The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. W... more The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. We employ exact expressions for classical harmonic oscillators by considering the unnormalized constraints. As q→1, we show that these approximations agree with the result of Gaussian network model.
This work presents our study on the atomic, electronic, magnetic structures, and phonon modes of ... more This work presents our study on the atomic, electronic, magnetic structures, and phonon modes of the low-temperature orthorhombic phase of undoped BaFe2As2 crystal. The electronic structure is characterized by a sharp Fe-3d peak close to the Fermi level and is dominated by Fe-3d- and As-4p-hybridized states. Ba contribution occurs only at lower energies. The spin ordering of the magnetic ground state, which is determined by minimizing the total energy of different spin alignments on Fe atoms in the conventional cell, is in agreement with experimental findings but is different from the antiferromagnetic spin ordering obtained by assigning antiparallel spin directions on two Fe atoms in the primitive unit cell. Valuable information about the charge transfer and bonding is revealed through the analysis of the charge density. Electrons are transferred from Ba to Fe-As layers and also from Fe to As atoms. The magnetic phonon calculations of the ground state are carried out to predict Raman and infrared-active modes. Softening of some calculated spin-dependent phonon modes corroborates the contribution of spin-lattice coupling to the structural phase transition from I4/mmm to Fmmm.
We have investigated the structure of cyclohexene-2-ethanamine molecule both theoretically and ex... more We have investigated the structure of cyclohexene-2-ethanamine molecule both theoretically and experimantally. Theoretical investigation is based on a first principle technique Density Functional Theory (DFT) using plane wave basis sets and ultrasoft pseudo-potentials while the experimental technique is infrared (IR) spectroscopy. Exchange-correlation potential of DFT was approximated in the frame of both local density approximation (LDA) and generalized gradient approximation (GGA) schemes. Vibrational properties of this molecule are given by the assignments in the range for wavenumber 4000-400 $cm^{-1}$. Stable equilibrium structure of the molecule was also obtained by using LDA and GGA. Obtained optimized geometrical structure was used to calculate vibrational properties and STM images. A remarkable agreement was obtained between theory and experiment, especially in the symmetric and asymmetric vibrations of NH groups.
Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investig... more Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investigated. The joint entropy so called Leipnik's entropy is calculated by using time dependent wave function obtained by the Feynman path integral method. It is shown that, Leipnik's entropy fluctuates with time. However in constant mass and time dependent frequency case, entropy increases monotonically with time.
Time dependent entropy of constant force motion is investigated. Their joint entropy so called Le... more Time dependent entropy of constant force motion is investigated. Their joint entropy so called Leipnik's entropy is obtained. The main purpose of this work is to calculate Leipnik's entropy by using time dependent wave function which is obtained by the Feynman path integral method. It is found that, in this case, the Leipnik's entropy increase with time and this result
The time dependent entropy (or Leipnik's entropy) of harmonic and damped harmonic oscillators... more The time dependent entropy (or Leipnik's entropy) of harmonic and damped harmonic oscillators is extensively investigated by using time dependent wave function obtained by the Feynman path integral method. Our results for simple harmonic oscillator are in agrement with the literature. However, the joint entropy of damped harmonic oscillator shows remarkable discontinuity with time for certain values of damping factor.
Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investig... more Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investigated. The joint entropy so called Leipnik's entropy is calculated by using time dependent wave function obtained by the Feynman path integral method. It is shown that, Leipnik's entropy fluctuates with time. However in constant mass and time dependent frequency case, entropy increases monotonically with time.
This paper presents our comparative study on atomic, electronic, magnetic and phonon properties o... more This paper presents our comparative study on atomic, electronic, magnetic and phonon properties of three, two and one dimensional honeycomb structures of molybdenum disulfide (MoS$_2$) using first-principles plane wave method. The cohesion and interlayer interactions in graphitic MoS$_{2}$ are analyzed. Two dimensional, single layer MoS$_2$, which consists of a positively charged molybdenum atomic plane between two negatively charged sulfur atomic
We present our study on the adsorption of C, Si and Ge adatoms on binary compound germanium carbi... more We present our study on the adsorption of C, Si and Ge adatoms on binary compound germanium carbide (GeC) honeycomb structure based on density functional theory using the generalized gradient approximation. We found that C atom is bound at bridge site, while Si and Ge prefer to adsorb to top site above the top of carbon. The electronic and magnetic properties of GeC can be modified by the adsorption of these adatoms. Nonmagnetic semiconductor GeC is either metal or narrow band gap semiconductor depending on the adatoms coverage. One of the reason of this effect is the bonding combination of adatom-p and GeC-sp 2 orbitals. All the adatom adsorptions on GeC have zero net magnetic moment, except Ge adsorption at low coverage, which has a net magnetic moment of = 2.0 B per cell. Our results also indicate that because of the charge transfer, the adsorption of C and Si/Ge on a GeC surface allow us to obtain pand n-type doping, respectively. Therefore, adatom covered GeC can serve as an interesting alternative for the nanodevice applications.
