Modulated Wave Packets in DNA and Impact of Viscosity

We study the nonlinear dynamics of a DNA molecular system at physiological temperature in a viscous media by using the Peyrard-Bishop model. The nonlinear dynamics of the above system is shown to be governed by the discrete complex Cinzburg-Landau equation. In the non-viscous limit, the equation reduces to the nonlinear Schroedinger equation. Modulational instability criteria are derived for both the cases. On the basis of these criteria, numerical simulations are made, which confirm the analytical predictions. The planar wave solution used as the initial condition makes localized oscillations of base pairs and causes energy localization. The results also show that the viscosity of the solvent in the surrounding damps out the amplitude of wave patterns.     

Long-range interactions and wave patterns in a DNA model

The three-dimensional structures of elastin-like polypeptides Val1-Pro2-Gly3-Xaa4-Gly5 were investigated by using the multicanonical Monte Carlo (MC) simulation procedure. By substituting different amino acids in the fourth position of the sequence, the thermodynamical variables are calculated in vacuo and in solvent to determine the hydrophobicity dependence of the conformational transition temperatures of the peptides. Resultant hydrophobicity scale is in good agreement with many hydrophobicity scales.     

Heavy ion–acoustic rogue waves in magnetized electron–positron multi-ion plasmas

Non-linear heavy ion-acoustic waves (HIAWs) are studied in a homogeneous magnetized four-component multi-ion plasma composed of inertial heavy negative ions, light positive ions, and inertia-less non-extensive electrons and positrons. The non-linear Schrödinger equation is derived in this model using the perturbation method. The criteria for modulational instability of HIAWs and the basic features of finite-amplitude heavy ion acoustic rogue waves (HIARWs) are investigated. The presence of the magnetic field was found to reduce the amplitude of HIARWs and enhances the stability. It is interesting to note that increasing positive ion mass causes decreases in the amplitude and width of rogue waves, which is opposite behaviour to that demonstrated in the previous study of these waves in an unmagnetized plasma. Furthermore, it is also shown that striking parameters, such as the non-extensive parameter, the positron number density, the electron number density, the electron temperature, and the magnetic field parameter, play an undeniable role on the stability of waves packets. The findings of the present investigation may be of wide relevance to some plasma environments, such as active galactic nuclei, pulsar magnetospheres, and other magnetic confinement systems.     

Synthesis of N-morpholine or N,N-diethyl, N′-monosubstituted benzoyl thiourea copper complexes: characterization and electrochemical investigations

A series of N-morpholine or N,N-diethyl, N′-substituted benzoyl thioureas (R = Cl, Br, OMe or NO₂ in ortho, meta or para position) have been synthesized by condensation of morpholine or diethylamine with substituted benzoyl isothiocyanates. All CuL₂ complexes have been characterized. Cyclic voltammetry has shown that the irreversible process copper(II)/copper(I) redox systems are influenced slightly by the substitution, whereas the quasi-reversible copper(III)/copper(II) redox systems are not.     

Synthesis,characterization and X-ray crystal structures of two non-molecular coordination polymers of manganese(II) and copper(II) with <Emphasis Type="Italic">N</Emphasis>-(2-pyridylmethyl)-<Emphasis Type="SmallCaps">l</Emphasis>-alanine and isothiocyanato ligands

The reduced Schiff base, N-(2-pyridylmethyl)-l-alanine (Pyala), has been prepared and used as a ligand for the synthesis of two new non-centrosymmetrical isothiocyanate mixed-ligand coordination polymers, [MnPyalaSCN] _n and [CuPyalaSCN] _n . Pyala and the metal complexes were characterized by physico-chemical and spectroscopic methods. The single-crystal X-ray structures of the complexes reveal both compounds to be non-molecular coordination polymers which crystallize in the orthorhombic system. The ligand acts as a bridge between two metal centres in both compounds, forming two six-membered rings around each Mn atom and two five-membered rings around each Cu centre. The 1D chains are assembled via N–H?O, N–H?S hydrogen bonds and S–S interactions building 3D helical supramolecular networks in both compounds. Packing of the polymers of both compounds along the b-axis gives chiral channels.     

