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.     

Making MRI quieter

We have mitigated acoustic noise in a 1.5 T cylindrical MRI scanner equipped with epoxy-potted, shielded gradients. It has been widely assumed that MRI acoustic noise comes overwhelmingly from vibrations of the gradient assembly. However, with vibration-isolated gradients contained in an airtight enclosure, we found the primary sources of acoustic noise to be eddy-current-induced vibrations of metal structures such as the cryostat inner bore and the rf body coil. We have elucidated the relative strengths of source-pathways of acoustic noise and assembled a reduced-acoustic-noise demonstration MRI system. This scanner employed a number of acoustic noise reduction measures including a vacuum enclosure of a vibrationally isolated gradient assembly, a low-eddy-current rf coil and a non-conducting inner bore cryostat. The demonstration scanner reduced, by about 20 dBA, the acoustic noise levels in the patient bore to 85 dBA and below for several typical noisy pulse sequences. The noise level standing near the patient bore is 71 dBA and below. We have applied Statistical Energy Analysis to develop a vibroacoustic model of the MR system. Our model includes vibrational sources and acoustic pathways to predict acoustic noise and provides a good spectral match above 400 Hz to experimentally measured sound levels. This tool enables us to factor acoustics into the design parameters of new MRI systems.     

Simple LC method for determination of chloramphenicol in equine, canine, and feline serum

A simple and sensitive high-performance liquid chromatographic (HPLC) method is developed for the determination of chloramphenicol (CAP) concentrations in equine, canine, and feline serum. Serum samples are diluted, then ultrafiltered using a microconcentrator with a 30,000 MW cutoff filter. CAP is separated and quantitated directly from the ultrafiltrate on a reversed-phase column using a buffered methanol mobile phase and a variable wavelength UV detector set at 278 nm. The recovery of CAP from 5 micrograms/mL spiked serum samples is determined using 10 serum samples from each of the three species. This method of sample preparation yields recoveries of 99.8%, 92.0%, and 88.6% with coefficients of variation of 1.2%, 1.3%, and 1.0% in equine, canine, and feline sera, respectively. Concentrations of CAP between 0.5 and 400 micrograms/mL as determined by peak area are found to have a linear relationship (correlation coefficient = 0.99997, n = 10), although amounts as low as 0.025 microgram/mL can be detected.     

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.