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a sim... more We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method samples the whole rugged energy landscape, in particular the low-energy part, and enables one to better understand the critical behaviors and visualize the folding pathways of the considered protein model.
ABSTRACT The adsorption of alanine dipeptide on a Si(100)-2 × 1 asymmetric surface is studied by ... more ABSTRACT The adsorption of alanine dipeptide on a Si(100)-2 × 1 asymmetric surface is studied by using pseudopotential plane wave approach based on Density Functional Theory (DFT). Adsorption energies for different surface sites of various conformations are calculated and the groove site is found to be energetically most favorable. We observed that the molecule-surface interactions might modify surface reconstruction: asymmetric surface dimers reconstruct to asymmetric dimers in opposite directions doubling the surface periodicity, which in turn gives the surface metallic properties.
Using first-principles plane wave calculations we predict that electronic and magnetic properties... more Using first-principles plane wave calculations we predict that electronic and magnetic properties of graphene nanoribbons can be affected by defect-induced itinerant states. The band gaps of armchair nanoribbons can be modified by hydrogen saturated holes. Defects due to periodically repeating vacancy or divacancies induce metallization, as well as magnetization in non-magnetic semiconducting nanoribbons due to the spin-polarization of local defect states. Antiferromagnetic ground state of semiconducting zigzag ribbons can change to ferrimagnetic state upon creation of vacancy defects, which reconstruct and interact with edge states. Even more remarkable is that all these effects of vacancy defects are found to depend on their geometry and position relative to edges. It is shown that these effects can, in fact, be realized without really creating defects
This paper presents a systematic study of two and one dimensional honeycomb structure of boron ni... more This paper presents a systematic study of two and one dimensional honeycomb structure of boron nitride (BN) using first-principles plane wave method. Two-dimensional (2D) graphene like BN is a wide band gap semiconductor with ionic bonding. Phonon dispersion curves demonstrate the stability of 2D BN flakes. Quasi 1D armchair BN nanoribbon are nonmagnetic semiconductors with edge states. Upon passivation of B and N with hydrogen atoms these edge states disappear and band gap increases. Bare zigzag BN nanoribbons are metallic, but become a ferromagnetic semiconductor when their both edges are passivated with hydrogen. However, their magnetic ground state, electronic band structure and band gap are found to be strongly dependent on whether B-or Nedge of the ribbon is saturated with hydrogen. Vacancy defects in armchair and zigzag nanoribbons affects also magnetic state and electronic structure. In order to reveal dimensionality effects these properties are contrasted with those of various 3D BN crystals and 1D BN atomic chain.
Using first-principles plane-wave calculations we predict that electronic and magnetic properties... more Using first-principles plane-wave calculations we predict that electronic and magnetic properties of graphene nanoribbons can be modified by the defect-induced itinerant states. Structure optimization gives rise to significant reconstruction of atomic structure, which is in good agreement with transmission electron microscope images. The band gaps of armchair nanoribbons can be modified by hydrogen-saturated holes. The band-gap changes depend on the width of the ribbon as well as on the position of the hole relative to the edges of the ribbon. Defects due to periodically repeating vacancy or divacancies induce metallization as well as magnetization in nonmagnetic semiconducting nanoribbons due to the spin polarization of local defect states. Antiferromagnetic ground state of semiconducting zigzag ribbons can change to ferrimagnetic state upon creation of vacancy defects, which reconstruct and interact with edge states. Even more remarkable is that all these effects of vacancy defects are found to depend on their geometry and position relative to the edges. It is shown that these effects can, in fact, be realized without really creating defects.
Using first-principles density functional theory calculations, we have investigated the structura... more Using first-principles density functional theory calculations, we have investigated the structural, electronic and magnetic properties of monolayer boron-nitride (BN) honeycomb structure which is functionalized by adatom adsorption and by substituting B and N atoms with foreign atom. We considered low and high density coverage of foreign atoms. Generally most of 3d transition metal atoms, some of group 4A, 5A, and
The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. W... more The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. We employ exact expressions for classical harmonic oscillators by considering the unnormalized constraints. As q→1, we show that these approximations agree with the result of Gaussian network model.
