39 citations · 191 across the 18 of their papers we have counts for
18 papers
Nested canalizing functions minimize sensitivity and simultaneously promote criticality
H. Coban, A. Kabakcioglu
We prove that nested canalizing functions are the minimum-sensitivity Boolean functions for any given activity ratio and we characterize the sensitivity boundary which has a nontri…
Role of helicity in DNA hairping folding dynamics
Huaping Li, Alkan Kabakcioglu
We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time . We find that the…
Coherent organization in gene regulation: a study on six networks
N. Aral, A. Kabakcioglu
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible…
Coherent regulation in yeast cell cycle network
Nese Aral, Alkan Kabakcioglu
We define a measure of coherent activity for gene regulatory networks, a property that reflects the unity of purpose between the regulatory agents with a common target. We propose…
Mode-coupling points to functionally important residues in Myosin II
Onur Varol, Deniz Yuret, Burak Erman +1
Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evid…
Denaturation of Circular DNA: Supercoils and Overtwist
Amir Bar, Alkan Kabakçıoğlu, David Mukamel
The denaturation transition of circular DNA is studied within a Poland-Scheraga type approach, generalized to account for the fact that the total linking number (LK), which measure…