My main research interests are
- Statistical physics of complex systems
Recent
scientific advances in our understanding of biological systems and
other organizations composed of diverse units (such as the internet,
social/scientific collaborations, etc.) gave birth a new
interdiciplinary field of research, coined "complex systems". It
investigates interesting problems related to the organizing
principles, stability, evolution, dynamics, etc. of such complex
networks. Examples are diverse: protein and gene interactions in
cells, mutual evolution of species, power-lines, world-wide-web,
nature of scientific collaborations, earthquakes, etc. I am
interested in the mechanisms that determine the connective topology of
these interacting systems and the interplay between their structure
and dynamical behaviour.
- Statistical physics and dynamics of (bio)polymers
Many biologically important macropolymers fold into a specific
conformation in favorable conditions. For example, proteins have very
specific 3-dimensional shapes that can be determined by X-ray
crystallography or NMR. Similarly, RNA chains form particular
structures called pseudoknots that are known to play an important role
during the translation of the genetic information from the mRNA into a
protein. The frequency of pseudoknots observed in RNA structures
deviates significantly from our theoretical expectations. As for the
DNA, despite the decades since Watson and Crick's discovery, little is
known about the effect of its inherent twist on some of its physical
properties (such as, its thermal denaturation which I am interested
in). I investigate conformational properties and dynamics of these
molecules and try to come up with simple models that capture their
physics. I collaborate with Prof. Sayar from Koc Univ. in developing a
microscopic model to study various mechanical properties of DNA and
with Prof. Mukamel (Weizmann Inst) on phase transitions in related
analytical models. Also, I recently started working on mode-coupling
in protein dynamics. We developed a new tool for predicting
functionally important sites on allosteric proteins by means of their
relevance to energy transfer between different vibrational modes.
- Biological interactions
This line of research is intimately related to the complex systems
research outlined earlier. Many complex biological systems involve a
reasonably large number of interacting agents (such as, proteins,
genes, or species in an ecosystem). These interactions are believed to
be tuned by evolutionary pressure to maintain the near-optimal
operational efficiency under varying environmental conditions. This
implies a trade-off between robustness and efficiency (the Kaufmann
doctrine), not unlike that between the energy and the entropy in
isolated systems. My goal is to understand the "modus operandi" of
such systems by means of models that capture their dynamical behaviour
at a coarse resolution. On the side, I also collaborate with members
of the molecular biology department at Koc, helping them in
interpreting the output of their experiments which try to elucidate
regulatory processes involved in brain development or microRNA
interactions.
- Phase transitions in disordered systems
Small impurities inside a material may change its nature in dramatic
ways. Such changes may be desired as in the case of steel, where
adding carbon into iron prevents dislocations from sliding past one
another, hence hardening the material. A similar role is played by
magnetic impurities in superconducting magnets which pin the magnetic
flux lines, preventing energy dissipation. Phase transitions in
certain materials also get modified upon introducing
'quenched-randomness'. Randomness is an important component in
surface-growth (applications in litography) as well, where the final
topography depends on statistical features of particle deposition and
surface diffusion. I use both theoretical and numerical techniques to
explore scaling properties of phase transitions and dynamics in such
systems.