Mite Mijalkov defended his PhD Thesis. Congrats!

Mite Mijalkov defended his PhD Thesis on 24 April 2018 in the Physics Department seminar room (SA240).

Assoc. Prof. Hande Toffoli (Middle-East Technical University), Prof. Tayfun Ozcelik (Bilkent University), Assoc. Prof. Alpan Bek (Middle-East Technical University), Assist. Prof. Seymur Cahangirov (Bilkent Unievrsity) and Assist. Prof. Giovanni Volpe (Bilkent University) will be the thesis committee members.

Thesis title: Graph Theory Study of Complex Networks in the Brain

Thesis abstract: The brain is a large-scale, intricate web of neurons, known as the connectome. By representing the brain as a network i.e. a set of nodes connected by edges, one can study its organization by using concepts from graph theory to evaluate various measures. We have developed BRAPH – BRain Analysis using graPHtheory, a MatLab, object-oriented freeware that facilitates the connectivity analysis of brain networks. BRAPH provides user-friendly interfaces that guide the user through the various steps of the connectivity analysis, such as, calculating adjacency matrices, evaluating global and local measures, performing group comparisons by non-parametric permutations and assessing the communities in a network. Furthermore, using graph theory, we showed that structural MRI undirected networks of stable MCI (sMCI) subjects, late MCI converters (lMCIc), early MCI converters (eMCIc), and AD patients show abnormal organization. This is indicated, at global level, by decreases in clustering and transitivity accompanied by increases in path length and modularity and, at nodal level, by changes in nodal clustering and closeness centrality in patient groups when compared to controls. In samples that do not exhibit differences in the undirected analysis, we propose the usage of directed networks to assess any topological changes due to a neurodegenerative disease. We demonstrate that such changes can be identified in Alzheimer’s and Parkinson’s patients by using directed networks built by delayed correlation coefficients. Finally, we put forward a method that improves the reconstruction of the brain connectome by utilizing the delays in the dynamic behavior of the neurons. We show that this delayed correlationmethod correctly identifies 70% to 80% of the real connections in simulated networks and performs well in the identification of their global and nodal properties.

Name of the PhD programme: Material Science and Nanotechnology Graduate Program
Thesis Advisor  Giovanni Volpe, Department of Physics, Bilkent University

Place: Physics Department seminar room (SA240), Bilkent University
Time: 24 April, 2018, 11:00

Erçağ Pinçe defended his PhD Thesis. Congrats!

Erçağ Pinçe defended his PhD thesis on 21 October 2016. Assist. Prof. Evren Doruk Engin (Ankara University), Assist. Prof. Giovanni Volpe (Bilkent University), Assist. Prof. Balázs Hétenyi (Bilkent University), Assoc. Prof. Fatih Ömer İlday (Bilkent University) and Prof. Alper Kiraz (Koç University) participated as thesis committee members.

Erçağ Pinçe investigated the role that spatial disorder can play to alter collective dynamics in a colloidal living active matter system where motile E. Coli bacteria are present. The results suggested that the level of heterogeneity present in the background changes the long-term spatial dynamics in a colloidal ensemble coupled to a bacterial bath. This work provided insights about statistical behavior and far-from-equilibrium interactions in an active matter system.

Thesis title: Manipulation and control of collective behavior in active matter systems

Thesis advisor: Giovanni Volpe

Thesis abstract: Active matter systems consist of active constituents that transform energy into directed motion in a non-equilibrium setting. The interaction of active agents with each other and with their environment results in collective motion and emergence of long-range ordering. Examples to such dynamic behaviors in living active matter systems are pattern formation in bacterial colonies, ocking of birds and clustering of pedestrian crowds. All these phenomena stem from far-from-equilibrium interactions. The governing dynamics of these phenomena are not yet fully understood and extensively studied. In this thesis, we studied the role that spatial disorder can play to alter collective dynamics in a colloidal living active matter system. We showed that the level of heterogeneity in the environment in uences the long-range order in a colloidal ensemble coupled to a bacterial bath where the non-equilibrium forces imposed by the bacteria become pivotal to control switching between gathering and dispersal of colloids. Apart from studying environmental factors in a complex active matter system, we also focused on a new class of active particles, \bionic microswimmers”, and their clustering behavior. We demonstrated that spherical bionic microswimmers which are fabricated by attaching motile E. coli bacteria on melamine particles can agglomerate in large colloidal structures. Finally, we observed the emergence of swimming clusters as a result of the collective motion of bionic microswimmers. Our results provide insights about statistical behavior and far-from-equilibrium interactions in an active matter system.