sahin uyaver - Academia.edu (original) (raw)
Papers by sahin uyaver
We report magnetization, resistivity and heat capacity measurements on samples of BaFe2As2 and Ba... more We report magnetization, resistivity and heat capacity measurements on samples of BaFe2As2 and Ba(1-x)LaxFe1.9Pt0.1As2 (x =0, 0.03, 0.05, 0.1, 0.3, 0.4, 0.6, 0.8, 0.95) prepared by solid state reaction. All samples crystallize with the ThCr2Si2-type structure. Lattice parameters are found to be in the 3.992-3.964 Å interval for a=b; and 13.057-13.001 Å for c. Both c and a decrease significantly with La doping up to x=0.3 and then stay almost constant. We have investigated in detail the superconducting state with magnetization measurements in the temperature range 5-400 K, up to a field of 9 T. Substitution of La for Ba produced an electron-doped situation; here we also study the results of direct substitution of non-isoelectronic Pt for Fe. Based on magnetization data, we observe that the superconducting critical temperature (Tc) decreases with La from 22.5 K for x=0 to 20.4 K for x=0.1, and then increases smoothly up to x=0.6 with a maximum Tc=23.5 K. The phase diagram (Tc versus x...
The proceedings of the conference "International 2nd Conference on Sustainable Energy and En... more The proceedings of the conference "International 2nd Conference on Sustainable Energy and Energy Calculations 2020"
Sakarya University Journal of Science
Monte Carlo simulations are used to simulate a single polymer chain in a more generalized model. ... more Monte Carlo simulations are used to simulate a single polymer chain in a more generalized model. The more generalized model differs from the simpler models by including dipole-dipole interactions. The polymer chain is modeled as a freely rotating chain where the neighboring beads are connected by harmonic spring. Excluded volume effects are included employing modified Lennard-Jones potential. As the extension in this work, each monomer unit carries permanently a freely-rotating electric dipole moment. After getting the system equilibrated the average values are measured and Θ-temperature of the system is determined. The effects of the presence of the dipole moments to the Θ-temperature of the system are investigated. The results are analyzed in comparison with a bare model.
ABSTRACT We present Monte Carlo simulations on annealed polyelectrolytes in poor solvent. Increas... more ABSTRACT We present Monte Carlo simulations on annealed polyelectrolytes in poor solvent. Increasing the chemical potential of the charges, which is equal to the pH of the solution except for a trivial additive constant, we find the first-order phase transition between a weakly charged globule and a highly charged extended chain predicted by theory. Starting from an elongated highly charged conformation and increasing the coupling strength u = λB/b, the degree of stretching of the chain at first increases similarly to quenched polyelectrolytes. However, on reaching some upper threshold u*, the chain collapses back into a weakly charged state.
The Journal of Chemical Physics, 2014
Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are... more Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain. © 2014 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4897161]
The Journal of Chemical Physics, 2014
One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We... more One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We recently suggested that the rate-limiting step in the folding of the βαβ protein is the formation of the central helix that then provides a scaffold for the parallel β-sheet formed by the two chain ends. In the present report we investigate whether and how this folding mechanism depends on the energy function, and compare the efficiency of molecular dynamics and Monte Carlo implementations of multicanonical sampling. While we find the native structure with similar frequency as in our previous simulations, we observe that the folding mechanism differs for both force fields.
Macromolecules, 2009
ABSTRACT Using grand canonical Monte Carlo simulations of a polyelectrolyte chain where the charg... more ABSTRACT Using grand canonical Monte Carlo simulations of a polyelectrolyte chain where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in a poor solvent. We address the influence of variable screening of the electrostatic interaction on the chain structure for rather poor solvents as well as in the close-to-Θ-point regime. For the latter case, we demonstrate that a fine tuning of the chain structure is attainable by varying screening. With growing screening length, that is, by reducing the salt concentration, the degree of charging is reduced and the pearl distribution can be shifted toward a smaller number of pearls. In addition, we find that pearl necklaces can also occur at high charging provided the screening is very strong. In the rather-poor-solvent regime, the position of the discrete transition from a highly charged, stretched chain to a weakly charged globule can be shifted by the variation of screening. By reducing the screening of electrostatic repulsion, we observe in both regimes a nonmonotonic stretching of the polyelectrolyte. After reaching a maximum of stretching, the chains relax back to an asymptotic value at vanishing screening, which depends on pH. For rather poor solvents, at large screening lengths, the chains collapse into an almost uncharged globule provided that high ionization is not pinned by a large chemical potential of the charges.
