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: 28/02/2018 



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.  

                                                                                                       [Google Scholar]

                                                                                   [Researcher ID: A-7805-2011]

Selected Recent Publications  

M. S. Manna, Y. T. Tamer, I. Gaszek, N. Poulides, A. Ahmed, X. Wang, F. C. R. Toprak, D. R. Woodard, A. Y. Koh, N. S. Williams, D. Borek, A. R. Atilgan, J. D. Hulleman, C. Atilgan, U. Tambar, and E. Toprak, "A trimethoprim derivative impedes antibiotic resistance evolution," Nature Communications, Vol. 12, 2021, 2249/1-10. [LINK]

Guclu, T. F., A. R. Atilgan, and C. Atilgan, "Dynamic Community Composition Unravels Allosteric Communication in PDZ," The Journal of Physical Chemistry B, Vol. 125 (9), 2021, pp. 2266 - 2276. [LINK]

Guclu, T. F., N. Kocatug, A. R. Atilgan, and C. Atilgan, "N-Terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding ," Journal of Chemical Information and Modeling, Vol. 61 (1), 2021, pp. 347 - 357. [LINK]

Abdizadeh, H., F. Jalalypour, A. R. Atilgan, and C. Atilgan, "A coarse-grained methodolody identifies intrinsic mechanisms that dissociate interacting protein pairs," Frontiers in Molecular Biosciences, Vol. 7, 210, 2020, pp. 1 - 18. [LINK]

Tamer, Y. T., I. K. Gaszek, H. Abdizadeh, T. Bature, K. Reynolds, A. R. Atilgan, C. Atilgan, and E. Toprak, "High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection," Molecular Biology and Evolution, Vol. 36 (7), 2019, pp. 1533 - 1550. [LINK]

Ross, C. J., B. Nizami, M. Glenister, O. S. Amamuddy, A. R. Atilgan, C. Atilgan, and O. T. Bishop, "MODE-TASK: Large-scale Protein Motion Tools," Bioinformatics, Vol. 34 (21), 2018, pp. 3759 - 3763. [LINK] 

Ross, C. J., A. R. Atilgan, O. T. Bishop, and C. Atilgan, "Unraveling the Motions behind Enterovirus 71 Uncoating," Biophysical Journal, Vol. 114(4), 2018, pp. 822 - 838. [LINK] Also find a [movie] visualizing first non-degenerate mode of pentamer complex, which is the minimal functional unit explaining virus deformations.

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]

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]


Graduating Class Award, selected by the senior students of the Sabanci University, 2012 (first place), 2016 (second place), 2017 (first place). [LINK]

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.

Recent Talks

"Empirically Tractable Antibiotics Time Machines," [VI. Ecology and Evolutionary Biology Symposium],    Ankara University, 10-12 July 2019.

"Overhauling A Popular Introductory Engineering Course: ENS 208," [The Second Education Conference],    Sabanci University, 28-29 May 2019 [Abstracts].

"Morphogenesis a la Schelling," [Queen Mary University of London], 24 January 2019.

"Unraveling the Motions behind Enterovirus 71 Uncoating," 17th European Conference on Computational Biology, Highlights - Proteins, Athens, 8-12 September 2018 [Programme].

"Biological physics of enterovirus coarsening," 4th International Scientific and the 5th MC meeting of the COST Action CM1306 'Understanding Movement and Mechanisms in Molecular Machines,' Zagreb, 21-24 March 2018 [Programme].

"The spread of influence through a network society," ESRC Business and Local Government, [BLG Data Research] Center, 31 January 2018, [Webinar].

"To be a part of a network or not to be," [University of Essex], 24 January 2018.

"Maze generators and collective action in networks," [McCormick-Civil and Environmental Engineering], Northwestern University, 10 November 2017.

"Collective action in social networks," [24th Statistical Physics Days], [Izmir Institute of Technology], 29 June - 2 July 2017.


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.
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.


WORKSHOP - 19-20 April 2018 Bounce forward: Moving communities from crisis to resilience [link] organized by the center for resilient communities [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].  

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.

Professor Philip Kitcher [home] speaks at Sabanci University on March 29, 2012. His recent book is "[The Ethical Project]." Please refer to the [link] for the abstract of the talk.

2007 MIDST Lab.

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