Effects of ELF Magnetic Field in Combination with Iron(III) Chloride (FeCl3) on Cellular Growth and Surface Morphology of Escherichia coli (E. coli)

This study investigated the effects of extremely low frequency (ELF) magnetic field with/without iron(III) chloride (FeCl₃) on bacterial growth and morphology. The ELF exposures were carried out using a pair of Helmholtz coil-based ELF exposure system which was designed to generate 50 Hz sinusoidal magnetic field. The field was approximately uniform throughout the axis of the coil pair. The samples which were treated or non-treated with different concentrations FeCl₃ were exposed to 50 Hz, 2 millitesla (mT) magnetic field for 24 h. ELF effect on viability was assessed in terms of viable colony counts (in colony-forming unit per milliliter) with the standard plate count technique. Scanning electron microscopy was used to investigate the magnetic field effect on surface morphology of Escherichia coli. No significant results were seen in terms of cell viability between ELF and sham-exposed bacterial strains. Similarly, FeCl₃ treatment did not change cell viability of E. coli samples. However, we observed some morphological changes on E. coli cell surfaces. Pore formations and membrane destruction were seen on the surface of 24 h ELF field-exposed cells. We concluded that ELF magnetic field exposure at 2 mT does not affect cell viability; however, it may affect bacterial surface morphology.     

Relationships between unfolded configurations of proteins and dynamics of folding to the native state

We compare folding trajectories of chymotrypsin inhibitor (CI2) using a dynamic Monte Carlo scheme with Go-type potentials. The model considers the four backbone atoms of each residue and a sphere centered around C^β the diameter of which is chosen according to the type of the side group. Bond lengths and bond angles are kept fixed. Folding trajectories are obtained by giving random increments to the φ and ψ torsion angles with some bias toward the native state. Excluded volume effects are considered. Two sets of 20 trajectories are obtained, with different initial configurations. The first set is generated from random initial configurations. The initial configurations of the second set are generated according to knowledge-based neighbor dependent torsion probabilities derived from triplets in the Protein Data Bank. Compared to chains with randomly generated initial configurations, those generated with neighbor-dependent probabilities (i) fold faster, (ii) have better defined secondary structure elements, and (iii) have less number of non-native contacts during folding. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3667–3678, 2006     

Aurones: Small Molecule Visible Range Fluorescent Probes Suitable for Biomacromolecules

Aurones, derivatives of 2-benylidenebenzofuran-3(2H)-one, are natural products that serve as plant pigments. There have been reports that some of these substances fluoresce, but little information about their optical properties is in the literature. In this report, series of aurone derivatives were synthesized as possible fluorescent probes that can be excited by visible light. We found that an amine substituent shifted the lowest energy absorption band from the near-UV to the visible region of the electromagnetic spectrum. Four amine-substituted aurone derivatives were synthesized to explore the effect of this substituent on the absorption and emission properties of the aurone chromophore. The emission maxima and intensities of the molecules are strongly dependent on the nature of the substituent and the solvent polarity. Overall, the emission intensity increases and the maximum wavelength decreases in less polar solvents; thus, the aurones may be useful probes for hydrophobic sites on biological molecules. A limited investigation with model protein, nucleic acid and fixed cells supports this idea. It is known that the sulfur analog of aurone can undergo photo-induced E/Z isomerization. This possibility was investigated for one of the aminoaurones, which was observed to reversible photoisomerize. The two isomers have similar absorption spectra, but the emission properties are distinct. We conclude that appropriately substituted aurones are potentially useful as biological probes and photoswitches.     

Compressed images for affinity prediction (CIFAP): a study on predicting binding affinities for checkpoint kinase 1 protein inhibitors

Analyses of known protein–ligand interactions play an important role in designing novel and efficient drugs, contributing to drug discovery and development. Recently, machine learning methods have proven useful in the design of novel drugs, which utilize intelligent techniques to predict the outcome of unknown protein–ligand interactions by learning from the physical and geometrical properties of known protein–ligand interactions. The aim of this study is to work through a specific example of a novel computational method, namely compressed images for affinity prediction (CIFAP), in which binding affinities for structurally related ligands in complexes with human checkpoint kinase 1 (CHK1) are predicted. The CIFAP algorithm presented here relates published pIC ₅₀ values of 57 compounds, derived from a thienopyridine pharmacophore, in complexes with CHK1 to their two‐dimensional (2D) electrostatic potential images compressed in orthogonal dimensions. Patterns obtained from the 2D images are then used as inputs in regression and learning algorithms such as support vector regression (SVR) and adaptive neuro‐fuzzy inference system (ANFIS) methods to validate the experimental pIC ₅₀ values. This study revealed that the 2D image pixels in the vicinity of bound ligand surfaces provide more relevant information to make correlations with the empirical pIC ₅₀ values. As compared with ANFIS, SVR gave rise to the lowest root mean square errors and the greatest correlations, suggesting that SVR could be a plausible choice of machine learning methods in predicting binding affinities by CIFAP. Copyright © 2013 John Wiley & Sons, Ltd.     

A three-component,one-pot synthesis of 1,8-naphthyridine and isoxazole derivatives and computational elucidation of the mechanism

Research on Chemical Intermediates - An efficient and general method for the synthesis of substituted 3,4-dimethylisoxazolo[5,4-b]pyridine-5-carboxamide and benzo[b][1,8]naphthyridine-3-carboxamide...     

