PhD Candidate
Carnegie Mellon University - University of Pittsburgh
Joint Program in Computational Biology

I work with Dr. Ivet Bahar and Dr. James Faeder at the University of Pittsburgh in development of multiscale models and simulators for neurobiological systems. Our focus is to investigate the synaptic signaling dynamics for different types of neurons. We aim to understand the effect of spatial complexity and distribution of molecules on signaling. Our models utilize molecular and cellular information with image data. A list of my publications can be found here.

Recent Work

Spatial Effects in Dopamine Neurons

Efficient clearance of neurotransmitters from the synapse is key to regulating dopamine neurotransmission in the central nervous system. We modeled and simulated the dynamics of transporters using a combination of structure-based tools to identify the most probable functional states, their populations as well as relative rates of transitions. These were used to build realistic kinetic schemes which were in turn adopted in MCell simulations performed in cellular environment reconstructed from experimental data. Spatial distribution of transporters as well as structural heterogeneities near the dopamine release site were observed to alter the efficiency of transporter function inviting attention to the significance of a realistic representation of structure and environment for gaining deeper insights into neurotransmission regulation.

Hybrid Models of Hippocampal Neurons

Learning and memory are two of the most fundamental and widely studied processes in neuroscience. Through the modulation of synapse strength depending on the activity of neurons, synaptic plasticity reshapes the neural network over time. Synaptic plasticity in excitatory synapses is caused by the release of glutamate from pre-synaptic neurons and the activity of the synapse is mediated by various receptors, transporters and kinases. The crucial mechanism is that the ion transport into the post-synaptic compartment through receptor modulates the level of ion conductance and the number of receptors on postsynaptic cell membrane. In this study, a unified model incorporating pre-synaptic and post-synaptic transport is developed. The limitations on the simulations due to complexity and size are alleviated by implementation of hybrid methods.

Connecting sequence and structure data to protein-protein interaction networks

In post-genomic era, data is generated with an uncontrolled manner which requires development of new methodologies to handle different fields of biology. The structure and function of proteins are mediated by the evolutionary properties. A large portion of proteins are functioning in multimeric form and with the introduction of multiple isoforms of proteins, the task of understanding how proteins function as multimers becomes more challenging. The interfacial contacts between monomers of similar or different proteins are mediator of the activity and function. Therefore, understanding the relationship between sequence, structure and dynamics is crucial to understand the activity of protein complexes.

Software for Protein Dynamics Analysis

ProDy is an integrative and scalable application programming interfacefor efficient evaluation and visualization of protein dynamics. Our goal is to develop and implement new modules and functions that will take advantage of the rapidly growing structural data, as well as advances in computational technology. We would like to build tools for increasingly larger systems, and focus on the dynamics of interacting proteins, biological assemblies, or oligomers, toward a better understanding of the role of intermolecular dynamics in cell function. Also, we would like implement hybrid methodologies and protocols to augment the spatiotemporal range and precision of dynamic processes. Prody is available here.


I graduated from Bogazici University in 2010 with B.S in Chemical Engineering and B.S in Physics. I also get my Masters in Chemical Engineering in Bogazici University in 2013. I worked 5 years at Polymer Research center to study motor protein dynamics and developed allosteric pathway determination tools.

Contact Me

Reach me by email cihank [at] pitt [dot] edu.