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
BNT Research Highlights

CONFERENCE PRESENTATIONS

(74 listed: 16 invited/keynote, 39 talks, 19 posters).

Invied/Keynote Talks
  1. E. E. Oren “Bionanodesign: Computational Methods in Bionanotechnology” Department of Chemical Engineering, Shriram Center for Bioengineering & Chemical Engineering, Stanford University, Palo Alto, CA, USA, March 06, 2017.
  2. E. E. Oren “Bionanodesign: Computational Methods in Bionanotechnology” Department of Biomedical Engineering, METU, Ankara, Turkey, November 10, 2016.
  3. E. E. Oren “Bionanodesign” 2nd Turkish-Mexican Workshop on Science and Technology, CONACYT, Mexico City, Mexico, June 11, 2015.
  4. E. E. Oren “Quantum dot formation models: Topologic instabilities in epitaxially strained solids” 20th Condensed Matter Physics Conference, Hacettepe University, Ankara, Turkey, December 26, 2014.
  5. E. E. Oren “Computational Methods in Bionanotechnology” Department of Chemistry, Gazi University, Ankara, Turkey, November 12, 2014.
  6. E. E. Oren “Computational Methods in Bionanotechnology” National Nanotechnology Research Center (UNAM), Bilkent, Ankara, Türkiye, December 27, 2013.
  7. E. E. Oren “Computational Methods in Bionanotechnology” Institute of Applied Mathematics, METU, Ankara, Turkey, April 30, 2013.
  8. E. E. Oren “Homology Modeling in Membrane Proteins” Molecular Dynamics Workshop II, Ankara, Turkey, September 13, 2011.
  9. E. E. Oren “Morphological evolution of surfaces and interfaces: Electromigration - Grain grooving - Thin film growth” Seminar: Nanoscale Devices, Univ. of Washington, Seattle, WA, USA, July 5, 2011.
  10. E. E. Oren “Bioinformatics design of solid binding peptides for bionanotechnology” Biomaterials Seminar, Univ. of Washington, Seattle, WA, USA, March 11, 2010.
  11. E. E. Oren and R. Samudrala “Knowledge-based peptide design” Molecular Biomimetics & Bionanotechnology-IV: Protein-based Materials & Systems for Technology & Medicine, Friday Harbor, WA, USA, August 24-28, 2009.
  12. E. E. Oren, R. Samudrala, C. Tamerler and M. Sarikaya “Knowledge-based design of GEPIs as molecular building blocks in bionanotechnology” SimBioMa Workshop: Challenges in modeling the interface between biomolecules and inorganic surfaces, Mainz, Germany, March 18-20, 2009.
  13. E. E. Oren, “Design of inorganic binding peptides for nanotechnology applications” Nanotechnology Research Center, Bilkent Univ., Ankara, Turkey, July 18, 2008.
  14. E. E. Oren, “Modeling biomolecules on inorganic surfaces” Centre for Scientific Computing, Department of Chemistry, University of Warwick, Coventry, UK, July 9-15, 2008.
  15. E. E. Oren, “Knowledge based design of inorganic binding peptides” 5th Annual Conference on Foundations of Nanoscience: Self-assembled architectures and devices, Symposium: Self-assembly of peptide/protein nanostructures, Snowbird, UT, USA, April 18-21, 2008.
  16. 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  – 2, Kraków-Krynica, Poland, December 3-8, 2000.
Oral Presentations
  1. N. S. Aydın and E. E. Oren “Theory and Simulation of Quantum Dot Formation in Heteroepitaxialy Grown Thin Films under External Forces” TMS 2017, Symposium: Computational Thermodynamics and Kinetics, San Diego, CA, USA, February 26-March 02, 2017.
  2. N. S. Aydın and E. E. Oren “Design of Heteroepitaxialy Grown Quantum Dots Under External Force Fields” TMS 2017, Symposium: Computational Approaches to Materials for Energy Applications, San Diego, CA, USA, February 26-March 02, 2017.
  3. N. S. Aydın, M. Y. Sengul and E. E. Oren “Design of quantum dots via adjusting the material and process properties in heteroepitaxial growth” IMRC 2016, Symposium A2: Bionanodesign, Cancun, Mexico, August 14-19, 2016.
  4. G. Gokce, E. Candas, N. S. Aydın and E. E. Oren “Forecasting antiviral drug resistance development among influenza viruses” IMRC 2016, Symposium A2: Bionanodesign, Cancun, Mexico, August 14-19, 2016.
  5. H. T. Yener, M. Sahin and E. E. Oren “Controlled drug release systems from bulk-degrading polymers” IMRC 2016, Symposium A2: Bionanodesign, Cancun, Mexico, August 14-19, 2016.
