About the Project
Applications accepted until June 16, 2017 for Fall 2017 admission into the PhD program.
Competitve public sector funded project (open to 1 student from all nationalities)
About This PhD Project
Dynamical behavior of long, helical molecules, such as DNA and folded RNA which assume central functions in cellular biochemistry, is still poorly understood due to their inherent entangled structure. In addition to their well-known role in biological organisms, these molecules are also of importance due to their newly found applications in microbiology, biophysics and bionanotechnology, thanks to recent technological advances in these areas.
The preliminary goal of the present project is to develop a coarse-grained DNA model, in order to address the role of helicity in these molecules by computational means.
Upon completion of the model, we will investigate the hydrogen-bond formation/breakage dynamics in DNA, and further dynamical properties stemming from the interplay between the partially melted two-phase (ssDNA+dsDNA) structure and the associated helical rearrangement within the molecule. DNA melts in water around 350 K and this physical aspect of the molecule is utilized by PCR technology, which is one of the foundational cornerstones of the modern revolution in molecular biology.
Recent theoretical studies of the PI considered the influence of overtwisting and writhing on the physics of DNA melting and proposed a novel melting scenario. The current project will allow a validation of these theoretical findings on a much more realistic, computational platform. The mentioned theoretical studies point at the possibility of a Bose-Einstein condensation mechanism triggered by the coalescing of denaturation bubbles in plasmid DNAs with circular topology.
A goal of the project is to observe this condensation by means of realistic molecular dynamics simulations. Another topic of interest is the diffusion dynamics associated with the inhomogeneous twist distribution triggered by the partial melting of the chain, in particular the twist/writhe accommodated by the denaturation bubbles and the kinetic barriers they form against twist diffusion. The output of the planned investigations is also expected to contribute to recent experimental research. For example, force-induced denaturation times of around 10-100 microseconds were measured for DNA/RNA hairpins by means of FRET measurements. Later experiments using optical traps found faster transition path times which were claimed to be independent of geometry.
Another question we plan to investigate is how much these dynamic properties are shaped by the helical nature of the molecules. We will investigate whether/how the impact of helicity changes and the observed melting times scale with the molecular weight (backbone length), as well as the fold shape for the case of RNA.
Current research on nucleic acids has moved well beyond the territory of biology. These molecules now serve as building blocks in drug delivery technologies and bio-nano design studies. Research studies aiming at a better understanding of their structural and dynamical properties and the interplay between the two, therefore, are not only of pure scientific value, but also carry potential technological and economic benefits in the long run.
Proposed research is expected to last 36 months under the guidance of Dr. Alkan Kabakçıoğlu (Koç University, Physics Dept. faculty member) as the principal investigator. The investigations are planned to be conducted in collaboration with Dr. Mehmet Sayar (Koç University, Mechanical Eng. Dept. faculty member) as researcher, a full-term Ph.D. student, and a post-doctoral fellow in the last 2 years.
PhD students should have experience in linux-based computing/programming in addition to a strong background in physics.
More information can be found here: http://home.ku.edu.tr/~akabakcioglu/research/research.htm
Email now
Contact the project director Prof. Kabakcioglu [Email Address Removed] and make sure you submit your online application to the PhD program at https://gradapp.ku.edu.tr/login.php
Funding Notes
This project is available to students who have completed a BSc or MSc in a related field applying for funded PhD studentships in the Phd in Computational Sciences or Phd in Physics program and may be altered or withdrawn.
Studentships will be awarded to successful applicants from all applications received. Applicants must satisfy all admission criteria required by the PhD program at the Graduate School of Sciences and Engineering. For more information please visit: https://gsse.ku.edu.tr/en/
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