In silico Complexes of Amino Acids and Diamondoids

We report on the specific interaction of a small diamond-like molecule, known as diamondoid, with single amino-acids forming nano/bio molecular complexes. Using time-dependent density-functional theory calculations we have studied two different relative configurations of three prototypical amino acids, phenylalanine, tyrosine, and tryptophan, with the diamondoid. The optical and charge-transfer properties of these complexes exhibit amino acid and topology specific features which can be directly utilized for in the direction of novel biomolecule detection schemes.     

Analysis of U87 glioma cells by dielectrophoresis

Glioblastoma multiforme is the most aggressive and invasive brain cancer consisting of genetically and phenotypically altering glial cells. It has massive heterogeneity due to its highly complex and dynamic microenvironment. Here, electrophysiological properties of U87 human glioma cell line were measured based on a dielectrophoresis phenomenon to quantify the population heterogeneity of glioma cells. Dielectrophoretic forces were generated using a gold-microelectrode array within a microfluidic channel when 3 V_pp and 100, 200, 300, 400, 500 kHz, 1, 2, 5, and 10 MHz frequencies were applied. We analyzed the dielectrophoretic behavior of 500 glioma cells, and revealed that the crossover frequency of glioma cells was around 140 kHz. A quantifying dielectrophoretic movement of the glioma cells exhibited three distinct glioma subpopulations: 50% of the glioma cells experienced strong, 30% of the cells were spread in the microchannel by moderate, and the rest of the cells experienced very weak positive dielectrophoretic forces. Our results demonstrated the dielectrophoretic spectra of U87 glioma cell line. Dielectrophoretic responses of glioma cells linked population heterogeneity to membrane properties of glioma cells rather than their size distribution in the population.     

Backward substitution method based on Müntz polynomials for solving the nonlinear space fractional partial differential equations

A computational technique based on the Müntz polynomials and meshless method has been presented for the solution of nonlinear and linear space fractional partial differential equations (PDEs). The meshless method that is used in this study is the new version of backward substitution method (BSM). First, the time-derivative term is discretized by the Crank-Nicolson method. Then, the approximate solution is given as the separation of the approximation of the boundary data and the correcting functions using the Müntz polynomials. In general form, this approximate solution that does not necessarily satisfy the original equation is shown as the sum of the system basics in which it consists free parameters. Finally, these parameters are determined by the BSM method inside the domain. The main advantage of the method is efficiency and reliability that is examined by six numerical experiments.     

New porphyrins: synthesis,characterization, and computational studies

Molecular Diversity - New trans-A2B2-porphyrins substituted at phenyl positions were synthesized from 4-methylphthalic acid as a starting material through sequential multistep reactions. These...     

Presentation of a new index for estimation of aromaticity in halo‐ and cyanobenzenes: The role of potential energy in aromaticity

A linear correlation has been obtained between average values of Hamiltonian kinetic energy ( ) and potential energy ( ) calculated at the bond critical points using atoms in molecules method. This relation was used to introduce a new index ( ) for estimation of aromaticity in halo‐ and cyanobenzenes. Potential energy has different terms such as attraction between nuclei and electrons, also repulsion of electrons which affect the inertia and mobility of electrons, respectively. Therefore, contribution of potential energy in this relation must be controlled. Contribution of potential energy in aromaticity has been managed using a fitting parameter. This parameter was obtained by fitting the aromaticity stabilization energy data with values of aromaticity calculated by index for halo‐ and cyanobenzenes. The contribution of potential energy in index is complete when molecule is nonaromatic and is negligible when molecule is antiaromatic. Indeed, molecule is aromatic when contribution of potential energy in index lies between above limits. © 2013 Wiley Periodicals, Inc.     

Measurement of the thermal conductivity of MWCNT-CuO/water hybrid nanofluid using artificial neural networks (ANNs)

Journal of Thermal Analysis and Calorimetry - In this paper, artificial neural networks (ANNs) are developed to predict the thermal conductivity ( $$k_{\text{nf}}$$ ) of multi-walled carbon...     

Efficient “On‐the‐Fly” calculation of Raman Spectra from Ab‐Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second‐generation Car‐Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed‐up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite‐temperature Raman spectra “on‐the‐fly” by means of ab‐initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.