PROF.DR. HANDAN OLĞAR    
Name : HANDAN
Surname : OLĞAR
E-Mail : holgar@eng.ankara.edu.tr
Phone Number : 203 3455
Title : PROF.DR.
Unit : FACULTY OF ENGINEERING
Department :
Personal Information

Name, Surname:  Prof. Dr.  Handan Arkın Olğar                        

Born:  4 November 1974, Berlin

 

Academic Degrees:

 

Assos. Prof.  Degree Condensed Matter Physics,  November  2005

     PhD.   Physics Engineering,  March 2003 Hacettepe  University, Ankara, Turkey.

M.Sc. Physics Engineering,  August 2000 Hacettepe  University, Ankara, Turkey.

B.Sc.  Physics Engineering, June 1997 Hacettepe  University, Ankara, Turkey

 

Professional Affiliations

November  2011 – present    Prof.  Dr.  , Ankara University, Department of Physics Engineering

March 2008 – November 2011  Assos.  Prof.  Dr.  , Ankara University, Department of Physics Engineering

March 2007 – February 2008   Postdoctoral Fellowship, Ankara University, Department  of Physics Engineering

June 2004- October 2004, Postdoctoral Fellowship, Institute of Theoretical Physics, University of Leipzig.

July 2003- October 2003, Postdoctoral Fellowship, Institute of Theoretical Physics, University of Leipzig.

January 1998 – March 2007 Teaching and Research Assistant, Hacettepe University, Department of Physics Engineering.

 

Awards:

·         Turkish Scientific and Technological research Council  Young Researcher Carrier Program  2004

·         L’ OREAL  Young Women Scientist Award 2005

  • Turkish Academy of Sciences (TÜBA) Outstanding  Young Scientist Award 2006
  • Alexander von HUMBOLDT Foundation Experienced Resercher Fellowship 2010

 

 

Fellowships:

 

  • Turkish Scientific and Technological research Council, Master  fellowship  (1998-2000)
  • Turkish Scientific and Technological research Council,  PhD fellowship  (2000- 2003)
  • DFG (Deutsche Forschungsgemeinschaft)  International Scientific  Exchange Program  (Theoretical Physics Institute, University of Leipzig, Germany, July-October 2003)
  • DFG  (Deutsche Forschungsgemeinschaft) International Scientific  Exchange Program  (Theoretical Physics Institute, University of Leipzig, Germany, June-October 2004)
  • Turkish Scientific and Technological research Council, Postdoc  fellowship, Ankara University, Dept. Physics Engineering  (2007- 2008)
  • Alexander von Humboldt Foundation Return Fellowship 2013 - 2014

 

 

 

 

 

 

 

 

Projects:

  • “Investigation of Biologically Motivated Problems in Statistical Physics: Molecular Modeling”, The Scientific and Technological Research Council of Turkey: Young Sceintist Career Project,  No: 150T146, 2005-2011, Director of Project.
  • “Simulations of Biological Molecules and Development of New Algorithms”, Hacettepe University,Research Project No: 03.01.602.002, 2003, Director of Project.
  • “Development of Searching algorithms for  Conformational Space of Biological Molecules” Hacettepe University Research Project No: 02.02.602.010, 2003, Researcher.
  • “Multicanonical Simulations of  Peptides and Proteins” Hacettepe University Reseacrh Project No: 02.01.602.006, 2002, Researcher.
  • “Simulations of Biological Molecules by General Update Algorithms, Hacettepe University Research Project,  No: 01.01.602.006, 2001, Researcher.
  • “Multicanonical Simulations of Some Peptides” Hacettepe University Reseacrh Project No: 01.00.602.001, 2000, Researcher.

 

Courses Given:

121 Physics I

122 Physics II

305 Quantum Mechanics I

306 Quantum Mechanics II

405  Advanced Quantum Mechanics I

406  Advanced Quantum Mechanics II

422 Computer Applications in Physics

516 Advanced Numerical Applications in Statistical Physics

 

Thesis Supervised:

·         “Investigation of the conformational transitions of elastin-based peptid chains.”, Mustafa Bilsel, July 2009, master thesis.

·         “Investigation of the adsorption of hydrophobic-polar model proteins on different surfaces”, Hakan Alaboz, July 2010, master thesis.