Using (semi-)grand canonical Monte Carlo simulations of a polyelectrolyte chain of length N where... more Using (semi-)grand canonical Monte Carlo simulations of a polyelectrolyte chain of length N where the charges are in contact with a reservoir of constant chemical potential µ given by the solution pH, we study the behavior of annealed polyelectrolytes in a poor solvent. We focus on the conformational properties in the close-to-Θ-point regime τ < τ* ∼ N -1/5 u -3/5 , which can be reached either by reducing electrostatic interaction strength u ) λ B /b or by improving solvent quality, i.e., by reducing τ ) (Θ -T)/Θ. We investigate the conformations with regard to parameters u, τ, and µ and explore in which conditions pearl-necklace-like structures are stable. Most of the pearl-necklace parameters are found to obey the scaling relations predicted for quenched polyelectrolytes. However, similarly to the behavior known for this class of polyelectrolytes, we obtain large fluctuations in pearl number and size. In agreement with theoretical predictions we find a nonuniform charge distribution between pearls and strings. For τ , 1 and moderate interaction strength we demonstrate that a cascade of pearl-necklace transitions can be initiated by changing µ, i.e., by tuning the solution pH.
Using Monte Carlo simulations, the cascade transition of a single polyelectrolyte chain having pe... more Using Monte Carlo simulations, the cascade transition of a single polyelectrolyte chain having permuted charge distribution is investigated. The polyelectrolyte chain is simulated at various solvent regimes. The effect of the electrostatic interaction strength is studied. The structures are analyzed with respect to the scaling laws. The effect of permuted charge distribution is investigated in comparison to the other charge distribution in the literature.
Fundamentals, Methods and Applications, 2012
Using molecular dynamics, we study the selfassembly of phenylalanine with charged end-groups at v... more Using molecular dynamics, we study the selfassembly of phenylalanine with charged end-groups at various temperatures and concentrations. As in the case of diphenylalanine, we observe the formation of nanotubes; however, phenylalanine aggregates in layers of four, not six, molecules. The observed aggregates are consistent with recent experimental measurements of fibrils obtained from mice with phenylketonuria. We investigate the stability and the mechanism by which these tubular structures form and discuss potential toxicity mechanisms.
We report magnetization, resistivity and heat capacity measurements on samples of BaFe2As2 and Ba... more We report magnetization, resistivity and heat capacity measurements on samples of BaFe2As2 and Ba(1-x)LaxFe1.9Pt0.1As2 (x =0, 0.03, 0.05, 0.1, 0.3, 0.4, 0.6, 0.8, 0.95) prepared by solid state reaction. All samples crystallize with the ThCr2Si2-type structure. Lattice parameters are found to be in the 3.992-3.964 Å interval for a=b; and 13.057-13.001 Å for c. Both c and a decrease significantly with La doping up to x=0.3 and then stay almost constant. We have investigated in detail the superconducting state with magnetization measurements in the temperature range 5-400 K, up to a field of 9 T. Substitution of La for Ba produced an electron-doped situation; here we also study the results of direct substitution of non-isoelectronic Pt for Fe. Based on magnetization data, we observe that the superconducting critical temperature (Tc) decreases with La from 22.5 K for x=0 to 20.4 K for x=0.1, and then increases smoothly up to x=0.6 with a maximum Tc=23.5 K. The phase diagram (Tc versus x...
The proceedings of the conference "International 2nd Conference on Sustainable Energy and En... more The proceedings of the conference "International 2nd Conference on Sustainable Energy and Energy Calculations 2020"
Sakarya University Journal of Science
Monte Carlo simulations are used to simulate a single polymer chain in a more generalized model. ... more Monte Carlo simulations are used to simulate a single polymer chain in a more generalized model. The more generalized model differs from the simpler models by including dipole-dipole interactions. The polymer chain is modeled as a freely rotating chain where the neighboring beads are connected by harmonic spring. Excluded volume effects are included employing modified Lennard-Jones potential. As the extension in this work, each monomer unit carries permanently a freely-rotating electric dipole moment. After getting the system equilibrated the average values are measured and Θ-temperature of the system is determined. The effects of the presence of the dipole moments to the Θ-temperature of the system are investigated. The results are analyzed in comparison with a bare model.
