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
degree distributions. These activities find technological applications
molecular machines and system identification tools.
Selected Recent Publications
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.
H., Y. T. Tamer, O. Acar, E. Toprak, A. R. Atilgan, and C. Atilgan,
"Increased Substrate Affinity in the Escherichia Coli L28R
Dihydrofolate Reductase Mutant Causes Trimethoprim Resistance," Physical Chemistry Chemical Physics, Vol. 19, 2017, pp. 11416 - 11428. [LINK]
G., A. R. Atilgan, and C. Atilgan, "In Silico Mutational Studies of
Hsp70 Disclose Sites with Distinct Functional Attributes," Proteins:
Bioinformatics, Vol. 83, No. 11 [Cover Image] 2015, pp. 2077 - 2090. [LINK]
Aykut, O. A., A. R. Atilgan, and
Atilgan, "Designing Molecular Dynamics Simulations to Shift
Populations of the Conformational States of Calmodulin,” PLoS Computational
Vol. 9, 2013, pp. e1003366(1 - 12). [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]
Newton Mobility Grant (NMG2R2\100183), 2018.
International Fellow, awarded by the University of Essex, 2018.
Outstanding Achievement in Education
Prize, awarded by the Bogazici
Outstanding Achievement in Research Prize, awarded by the Bogazici
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.
"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.
Aerospace Engineering, September 1989, Georgia Institute of Technology,
M.S. in Aerospace Engineering, June 1987, Georgia Institute of Technology, Atlanta, Georgia.
B.S. in Aeronautical Engineering, June 1984, Istanbul Technical University, Istanbul.
February 2006 - Present. School of
Engineering and Natural Sciences, Sabanci University, Istanbul.
February 2002 - Present. Financial Engineering Program,
January 2007 - Present. Adjunct Professor, Department of Civil Engineering, Bogazici
August 1993 - February 2006. Department of Civil Engineering, Bogazici
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.