·         “Investigation of the energy landscape of the hydrophobic-polar model proteins, Buket Tasdizen, December 2012, currently my Phd Student.

 

 

Important Seminars and Colloquia:

 

  • Comformational Behavior of a polymer chain  in an Attractive Spherical Cage, Sonder Forschung Bereich SFB/TR102  Fall Meeting Miniworkshop Brehna,  19 October 2012, Brehna, Germany.
  • “Simulations of Biological Molecules, SPG Kick-Off Meeting, 24 June 2011, Leipzig, Germany.

·         “Structural Transitions Mechanism  in Protein Models”,  L’oreal   Young Women Scientist Meeting, 16 May 2009, İstanbul, Turkey.

 

  • “Generalized Ensemble Simulations of off-lattice Protein Models” Turkish Academy of Sciences Outstanding  Young Scientist Annual Meeting, September 2007,  Atatürk University, Erzurum, Turkey.

·          “Simulations of Biological Molecules by Generalized-Ensemble Algorithms”, Statistical Physics Days (invited) July 2005, İstanbul, Turkey.

·         “Generalized-Ensemble Simulations of Peptides and Proteins, NTZ- Kolloquium, October 2004, University of Leipzig, Leipzig, Germany.

 

·         “Structure of Energy Landscape of Peptides and Proteins”, Institute of Theoretical Physics, June 2003, University of Leipzig, Leipzig, Germany.

·         “Multicanonical Simulations of Biological Molecules”, Physics Department Seminar Series, September 2003, Hacettepe University, Ankara, Turkey.

 

 

Publications:

 

B) Articles in journal / contributions to boks

B1. Arkın, H., Janke W., (2013): Gyration Tensör Based Analysis of the Shapes of the Polymer Chain in an Attractive Spherical Cage, J. of Chem. Phys.  138, 054904.

B2.  Arkın, H,  Janke W., (2013):  Polymer-Attractive Spherical Cage System,  Eur. Phys. J. Special Topics, 216, 181.

B3. Arkın, H., Janke W., (2012): Ground State Properties of a Polymer Chain inside an Attractive Sphere, J. Phys. Chem B, 116 (34) 10379.

B4. Arkın, H., Janke W., (2012): Structural Behavior of a Polymer Chain inside an Attractive Sphere, Phys. Rev. E85, 051802.

B5. Marenz, M., Zierenberg, J., Arkın, H., and Janke, W., (2012): Simple Flexible Polymers in a Spherical Cage, J. Cond. Matter Phys., Vol. 15, No:4, 43008.

B6. Bilsel, M.,  Taşdizen B., Arkın, H.,  Janke W., (2012): Effects of Confinement on the Thermodynamics of a Model Protein, John von Neumann Institute for Computing, Jülich, IAS Series Vol. 8, pp. 21 – 24.

B7.  Bilsel, M and Arkin,  H. (2010):  Residue Length and Solvation Model Dependency of Elastin-like Polypeptides, Phys. Rev. E, 81, 051906.

B8. Arkin, H. and Bilsel, M (2010):  How conformational Transitions Depends on hydrophobicity of  Elastin-Like Polypeptides,  Eur.  Phys.  J. E, Vol. 31(3), 327- 332.

B9. Arkin, H. (2010):  Comparison of the Paralel Tempering Algorithm and Multicanonical Method as Applied to Coarse-Grained Off-Lattice Models for Folding Heteropolymers, J. Of Statistical Phys. Vol. 139(2),  326-332.

 

B10. Aktürk, E.,  Gülseren, O.,  Arkın, H. and Çelik, T. (2010):  First Principles Investigation of Amino Acid Adsorption on Si(100)-2x1 Asymmetric Surface. Int. J. Of  Mod. Phys. C, Vol. 21(1), 97-106.

 

 

 

 

B11. Arkın, H. (2010): Conformational properties of surfactant-like peptides with variable   glycine tails. Physica A 389, 265-272.

B12. Arkın, H. (2009): Adsorption of a hydrophobic-polar-model heteropolymer in an attractive nanotube.  Phys. Rev. E 80, 041910. Virtual Journal of Nanoscale Science & Technology, Oct. 19 (2009);  Virtual Journal of Biological Physics Research, Oct. 2009.

