Ali Rana  Atılgan

Türkçe sürüm

Ali Rana Atılgan

E-mail : atilgansabanciuniv.edu

Personal web page

Education :

Ph.D. in Aerospace Engineering, September 1989, Georgia Institute of Technology, Atlanta, Georgia, USA.

M.S. in Aerospace Engineering, June 1987, Georgia Institute of Technology, Atlanta, Georgia, USA.

B.S. in Aeronautical Engineering, June 1984, Istanbul Technical University, Istanbul, Turkey.

Work Experience :

Professor; February 2006 ? present. School of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.

Adjunct Professor; January 2007 - present. Department of Civil Engineering, Bogazici University, Istanbul, Turkey.

Professor; May 1998 ? February 2006. Department of Civil Engineering, Bogazici University, Istanbul, Turkey.

Associate Professor; August 1993 ? May 1998, Department of Civil Engineering, Bogazici University, Istanbul, Turkey;
October 1992 ? August 1993, Department of Civil Engineering, Istanbul Technical University, Istanbul, Turkey.

Assistant Professor; May 1991 ? October 1992, Department of Civil Engineering, Istanbul Technical University, Istanbul, Turkey.

Post Doctoral Fellow; September 1989 ? March 1991, School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.

Core Faculty; September 1994 ? December 2003. Polymer Research Center, TUBITAK Advanced Polymeric Materials Research Center, Bogazici University, Istanbul, Turkey.

Visiting Scientist; June 1995 ? September 1995, Boeing Commercial Airplane Group, Seattle, Washington, USA.
July 1992 ? September 1992; July 1993 ? August 1993; School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.

Areas of Interest :

Biological physics • Systems science

Awards :

  • Graduating Class Award (Second Place) - Sabanci University  2016
  • Graduating Class Award (First place) - Sabanci University  2012
  • Outstanding Achievement in Education Prize (Eğitimde Üstün Başarı Ödülü) - Bogazici University  1999
  • Outstanding Achievement in Research Prize (Araştırmada Üstün Başarı Ödülü) - Bogazici University  1998
  • Young Scientist Encouragement Prize (nationwide) (TÜBİTAKTeşvik Ödülü) - Scientific and Technical Research Council of Turkey  1995
  • Jefferson Goblet Paper Award (nationwide, first place)(Jefferson Goblet Makale Ödülü ) - the American Institute of Aeronautics and Astronautics,  1989

Publications :

