On deflection fields, weak-focusing and strong-focusing storage rings for polar molecules

In this paper, we analyze electric deflection fields for polar molecules in terms of a multipole expansion and derive a simple but rather insightful expression for the force on the molecules. Ideally, a deflection field exerts a strong, constant force in one direction, while the force in the other directions is zero. We show how, by a proper choice of the expansion coefficients, this ideal can be best approximated. We present a design for a practical electrode geometry based on this analysis. By bending such a deflection field into a circle, a simple storage ring can be created; the direct analog of a weak-focusing cyclotron for charged particles. We show that for realistic parameters a weak-focusing ring is only stable for molecules with a very low velocity. A strong-focusing (alternating-gradient) storage ring can be created by arranging many straight deflection fields in a circle and by alternating the sign of the hexapole term between adjacent deflection fields. The acceptance of this ring is numerically calculated for realistic parameters. Such a storage ring might prove useful in experiments looking for an EDM of elementary particles.     

Electric field-derived point charges to mimic the electrostatics in molecular crystals

Because of the way the electrostatic potential is defined in a crystal, it is not possible to determine potential-derived charges for atoms in a crystal. To overcome this limitation, we present a novel method for determining atomic charges for a molecule in a crystal based on a fit to the electric field at points on a surface around the molecule. Examples of fits to the electric field at points on a Hirshfeld surface, using crystal Hartree-Fock electron densities computed with a DZP basis set are presented for several organic molecular crystals. The field-derived charges for common functional groups are transferable, and reflect chemical functionality as well as the subtle effects of intermolecular interactions. The charges also yield an excellent approximation to the electric field surrounding a molecule in a crystal for use in cluster calculations on molecules in solids.     

Fast choice of separation conditions for analyses by capillary zone electrophoresis using an information system Xemic

An information system Xemic applicable in analytical chemistry is described and its use in capillary electrophoresis for searching suitable separation conditions is demonstrated. This system is capable to provide suitable separation conditions even for analytes for which no electrophoretic experiments have been published so far. The system works with a database of components of anionic character the analyses of which have been performed, published in reviewed scientific journals, and included into a database created by an expert. Moreover, the system learned to search also in abstracts or complete scientific articles to find articles dealing with the determination of a substance in a given sample matrix. When no experiments have been published so far for a defined substance in a specific matrix, Xemic shows the separation conditions for determination of the substance regardless of the matrix. When no response can be found for the analyte of interest at all, the system Xemic works like an expert in the field and searches chemically similar substances and offers a series of substances the physicochemical properties of which are close to the followed analyte with respect to the behavior in the electric field, and shows working conditions for their analysis. Thus, the analyst puts only the order in the form of a given analyte in a given matrix and obtains a recommendation of a separation system that should enable to perform a successful separation. The system is not rigid and enables the operator to change the importance of individual attributes used in similarity search so as to obtain a broader or narrower group of similar components. With a certain probability the analyte of interest can be successfully analyzed under separation conditions that suited for the analysis of the most similar substances in the given matrix.     

Numerical Simulation of Rayleigh–Bènard Instability in Solutions Containing Ions of Three Types

The conditions for appearance of a Rayleigh–Benard instability (RBI) induced by a constant current between two horizontal electrodes in solution containing electroactive ions and indifferent electrolyte (system with three kinds of ions) are analyzed. It is taken into account that all the components take part in the formation of buoyant forces. The problem is solved for a stationary case (as an expansion to a series by a small parameter), and then equations for low perturbations are solved by the Galerkin method. The calculation is performed with a program that accounts for any number of members in a Galerkin expansion. A diagram is obtained, which determines conditions for the RBI emergence in terms of ratios of partial Raleigh numbers. The ratio of diffusion coefficients for supporting cations and anions significantly affects position of the boundary dividing ranges of convective stability and RBI in a diagram of nonequilibrium phase transitions.     

