The Computational Chemistry Prototyping Environment

Evolving technologies, as exemplified by computational grids and Web services, have made it possible to solve new scientific problems that would not have been feasible previously. In order to make such advances available to the community in general and to be able to solve new problems, not necessarily from the same discipline, it is imperative to build tools that provide a common user interface in order that application programmers and users do not have to be concerned with particulars of Web services and their underlying code, computational platforms, or with data file formats. We will describe our efforts in creating a computational chemistry environment that encompasses a general scientific workflow environment, a domain specific example for quantum chemistry, our ongoing design of a workflow user interface, and our efforts at database integration.     

Radar cross-section study of cylindrical cavity-backed apertureswith outer or inner material coating: the case of H-polarization

A dual-series-based solution is obtained for the scattering of an H-polarized plane wave from a slitted infinite circular cylinder coated with absorbing material from inside or outside. For both cases, numerical results are presented for the radar cross section and comparisons are given for two different realistic absorbing materials. The radar cross-section dependencies are also given for the aspect angle of the scatterer and the thickness of the absorbing layer     

Determination of the Free Radical Scavenging Activity of Lycium Extracts

Lycium species growing in Turkey have not so far been studied sufficiently. For this reason, non-polar and polar extracts obtained from the fruits of Lycium barbarum L. and L. Ruthenicum Murray (Solanaceae) were assessed both in vitro for their potential as free radical scavenger crude extracts and their phenolic composition. Fruits of Lycium species were sequentially extracted with petroleum ether, ethyl acetate, methanol, n-butanol, and water in a Soxhlet extractor. All the extracts were assessed for the scavenging of the nitrogen-centered free radical 1,1-diphenyl-2-picrylhydrazyl (DPPH^.) by in vitro method. Furthermore, the composition of each extract was investigated both in terms of its Folin-Ciocalteau reactive components and its qualitative content. The phenolic compounds within the extracts were determined as benzoic acid and hydroxycinnamic acid derivatives, flavonoids, and anthocyanins according to their retention time and UV spectral data by HPLC-DAD system.     

Determination of aminothiols by liquid chromatography with amperometric detection at a silver electrode: Application to white wines

Liquid chromatography coupled to a silver electrode based flow-through amperometric detector (LC-EC-Ag) was developed for the determination of aminothiols in white wines. The C18 reversed phase LC system operated in the isocratic mode at 0.7 mL min⁻¹ and used an acidic mobile phase composed of formic acid, EDTA, sodium nitrate, sodium hydroxide, and methanol 1% (v/v) at pH 4.5. The working electrode operated at 0.08 V vs Ag/AgCl, 3 M KCl and its manual cleaning was realized once a month by smoothing on a polishing cloth. The analyzed aminothiols were resolved and eluted within 4 min, and all standard curves were linear in the range 2 × 10⁻⁷–2 × 10⁻⁵ M. The analyzed wine samples needed no preparation other than dilution with the mobile phase. The concentration of cysteine (CYS), homocysteine (HCYS), glutathione (GSH) and N-acetylcysteine (NAC) in bottled white wines, determined by the method of standard addition, was found to be in the low μM range (0.2–2 mg L⁻¹) depending on the wine type and its age.     

Papain Loaded Poly(ε-Caprolactone) Nanoparticles<Emphasis Type="Italic">: In-silico and</Emphasis><Emphasis Type="Italic">In-Vitro</Emphasis> Studies

Papain is a protease enzyme with therapeutic properties that are very valuable for medical applications. Poly(ε-caprolactone) (PCL) is an ideal polymeric carrier for controlled drug delivery systems due to its low biodegradability and its high biocompatibility. In this study, the three-dimensional structure and action mechanism of papain were investigated by in vitro and in silico experiments using molecular dynamics (MD) and molecular docking methods to elucidate biological functions. The results showed that the size of papain-loaded PCL nanoparticles (NPs) and the polydispersity index (PDI) of the NPs were 242.9 nm and 0.074, respectively. The encapsulation efficiency and loading efficiency were 80.4 and 27.2%, respectively. Human embryonic kidney cells (HEK-293) were used for determining the cytotoxicity of papain-loaded PCL and PCL nanoparticles. The in vitro cell culture showed that nanoparticles are not toxic at low concentrations, while toxicity slightly increases at high concentrations. In silico studies, which were carried out with MD simulations and ADME analysis showed that the strong hydrogen bonds between the ligand and the papain provide stability and indicate the regions in which the interactions occur.     