This work presents our study on the atomic, electronic, magnetic structures, and phonon modes of ... more This work presents our study on the atomic, electronic, magnetic structures, and phonon modes of the low-temperature orthorhombic phase of undoped BaFe2As2 crystal. The electronic structure is characterized by a sharp Fe-3d peak close to the Fermi level and is dominated by Fe-3d- and As-4p-hybridized states. Ba contribution occurs only at lower energies. The spin ordering of the magnetic ground state, which is determined by minimizing the total energy of different spin alignments on Fe atoms in the conventional cell, is in agreement with experimental findings but is different from the antiferromagnetic spin ordering obtained by assigning antiparallel spin directions on two Fe atoms in the primitive unit cell. Valuable information about the charge transfer and bonding is revealed through the analysis of the charge density. Electrons are transferred from Ba to Fe-As layers and also from Fe to As atoms. The magnetic phonon calculations of the ground state are carried out to predict Raman and infrared-active modes. Softening of some calculated spin-dependent phonon modes corroborates the contribution of spin-lattice coupling to the structural phase transition from I4/mmm to Fmmm.
We have investigated the structure of cyclohexene-2-ethanamine molecule both theoretically and ex... more We have investigated the structure of cyclohexene-2-ethanamine molecule both theoretically and experimantally. Theoretical investigation is based on a first principle technique Density Functional Theory (DFT) using plane wave basis sets and ultrasoft pseudo-potentials while the experimental technique is infrared (IR) spectroscopy. Exchange-correlation potential of DFT was approximated in the frame of both local density approximation (LDA) and generalized gradient approximation (GGA) schemes. Vibrational properties of this molecule are given by the assignments in the range for wavenumber 4000-400 $cm^{-1}$. Stable equilibrium structure of the molecule was also obtained by using LDA and GGA. Obtained optimized geometrical structure was used to calculate vibrational properties and STM images. A remarkable agreement was obtained between theory and experiment, especially in the symmetric and asymmetric vibrations of NH groups.
Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investig... more Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investigated. The joint entropy so called Leipnik's entropy is calculated by using time dependent wave function obtained by the Feynman path integral method. It is shown that, Leipnik's entropy fluctuates with time. However in constant mass and time dependent frequency case, entropy increases monotonically with time.
Time dependent entropy of constant force motion is investigated. Their joint entropy so called Le... more Time dependent entropy of constant force motion is investigated. Their joint entropy so called Leipnik's entropy is obtained. The main purpose of this work is to calculate Leipnik's entropy by using time dependent wave function which is obtained by the Feynman path integral method. It is found that, in this case, the Leipnik's entropy increase with time and this result
The time dependent entropy (or Leipnik's entropy) of harmonic and damped harmonic oscillators... more The time dependent entropy (or Leipnik's entropy) of harmonic and damped harmonic oscillators is extensively investigated by using time dependent wave function obtained by the Feynman path integral method. Our results for simple harmonic oscillator are in agrement with the literature. However, the joint entropy of damped harmonic oscillator shows remarkable discontinuity with time for certain values of damping factor.
Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investig... more Time dependent entropy of harmonic oscillator with time dependent mass and frequency are investigated. The joint entropy so called Leipnik's entropy is calculated by using time dependent wave function obtained by the Feynman path integral method. It is shown that, Leipnik's entropy fluctuates with time. However in constant mass and time dependent frequency case, entropy increases monotonically with time.
This paper presents our comparative study on atomic, electronic, magnetic and phonon properties o... more This paper presents our comparative study on atomic, electronic, magnetic and phonon properties of three, two and one dimensional honeycomb structures of molybdenum disulfide (MoS$_2$) using first-principles plane wave method. The cohesion and interlayer interactions in graphitic MoS$_{2}$ are analyzed. Two dimensional, single layer MoS$_2$, which consists of a positively charged molybdenum atomic plane between two negatively charged sulfur atomic
We present our study on the adsorption of C, Si and Ge adatoms on binary compound germanium carbi... more We present our study on the adsorption of C, Si and Ge adatoms on binary compound germanium carbide (GeC) honeycomb structure based on density functional theory using the generalized gradient approximation. We found that C atom is bound at bridge site, while Si and Ge prefer to adsorb to top site above the top of carbon. The electronic and magnetic properties of GeC can be modified by the adsorption of these adatoms. Nonmagnetic semiconductor GeC is either metal or narrow band gap semiconductor depending on the adatoms coverage. One of the reason of this effect is the bonding combination of adatom-p and GeC-sp 2 orbitals. All the adatom adsorptions on GeC have zero net magnetic moment, except Ge adsorption at low coverage, which has a net magnetic moment of = 2.0 B per cell. Our results also indicate that because of the charge transfer, the adsorption of C and Si/Ge on a GeC surface allow us to obtain pand n-type doping, respectively. Therefore, adatom covered GeC can serve as an interesting alternative for the nanodevice applications.