Article
Şensoy, Özge and Atılgan, Ali Rana and Atılgan, Canan (2017) "FbpA iron storage and release are governed by periplasmic microenvironments", Physical Chemistry Chemical Physics, Vol.19, No.8, 6064-6075 (SCI)
Abdizadeh, Haleh and Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2015) "Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability", Journal of Enzyme Inhibition and Medicinal Chemistry, Vol.30, No.6, 867-873 (SCI)
Özbaykal, Gizem and Atılgan, Ali Rana and Atılgan, Canan (2015) "In silico mutational studies of Hsp70 disclose sites with distinct functional attributes", Proteins: Structure, Function and Bioinformatics, Vol.83, No.11, 2077-2090 (SCI)
Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2015) "Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH", Journal of Biological Inorganic Chemistry, Vol.20, No.4, 705-718 (SCI)
Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2014) "Protonation states of remote residues affect binding-release dynamics of the ligand but not the conformation of apo ferric binding protein", Journal of Physical Chemistry B, Vol.118, No.40, 11677-11687 (SCI)
Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2013) "Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin", PLoS Computational Biology, Vol.9, No.12 (SCI)
Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana (2012) "On modifying properties of polymeric melts by nanoscopic particles", Journal of Polymer Science Part B: Polymer Physics, Vol.50, No.23, 1653-1662 (SCI)
Atılgan, Ali Rana and Atılgan, Canan (2012) "Local motifs in proteins combine to generate global functional moves", Briefings in Functional Genomics (Sl), Vol.11, No.6, 479-488 (SCI)
Negi, Sunita and Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2012) "Calmodulin readily switches conformation upon protonating high pK(a) acidic residues", Journal of Physical Chemistry B, Vol.116, No.24, 7145-7153 (SCI)
Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2012) "Network-based models as tools hinting at nonevident protein functionality", Annual Review of Biophysics, Vol.41, 205-225 (SCI)
Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan (2011) "Subtle pH differences trigger single residue motions for moderating conformations of calmodulin", Journal of Chemical Physics, Vol.135, No.15 (SCI)
Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2010) "How orientational order governs collectivity of folded proteins", Proteins: Structure, Function, Bioinformatics, Vol.78, No.16, 3363-3375 (SCI)
Turgut, Deniz and Atılgan, Ali Rana and Atılgan, Canan (2010) "Assortative mixing in close-packed spatial networks", PLoS One, Vol.5, No.12 (SCI)
Atılgan, Canan and Gerek, Z. N. and Özkan, S. B. and Atılgan, Ali Rana (2010) "Manipulation of conformational change in proteins by single-residue perturbations", Biophysical Journal, Vol.99, No.3, 933-943 (SCI)
Servantie, James and Atılgan, Canan and Atılgan, Ali Rana (2010) "Depth dependent dynamics in the hydration shell of a protein", Journal of Chemical Physics, Vol.133, No.8 (SCI)
Atılgan, Canan and Atılgan, Ali Rana (2009) "Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein", PLoS Computational Biology, Vol.5, No.10, 1-14 (SCI)
Okan, Osman Burak and Atılgan, Ali Rana and Atılgan, Canan (2009) "Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics", Biophysical Journal, Vol.97, No.7, 2080-2088 (SCI)
Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana (2008) "Collective behavior of El Farol attendees", Advances in Complex Systems, Vol.11, No.4, 629-639 (SCI)
Atılgan, Canan and Aykut, Ayşe Özlem and Atılgan, Ali Rana (2008) "How a vicinal layer of solvent modulates the dynamics of proteins", Biophysical Journal, Vol.94, 79-89 (SCI)
Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) "Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication", Biophysical Journal, Vol.92, No.9, 3052-3062 (SCI)
Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) "A Few designed-in interactions imposed on chain connectivity are sufficient for robust residue communications ", Biophysical Journal , Vol.Suppl S, No.Abstract Issue, 217A-218A (SCI)
Atılgan, Canan and Sezerman, Ayşe Özlem and Baloğlu, Çetin and Sirer, Irmak and Okan, Osman Burak and Atılgan, Ali Rana (2007) "Solvent mobility and surface group flexibility at the dynamical transition", Biophysical Journal, Vol.Suppl S, No.Abstract issue, 405A-406A (SCI)
Okan, Osman Burak and Atılgan, Ali Rana and Baysal, Canan (2005) "Distribution of relaxation times on the pico-nano time scales for a functional protein (ABSTRACT)", Biophysical Journal, Vol.88, No.1, 16A-16A (SCI)
Atılgan, Ali Rana and Atılgan, Canan (2004) "Thermodynamics of residue networks in folded proteins", WSEAS Transactions in Biology and Biomedicine, Vol.1, No.2, 205-209
Papers in Conference Proceedings
Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan, "Computational modeling of iron binding and release in human serum transferrin", 41st FEBS Congress on Molecular and Systems Biology for a Better Life, Wiley Online Library, September 2016, 73-73
Abdizadeh, Haleh and Acar, Ömer and Güçlü, Tandaç Fürkan and Tamer, Yusuf Talha and Altınuşak, Tuğçe and Toprak, Erdal and Atılgan, Ali Rana and Atılgan, Canan, "Computational assessment of trimethoprim resistance in dihydrofolate reductase", 60th Annual Meeting of the Biophysical Society, Cell Press, February 2016, 47A-48A
Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan, "Non-equilibrium fluctuation theorems, redundant paths in proteins, and elucidating conformational changes by single-residue perturbations", 57th Annual Meeting of the Biophysical-Society, Cambridge, MA, USA: Biophysical Society, January 2013, 70A-70A
Atılgan, Canan and Güven, Gökçe and Atılgan, Ali Rana, "Structural basis of how ferric binding proteins utilize pH differences for controlled release of iron", 57th Annual Meeting of the Biophysical-Society, Cambridge, MA, USA: Biophysical Society, January 2013, 212A-212A
Negi, Sunita and Atılgan, Ali Rana and Atılgan, Canan, "Driving calmodulin protein towards conformational shift by changing ionization states of select residues", Stocks, G. M. and Troparevsky, M. C. (eds.), 23rd IUPAP C20 Conference on Computational Physics (CCP 2011), Bristol, England: Institute of Physics, December 2012
Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana, "Effect of van der Waals interaction strength and nanocluster size on the dynamical and mechanical properties of 1,4-cis-polybutadiene melts", Materials Research Society Fall Meeting 2011 , Boston: Materials Research Society, February 2012
Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan, "Molecular recognition mechanisms of calmodulin examined by perturbation-response scanning", 2010 MRS Fall Meeting, UK: Cambridge University Press Academic and Professional Books 2011
Özden Yenigün, Elif and Atılgan, Ali Rana and Bilge, Kaan and Menceloğlu, Yusuf Z. and Atılgan, Canan and Papila, Melih, "Designed-in molecular interactions lead to superior thermo-mechanical properties in nanocomposites", 2010 MRS Fall Meeting, UK: Cambridge University Press Academic and Professional Books 2011
Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana, "Long-range structural regularities and collectivity of folded proteins", Levitz, P. and Metzler, R. and Reichman, D. (eds.), 2009 MRS Fall Meeting, Warrendale, PA: MRS (Materials Research Society) 2010
Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana, "Landscape Dynamics of El Farol Attendees", The 2007 International Conference of the System Dynamics Society, Boston, Massachusetts, USA: System Dynamics Society, October 2007
Before SU Publications:

Selected Publications: Lus, H., Aydin, C.A., Keten, S., Unsal, H.I., and Atilgan A.R., "El Farol Revisited," Physica A, Vol. 346, 2005, pp. 651 - 656. Yilmaz, L. S. and Atilgan, A. R., "Identifying the Adaptive Mechanism in Globular Proteins: Fluctuations in Densely Packed Regions Manipulate Flexible Parts," Journal of Chemical Physics, Vol. 113, No. 10, 2000, pp. 4454 - 4464. Alparslan, A. K., Sayar, M., and Atilgan, A. R., “A State-Space Prediction Model for Chaotic Time Series,” Physical Review E, Vol. 58, 1998, 2640 – 2643. Atilgan, A. R., “A Nonlinear Model for the Kinking Behavior of Unidirectional Polymer Matrix Composites,” Zeitschrift fur Angewandte Mathematik und Mechanik (ZAMM), Vol. 78, 1998, 212 - 216. Atilgan, A. R., "Analogy between Dislocation Mechanics and Aerodynamics," Zeitschrift fur Angewandte Mathematik und Mechanik (ZAMM), Vol. 77, No. 8, 1997, pp. 631 - 634. Hodges, D. H., Atilgan, A. R., Fulton, M. V., and Rehfield, L. W., “Free-Vibration Analysis of Composite Beams,” Journal of the American Helicopter Society, Vol. 36, 1991, 36 - 47.