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
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, published on website, 29 May, to appear in print, 2018. [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]
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.
"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.