B13. Arkın, H. (2008):  Determination of the structure of the energy landscape for coarse-grained off-lattice models of folding heteropolymers.  Phys. Rev. E 78, 041914.

B14. Aktürk, E.,  Arkın, H. and   Çelik, T. (2007):  The structure of the free energy surface of coarse-grained off-lattice protein models.  Int. J. of  Mod. Phys C, 18(1), 99- 106.

 

B15. Aktürk, E. and  Arkın, H. (2007):  Nonextensive Statistical Mechanis Application to Vibrational Dynamics of  Protein Folding.  Int. J. of  Theo. Phys. 46(11), 2945- 2949.

 

B16. Bachmann, M., Arkın, H. and   Janke, W. (2005):  Multicanonical Study of Coarse-Grained   Off-Lattice Models for  Folding Heteropolymers.   Phys. Rev. E, 71, 031906; Virt. J. Biol.  Phys. Res. 9.

B17. Gökoğlu, G.,   Arkın, H.,  Aktürk, E. and   Çelik, T. (2005):  Solvation Effects on Free Energy Surface of Polyalanine.  Int. J. of Mod. Phys. C 16 (9), 1489-1496.

B18. Arkın, H. (2005): Study of Conformational Structure of Elastin Sequences With Solvent-Incuded Force-Field.  Int. J. Of Mod. Phys. C 16(9), 1339-1346.

B19. Gökoğlu, G.,  Arkın, H. and  Çelik, T. (2005): Conformational Analysis of Polyalanine Chains.  Int. J. of  Mod. Phys. C 16(3), 455-463.

B20. Arkın, H. (2004):  A Combination of Replica Exchange Monte Carlo and Energy Landscape Paving Algorithms to Increase The Effectiveness of Conformational Sampling.  Int. J. of  Modern Physics C, 15(7), 933-937.

B21. Arkın, H. (2004): Searching Low-Energy Conformations of Two Elastin Sequences.  Eur. Phys.  Jour.  B, 37, 223-228.

B22. Arkın, H. (2004):  Simulations of  Peptide Models in a Solvent.  Int. J. of Modern Physics C, 15(2), 223-231.

B23. Arkın, H. and  Çelik, T. (2003):  A Fast and Effective Conformational Search Method for  Peptides.  Int. J. of Modern Physics C, 14(7), 985-991.

B24. Arkın, H. and  Çelik, T. (2003):  Determination of Conformational Transitions of Peptides from Energy Landscape.  Int. J. of Modern Physics C, 14(5), 567-574.

B25. Arkın, H. and   Çelik, T. (2003):  Structure of The Energy Landscape of Short Peptides.  Int. J. of Modern Physics C, 14(1), 113-120.

B26. Arkın, H. and   Çelik, T. (2002): Comparison of The Energy Landscape Paving and Multicanonical Methods in Simulation of The Heptapeptide Deltorphin.  Eur. Phys.  Jour. B, 30, 577-580.

B27. Yaşar, F.,  Arkın, H., Çelik, T., Berg, B. A. and  Meirovitch, H. (2002):  Efficiency of The Multicanonical Method as Applied To Peptides of Increasing Size: The Heptapeptide Deltorphin.  J. Computational Chem., Vol: 23(12), 1127-1134.

B28. Arkın, H.,  Yaşar, F.,  Köksel, H.,  Çelik, S. and  Çelik, T. (2001):  Molecular Modeling of The Pentapeptide and Tetrapeptide Sequences of C-Hordein.  J. of The Instıtute of Brewing, 107(6), 383-388.

 

 

 

 

B29. Arkın, H.,  Yaşar, F.,  Köksel, H.,  Çelik, S. and  Çelik, T. (2001):   Molecular Modeling of  Two Hexapeptide Repeat Motifs HMW Glutenin Subunits.  Int. J. of Modern Physics C, 12(2), 281-292.

B30. Arkın, H.,  Yaşar, F.,  Köksel, H.,  Çelik, S. and  Çelik, T. (2000):  Molecular Modeling of  Five Tetrapeptide Sequences in the Central Domain of  HMW Glutenin.  Int. J. of Modern Physics C, 11(8), 1595-1606.

B31. Arkın, H. and   Çelik, T. (2000):   Study of Phase Conversion in Three Dimensional q = 3  Potts Model.  Int. J. of Modern Physics C, 11(7), 1313-1320.

