Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase

We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three‐dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D‐RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI‐272 bound form of HIV‐1 protease and predicting both sodium ions and water molecules near the rotor ring of F‐adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39–0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D‐RISM output within minutes. It is extremely useful for examining multiple specific solvent–solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.     

Development of an automated sequential injection on-line solvent extraction-back extraction procedure as demonstrated for the determination of cadmium with detection by electrothermal atomic absorption spectrometry

An automated sequential injection (SI) on-line solvent extraction-back extraction separation/preconcentration procedure is described. Demonstrated for the assay of cadmium by electrothermal atomic absorption spectrometry (ETAAS), the analyte is initially complexed with ammonium pyrrolidinedithiocarbamate (APDC) in citrate buffer and the chelate is extracted into isobutyl methyl ketone (IBMK), which is separated from the aqueous phase by means of a newly designed dual-conical gravitational phase separator. A metered amount of the organic eluate is aspirated and stored in the PTFE holding coil (HC) of the SI-system. Afterwards, it is dispensed and mixed with an aqueous back extractant of dilute nitric acid containing Hg(II) ions as stripping agent, thereby facilitating a rapid metal-exchange reaction with the APDC ligand and transfer of the Cd into the aqueous phase. The aqueous phase is separated in a second dual-conical gravitational phase separator, and 30 μl of it is entrapped and metered in a sample loop (SL) and subsequently introduced via air segmentation into the graphite tube for analyte quantification. The ETAAS determination is performed in parallel with the separation/preconcentration process of the ensuing sample. An enrichment factor of 21.4, a detection limit of 2.7 ng l⁻¹, along with a sampling frequency of 13 h⁻¹ were obtained at a sample flow rate of 6.0 ml min⁻¹. The precision (R.S.D.) at the 0.4 μg l⁻¹ level was 1.8% as compared to 3.2% when quantifying the organic extractant directly. The applicability of the procedure is demonstrated for the determination of trace levels of cadmium in three certified reference materials.     

On the Integrability of Strong Maximal Functions Corresponding to Different Frames

For the frame in ⁿ, let B₂()()( ⁿ) be a family of all n-dimensional rectangles containing x and having edges parallel to the straight lines of , and let M_{B 2()} be a maximal operator corresponding to B ₂(). The main result of the paper is the following Theorem. For any function fL(1+1n⁺ L)( ⁿ ) (n2) there exists a measure preserving and invertible mapping ^{n n} such that

A Goal Programming model of the reference point method

Real-life decision problems are usually so complex they cannot be modeled with a single objective function, thus creating a need for clear and efficient techniques of handling multiple criteria to support the decision process. The most commonly used technique is Goal Programming. It is clear and appealing, but in the case of multiobjective optimization problems strongly criticized due to its noncompliance with the efficiency (Pareto-optimality) principle. On the other hand, the reference point method, although using similar control parameters as Goal Programming, always generates efficient solutions. In this paper, we show how the reference point method can be modeled within the Goal Programming methodology. It allows us to simplify implementations of the reference point method as well as shows how Goal Programming with relaxation of some traditional assumptions can be extended to a multiobjective optimization technique meeting the efficiency principle.     

The EC networking on elemental speciation revisited

In Europe, the EC-funded Thematic Network Speciation 21 was instrumental in disseminating the existing knowledge about chemical speciation of trace elements. It created a forum in which analytical chemists working in method development were mixed with potential users from industry and representatives of legislative bodies. This endeavour is continuing in the currently established European Virtual Institute for Speciation Analysis (EVISA). Although there already exists substantial know-how in Europe for the speciation of a number of substances, such as organo-arsenic, organo-tin and organo-mercury compounds, to name just these three groups, there is an urgent need to enforce the analytical potential in speciation analysis on a much wider scope of compounds capable of providing data of a suitable quality. The ensuing need for quality assurance of the analytical procedures requires the analysis of representative reference materials, certified for the relevant species. Last but not least, where applicable, the European-wide legislation should be adapted to focus on toxic species of the elements, rather than the total element.Presented at BERM-9—Ninth International Symposium on Biological and Environmental Reference Materials, June 15–19, 2003, Berlin, Germany. Disclaimer The opinions expressed in the present article are entirely those of the authors. They do not represent the opinion of the European Community.     

A Polymer-Based All-Solid-State Internal Reference System for pH Glass Electrodes – Performance and Charge Transfer

An all-solid-state internal reference system for pH glass electrodes employing polypyrrole (PPy)-Nafion® composites is described. pH sensors based on this reference system are characterised at 23±3°C. The observed characteristics of the resulting all-solid-state sensors, i.e. slope and linearity of the calibration plot, response behaviour, and signal stability, are very promising, and the differences with respect to the parameters of conventional liquid filled sensors are negligible. The values of the zero potential point, which differ from those of conventional pH glass electrodes, could be controlled within limits via the composition of the PPy-Nafion composite.The excellent sensor performance observed seems to be the consequence of a reversible charge transfer between the ion-conducting membrane, the mixed conducting PPy-Nafion interlayer, and the metal wire. A first discussion of the mechanism of this charge transfer is given.     

The need for new SI-traceable magnesium isotopic reference materials

Recent measurements revealed that commercial magnesium standard solutions showed isotopic abundance variations, which cannot clearly be distinguished from each other by calibrating against the only available isotopic reference material, SRM 980, or reference materials made from SRM 980 like IRMM-009. Therefore new SI-traceable magnesium isotopic reference materials are required.     

All frame-spun knots are slice

Frame-spun knots are constructed by spinning a knot of lower dimension about a framed submanifold of . We show that all frame-spun knots are slice (null-cobordant).

     

Metric and Complete Metric σ-Frames

A -frame is a lattice in which countable joins exist and binary meets distribute over countable joins. In this paper, the category MFrm, of metric -frames, is introduced, and it is shown to be equivalent to the category MLFrm _u, of metric Lindelöf frames.Finally, it is shown that the complete metric -frames are exactly the cozero parts of complete metric Lindelöf frames.