  6. B. Demir, J. Qi, S. Gokce, E. E. Oren and M. P. Anantram “Environmental effects on DNA backbone and conductance” IMRC 2016, Symposium A2: Bionanodesign, Cancun, Mexico, August 14-19, 2016.
  7. E. Candas, G. Gokce, B. Demir, G. Demirel and E. E. Oren “Modeling of morphological versatility in self-assembly of Val-Ala and Ala-Val dipeptides” MRS 2015 Fall Meeting, Symposium WW: Modeling and theory-driven design of soft materials, Boston, MA, USA, November 29 - December 4 , 2015.
  8. E. Kayali, E. Mercan, M. Sahin, H. T. Yener, N. S. Aydin, G. K. Dogu E. E. Oren and G. C. Buke “Investigation of catalyst effect on the formation of 1D carbon nanostructures via low temperature vacuum decomposition of SiC” MRS 2015 Fall Meeting, Symposium Q: Nano carbon materials - 1D to 3D, Boston, MA, USA, November 29 - December 4 , 2015.
  9. M. Y. Sengul, S. Haddadian, A. Celik, T. O. Ogurtani and E. E. Oren “Simulation of Strained-Heteroepitaxial Quantum Dot Formation Under the Effect of Anisotropic Surface Properties” MRS 2014 Spring Meeting, "Symposium WW: Materials by Design—Merging Advanced In-Situ Characterization with Predictive Simulation, San Francisco, CA, ABD, April 21-25, 2014.
  10. T. O. Ogurtanı, A. Celik, O. Akyıldız and E. E. Oren “Nonequilibrium thermodynamics of surfaces and interfaces in solids with applications” IWPMEO II: International Workshop on the Physics based Modeling of Material Properties & Experimental Observations, Antalya, Turkey, May 15-17, 2013.
  11. T. O. Ogurtani, L. N. Brush and E. E. Oren “Effects of electromigration stressing on the topological instabilities of the Stranski-Krastanow islanding” MRS 2012 Spring Meeting, "Symposium XX: Computational Materials Design in Heterogeneous Systems, San Francisco, CA, ABD, April 9-13, 2012.
  12. J. Qi, S. Edirisinghe, E. E. Oren, M. P. Anantram “Charge transport in biomolecules” IWPSD 2011: XVI International Workshop on the Physics of Semiconductor Devices, Kanpur, India, December 19-22, 2011.
  13. E. E. Oren, R. Samudrala, J. S. Evans, Malcolm L. Snead, Martha J. Somerman, C. Tamerler and M. Sarikaya “Computational biomimetic design of materials specific peptides” TMS 2010 139th Annual Meeting & Exhibition" Bio-inspired Materials Design and Processing I: Macromolecular Concepts and Applications, Seattle, WA, USA, February 14-18, 2010.
  14. C. So, M. Noyes, E. E. Oren, H. Meskine, H. Yazici, P. Mulheren, C. Tamerler, J. Evans and M. Sarikaya “Binding and assembly of material-specific peptides on solid substrates by atomic force microscopy” TMS 2010 139th Annual Meeting & Exhibition" Biological Materials Science: Computational Materials Science, Seattle, WA, USA, February 14-18, 2010.
  15. Y. Hayamizu, M. Hnilova, E. E. Oren, C. Zhong, C. Tamerler, M. Rolandi and M. Sarikaya “Electronic transport through solid-binding peptides” TMS 2010 139th Annual Meeting & Exhibition" Biological Materials Science: Bio-inspired Materials Design and Processing I: Macromolecular Concepts and Applications, Seattle, WA, USA, February 14-18, 2010.
  16. T. Kacar, M. Hnilova, B. Taktak, Y. Hayamizu, E. E. Oren, J. Evans, C. Tamerler, and M. Sarikaya “Bridging inorganic nanoparticles and biomolecules via genetically engineered peptides” TMS 2010 139th Annual Meeting & Exhibition" Biological Materials Science: Bio-inspired Materials Design and Processing I: Macromolecular Concepts and Applications, Seattle, WA, USA, February 14-18, 2010.
  17. E. E. Oren, R. Samudrala, C. Tamerler and M. Sarikaya. “In silico design of solid binding peptides as molecular building blocks in technology and medicine” 237th ACS National Meeting Division of Medicinal Chemistry, Salt Lake City, UT, USA, March 22-26, 2009.
  18. T. Kacar, J. Ray, M. Gungormus, E. E. Oren, C. Tamerler and M. Sarikaya. “Quartz binding peptides as molecular linkers for co-assembling nanoentities on multifunctional micropatterned substrates” 237th ACS National Meeting Division of Medicinal Chemistry, Salt Lake City, UT, USA, March 22-26, 2009.
  19. M. Gungormus, H. Fong, E. E. Oren, C. Tamerler, M. Somerman and M. Sarikaya. “Cementum-analogs using hydroxyapatite binding peptides: Toward periodontal regeneration” 237th ACS National Meeting Division of Medicinal Chemistry, Salt Lake City, UT, USA, March 22-26, 2009.
