnects with special reference to computer simulation.
Research Adviser: Prof. Dr. Tarik Omer Ogurtani

Sep 1992 - Jun 1997
B. Sc. in Materialsand Metallurgical Engineering,
Middle East Technical University, Ankara, Turkey

Sep 1994 - Jun 1997
Minor in Solid State Physics in the Department of Physics
Middle East Technical University, Ankara, Turkey

PROFESSIONAL EXPERIENCE

Research Associate, July 2003-present
Department of Materials Science & Engineering, University of Washington, Seattle, WA, USA.

Visiting Scientist, June 2001-September 2001
Max-Planck-Institut für Metallforschung, Seestrasse 92, D-70174, Stuttgart, Germany.
Research topics: Electromigration and Fatigue Reliability.

Research Assistant, September 1997- June 2003
Materials and Metallurgical Engineering, Middle East Technical University, Ankara, Turkey.

AWARDS AND FELLOWSHIPS

(1) Prof. Dr. Mustafa N. Parlar Education & Research Foundation, Middle East Technical University, The Best Thesis Award 2000.

(2) Scientific and Technical Research Council of Turkey (TUBITAK)-NATO-A2 Research Grant for visiting Max-Planck-Institut für Metallforschung, Seestrasse 92, D-70174, Stuttgart, Germany.

SCIENTIFIC PUBLICATIONS

Thesis

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.

Papers in Refereed Journals

1. E. E. Oren, C. Tamerler, D. Sahin, M. Hnilova, U. O. S. Seker, M. Sarikaya and R. Samudrala
A novel knowledge-based approach to design inorganic binding peptides.
Bioinformatics, (in print, 2007)

2. T. O. Ogurtani, A. Celik and 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).

3. U. O. S. Seker, B. Wilson, S. Dincer, I. W. Kim, E. E. Oren, J. S. Evans, C. Tamerler, and M. Sarikaya
Adsorption behavior of linear and cyclic genetically engineered platinum binding peptides.
Langmuir, 23, 7895-7900 (2007).

4. C. Tamerler, M. Duman, E. E. Oren, M. Gungormus, X. Xiong, B. A. Parviz and M. Sarikaya
Materials specificity and directed assembly of a gold binding peptide
Small, 2 (11), 1372-1378 (2006).

5. C. Tamerler, E. E. Oren, M. Duman, E. Venkatasubramanian and 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).

6. E. E. Oren, C. Tamerler and M. Sarikaya
Metal recognition of septapeptides via polypod molecular architecture
Nano Letters, 5 (3), 415-419 (2005).

7. T. O. Ogurtani and 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).

8. T. O. Ogurtani and 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).

9. A. Kalkanli and E. E. Oren
Effect of spraying rate on microstructure of spray deposited Al-Fe-V-Si alloy
Powder Metallurgy, 46 (4), 324-328 (2003).

10. T. O. Ogurtani, M. R. Gungor and 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).

11. T. O. Ogurtani, M. R. Gungor and 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).

12. T. O. Ogurtani and 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).

13. E. E. Oren and A. C. Tas
Hydrothermal synthesis of pure and Dy doped BaTiO3 powders at 90 oC
Metallurgical and Materials Transactions B, 30, 1089-1093 (1999).

14. E. E. Oren, E. Taspinar and A. C. Tas
Preparation of lead zirconate (PbZrO3) by homogeneous precipitation and calcination
Journal of American Ceramic Society, 80 (10), 2714-2716 (1997).

Papers in Review

1. E. E. Oren, R. Samudrala, D. Sahin, M. Hnilova, S. Cetinel, N. Gul-Karaguler, C. Tamerler and M. Sarikaya
In silico design of inorganic-binding peptides.
Nature Materials, submitted for publication (June, 2007).

2. C. So, J. L. Kulp, E. E. Oren, H. Zareie, C. Tamerler, J. S. Evans and M. Sarikaya
Molecular basis for patterned self assembly of a genetically selected E. coli gold binding protein on Au {111} surfaces.
Nature Nanotechnology, submitted for publication (July, 2007).

3. T. O. Ogurtani, O. Akyildiz and 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, submitted for publication (August, 2007).

Proceedings of Refereed Conferences

1. E. E. Oren and T. O. Ogurtani
Void intergranular motion under the action of electromigration forces in thin film interconnects with bamboo structure
Thin Films: Stresses and Mechanical Properties IX, Vol. 695, pp L5.5.1-L5.5.7. Editors: C. S. Ozkan, R. C. Cammarata, L. B. Freund, H. Gao Materials Research Society, Fall Meeting, Boston, MA, USA, November 26-30, 2001.

2. E. E. Oren and T. O. Ogurtani
The effect of initial void configuration on the morphological evolution under the action of normalized electron wind forces
Materials, Technology and Reliability for Advanced Interconnects and Low-k Dielectrics II, Vol 714E, pp L9.2.1-L9.2.6. Editor: S. Lahiri, Materials Research Society, Spring Meeting, San Francisco, CA, USA, April 16-20, 2001.

