SABANCI UNIVERSITY Faculty of Engineering and Natural Sciences

Research interets : Biological Physics and Systems ScienceResearch interets : Biological Physics and Systems ScienceResearch interets : Biological Physics and Systems ScienceResearch interets : Biological Physics and Systems Science


Last Update: 14/03/2012 



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Ali Rana ATILGAN


Current Research Activities

We identify molecular interactions and trace their communication pathways on different time and length scales. We ferret out the relationships between local motifs and global patterns in complex networks with arbitrary degree distributions. These activities find technological applications in devising molecular machines and system identification tools.  


Recent Publications

Ozbaykal, G., A. R. Atilgan, and C. Atilgan, "In Silico Mutational Studies of Hsp70 Disclose Sites with Distinct Functional Attributes," Proteins: Structure, Function, Bioinformatics, Vol. 83, No. 11 [Cover image] 2015, pp. 2077 - 2090. [LINK]

Abdizadeh, H., A. R. Atilgan, and C. Atilgan, “Detailed Molecular Dynamics Simulations of Human Transferrin Provide Insights on Iron Release Dynamics at Serum and Endosomal pH,” Journal of Biological Inorganic Chemistry, Vol. 20, 2015, pp. 705 - 718. [LINK]

Abdizadeh, H., G. Guven, A. R. Atilgan, and C. Atilgan, "Perturbation Response Scanning Specifies Key Regions in Subtilisin Serine Protease for both Function and Stability," Journal of Enzyme Inhibition and Medicinal Chemistry, Early Online, 2015. [LINK]

Guven, G., A. R. Atilgan, and C. Atilgan, "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, 118, 2014, pp. 11677 - 11687. [LINK]

Aykut, O. A.,  A. R. Atilgan, and C. Atilgan, "Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin,” PLoS Computational Biology, Vol. 9, 2013, pp. e1003366(1 - 12). [LINK]

Atilgan, C., I. Inanc, A. R. Atilgan, "On Modifying Properties of Polymeric Melts by Nanoscopic Particles," Journal of Polymer Science B: Polymer Physics,  Vol. 50, No. 23 [Cover Image] 2012, pp. 1653 - 1662. [LINK]

Atilgan, A. R. and C. Atilgan, “Local Motifs in Proteins Combine to Generate Global Functional Moves,” Briefings in Functional Genomics, Vol. 11, No. 6, 2012, pp. 479 - 488. [LINK]

Negi, S., A. O. Aykut, A. R. Atilgan, and C. Atilgan, “Calmodulin Readily Switches Conformation upon Protonating High pKa Acidic Residues,” Journal of Physical Chemistry B, Vol. 116, 2012, pp. 7145 - 7153. [LINK]

Atilgan, C., O. B. Okan, and A. R. Atilgan, "Network-based Models as Tools Hinting at Non-evident Protein Functionality," Annual Review of Biophysics, Vol. 41, 2012, pp. 205 - 225. [LINK]

Atilgan, A. R., A. O. Aykut, and C. Atilgan, "Subtle pH Differences Trigger Single Residue Motions for Moderating Conformations of Calmodulin," Journal of Chemical Physics, Vol. 135, 2011, pp. 155102(1-11). [LINK]

Turgut, D., A. R. Atilgan, and C. Atilgan, "Assortative Mixing in Close-Packed Spatial Networks," PLoS ONE, Vol. 5, No.12, 2010, pp. e15551(1 - 9). [LINK]

Servantie, J., C. Atilgan, and A. R. Atilgan, "Depth Dependent Dynamics in the Hydration Shell of a Protein," Journal of Chemical Physics, Vol. 133, 2010, pp. 085101(1 - 8)[LINK]

Atilgan, C., O. B. Okan, and A. R. Atilgan, "How Orientational Order Governs Collectivity of Folded Proteins," Proteins: Structure, Function, Bioinformatics, Vol. 78, 2010, pp. 3363 - 3375[LINK]

Atilgan, C., Z. N. Gerek, S. B. Ozkan, and A. R. Atilgan, "Manipulation of Conformational Change in Proteins by Single Residue Perturbations," Biophysical Journal, Vol. 99, 2010, pp. 933 - 943. [LINK]