We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a sim... more We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method samples the whole rugged energy landscape, in particular the low-energy part, and enables one to better understand the critical behaviors and visualize the folding pathways of the considered protein model.
ABSTRACT The adsorption of alanine dipeptide on a Si(100)-2 × 1 asymmetric surface is studied by ... more ABSTRACT The adsorption of alanine dipeptide on a Si(100)-2 × 1 asymmetric surface is studied by using pseudopotential plane wave approach based on Density Functional Theory (DFT). Adsorption energies for different surface sites of various conformations are calculated and the groove site is found to be energetically most favorable. We observed that the molecule-surface interactions might modify surface reconstruction: asymmetric surface dimers reconstruct to asymmetric dimers in opposite directions doubling the surface periodicity, which in turn gives the surface metallic properties.
Using first-principles plane wave calculations we predict that electronic and magnetic properties... more Using first-principles plane wave calculations we predict that electronic and magnetic properties of graphene nanoribbons can be affected by defect-induced itinerant states. The band gaps of armchair nanoribbons can be modified by hydrogen saturated holes. Defects due to periodically repeating vacancy or divacancies induce metallization, as well as magnetization in non-magnetic semiconducting nanoribbons due to the spin-polarization of local defect states. Antiferromagnetic ground state of semiconducting zigzag ribbons can change to ferrimagnetic state upon creation of vacancy defects, which reconstruct and interact with edge states. Even more remarkable is that all these effects of vacancy defects are found to depend on their geometry and position relative to edges. It is shown that these effects can, in fact, be realized without really creating defects
This paper presents a systematic study of two and one dimensional honeycomb structure of boron ni... more This paper presents a systematic study of two and one dimensional honeycomb structure of boron nitride (BN) using first-principles plane wave method. Two-dimensional (2D) graphene like BN is a wide band gap semiconductor with ionic bonding. Phonon dispersion curves demonstrate the stability of 2D BN flakes. Quasi 1D armchair BN nanoribbon are nonmagnetic semiconductors with edge states. Upon passivation of B and N with hydrogen atoms these edge states disappear and band gap increases. Bare zigzag BN nanoribbons are metallic, but become a ferromagnetic semiconductor when their both edges are passivated with hydrogen. However, their magnetic ground state, electronic band structure and band gap are found to be strongly dependent on whether B-or Nedge of the ribbon is saturated with hydrogen. Vacancy defects in armchair and zigzag nanoribbons affects also magnetic state and electronic structure. In order to reveal dimensionality effects these properties are contrasted with those of various 3D BN crystals and 1D BN atomic chain.
Using first-principles plane-wave calculations we predict that electronic and magnetic properties... more Using first-principles plane-wave calculations we predict that electronic and magnetic properties of graphene nanoribbons can be modified by the defect-induced itinerant states. Structure optimization gives rise to significant reconstruction of atomic structure, which is in good agreement with transmission electron microscope images. The band gaps of armchair nanoribbons can be modified by hydrogen-saturated holes. The band-gap changes depend on the width of the ribbon as well as on the position of the hole relative to the edges of the ribbon. Defects due to periodically repeating vacancy or divacancies induce metallization as well as magnetization in nonmagnetic semiconducting nanoribbons due to the spin polarization of local defect states. Antiferromagnetic ground state of semiconducting zigzag ribbons can change to ferrimagnetic state upon creation of vacancy defects, which reconstruct and interact with edge states. Even more remarkable is that all these effects of vacancy defects are found to depend on their geometry and position relative to the edges. It is shown that these effects can, in fact, be realized without really creating defects.
Using first-principles density functional theory calculations, we have investigated the structura... more Using first-principles density functional theory calculations, we have investigated the structural, electronic and magnetic properties of monolayer boron-nitride (BN) honeycomb structure which is functionalized by adatom adsorption and by substituting B and N atoms with foreign atom. We considered low and high density coverage of foreign atoms. Generally most of 3d transition metal atoms, some of group 4A, 5A, and
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