Stability of matter–wave soliton in a time-dependent complicated trap

We examine the possibility to generate localized structures in effectively one-dimensional Gross–Pitaevskii with a time-dependent scattering length and a complicated potential. Through analytical methods invoking a generalized lens-type transformation and the Darboux transformation, we present the integrable condition for the Gross–Pitaevskii equation and obtain the exact analytical solution which describes the modulational instability and the propagation of bright solitary waves on a continuous wave background. The dynamics and stability of this solution are analyzed. Moreover, by employing the extended tanh-function method we obtain the exact analytical solutions which describes the propagation of dark and other families of solitary waves.     

Modulational instability in the anharmonic Peyrard-Bishop model of DNA

We report on the presence of modulational instability and the generation of soliton-like excitations in DNA nucleotides. Taking the Peyrard-Bishop-Dauxois model of DNA dynamics as an example, we show that the original difference equation for the DNA dynamics can be reduced to the Salerno equation. We derive the MI criterion in this case. The effect of the anharmonic stacking term on the domain of instability/stability is pointed out. Numerical simulations show the validity of the analytical approach with the generation of wave packets provided that the wave numbers fall in the instability domain. The impact of the anharmonic stacking interactions is investigated and these are found to give rise to a spectrum of behaviours which corroborates experimental facts.     

Internal path investigation of the acting electrons during the photocatalysis of panchromatic ruthenium dyes in dye-sensitized solar cells

A series of heteroleptic Ru(II) complexes were theoretically investigated using time-dependent density functional theory. These dyes, including K8 and N3, are based on a common motif formed by Ru center, NCS, and polypyridyl ligands, but differ only by the nature of the added group in para position of each pyridyl. The presence of these ligands will enable the evaluation of the electronic effects ±I and ±M. This work focuses on the localization of the part, among the metal, the NCS, the polypyridyl ligands, and the added group R, which is most actively involved in the photocatalysis process. We dealt with both ground and excited states as well as the electronic transitions between them. To illustrate the effect of each functional group R on its photophysical properties, the geometries of five dyes were optimized in the molecular and univalent cationic states. All molecules are asymmetrical in shape with a distorted octahedral coordination of the RuN6 core. Atomic charge and spin density distributions show that a charge transfer process occurs from the NCS/Ru to polypyridyl ligand. Analysis of the electronic absorption spectra reveals that the band with the highest wavelength value is assigned to metal-to-ligand charge transfer transition. On the contrary, two other bands are assigned to multitransitions Ru/NCS to polypyridyl–π*. These attributions have been confirmed by the localization of all atoms intervening in them. We also introduced an adapted way to estimate the ionization probability values in each atomic center in the ground and first excited states. Phenomenal properties such as mobility, redox potential, electronic spectrum, ionization potential, and optical gap of the most efficient dye, which is the N3, fit well with experimental values.     

Two-dimensional third- and fifth-order nonlinear evolution equations for shallow water waves with surface tension

Nonlinear Dynamics - We derive two new two-dimensional third- and fifth-order nonlinear evolution equations that model a unidirectional wave motion in shallow water waves with surface tension....     

Matter-wave solutions of Bose—Einstein condensates with three-body interaction in linear magnetic and time-dependent laser fields

We construct, through a further extension of the tanh-function method, the matter-wave solutions of Bose-Einstein condensates (BECs) with a three-body interaction. The BECs are trapped in a potential comprising the linear magnetic and the time-dependent laser fields. The exact solutions obtained include soliton solutions, such as kink and antikink as well as bright, dark, multisolitonic modulated waves. We realize that the motion and the shape of the solitary wave can be manipulated by controlling the strengths of the fields.