  20. C. Tamerler, R. Samudrala, E. E. Oren, J. Evans, B. Traxler and M Sarikaya. “Molecular biomimetics – coupling peptides and nanoparticles for nanotechnology and medicine” 6th Annual Conference on Foundations of Nanoscience: Biomedical Nanotechnology, Snowbird, UT, USA, April 20-24, 2009.
  21. E. E. Oren, R. Samudrala, J. S. Evans, C. Tamerler and M. Sarikaya “Bioinformatics-based design of multifunctional solid-binding peptides” MRS 2008 Fall Meeting, "Symposium UU: Molecular Biomimetics and Materials Design, Boston, MA, USA, December 1-2, 2009.
  22. C. So, J. Kulp, H. Meshine, P. Mulheran, E. E. Oren, C. Tamerler, J. S. Evans and M. Sarikaya. "Binding, molecular recognition, and supramolecular assembly of solid binding peptides on solid substrates: a multi-scale perspective" MRS 2009 Fall Meeting, Symposium UU: Biomimetics and Materials Design, Boston, MA, USA, November 30-December 2, 2009.
  23. T. Kacar, M. Gungormus, Y. Hayamizu, E. E. Oren, J. S. Evans, C. Tamerler,  and M. Sarikaya. "Nanoparticle assembly via bifunctional genetically engineered peptides for inorganics" MRS 2009 Fall Meeting, Symposium TT: Nanobiotechnology and Nanobiophotonics--Opportunities and Challenges, Boston, MA, USA, November 30-December 2, 2009.
  24. E. E. Oren, R. Samudrala, J. A. Horst, M. Gungormus, H. Fong, Hnilova, C. Tamerler and M. Sarikaya. “In silico prediction of functional binding domains of natural proteins” MRS 2008 Spring Meeting, Symposium DD: From biological materials to biomimetic material synthesis, San Francisco, CA, USA, March 24-28, 2008.
  25. T. Kacar, M. Gungormus, M. Hnilova, E. E. Oren, C. Tamerler and M. Sarikaya. "Optically Active Metal Nanoparticle and Quantum Dot Co-Immobilization Using Genetically Engineered Peptides for Inorganics" MRS 2008 Fall Meeting, Symposium FF: Nanofunctional Materials, Structures, and Devices for Biomedical Applications, Boston, MA, USA, December 1-5, 2008.
  26. E. E. Oren, M. Gungormus, R. Samudrala, J. A. Horst, H. Fong, M. Hnilova, J. Evans, M. Snead, M. Somerman, C. Tamerler and M. Sarikaya. “A knowledge-based quest for amelogenin function in enamel biomineralization”  MRS 2008 Fall Meeting, "Symposium Y: Biomineral Interfaces – From Experiment to Theory Boston, MA, USA, December 1-5, 2008.
  27. 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, San Francisco, CA, USA, April 10-13, 2007.
  28. 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, Lyon, France, July 25-27, 2007.
  29. 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, Boston, MA, USA, November 26-30, 2007.
  30. J. S. Evans. W. K. Il, J. L. Kulp, S. Collino, K. Delak, U. O. S. Seker, C. So, E. E. Oren, C. Tamerler and M. Sarikaya. "Molecular structures of engineered inorganic-binding peptides" MRS 2007 Fall Meeting, Symposium NN: Protein and Peptide Engineering for Therapeutic and Functional Materials, Boston, MA, USA, November 26-28, 2007.
  31. C. So, E. E. Oren, U. Seker, B. R. Wilson, J. Kulp, C. Tamerler, J. S. Evans and M. Sarikaya. "Supramolecular Self-Assembly of a Metal-binding Polypeptide and Implications for Molecular Recognition" MRS 2007 Fall Meeting, Symposium NN: Protein and Peptide Engineering for Therapeutic and Functional Materials, Boston, MA, USA, November 26-28, 2007.
  32. 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, San Francisco, CA, USA, April 12-16, 2004.
  33. 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, Alberta, Canada, October 17-22, 2004.
  34. E. Venkatasubramanian, M. Duman, T. Kacar, D. Heidel, E. E. Oren, C. Tamerler and M. Sarikaya. "Binding and Specificity of Engineered Polypeptides on Functional Inorganics" MRS 2004 Fall Meeting, Symposium Z: Bio-Inspired and Bio-Derived Materials and Processes, Boston, MA, USA, November 29-December 2, 2004.
  35. 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, Boston, MA, USA, November 29-December 2, 2004.
  36. 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, Ankara and Konya, Turkey, April 2-6, 2001.