3. T. O. Ogurtani and E. E. Oren
A computer simulation of void dynamics under the action of electromigration and capillary forces in narrow thin interconnects
Advanced Metallization Conference 2000 (AMC 2000), Vol 16, pp 483-487. Editors: D. Edelstein, G. Dixit, Y. Yasuda, T. Ohba Advanced Metallization Conference, San Diego, CA, USA, October 3-5, 2000.

4. E. E. Oren and 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
Ceramic Transactions, Vol. 100, pp. 95-104, Editors: K. M. Nair and A. S. Bhalla, American Ceramic Society, Cincinnati, OH, USA, May 3-6, 1998.

5. E. E. Oren and A. C. Tas
Preparation of piezoelectric lead zirconate titanate (PbZr0.52Ti0.48O3) powders by homogeneous precipitation and calcination
Ceramic Transactions, Vol. 100, pp. 105-114, Editors: K. M. Nair and A. S. Bhalla, American Ceramic Society, Cincinnati, OH, USA, May 3-6, 1998.

Presentations at conferences

1. E. E. Oren, R. Samudrala, D. Sahin, T. Kacar, M. Hnilova, C. Tamerler and M. Sarikaya
Design of multifunctional binding peptides
MRS 2007 Fall Meeting, "Symposium NN: Protein and peptide engineering for therapeutic and functional materials"
Submitted for Oral Presentation, Boston, MA, USA, November 26-30, 2007.

2. J. S. Evans, J. L. Kulp, I. W. Kim, S. Collino, E. E. Oren, H. Zareie, C. So, C. Tamerler and M. Sarikaya
Guiding theory: Materials genomics and lessons learned from polypeptide “interactions” with natural and artificial inorganic solids
Centre Europeen de Calcul Atomique et Moleculaire (CECAM) Workshop on “Modeling the interaction of biomolecules with inorganic surfaces”
Oral Presentation, Lyon, France, July 25-27, 2007.

3. E. E. Oren, R. Samudrala, D. Sahin, M. Hnilova, U.O.S. Seker, M. Gungormus, S. Cetinel, N.G. Karaguler, C. Tamerler and M. Sarikaya
In silico design of inorganic binding peptides
Molecular biomimetics and bionanotechnology workshop
Poster Presentation, Istanbul, Turkey, May 21-23, 2007.

4. E. E. Oren, R. Samudrala, D. Sahin, M. Hnilova, C. Tamerler and M. Sarikaya
In silico design of inorganic binding peptides
4th Annual Conference on Foundations of Nanoscience: Self-assembled architectures and devices “Symposium: Self-assembly of Peptide-Protein Nanostructures”
Poster Presentation, Snowbird, UT, USA, April 18-21, 2007.

5. C. So, E. E. Oren, J. Kulp, H. Zareie, C. Tamerler, J. Evans and M. Sarikaya
Molecular Basis for Patterned Supramolecular SelfAssembly of a Genetically Engineered Gold Binding Protein on Au {111}
4th Annual Conference on Foundations of Nanoscience: Self-assembled architectures and devices “Symposium: Self-assembly of Peptide-Protein Nanostructures”
Poster Presentation, Snowbird, UT, USA, April 18-21, 2007.

6. E. E. Oren, R. Samudrala, D. Sahin, M. Hnilova, M. Gungormus, U. O. S. Seker, S. Cetinel, A. Cebeci, N. G. Karaguler, C. Tamerler and M. Sarikaya
A novel informatics-based approach for the design of inorganic binding peptides
MRS 2007 Spring Meeting, "Symposium T: The nature of design--utilizing biology’s portfolio"
Oral Presentation, San Francisco, CA, USA, April 10-13, 2007.

7. M. Hnilova, E. E. Oren, U. O. S. Seker, B. Wilson, X. Xiorong, C. Tamerler and M. Sarikaya
Selection of specific gold-binding peptides via cell surface display
MRS 2007 Spring Meeting, "Symposium T: The nature of design--utilizing biology’s portfolio"
Poster Presentation, San Francisco, CA, USA, April 10-13, 2007.

8. C. Tamerler, M. Gungormus, H. Fong, D. Sahin, E. E. Oren, S. Cetinel, N. G. Karaguler, and M. Sarikaya
Post-selection genetic engineering of inorganic binding peptides for practical materials applications
TMS 2007 Annual Meeting & Exhibition, "Symposium: Biological Materials Science: Biological Materials I"
Oral Presentation, Orlando, FL, USA, February 25-March 1, 2007.

9. E. E. Oren, C. Tamerler, M. Sarikaya and R. Samudrala
A novel informatics-based approach for the design of inorganic binding peptides
Molecular Biomimetics I: Protein Based Materials for Technology and Medicine
Poster Presentation, San Juan Island, WA, USA, September 6-8, 2006.

