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Yayın Monitoring diffusion of reptating polymer chains by a direct energy transfer method: A Monte Carlo simulation(Wiley-Blackwell, 2002-07-29) Tüzel, Erkan; Kısacıkoğlu, Kemal Batuhan; Pekcan, Mehmet ÖnderA kinetic Monte Carlo method was used to simulate the diffusion of reptating polymer chains across an interface. A time-resolved fluorescence technique in conjunction with a direct energy transfer method was used to measure the extent of diffusion of dye-labeled reptating polymer chains. The diffusion of donor- and acceptor-labeled polymer chains between adjacent compartments was randomly generated. The fluorescence decay profiles of donor molecules were simulated at several diffusion steps to produce mixing of the polymer chains. Mixing ratios of donor- and acceptor-labeled polymer chains in compartments were measured at various stages (snap-shots) of diffusion. It was observed that for a given molecular weight, the average interpenetration contour length was found to be proportional to the mixing ratio. Monte Carlo analysis showed that the curvilinear diffusion coefficient is inversely proportional to the weight of polymer chains during diffusion.Yayın The statistics of energy states of a Hookean model for proteins(TÜBİTAK, 2000) Erzan, Ayşe; Tüzel, ErkanA generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobia residues, reproduces the energy probability distribution of real proteins over a very large range of energies. We show that this system with harmonic interactions, under dissipative dynamics driven by random noise, leads to a distribution of energy states obeying a modified one-dimensional Ornstein-Uhlenbeck process with reflecting boundary conditions, and giving rise to distributions of the Wigner or inverse Gaussian form. A continuum approximation leads to a path integral formulation of the problem.Yayın Testing a hypothesis for the evolution of sex(World Scientific Publishing Company, 2000-07-11) Örçal, Bora; Tüzel, Erkan; Sevim, Volkan; Jan, Naeem; Erzan, AyşeAn asexual set of primitive bacteria is simulated with a lit-string Penna model with a Fermi function for survival. A recent hypothesis by Jan, Stauffer, and Moseley on the evolution of sex from asexual cells as a strategy for trying to escape the effects of deleterious mutations is checked. This strategy is found to provide a successful scenario for the evolution of a stable macroscopic sexual population.