On-chip screening method for cell migration genes based on a transfection microarray

Cell migration plays a major role in a variety of biological processes and a detailed understanding of associated mechanisms should lead to advances in the medical sciences, for example, in drug discovery for cancer therapy. However, the traditional methods used for analysis of cell migration cannot easily be scaled up for high-throughput screening. In this study, we have attempted to develop a novel simple method for high-throughput phenotypic screening for the identification of genes that are required for cell migration. As the appropriate cell line for the method, we found NBT-L2b cells that would be suitable for screening of migration-related genes in our method without influence by other cellular processes. Moreover, the idea for printing both the labeled fibronectin, for identification of the starting region of a cell, and the green fluorescent protein (GFP) expression vector, for identification of cells that had been transfected with siRNA and of the end point of migration, brings a rapid and efficient high-throughput screening procedure. Our new method will lead to an enhanced understanding of cell migration.     

Development and validation of a liquid chromatography/tandem mass spectrometry method for the quantification of flucloxacillin and cloxacillin in microdialysis samples

In the present study we developed and validated a liquid chromatography/tandem mass spectrometry (LC‐MS/MS) assay for the determination of flucloxacillin in human plasma and microdialysis samples and cloxacillin in microdialysis samples, using oxacillin as the internal standard for the assay. The samples were separated on a UPLC BEH C₁₈,1.7 µm column (2.1 × 50 mm) and analyzed by a tandem–quadrupole mass spectrometer in multiple reaction monitoring mode using an electronspray ionization interface. For flucloxacillin the method was demonstrated to be accurate and precise in the linearity range of 1–30 mg/L in plasma and 0.05–5.0 mg/L for microdialysate with a regression coefficient (r) of 0.9986 and 0.9989 in plasma and microdialysate respectively. For cloxacillin it was accurate and precise in the range of 0.1–5.0 mg/L for microdialysate with a regression coefficient of 0.9972. The method presents a high sensitivity for flucloxacillin (lower limit of quantification of 1 mg/L for plasma and 0.05 mg/L for microdialysis samples) combined with a low within‐ and between‐day variation (<5.0% for flucloxacillin and cloxacillin in microdialysis samples and <6.5% for plasma samples of flucloxacillin). The validation experiments for the microdialysis probes showed a relative recovery of 85.5% for flucloxacillin at a flow rate of 1.0 μL/min. The results justify the use of this assay for clinical studies for measuring free unbound tissue concentrations of flucloxacillin in patients with a Staphylococcus aureus bacteremia. Copyright © 2014 John Wiley & Sons, Ltd.     

Retrieving definitional content for ontology development

Ontology construction requires an understanding of the meaning and usage of its encoded concepts. While definitions found in dictionaries or glossaries may be adequate for many concepts, the actual usage in expert writing could be a better source of information for many others. The goal of this paper is to describe an automated procedure for finding definitional content in expert writing. The approach uses machine learning on phrasal features to learn when sentences in a book contain definitional content, as determined by their similarity to glossary definitions provided in the same book. The end result is not a concise definition of a given concept, but for each sentence, a predicted probability that it contains information relevant to a definition. The approach is evaluated automatically for terms with explicit definitions, and manually for terms with no available definition.     

Development of an iminocoumarin-based zinc sensor suitable for ratiometric fluorescence imaging of neuronal zinc

Ratiometric imaging is a technique to reduce artifacts by minimizing the influence of extraneous factors on the fluorescence of a sensor and is particularly useful for cellular imaging studies. Here we characterized the iminocoumarin fluorophore as a new scaffold for sensors for ratiometric imaging. The iminocoumarin 4 showed a high quantum yield in aqueous media on excitation in the visible wavelength region, while its coumarin analogue showed little fluorescence. We therefore developed a novel fluorescence probe, ZnIC, for ratiometric imaging of Zn2+, using iminocoumarin as a fluorophore and (ethylamino)dipicolylamine as a Zn2+ chelator. ZnIC exhibited almost the same fluorescence properties as 4, and the emission spectrum of this probe was red-shifted on addition of Zn2+ under physiological conditions. ZnIC is selective for Zn2+ over other biologically important metal ions, such as Ca2+ and Mg2+, and has high affinity for Zn2+. To confirm the suitability of ZnIC for biological applications, we employed it for the ratiometric detection of changes in intracellular Zn2+ in cultured cells and in rat hippocampal slices. The results indicate that iminocoumarin is a useful fluorophore for fluorescence microscopic imaging and that ZnIC should be useful for studies on the biological functions of Zn2+.     

