Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach

Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.     

Spin-correlation function of the fully frustrated Ising model and ± J Ising spin glass on the square lattice

In this work we study the correlation function of the ground state of two-dimensional fully frustrated Ising model as well as spin glass. The Pfaffian method is used to calculate free energy and entropy as well as correlation function. We estimate the exponent of spin correlation function for fully frustrated model and spin glass. In this paper an overview of the latest results on the spin correlation function is presented.     

Impact of composition ratio on the structure and optical properties of (1-x)MnFe2O4/(x)ZnMn2O4 nanocomposite

($1-x$)MnFe$_{2}$O$_{4}$ (MFO)/$x$ZnMn$_{2}$O$_{4}$ (ZMO) ($x=0$, 0.2, 0.5, 0.8, and 1.0) nanocomposite samples were prepared using co-precipitation procedure. The phase percentage, cell parameters, and crystallite size of MFO and ZMO phases in each nanocomposite sample were calculated using Rietveld refinement procedure. The x-ray diffraction (XRD) analysis and Fourier-transform infrared spectroscopy techniques established the variation in the lattice parameters of each phase are due to permutation of all cations among the octahedral and tetrahedral sites of MFO and ZMO. The different oxidation states of different ions in all samples were determined using x-ray photoelectron spectroscopy (XPS) technique. The variation in absorbance of the nanocomposite samples with composition parameter ($x$) is dependent on the wavelength region. The optical bandgap of the nanocomposite samples is decreased as the content of ZMO phase increased. The effect of alloying on the refractive index, extinction coefficient, dielectric constant, optical conductivity, and the nonlinear optical behaviors of all samples were studied in detail. The nanocomposite sample $x=0.5$ disclosed upgraded optical parameters with the highest refractive index, optical conductivity, and PL intensity, which nominate it to be functional in various application fields.     

Host–guest system of etodolac in native and modified β-cyclodextrins: preparation and physicochemical characterization

Etodolac, being a practically insoluble candidate, exhibits certain toxic effects and a limited bioavailability. Upon chronic use, it causes gastro-intestinal injury and increases the risk of ulcer complications. The approach of this study was to improve the physicochemical properties of the drug utilizing complexation phenomenon with β-, methyl-β- and hydroxypropyl-β-cyclodextrins, which may enhance the aqueous solubility and dissolution rate of etodolac, in an effort to increase oral bioavailability. In certain instances, this approach can be used to increase drug solubility, improve organoleptic properties and maximize the gastrointestinal tolerance by reducing drug irritation after oral administration. Differential UV measurements as well as continuous variation plots revealed the formation of equimolar complex with hydroxypropyl-β-cyclodextrin and 1:2 complexes with β-cyclodextrin and its methyl derivative. Differential scanning calorimetry (DSC), X-ray and FT-IR measurements were applied to prove inclusion complex formation and characterize the complexes. These results lend support to the idea that solubilization of etodolac is mainly related to inclusion complex formation and to a lesser extent to cyclodextrin aggregates. Understanding the factors that influence the performance of etodolac, will allow us to state that molecular encapsulation of the drug and other modifications with appropriate hydroxylation or methylation of parent β-cyclodextrin is able to overcome its problems and facilitate safe and efficient delivery of the drug.     

Phase-controlled atom-photon entanglement in a three-level Λ-type closed-loop atomic system

We study the entanglement of dressed atom and its spontaneous emission in a three-level Λ-type closed-loop atomic system in a multi-photon resonance condition and beyond it.It is shown that the von Neumann entropy in such a system is phase-dependent,and it can be controlled by either the intensity or relative phase of applied fields.It is demonstrated that for the special case of the Rabi frequency of applied fields,the system is disentangled.In addition,we take into account the effect of Doppler broadening on the entanglement and it is found that a suitable choice of laser propagation direction allows us to obtain the steady state degree of entanglement(DEM) even in the presence of the Doppler effect.     

Critical properties of mixed spin-1 and spin-5/2 with equal and unequal crystal fields

The effects of assuming equal or unequal crystal fields (CF) on the phase diagrams of a mixed spin-1 and spin-5/2 system are investigated in terms of the recursion relations on the Bethe lattice (BL). The equal CF case was considered for the coordination numbers q=3, 4, and 6, while for q=3 the unequal CF case was also studied. It was found that for the equal CF case, the model exhibits second-order phase transitions and two compensation temperatures for all q, the reentrant behavior for q=4 and first-order phase transitions and tricritical point (TCP) for q=6. In the unequal CF case for q=3, the system yields first- and second-order phase transitions, TCP's, and three compensation temperatures. In addition, the TCP's in a very short range are classified as the stable and unstable ones depending on their free energies.     

Synthesis of 1-aryl-substituted-4-chloroimidazo[1,2-a]quinoxalines catalyzed by PdCl2 in water

The reaction of 2-chloro-3-propargylaminoquinoxaline with various aryl iodides and bromides catalyzed by Pd–Cu in the presence of potassium carbonate as the base in water leads to the one-pot formation of 1-aryl-substituted-4-chloroimidazo[1,2-a]quinoxalines in moderate-to-high yields.     

Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3

The molecular interactions between phosphorous ylide (PY) and HX molecules (X?=?F, CN, and N₃) were investigated using the MP2 method at 6-311++G(2d,2p) basis set. Three different patterns including non-classical hydrogen bond H···C, X···P interaction and classical hydrogen bond H···X were found for complex formation between PY and HX molecules. From the predicted models, stability of the H···C type complexes are greater than other types. Quantum theories of atoms in molecules and natural bond orbitals methods have been applied to analyze the intermolecular interactions. Good correlations have been found between the interaction energies (SE), the second-order perturbation energy E ⁽²⁾, and the charge transfer qCT in the studied systems.