10. E. E. Oren, C. Tamerler and M. Sarikaya
Metal recognition of GEPI’s via polypod molecular architecture
Molecular Biomimetics I: Protein Based Materials for Technology and Medicine
Poster Presentation, San Juan Island, WA, USA, September 6-8, 2006.

11. D. Sahin, E. E. Oren, C. Tamerler and M. Sarikaya
Genetic construction of peptide-protein molecular hybrids for materials applications
Molecular Biomimetics I: Protein Based Materials for Technology and Medicine
Poster Presentation, San Juan Island, WA, USA, September 6-8, 2006.

12. E. E. Oren, R. Samudrala, D. Sahin, S. Dincer, C. Tamerler and M. Sarikaya
De novo design of inorganic binding polypeptides
MRS 2005 Fall Meeting, "Symposium LL: Combinatorial methods and informatics in materials science"
Poster Presentation, Boston, MA, USA, November 28-December 1, 2005.

13. E. E. Oren, R. Samudrala, D. Sahin, N. Gul-Karaguler, C. Tamerler and M. Sarikaya
Bioinformatics-based de novo design of biocombinatorially pregenerated quartz binding peptides
Nanoscale Science and Technology Workshop
Poster Presentation, Seattle, WA, USA, September 20-21, 2005.

14. E. E. Oren, R. Samudrala, D. Sahin, C. Tamerler and M. Sarikaya
Structure prediction of biocombinatorially generated quartz binding peptides
Nanoscale Science and Technology Workshop
Poster Presentation, Snowbird, WA, USA, September 20-21, 2005.

15. E. E. Oren, R. Samudrala, D. Sahin, S. Dincer, C. Tamerler and M. Sarikaya
Similarity analysis of polypeptides generated via directed evolution
2nd Annual Conference on Foundations of Nanoscience: Self-assembled architectures and devices “Symposium: Principles and Theory of Self-Assembly”
Poster Presentation, Snowbird, UT, USA, April 24-28, 2005.

16. E. E. Oren, D. Sahin, C. Tamerler and M. Sarikaya
Similarity analysis of genetically engineered polypeptides for inorganics
MRS 2004 Fall Meeting, "Symposium Z: Bio-inspired and bio-derived materials and processes"
Poster Presentation, Boston, MA, USA, November 29-December 3, 2004.

17. U. O. S. Seker, E. E. Oren, C. Selcuki, C. Tamerler and M. Sarikaya
Molecular modeling of engineered polypeptides
MRS 2004 Fall Meeting, "Symposium Z: Bio-inspired and bio-derived materials and processes"
Oral Presentation, Boston, MA, USA, November 29-December 3, 2004.

18. M. Sarikaya, C. Tamerler, M. Duman, E. Venkatasubramanian, S. Dincer, E. E. Oren, H. Dai, C. Nguyen, D. T. Schwartz and F. Baneyx
Recognition and binding of engineered polypeptides on functional inorganics
MRS 2004 Spring Meeting, "Symposium Z: Hybrid Biological-Inorganic Interfaces"
Oral Presentation, San Francisco, CA, USA, April 12-16, 2004.

19. M. Sarikaya, C. Tamerler, E. E. Oren, M. H. Zaraie, H. Fong and F. Baneyx
Molecular Biomimetics: Biomaterialization and assembly using engineered polypeptides
8th International Conference on the Chemistry and Biology of Mineralized Tissues MRS 2004 Spring Meeting, "Symposium Z: Hybrid Biological-Inorganic Interfaces"
Poster Presentation, Alberta, Canada, October 17-22, 2004.

20. E. E. Oren and T. O. Ogurtani
Interactive computer simulation of dislocation damping spectra associated with the coupled motion of geometric kinks and point defects subjected to the bulk segregation
ICIFUAS 13
Poster Presentation, Bilbao, Spain, July 8-12, 2002.

21. E. E. Oren and T. O. Ogurtani
Mathematical modeling of the void evolution dynamics under the action of electromigration and capillary forces in thin interconnects
International Conference on Mathematical Modeling and Scientific Computing Middle East Technical University and Selçuk University
Oral Presentation, Ankara and Konya, Turkey, April 2-6, 2001.

22. T. O. Ogurtani, M. R. Gungor and E. E. Oren
Computer simulation of internal friction spectrum utilizing an interactive kink chain mobile foreign interstitials model
Second International School on Mechanical Spectroscopy MS - 2
Invited Presentation, Kraków-Krynica, Poland, December 3-8, 2000.

PROFESSIONAL SOCIETY MEMBERSHIPS

Member, Materials Research Society (MRS)

Member, METU Amateur Astronomy Society

 

FIELDS OF INTEREST 

Materials Science