DYNGA: a general purpose QM-MM-MD program. I. Application to water

We present a general purpose QM-MM-MD engine (DYNGA) designed to test alternative hybrid Hamiltonians geared towards the treatment of problems of interest in structural biology including the use of experimental data constraints. In this first presentation we use DYNGA to explore the behaviour of a traditional QM-MM approach in the treatment of the water—water interaction. We find the potential energy hypersurface for the water dimer computed with the HF 4–31G*/TIP3P hybrid Hamiltonian tends to be too flat. We also explore the effect of using traditional QM-MM techniques on proton wires and conclude there is a need for improvement, possibly addressed by using polarizable force fields.     

PAST AND FUTURE MANAGEMENT OF A COLLAPSED FISHERY: THE BAY OF BISCAY ANCHOVY

Abstract We analyze the efficiency of the international management of the Bay of Biscay anchovy. While a sharing agreement between France and Spain has been in place since 1992, the fish stock collapsed in 2005 and the fishery closed from 2005 to spring 2010. We consider differences in production technologies between both countries and calibrate our model using data from 1987 to 2009. Our results suggest two sources of rent dissipation under the existing sharing agreement: inefficient quota allocation and production inefficiencies due to inflexible national regulations. We discuss several alternatives to improve management.     

ConFlo III - an interface for high precision delta(13)C and delta(15)N analysis with an extended dynamic range

A newly developed interface coupling a CHN combustion device (elemental analyser 'EA') to an isotope ratio mass spectrometer is described and evaluated. The purpose of the device is to extend the dynamic range of delta(13)C and delta(15)N analysis from less than 2 orders of magnitude to more than 3 orders of magnitude. Carbon isotope ratio measurements of atropine as a model compound have been performed analysing between 1 μg to 5 mg C with acceptable to excellent precision (0.6 to 0.06 per thousand, delta-notation). The correction due to the blank signal is critical for sample amounts smaller than 4 μg C. The maximum sample weight is determined by the combustion capacity of the EA. Larger sample amounts are measured using dilution of a small part of the EA effluent with helium. The dilution mechanism works virtually free of isotope fractionation. Copyright 1999 John Wiley & Sons, Ltd.     

Fast‐scanning high‐flux microprobe for biological X‐ray fluorescence microscopy and microXAS

There is a growing interest in the biomedical community in obtaining information concerning the distribution and local chemical environment of metals in tissues and cells. Recently, biological X‐ray fluorescence microscopy (XFM) has emerged as the tool of choice to address these questions. A fast‐scanning high‐flux X‐ray microprobe, built around a recently commissioned pair of 200 mm‐long Rh‐coated silicon Kirkpatrick–Baez mirrors, has been constructed at BioCAT beamline 18ID at the Advanced Photon Source. The new optical system delivers a flux of 1.3 × 10¹² photons s^?1 into a minimum focal spot size of ～3–5 µm FWHM. A set of Si drift detectors and bent Laue crystal analyzers may be used in combination with standard ionization chambers for X‐ray fluorescence measurements. BioCAT's scanning software allows fast continuous scans to be performed while acquiring and storing full multichannel analyzer spectra per pixel on‐the‐fly with minimal overhead time (<20 ms per pixel). Together, the high‐flux X‐ray microbeam and the rapid‐scanning capabilities of the BioCAT beamline allow the collection of XFM and micro X‐ray absorption spectroscopy (microXAS) measurements from as many as 48 tissue sections per day. This paper reports the commissioning results of the new instrument with representative XFM and microXAS results from tissue samples.     

Hf, Ta, W and Re experimental L X-ray fluorescence cross-sections at 12, 13 and 14 keV with synchrotron radiation

Experimental determinations of L X-ray fluorescence cross-sections for elements with 72≤Z≤75 at 12, 13 and 14 keV were carried out with synchrotron radiation. The experimental set-up provided a linearly polarized monoenergetic photon beam producing a very low background, which improved the signal-to-noise ratio and reduced the experimental uncertainties. Results of the experimental cross-sections obtained for the L lines were grouped considering the transitions scheme, the energies of the emission lines and the detector's resolution. The data obtained were compared with theoretical ones using two different data tables. A very good agreement was found between our experimental values and the theoretical values calculated using Puri's data (X-Ray Spectrom. 22 (1993) 358–361).     

Intercalation of Toluidines into α-Zirconium Hydrogenphosphate

Intercalates of o-, m-, and p-toluidine into α-Zr(HPO₄)₂ · H₂O were prepared and characterized by powder X-ray diffraction, thermogravimetric analysis and infrared spectroscopy. As follows from IR, toludine molecules are protonated in the interlayer space. Toluidine molecules are arranged in a bimolecular way in the intercalates containing more than 1.5 toluidine molecules per Zr atom. On the other hand, a monolayer of the toluidine molecules is supposed in the intercalates with less than one toluidine molecule per Zr atom.