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
D. K., D. L. Penkler, O. S. Amamuddy, C. Ross, A. R. Atilgan, C.
Atilgan, and O. T. Bishop, "MD-TASK: A Software Suite for Analyzing
Molecular Dynamics Trajectories," Bioinformatics, published online 31 May, 2017.[LINK]
H., A. R. Atilgan, and C. Atilgan,
"Mechanisms by which Salt Concentration Moderates the Dynamics of Human Serum Transferrin," Journal of Physical Chemistry B, Vol. 121, 2017, pp. 4778 - 4789. [LINK]
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]
Sensoy, O., A. R. Atilgan, and C. Atilgan, "FbpA Iron Storage and Release are Governed by Periplasmic Microenvironments," Physical Chemistry Chemical Physics, Vol. 19, 2017, pp. 6064 - 6075. [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]
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
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., 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]
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]
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., 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]
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
Vol. 100, Issue 3, Supplement 1, 2011,
pp. 372a. [Abstract]
Atilgan, A.R., "Network Structure and
Dynamics," Stochastic Physics in
Biology – Gordon 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
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]
Graduating Class Award, selected by the
senior students of the Sabanci University, 2012 (first place), 2016 (second place). [LINK]
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.