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.     

The stoichiometry and kinetics of carbon combustion at low temperature: A surface complex approach

The stoichiometry and rate of carbon combustion at low temperature (673 K) were investigated. Oxidation and TPD experimental data provide quantification of gaseous products and stable surface complexes over a broad range of conversion. Our analysis distinguishes between surface complexes forming CO and CO₂ and has assumed a certain fraction of each complex type decomposes instantaneously upon formation, leaving the remainder on the surface as stable complexes, C(O) and C(O₂). This analysis suggests that a maximum of 25% of CO-complexes and 89% of CO₂-complexes are unstable upon formation. At low conversion, unstable complex formation is the dominant pathway for the CO product. As conversion increases, decomposition of stable CO-complexes eventually becomes the main source of CO. Formation of unstable CO₂-complexes is the dominant pathway for the CO₂ product at all times. The combustion rate is initially high due to a high availability of vacant active sites, decreases sharply as these sites are filled with stable complexes, and gradually increases as the stable complexes promote CO₂-complex formation, in turn, driving their decomposition. The dynamics of formation and decomposition of C(O) and C(O₂) dictates their ratio on the carbon surface at any moment, which may be measured by TPD. This work may help in developing new kinetic models of carbon combustion which can predict the stoichiometry as well as the rate.     

Gradient Formula for Linearly Self-Interacting Branes

 The computation of long range linear self-interaction forces in string and higher dimensional brane models requires the evaluation of the gradients of regularised values of divergent self-interaction potentials. It is shown that the appropriately regularised gradient in directions orthogonal to the brane surface will always be obtainable simply by multiplying the regularised potential components by just half the trace of the second fundamental tensor, except in the hypermembrane case for which the method fails. Whatever the dimension of the background this result is valid provided the codimension is two (the hyperstring case) or more, so it can be used for investigating brane-world scenarios with more than one extra space dimension. Received: 15 April 2002 / Accepted: 23 October 2002 Published online: 25 February 2003 Communicated by H. Nicolai