A numerical study of shock-induced cavity collapse

The flow field resulting from the interaction between a planar incident shock in a solid and an embedded ellipsoidal gas cavity is examined computationally. The study is motivated by the need for improved understanding of the role of embedded cavities in the initiation of reaction in a heterogeneous explosive following the application of a shock. The system is modeled as a compressible multi-fluid flow with a sufficiently strong shock in the solid. A high-resolution, Godunov-type capturing scheme is employed to solve the governing equations numerically. The calculations are performed in parallel and use adaptive mesh refinement to obtain well-resolved solutions. The goal is to identify regions in which the shock-cavity interaction results in pressures that are substantially higher than the post-shock pressure that existed prior to the beginning of the interaction. Also of interest are the ways in which the magnitude of the elevated pressure, the extent and location of the regions where it develops, and the mechanisms that underlie such a development are influenced by the strength of the shock and the geometry of the cavity.     

Principles of hierarchical meso- and macropore architectures by liquid crystalline and polymer colloid templating

The generation of porous silica with hierarchically organized bimodal mesoporosity of adjustable size and well-defined shape was investigated by using surfactant mixtures and the nanocasting procedure (liquid crystalline templating). A systematic study of combinations of various block copolymers (Pluronics F127, KLE (poly(omega-hydroxypoly(ethylene-co-butylene)-co-poly(ethylene oxide))) and SE (PS-co-PEO)) with smaller surfactants (Pluronics P123, C16mimCl, and CTAB) revealed that hierarchical bimodal mesopore architectures could only be obtained by the usage of block copolymers with a strong hydrophilic-hydrophobic contrast, such as KLE and SE, giving rise to pores between 6 and 22 nm. Furthermore, the ionic liquid (IL) C16mimCl appeared to have advantageous templating properties, resulting in 2-3-nm pores being located between the block copolymer mesopores, whereas phase separation was observed for Pluronics and CTAB as small templates. Thereby, the study provided also general insights into the mixing and co-self-assembly behavior of block copolymers and ionic surfactants in water and confirmed the special templating properties of ILs, as recently proposed. In addition to the bimodal mesoporosity, additional tunable macroporosity was created by the presence of poly(styrene) or poly(methyl methacrylate) spheres, leading to well-defined trimodal hierarchical pore architectures with the small pores being located in the walls of the respective larger pores. As a major improvement, due to the pore hierarchy, these large-pore materials showed relatively large surface areas and pore volumes, and the size of densely packed macropores could even be decreased down to 90 nm. The materials were characterized by electron microscopy, small-angle X-ray scattering, and nitrogen sorption using a proper NLDFT (nonlocal density functional theory) approach for calculations of the pore size distribution in the entire range of micro- and mesopores.     

Near-field performance analysis of locally-conformal perfectly matched absorbers via Monte Carlo simulations

In the numerical solution of some boundary value problems by the finite element method (FEM), the unbounded domain must be truncated by an artificial absorbing boundary or layer to have a bounded computational domain. The perfectly matched layer (PML) approach is based on the truncation of the computational domain by a reflectionless artificial layer which absorbs outgoing waves regardless of their frequency and angle of incidence. In this paper, we present the near-field numerical performance analysis of our new PML approach, which we call as locally-conformal PML, using Monte Carlo simulations. The locally-conformal PML method is an easily implementable conformal PML implementation, to the problem of mesh truncation in the FEM. The most distinguished feature of the method is its simplicity and flexibility to design conformal PMLs over challenging geometries, especially those with curvature discontinuities, in a straightforward way without using artificial absorbers. The method is based on a special complex coordinate transformation which is ‘locally-defined’ for each point inside the PML region. The method can be implemented in an existing FEM software by just replacing the nodal coordinates inside the PML region by their complex counterparts obtained via complex coordinate transformation. We first introduce the analytical derivation of the locally-conformal PML method for the FEM solution of the two-dimensional scalar Helmholtz equation arising in the mathematical modeling of various steady-state (or, time-harmonic) wave phenomena. Then, we carry out its numerical performance analysis by means of some Monte Carlo simulations which consider both the problem of constructing the two-dimensional Green’s function, and some specific cases of electromagnetic scattering.     

Quantum Contagion: A Quantum-Like Approach for the Analysis of Social Contagion Dynamics with Heterogeneous Adoption Thresholds

Modeling the information of social contagion processes has recently attracted a substantial amount of interest from researchers due to its wide applicability in network science, multi-agent-systems, information science, and marketing. Unlike in biological spreading, the existence of a reinforcement effect in social contagion necessitates considering the complexity of individuals in the systems. Although many studies acknowledged the heterogeneity of the individuals in their adoption of information, there are no studies that take into account the individuals’ uncertainty during their adoption decision-making. This resulted in less than optimal modeling of social contagion dynamics in the existence of phase transition in the final adoption size versus transmission probability. We employed the Inverse Born Problem (IBP) to represent probabilistic entities as complex probability amplitudes in edge-based compartmental theory, and demonstrated that our novel approach performs better in the prediction of social contagion dynamics through extensive simulations on random regular networks.     

Convergence theorem for I-asymptotically quasi-nonexpansive mapping in Hilbert space

Let H be a Hilbert space with inner product (⋅,⋅) and ‖⋅‖ norm, and let K be weakly compact a subset of H. Let be nonlinear mapping and be a nonlinear bounded mapping. In this paper, we define the I-asymptotically quasi-nonexpansive mapping in Hilbert space. If T is an I-asymptotically quasi-nonexpansive mapping, then we prove that , for u∈K as n→∞, is weakly almost convergent to its asymptotic center.