Students’ mathematical work on absolute value: focusing on conceptions,errors and obstacles

ZDM – Mathematics Education - This study investigates students’ conceptions of absolute value (AV), their performance in various items on AV, their errors in these items and the...     

cyc-DEP: Cyclic immunofluorescence profiling of particles collected using dielectrophoresis

Cancer is a highly heterogenous disease that requires precise detection tools and active surveillance methods. Liquid biopsy assays provide an agnostic way to follow the complex trajectory of cancer, providing better patient stratification tools for optimized treatment. Here, we present the development of a low-volume liquid biopsy assay called cyc-DEP (cyclic immunofluorescent imaging on dielectrophoretic chip) to profile biomarkers collected on a dielectrophoretic microfluidic chip platform. To enable on-chip cyclic imaging, we optimized a fluorophore quenching method and sequential rounds of on-chip staining with fluorescently conjugated primary antibodies. cyc-DEP allows for the quantification of a multiplex array of proteins using 25 µl of a patient plasma sample. We utilized nanoparticles from a prostate adenocarcinoma (LNCaP) cell line and a panel of six target proteins to develop our proof-of-concept technique. We then used cyc-DEP to quantify blood plasma levels of target proteins from healthy individuals, low-grade and high-grade prostate cancer patients (n = 3 each) in order to demonstrate that our platform is suitable for liquid biopsy analysis in its present form. To ensure accurate quantification of signal intensities and comparisons between different samples, we incorporated a signal intensity normalization method (fluorescent beads) and a custom signal intensity quantification algorithm that account for the distribution of signal across hundreds of collection regions on each chip. Our technique enabled a threefold improvement in multiplicity for detecting proteins associated with fluid samples, opening doors for early detection, and active surveillance through quantification of a multiplex array of biomarkers from low-volume liquid biopsies.     

Graphene oxide-octadecylsilane incorporated monolithic nano-columns with 50 μm id and 100 μm id for small molecule and protein separation by nano-liquid chromatography

In this study, graphene oxide-octadecylsilane incorporated monolithic nano-columns were developed for protein analysis by nano liquid chromatography (nano LC). The monolithic column with 100 μm id was first prepared by an in situ polymerization using ethylene dimethacrylate (EDMA), 3-chloro-2-hydroxypropylmethacrylate (HPMA-Cl), and methacryloyl graphene oxide nanoparticles (MGONPs). MGONPs were synthesized by the treatment of 3-(trimethoxysilyl)propylmethacrylate (TMSPM) and GO. Tetrahydrofuran (THF) and dodecanol were used as the porogenic solvent. The resulting column was functionalized by dimethyloctadecylch lorosilane (DODCS) for the enhancement of hydrophobicity. The functionalization greatly improved the baseline separation of hydrophobic compounds such as polyaromatic hydrocarbons (PAHs). The optimized monolith with respect to total polymerization mixture was characterized by using Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM) X-ray diffraction (XRD) and chromatographic analyses. The blank monoliths without functionalization exhibited poor separation while a good separation performance of MGONPs functionalized monoliths was achieved. The monolith with 100 μm id was evaluated in protein separation in nano LC using RNase A, Cytochrome C, Lysozyme, Trypsin, and Ca isozyme II as the test proteins. It was shown that protein separation mechanism was based on large π-system of GO and hydrophobicity of the monolithic structure. Theoretical plates number up to 57 600 plates were achieved. The nano-column with 50 μm id was also prepared using the same polymerization mixture under the same chemical conditions. These nano-columns were employed for protein separation by nano LC, and the dependence of both nano-column performance on the internal diameter was also discussed.