B32. Arkın, H.,  Çelik, T.,  Berg, B. A. and   Meyer-Ortmanns, H. (1999):  Study of Phase Separation in a First-Order Phase Transition: Nucleation vs.  Spinodal Decomposition.  Int. J. of Modern Physics C, 10, 1261-1269.

 

(Papers in Turkish)

B33. Arkın, H. (2007): Multikanomik simülasyon yöntemi ile peptidlerin enerji yüzeylerinin incelenmesi (Investigation of the energy landscape of peptides by Multicanonical Simulation Method). Anadolu University Journal of Science and Technology,  Vol: 8, o: 1, pp: 103-110.

B34. Arkın, H. (2007): Multikanonik Simülasyon Yöntemi ile Peptidlerin Sıvı İçindeki Yapılarının İncelenmesi ( Investigation of peptides in a Solvent by Multicanonical Simulation Method). Süleyman Demirel University,  Journal of Natural Sciences,  11, 1-7.

 

C) Published Contributions to Academic Conferences

 

C1. Bilsel M. and Arkın, H. (2009) : Conformational Transition in Elastin Polypeptide with Different Residue Length. AIP Proceedings  7th Balkan Physical Union General Conference Alexandroupolis, Greece.

C2. Arkın, H. and  Çelik, T. (2002):  Phase Separation in 3D Three State Potts Model.  Nuclear

Physics A Procedings of the International Symposium on Statistical QCD, Bielefeld, Germany,  P5,

Elsevier.

C3. Arkın, H.,  Yaşar, F.,  Çelik, T.,   Berg, B. A. and  Meirovitch, H. (2002):    Multicanonical

Simulations of Same Peptides.  Comput. Physics Commun., 147, 600-603.

 C4.  Arkın, H., Yaşar, F., Köksel, H.,  Çelik, S. and  Çelik, T. (2001): Multicanonical Simulations of

Five Tetrapeptide Sequences in The Central Domain of HMW Glutenin. AACC Annual Meeting,

Charlotte, North Carolina, 414.

 C5. Arkın, H and  Çelik, T. (2002): Spinodal Decomposition in 3D q= 3 Potts Model.  Nuclear Physics B (Proc. Suppl.), 106, 926-928.

C6. Arkın, H., Çelik, T., Berg, B. A. and  Meyer-Ortmanns, H. (1999):  Phase Separation in a Weak First-Order Phase Transition.  Physica A, 274, 320-324.

 

D) Academic Conferences

 

D1.   Arkın, H., Janke, W., (2012):“Thermodynamics of a polymer chain in a spherical cage”, Comphys12, 29 November – 1 December 2012, Leipzig, Germany.

 

 

D2.       Marenz, M., Zierenberg, J., Arkın, H., and Janke, W., (2012): “Polymers in a Spherical Cage”, Comphys12, 29 November – 1 December 2012, Leipzig, Germany.

D3.       Arkın, H., Janke, W., (2012): SFB/TR102  Fall Meeting Miniworkshop Brehna,  Comformational Behavior of a polymer chain  in an Attractive Spherical Cage, 19 October 2012, Brehna, Germany.

D4.  Arkın, H., Janke, W., (2012): Polymer Chain in an Attractive Spherical Confinement, StatMech Meeting, 19-21 September, Mainz, Germany

D5.  Arkın, H., Janke, W., (2012): Conformational Phase Diagram of a Polymer Chain inside an Attractive Sphere, Career in Polymers 2012, 28-30 June, Prag, Czech Republic.

D6. Arkın, H, Janke, W., (2012): Structure Formation of a Polymer Chain in an Attractive Sphere, CECAM Workshop, 21-23 May 2012, Paris, France. 

D7.  Arkın, H., Janke, W., (2012): Polymer Chain inside Confinement, Alexander von Humboldt Foundation, Network Meeting, 8-10 February 2012, Kiel, Germany.

D8.  Arkın, H., Janke W., (2012): Polymer Chain inside an Attractive Sphere, NIC Symposium 2012, 7- 8 February 2012, Jülich, Germany.

D9.  Arkın, H., (2011): Alexander von Humboldt Foundation,  1st  Bonn Award Winners Forum Frontiers in Macromolecular and Material Science,  12-16 October 2011, Bonn, Germany.