ABSTRACT We present Monte Carlo simulations on annealed polyelectrolytes in poor solvent. Increas... more ABSTRACT We present Monte Carlo simulations on annealed polyelectrolytes in poor solvent. Increasing the chemical potential of the charges, which is equal to the pH of the solution except for a trivial additive constant, we find the first-order phase transition between a weakly charged globule and a highly charged extended chain predicted by theory. Starting from an elongated highly charged conformation and increasing the coupling strength u = λB/b, the degree of stretching of the chain at first increases similarly to quenched polyelectrolytes. However, on reaching some upper threshold u*, the chain collapses back into a weakly charged state.
The Journal of Chemical Physics, 2014
Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are... more Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain. © 2014 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4897161]
The Journal of Chemical Physics, 2014
One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We... more One of the smallest proteins with end-to-end β-sheet is the designed 36-residue protein DS119. We recently suggested that the rate-limiting step in the folding of the βαβ protein is the formation of the central helix that then provides a scaffold for the parallel β-sheet formed by the two chain ends. In the present report we investigate whether and how this folding mechanism depends on the energy function, and compare the efficiency of molecular dynamics and Monte Carlo implementations of multicanonical sampling. While we find the native structure with similar frequency as in our previous simulations, we observe that the folding mechanism differs for both force fields.
Macromolecules, 2009
ABSTRACT Using grand canonical Monte Carlo simulations of a polyelectrolyte chain where the charg... more ABSTRACT Using grand canonical Monte Carlo simulations of a polyelectrolyte chain where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in a poor solvent. We address the influence of variable screening of the electrostatic interaction on the chain structure for rather poor solvents as well as in the close-to-Θ-point regime. For the latter case, we demonstrate that a fine tuning of the chain structure is attainable by varying screening. With growing screening length, that is, by reducing the salt concentration, the degree of charging is reduced and the pearl distribution can be shifted toward a smaller number of pearls. In addition, we find that pearl necklaces can also occur at high charging provided the screening is very strong. In the rather-poor-solvent regime, the position of the discrete transition from a highly charged, stretched chain to a weakly charged globule can be shifted by the variation of screening. By reducing the screening of electrostatic repulsion, we observe in both regimes a nonmonotonic stretching of the polyelectrolyte. After reaching a maximum of stretching, the chains relax back to an asymptotic value at vanishing screening, which depends on pH. For rather poor solvents, at large screening lengths, the chains collapse into an almost uncharged globule provided that high ionization is not pinned by a large chemical potential of the charges.
Using (semi-)grand canonical Monte Carlo simulations of a polyelectrolyte chain of length N where... more Using (semi-)grand canonical Monte Carlo simulations of a polyelectrolyte chain of length N where the charges are in contact with a reservoir of constant chemical potential µ given by the solution pH, we study the behavior of annealed polyelectrolytes in a poor solvent. We focus on the conformational properties in the close-to-Θ-point regime τ < τ* ∼ N -1/5 u -3/5 , which can be reached either by reducing electrostatic interaction strength u ) λ B /b or by improving solvent quality, i.e., by reducing τ ) (Θ -T)/Θ. We investigate the conformations with regard to parameters u, τ, and µ and explore in which conditions pearl-necklace-like structures are stable. Most of the pearl-necklace parameters are found to obey the scaling relations predicted for quenched polyelectrolytes. However, similarly to the behavior known for this class of polyelectrolytes, we obtain large fluctuations in pearl number and size. In agreement with theoretical predictions we find a nonuniform charge distribution between pearls and strings. For τ , 1 and moderate interaction strength we demonstrate that a cascade of pearl-necklace transitions can be initiated by changing µ, i.e., by tuning the solution pH.
Using Monte Carlo simulations, the cascade transition of a single polyelectrolyte chain having pe... more Using Monte Carlo simulations, the cascade transition of a single polyelectrolyte chain having permuted charge distribution is investigated. The polyelectrolyte chain is simulated at various solvent regimes. The effect of the electrostatic interaction strength is studied. The structures are analyzed with respect to the scaling laws. The effect of permuted charge distribution is investigated in comparison to the other charge distribution in the literature.
Fundamentals, Methods and Applications, 2012
Using molecular dynamics, we study the selfassembly of phenylalanine with charged end-groups at v... more Using molecular dynamics, we study the selfassembly of phenylalanine with charged end-groups at various temperatures and concentrations. As in the case of diphenylalanine, we observe the formation of nanotubes; however, phenylalanine aggregates in layers of four, not six, molecules. The observed aggregates are consistent with recent experimental measurements of fibrils obtained from mice with phenylketonuria. We investigate the stability and the mechanism by which these tubular structures form and discuss potential toxicity mechanisms.