Regularities of formation of emboli of liquid polymer solutions in aqueous medium

Work on creating the basis for embolic compositions for the treatment of a wide range of pathologies of various organs was conducted. This basis is a solution of a biocompatible water-insoluble polymer in a biocompatible water-soluble solvent. Formation of the embolus in such an aqueous medium takes place in the transition of the solvent into the aqueous phase and the formation of a solid polymer clot occluding a blood vessel. Criteria for selection of the polymer and the solvent for the basis were formulated, and a number of polymers and solvents that meet these criteria were selected for further research. Research on the solubility of the selected polymers in solvents was carried out, and the rheoviscometric characteristics of polymer solutions, as well as parameters of solid emboli formation of polymer solutions in aqueous media, were found. The solution of cellulose acetate plasticized with OPADRY CA 500F190000 polyethylene glycol in dimethylsulfoxide with concentration of no less than 60 g/L was recognized as optimal for further studies.     

Quantum solvation of phthalocyanine in superfluid helium droplets

We have measured quantum states of the solvent-solute system of phthalocyanine in superfluid helium droplets in a high resolution pump-probe experiment. This provides evidence for the attribution of a splitting effect in the emission spectra of phthalocyanine in helium droplets to the relaxation of the first helium layer upon electronic excitation, measured recently by us. Our experimental results are a strong indication for the first helium layer playing a key roll for the solvation of molecules in helium droplets and, thus, for their spectroscopic features.     

One-dimensional trapped atoms: critical coupling parameter and critical number of particles

In this paper we consider the case of a Bose gas in low dimension in order to illustrate the applicability of a method that allows us to construct analytical relations, valid for a broad range of coupling parameters, for a function which asymptotic expansions are known. The method is well suitable to investigate the problem of stability of a collection of Bose particles trapped in one- dimensional configuration for the case where the scattering length presents a negative value. The eigenvalues for this interacting quantum one-dimensional many particle system become negative when the interactions overcome the trapping energy and, in this case, the system becomes unstable. Here we calculate the critical coupling parameter and apply for the case of Lithium atoms obtaining the critical number of particles for the limit of stability.     

Effects of anharmonicity on nonadiabatic electron transfer: a model

The effect of anharmonicity in the intramolecular modes of a model system for exothermic intramolecular nonadiabatic electron transfer is probed by examining the dependence of the transition probability on the exoergicity. The Franck-Condon factor for the Morse potential is written in terms of the Gauss hypergeometric function both for a ground initial state and for the general case, and comparisons are made between the first-order perturbation theory results for transition probability for harmonic and Morse oscillators. These results are verified with quantum dynamical simulations using wave-packet propagations on a numerical grid. The transition-probability expression incorporating a high-frequency quantum mode and low-frequency medium mode is compared for Morse and harmonic oscillators in different temperature ranges and with various coarse-graining treatments of the delta function from the Fermi golden rule expression. We find that significant deviations from the harmonic approximation are expected for even moderately anharmonic quantum modes at large values of exoergicity. The addition of a second quantum mode of opposite displacement negates the anharmonic effect at small energy change, but in the inverted regime a significantly flatter dependence on exoergicity is predicted for anharmonic modes.     

β-Lactam ring stability and antibacterial potency: A novel eigenvalue problem

Low inoculum potency data in vitro for 16 clinical β-lactam antibiotics have been analyzed, and a physical model for interpreting the results of a number of bacterial strains has been derived. An analytic criterion for performing a unitary transformation on the potency data is developed following the identification of a physical vector present within the data which is attributable to an activation energy required for the transport of the β-lactam into a biological membrane. This vector has inverse slope relations in Gram positive and Gram negative bacteria and provides the basis for the analytic criterion for the unitary transformation. Compounds with similar potency spectra which differ only in the absolute magnitude of their effect will possess similar transport properties. It is shown that a slow rate of membrane entry for the β-lactam has overriding consequences on differences in fast rates of binding to the target enzymes and to β-lactamases, and a second primary vector is established directly from the biological data related to the ease of β-lactam ring opening. This vector offers precise evidence for testing the solvational and theoretical requirements for predicting the biological stability of novel β-lactam ring compounds.     