D10.  Arkın H., (2011): Simulations of Biological Molecules, SPG Kick-Off Meeting, 24 June 2011, Leipzig, Germany.

D11. Alaboz, H. and   Arkın H. (2009):  Study of the conformational changes of hydrophobic – polar  polymer chain near a hydrophobic chain,. MECO34:  34rd  Conference of the Middle European  Cooperation in Statistical Physics 29 March, 2 April 2009, Leipzig, Germany.

 

D12. Arkın, H. (2008):  The energy landscape of Hydrophobic-Polar Protein Model. Conference on Knots and Other Entaglements in Biopolymers: Topological and Geometrical Aspects of DNA, RNA and Protein Structures, 15-19 September 2008, ICTP, Trieste, Italy.

 

 D13. Aktürk, E., Gülseren, O., Arkın, H. and  Çelik, T. (2008):  First Principles  Investigation of

Amino Acid adsorption on a Surface,.  MECO33: 33rd  Conference of the Middle European

Cooperation in Statistical Physics, 14-16 April 2008, Puchberg-Wels, Austria.

D14.  Bilsel, M.,  Arkin, H., (2009):  Molecular Modeling of Elastin_like Polypeptides,   16. Statistical Physics Days, Istanbul Technical University, 25-27  June 2009,  Istanbul.

D15.  Alaboz, H.,  Arkin, H., (2009):  Determination of the Adsorption of Hydrophobic-Polar Models Proteins on Different Surfaces, 16. Statistical Physics Days, Istanbul Technical University, 25-27  June 2009,  Istanbul.

      

 

 

 

D16. Arkin, H., (2009):  Structural Transitions Mechanism  in Protein Models,  L’oreal Young

Women Scientist Meeting, 16 May 2009, İstanbul, Turkey.

D17. Arkin, H., (2007): Generalized Ensemble Simulations of off-lattice Protein Models,  Turkish Academy of Sciences Outstanding  Young Scientist Annual Meeting, September 2007,  Atatürk University, Erzurum, Turkey.

 

D18.  Aktürk, E.  Gülseren, O.,  Arkın, H. And   Çelik, T. (2006):  First Principles  Investigation of Amino Acid Adsorption on Si(100)-2x1 Asymetric Surface, 13. Statistical Physics Days,, 6- 8 July 2006, Boğaziçi University. İstanbul, Turkey

 

D19. Arkın, H. (2005): Simulations of Biological Molecules by Generalized-Ensemble Algorithms.  12. Statistical Physics Days, Istanbul Technical University, 30 June- 2 July 2005, Istanbul.

D20. Bachmann, M., Arkın, H. and Janke, W. (2004): Multicanonical Simulations of AB model.  Conference on Computational Physics,  Cenova, Italya, 31 august- 4 September 2004. 

D21. Gökoğlu, G., Arkın, H. and Çelik, T. (2004):  Multicanonical Simulations of Short Polyalanine Chains.  Workshop of Structure and Function of Biomolecules, Poland, 12-15 May  2004.

D22. Arkın, H. (2004): Conformational Search Algorithms for All-Atom Protein Models.  Workshop of Structure and Function of Biomolecules, Poland, 12-15 May  2004. 

D23. Bachmann, M., Janke, W. and Arkın, H. (2004):  Multicanonical Study of Effective Off-Lattice Models for  Heteropolymers.  29th Conference of the Middle European Cooperation in Statistical Physics, Bratislava (Slovakia), P1.

D24. Bachmann, M., Janke, W. and Arkın, H. (2004): Statistical Properties of Off-Lattice Heteropolymers.  Deutsche Physikalische Gesellschaft, Physik Tagungen, Regensburg, Germany, E-Verhandlungen2004.

D25. Arkın, H., Çelik, T., Berg, B. A. and Meyer-Ortmanns, H. (1999): Study of Phase Separation in a First-Order Phase Transition.  Monte Carlo and Structure Optimization Methods for Biology, Chemistry and Physics, Florida State University, Tallahassee, Florida, February 1999.

 D26.  Arkın, H.,  Aydın, M.,  Gündüç,  Y. and  Çelik, T. (1998):  Nucleation vs. Spinodal Decomposition in a First-Order Phase Transition, 5. Statistical Physics Days, Istanbul Technical University, 16-17 July 1998, Istanbul, Turkey.