Atilgan, C. and A. R. Atilgan, "Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein," PLoS Computational Biology, Vol. 5, 2009, pp. e1000544(1 - 14). [LINK]

Okan, O. B., A. R. Atilgan, and C. Atilgan, "Nanosecond Motions in Proteins Impose Bounds on the Timescale Distributions of Local Dynamics," Biophysical Journal, Vol. 97, 2009, pp. 2080 - 2088. [LINK]


Recent Talks

Atilgan, A. R., D. Turgut, A.O. Aykut, and C. Atilgan, "Orchestrating Population Shifts of Native Proteins in Different Environments," Biophysical Society 55rd Annual Meeting, 2004-Plat (Co-chair), Baltimore, MA, Mar 5 - 9, 2011. Abstract published in Biophysical Journal, Vol. 100, Issue 3, Supplement 1, 2011, pp. 372a. [Abstract]

Atilgan, A.R., "Network Structure and Dynamics," Stochastic Physics in BiologyGordon Research Conferences, (invited, session discussion leader), Ventura, CA, USA, 23-28 January 2011. [Conference]

Atilgan, A. R. and Atilgan, C., "A Coarsened Network Model Reveals Allosteric Machinery," Biophysical Society 53rd Annual Meeting, 27-Plat (Co-chair), Boston, MA, Feb 28 - Mar 4, 2009. Abstract published in Biophysical Journal, Vol. 96, Issue 3, Supplement 1, 2009, pp. 5a - 6a. [Abstract]

Atilgan, A. R. and Atilgan, C., “Three-dimensional Lattice-based Network Models Portray the Properties of Folded Proteins,” XXI Sitges Conference on Statistical Mechanics - Statistical Mechanics of Molecular Biophysics, Invited Talk, 2-6 June 2008, Sitges, Barcelona. [Conference]


Awards

Graduating Class Award, selected by the senior students of the Sabanci University, 2012.

Outstanding Achievement in Education Prize, awarded by the Bogazici University, 1999.

Outstanding Achievement in Research Prize, awarded by the Bogazici University, 1998.

Young Scientist Encouragement Prize (nationwide), given by the Scientific and Technical Research Council of Turkey, 1995.

Jefferson Goblet Paper Award (nationwide, first place) given by the American  Institute of Aeronautics and Astronautics, 1989.

 



Education

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

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

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

Academic Experience

February 2006 - Present. School of Engineering and Natural Sciences, Sabanci University, Istanbul.
ali_rana
February 2002 - Present. Financial Engineering Program, Bogazici University, Istanbul.

January 2007 - Present. Adjunct Professor, Department of Civil Engineering, Bogazici University, Istanbul.

August 1993 - February 2006. Department of Civil Engineering, Bogazici University, Istanbul.

May 1991 - August 1993, Department of Civil Engineering, Istanbul Technical University, Istanbul.

September 1989 - March 1991, School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia.


Announcements

Professor Philip Kitcher [home] speaks at Sabanci University on March 29. His recent book is "[The Ethical Project]." Please refer to the [link] for the abstract of the talk.

The Spring 2012 Issue of the Hedgehog Review [link] discusses the university, the market, and professors. A decade ago, the Fall 2000 Issue [link] already asked the question: "What's the University for?" 

Diane Ravitch's review about "improving the schools" appears in the March 8 [link] and March 22 [link] 2012 issues of the New York Review of Books.

Cubitt et al., have recently proved that deducing the dynamical equations that describe a system’s evolution is an NP-hard problem [link].

The Higgs Boson is explained by PhD comics [link]To discover more, we may need to change our education paradigms [link]. An example may be the Nesin Mathematics Village [link].  

"...We are all simultaneously experts and beginners, flaunting our talents while trying to cover our shortcomings the way an animal hides a wound..." says mathwithbaddrawings [link].

"...Science needs time to think. Science needs time to read, and time to fail [link]. Science does not always know what it might be at right now [link]...." says the slow science manifesto [link].    






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