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.     

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.     

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.     

Synthesis of 4-alkoxy-Δ3-pyrrolin-2-ones and tetramic acids

Acetoacetic ester is converted into 4-alkoxy-Δ³-pyrrolin-2-ones which can be hydrolyzed to give tetramic acids.     

Isotropic-nematic phase transition of single-walled carbon nanotubes in strong acids

We present the first quantitative assessment of the maximum amount of nanotubes that can exist in the isotropic phase () of single-walled carbon nanotubes (SWNTs) in Br?nsted-Lowry acids. We employ a centrifugation technique in conjunction with UV-vis-nIR spectroscopy to quantify , which is also the critical concentration of the isotropic-nematic transition of SWNTs in strong acids. Centrifugation of biphasic dispersions of SWNTs, that is, acid dispersions consisting of an isotropic phase in equilibrium with an ordered nematic liquid crystalline phase, results in a clear phase separation, where the isotropic phase is supernatant. Dilution of the isotropic phase with a known amount of acid followed by UV-vis-nIR absorbance measurements yields , that is, the maximum concentration of SWNTs that can exist in the isotropic phase in a given acid for a given SWNTs' length distribution. At low SWNT concentration (below 200 ppm) in superacids, light absorbance in the range from 400 to 1400 nm scales linearly with concentration. This Beer's law behavior yields calibration curves for measuring SWNTs' concentration in acids. We find that the critical concentration of the isotropic-nematic transition increases with acid strength in accordance with the previously proposed sidewall protonation mechanism for dispersing SWNTs in acids.     

Simultaneous forward- and backward-hemisphere elastic-light-scattering patterns of respirable-size aerosols

Two-dimensional angular optical scattering (TAOS) patterns of aerosols are measured simultaneously from the forward hemisphere 15 degrees < theta < 90 degrees as well as the backward hemisphere 90 degrees < theta < 165 degrees (detecting 63% of the 4pi sr of scattered light) by using an ellipsoidal reflector and an intensified CCD detector. TAOS patterns were obtained from polystyrene-latex spheres (individuals and aggregates) and from single Bacillus subtilis spores. These information-rich patterns, measured with a single laser pulse for individual particles on the fly, suggest that forward-TAOS and backward-TAOS measurements may be used for rapid classification of single aerosol particles.     

Static dielectric constants and molecular dipole distributions of liquid water and ice-Ih investigated by the PAW-PBE exchange-correlation functional

The static dielectric constants, ε(s), of ice-Ih and liquid water were calculated using density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the projector-augmented-wave (PAW) approach. Proton disordered ice configurations and uncorrelated liquid configurations were sampled with the electrostatic switching method using force fields specially designed to facilitate the ab initio free energy perturbation calculations. Our results indicate that PAW-PBE underestimates the ε(s) of both ice-Ih and liquid water but predicts the ratio of ice and water ε(s) in good agreement with experimental measurements. PAW-PBE gives average water dipole moments of 2.50 D in ice-Ih and 2.48 D in the liquid. Our results show that the fixed-charge water models developed by adaptive force matching can reproduce the PAW-PBE dipole moments with an error of approximately 5%. The ice and liquid models created in this work have polarizabilities of 1.32 ?(3) and 1.30 ?(3), respectively, along the HOH bisector direction.     

Dynamics of photon-induced degradation and fluorescence in riboflavin microparticles

An unexpected blue-fluorescence band (around 420 nm) from both micrometer-sized dried particles and aqueous droplets of riboflavin [7,8-dimethyl-10-(D-1^′-ribityl)-isoalloxazine] is observed when the microparticles are irradiated with a pulsed UV (355- or 351-nm) laser. The intensity of the band increases quadratically with input laser energy density (fluence) and is attributable to a one-photon-excited fluorescence of lumichrome (7,8-dimethyl-alloxazine) that is produced by photo-degradation of riboflavin. The well-known greenish-yellow fluorescence band (at 560 nm for dried particles and 535 nm for aqueous droplets) from riboflavin increases sublinearly with UV-laser fluence. With a laser input fluence above 5 J/cm² the riboflavin fluorescence decays earlier and the lumichrome fluorescence reaches a maximum later than the peak of the input laser pulse. The temporal dynamics of the 420- and 535-nm fluorescence peaks are consistent with a rate-equation simulation of photon-induced conversion of riboflavin to lumichrome and the subsequent fluorescence of lumichrome. Received: 28 September 2000 / Revised version: 11 December 2000 / Published online: 21 February 2001