On the applicability of the Born-Oppenheimer approximation in a theory of nonadiabatic charge transfer reactions: An exactly solvable model

The question concerning the applicability of the Born-Oppenheimer approximation (BOA) for the calculation of the transition probability for a nonadiabatic process of charge transfer in a polar environment with allowance made for temperature effects is investigated theoretically. Considered is the transfer of a quantum particle (proton) that interacts with a local vibration mode in a model of bound harmonic oscillators. The model admits an exact solution for wavefunctions of the initial and final states. A calculation shows that BOA is applicable even for very large distances of the proton transfer. At the same time, the exact result and the BOA result severely differ from a probability calculated in a crude Condon approximation. It is demonstrated that the non-Condon effects are in a general case temperature-dependent and may substantially influence the calculated values of the transition probability.     

Bead-bead interaction parameters in dissipative particle dynamics: relation to bead-size, solubility parameter, and surface tension

Dissipative particle dynamics (DPD) is a mesoscale modeling method for simulating equilibrium and dynamical properties of polymers in solution. The basic idea has been around for several decades in the form of bead-spring models. A few years ago, Groot and Warren established an important link between DPD and the Flory-Huggins chi-parameter theory for polymer solutions. We revisit the Groot-Warren theory and investigate the DPD interaction parameters as a function of bead size. In particular, we show a consistent scheme of computing the interfacial tension in a segregated binary mixture. Results for three systems chosen for illustration are in excellent agreement with experimental results. This opens the door for determining DPD interactions using interfacial tension as a fitting parameter.     

Simulation of DNA Extension in Nanochannels

We have used a realistic model for double stranded DNA and Monte Carlo simulations to compute the extension (mean span) of a DNA molecule confined in a nanochannel over the full range of confinement in a high ionic strength buffer. The simulation data for square nanochannels resolve the apparent contradiction between prior simulation studies and the predictions from Flory theory, demonstrating the existence of two transition regimes between weak confinement (the de Gennes regime) and strong confinement (the Odijk regime). The simulation data for rectangular nanochannels support the use of the geometric mean for mapping data obtained in rectangular channels onto models developed for cylinders. The comparison of our results with experimental data illuminates the challenges in applying models for confined, neutral polymers to polyelectrolytes. Using a Flory-type approach, we also provide an improved scaling result for the relaxation time in the transition regime close to that found in experiments.     

Benefits of the implementation of a metrological structure for water analyses

Traceability of measurements still often remains a non-operational notion for end-user chemists. A practical project, sponsored by the French Ministry of Research, has been conducted to evaluate and to demonstrate possible benefits of the implementation of a metrological structure for improvement of the quality of water analyses. LNE (Laboratoire National d'Essais) was in charge of the build up of the traceability chain in a concrete case of determination of some heavy metals (cadmium and lead) in a groundwater. Pure solutions for calibration and a matrix RM have been certified by LNE and then used by 46 labs (mainly French) in a inter-laboratory study. Results have shown a measurable bias in lead analysis in the groundwater for all methods in routine use by laboratories. This project has demonstrated the interest of a metrological approach for method calibration, method validation and estimation of measurement uncertainty.     

Determination of the reference value of nitrogen mass fraction in the reference material of Polish soil

Ensuring a traceability and meaningful of a measurements is one of the most important stages of each analysis, each measurement. It is especially important for measurement of the environmental samples, like soil, which is a very complex matrix. A certified reference materials (CRMs) should be routinely used for this purpose. The paper discusses the procedure for preparation of the soil samples for certification as CRM. As for agricultural reasons there is a growing demand for CRMs regarding a nitrogen mass fraction in the Polish soil, we prepared such a material and established the reference value with associated measurement uncertainty. Homogeneity and stability of the material were shown to be appropriate for the intended purpose. The presented approach can also be used in a process of manufacture of a laboratory reference material, which can be used for a routine quality control.