  37. E. E. Oren and T. O. Ogurtani. "Void Intergranual Motion under the Action of Electromigration Forces in Thin Film Interconnects with Bamboo Structure" MRS 2001 Fall Meeting, Symposium L: Thin Films, Stresses and Mechanical Properties IX, Boston, MA, USA, November 26-30, 2001.
  38. E. E. Oren and A. C. TAS, "Hydrothermal Synthesis of Pure and Dy:BaTiO3 Powders at 90°C, Their Sintering Behavior, and Microstructures of Dy:BaTiO3 Powders Heated on Ti-Strips" Journal of American Ceramic Society, 100th Annual Meeting & Exposition, Cincinnati, OH, USA. May 3-6, 1998.
  39. E. E. Oren and A. C. TAS, "Preparation of Piezoelectric Lead Zirconate Titanate (PbZr0.52Ti0.48O3) Powders by Homogeneous Precipitation and Calcination" Journal of American Ceramic Society, 100th Annual Meeting & Exposition, Cincinnati, OH, USA, May 3-6, 1998.
Poster Presentations
  1. M. Sahin, H. T. Yener, N. S. Aydin, E. Kayali, E. Mercan, G. C. Buke and E. E. Oren “Modeling of morphological evolution of catalyst for the synthesis of 1D carbon nanostructures on SiC”MRS 2015 Fall Meeting, Symposium TT: Topology in materials science - biological and functional nanomaterials, metrology and modeling, Boston, MA, USA, November 29 - December 4 , 2015.
  2. M. Y. Sengul, S. Haddadian, A. Celik, T. O. Ogurtanı and E. E. Oren “Strained-heteroepitaxial quantum dots with anisotropic surface properties” IWPMEO II: International Workshop on the Physics based Modeling of Material Properties & Experimental Observations, Antalya, Turkey, May 15-17, 2013.
  3. T. Kacar, M. Gungormus, M. Hnilova, C. So, E. E. Oren, C. Tamerler and M Sarikaya. “Optoelectronic properties of ZnO nanoparticles deposition on porous silicon” 6th Annual Conference on Foundations of Nanoscience: Nanoplasmonics & Nanophotovoltaics, Snowbird, UT, USA, April 20-24, 2009.
  4. M. Hnilova, B. Taktak, E. E. Oren, C. So, T. Kacar, C. Tamerler and M. Sarikaya. "Targeted immobilization of nanostructures and biomolecules through peptide-based biolinkers towards nanosensing platforms" MRS 2008 Fall Meeting, Symposium FF: Nanofunctional Materials, Structures, and Devices for Biomedical Applications, Boston, MA, USA, November 30-December 2, 2008.
  5. M. Gungormus, S. Cetinel, E. E. Oren, B. R. Wilson, C. So, M. Somerman, C. Tamerler and M. Sarikaya. "Surface Bio-Engineering Using Peptides for Enhanced Cell Adhesion and Proliferation" MRS 2008 Spring Meeting, Symposium DD: From Biological Materials to Biomimetic Material Synthesis, San Francisco, CA, USA, March 25-28, 2008.
  6. M. Hnilova, E. E. Oren, C. So, T. Kacar, B. A. Parviz, C. Tamerler and M. Sarikaya. "Peptide-Directed Immobilization of Optical Active Nanostructures and Flurophores towards Nanosensing Platforms" MRS 2008 Spring Meeting, Symposium DD: From Biological Materials to Biomimetic Material Synthesis, San Francisco, CA, USA, March 25-28, 2008.
  7. T. Kacar, M. Gungormus, E. E. Oren, M. Hnilova, C. Tamerler and M. Sarikaya. "LSPR Based Nanophotonic Detection of Biomolecules through Genetically Engineered Peptides and Molecular Constructs" MRS 2008 Spring Meeting, Symposium EE: Responsive Biomaterials for Biomedical Applications, Poster Presentation, San Francisco, CA, USA, March 25-28, 2008.
  8. C. So, E. E. Oren, J. Kulp, H. Zereie, C. Tamerler and J. Evans. “Molecular Basis for Patterned Supramolecular Self Assembly 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, Snowbird, UT, USA, April 18-21, 2007.
  9. 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, San Francisco, CA, USA, April 10-13, 2007.
  10. 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, Istanbul, Turkey, May 21-23, 2007.
  11. 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, Snowbird, UT, USA, April 18-21, 2007.
  12. 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, San Juan Island, WA, USA, September 6-8, 2006.
  13. 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, San Juan Island, WA, USA, September 6-8, 2006.
  14. 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, Boston, MA, USA, November 28-December 1, 2005.
  15. 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, Seattle, WA, USA, September 20-21, 2005.
  16. 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, Snowbird, WA, USA, September 20-21, 2005.
  17. 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, Snowbird, UT, USA, April 24-28, 2005.
  18. 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, Boston, MA, USA, November 29-December 3, 2004.
  19. 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, Bilbao, Spain, July 8-12, 2002.
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