Evolution of Biomolecular Networks

Why do higher organisms transcribe so much noncoding DNA?

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For mammals, almost the entirety of the genome (including the 98% noncoding portion) gets turned into RNA fragments, present at various concentrations. A fraction of these RNAs interact with other cellular components, forming a kind of shadow regulatory system we are only beginning to unravel. To what extent the noncoding part of genome is functional remains as a key biological mystery. To address this question, we make a cost efficiency analysis by estimating the metabolic costs of these regulation networks  and investigating their adaptive benefits. (the results for microRNA regulation in protein expression will be published soon...)

Disentangling the effect of metabolic costs in selection

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Collaboration with Michael Hinczewski

Active Phase Separation 

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The activity-driven phase separation plays an important role in living organisms, by promoting the self-organization and increasing the efficiency of biological functions inside the cell which are destined to operate in very crowded and noisy environment. The constant use of energy in unequal amounts for each subcomponent reflects variety in dynamical and chemical activity along with their innate physiological differences. In return, such activity gradient enhance the phase separation by creating an effective attraction between alike particles. Remarkably, we observe similar characteristics and governing principles at various length scales on diverse setups in biology, now also guiding the artificial models.

 

In binary active/passive mixtures, the activity differences in compartments or particles can be described by having two different temperatures in the system. The existence of a secondary temperature creates a non-zero flux in the system, and hence drives the system out of equilibrium. Various applications in different fields include biological organisms, polymeric systems, spin glasses and plasmas in the interstellar medium. It is widely employed since this simple realization already exhibits rich phenomena often sufficient to illustrate those systems. I am working on theory of phase separation in two temperature systems.

Collaboration with Jean-François Joanny

Physics of Biosensing

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In our collaboration at Case Western Reserve University with the labs of Guiseppe Strangi and Umut Gurkan, we design a comprehensive computational model of the entire sensor system, including diffusion of the biomolecule analytes, their binding to the functionalized surface, and the resulting changes in plasmon resonance and the reflectance spectrum. We are working closely with the experimental researchers, analyzing their data as well as giving theoretical feedback on optimal sensor design. This work has led to a device with record-breaking sensitivity, described in a recent article in Nature Materials (published article), and in another publication highlighted on the cover of Advanced Optical Materials (published article).

See other recent works in my publications

Controlled Growth Modes and Stability of Bimetallic Nano-structures

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Controlling the growth of metallic/bi-metallic nanostructures has become increasingly important as the morphology at this scale plays an essential role in determining the behavior of these materials in many industrially and technologically relevant phenomena such as catalysis, chemical reactivity, selectivity, and stability.  With the adequate conditions implemented on the nano-structure (forced configurational state), an environment in which the diffusion mechanisms (the diffusion in the surrounding solution and the surface diffusion on the nano cube) govern the formation of layers in the macroshape can be maintained. In other words, the kinetic product wins over the thermodynamic product.

In the light of experiments, we investigate the growth modes and stability related to this phenomena by using molecular dynamics (MD) simulations. (published article)

 

Collaboration with Prof. Sondan Durukanoglu

 Controlling Frustration and Chaos in Spin-Glass Systems

PhD thesis

Spin-glass theory came into life to validate a physical basis for problems raised by experimental peculiarities in magnetic systems. While answering some of the major concerns, its applications grew beyond its original purpose and became a new topic in statistical physics representing collective complex structures, even posing now its own questions and being innovative in its understanding. 

In the upper right figure,  an illustration of complex spin structure is shown, displaying different patterns of alignments on different regions. In fact, the spin configuration is dynamic, slowly changing in time, due to large relaxation times even larger than experimental observation timescales. In return, slowly relaxing magnetization can be observed. Furthermore, these systems may have very dissimilar equilibrium configurations, also with different portions of the system being not alike. The degeneracy in free energy minima can be better seen with the notion of ground-state entropy which can be injected into the system by bond randomness, thus frustration.

In the bottom right figure, we demonstrate how frustration can be adjusted, without changing the antiferromagnetic (AF) bond probability p, by using locally correlated quenched randomness. This manipulation gives an access to all frustration levels for spin-glass systems from unfrustrated (so-called Mattis spin glasses) to fully frustrated networks. By applying this idea using renormalization-group (RG) theory, we obtain a variety of phase diagrams, varying chaos in different frustration levels, including  spin-glass order in d=2 (with underfrustrated networks) and disappearance of spin-glass phase in d=3 (with overfrustrated networks). published article

Also see my other works:

 q-state clock spin-glass models with symmetry in ordering (even q-state clock models) are investigated up to reaching high q-values and thus XY model limit. published article

Spin-glass systems without symmetry in ordering of F and AF (odd q-state clock models) which belongs to a class of systems having ground-state entropy even without bond frustration (due lacking sublattice spin-reversal (θ→ θ  + π) symmetry). published article

 

Collaboration with Prof. A. Nihat Berker

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