Molecular dynamics simulation of fractures using an N-body potential

Molecular dynamics has been employed to model the fracture of a two dimensional triangular atomic lattice. The N-body Sutton-Chen potential developed for fcc metals and its extended version (Rafii-Tabar and Sutton) for fcc random binary alloys were used for the interatomic interactions. It is shown that at low temperatures cleavage fractures can occur in both an elemental metal and an alloy. At elevated temperatures the nucleation of dislocations is shown to cause a brittle-to-ductile transition. For the brittle crack propagation in the elemental metal, crack propagation speeds have been computed for different stress rates, and a crack instability found to exist as the speed reaches a critical value of about 32% of the Rayleigh wave speed. For the random alloy, we find that the dislocation movement can be affected by the distorted lattice.

Determining surface tension using DC magnetic levitation

The values of material physical properties are vital for the successful use of numerical simulations for electromagnetic processing of materials. The surface tension of materials can be determined from the experimental measurement of the surface oscillation frequency of liquid droplets. In order for this technique to be used, a positioning field is required that results in a modification to the oscillation frequency. A number of previous analytical models have been developed that mainly focus on electrically conducting droplets positioned using an A.C. electromagnetic field, but due to the turbulent flow resulting from the high electromagnetic fields required to balance gravity, reliable measurements have largely been limited to microgravity. In this work axisymmetric analytical and numerical models are developed, which allow the surface tension of a diamagnetic droplet positioned in a high DC magnetic field to be determined from the surface oscillations. In the case of D.C. levitation there is no internal electric currents with resulting Joule heating, Marangoni flow and other effects that introduce additional physics that complicates the measurement process. The analytical solution uses the linearised Navier-Stokes equations in the inviscid case. The body force from a DC field is potential, in contrast to the AC case, and it can be derived from Maxwell equations giving a solution for the magnetic field in the form of a series expansion of Legendre polynomials. The first few terms in this expansion represent a constant and gradient magnetic field valid close to the origin, which can be used to position the droplet. Initially the mathematical model is verified in microgravity conditions using a numerical model developed to solve the transient electromagnetics, fluid flow and thermodynamic equations. In the numerical model (as in experiment) the magnetic field is obtained using electrical current carrying coils, which provides the confinement force for a liquid droplet. The model incorporates free surface deformation to accurately model the oscillations that result from the interaction between the droplet and the non-uniform external magnetic field. A comparison is made between the analytical perturbation theory and the numerical pseudo spectral approximation solutions for small amplitude oscillations.

Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non-peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of 'expected' masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high-resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright (C) 2009 John Wiley & Sons, Ltd.

Vibrational spectroscopy and DFT calculations of di-amino acid cyclic peptides. Part I: cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly-Gly), cyclo(L-Ala-L-Ala) and cyclo(t-Ala-Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid-state and aqueous protonated samples, as well as their corresponding N-deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3-LYP/cc-pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas-phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di-amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C-2 and C-1 symmetries for the six-membered rings of cyclo(L-Ala-L-Ala) and cydo(L-Ala-Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cydo(L-Ala-L-Ala) and cyclo(L-Ala-Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L-AlaGly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis-peptide linkage are shown to be significantly different from those of the trans-peptides. For example, deuterium shifts have shown that the cis-amide I vibrations found in cyclo(Gly-Gly), cyclo(L-Ala-L-Ala), and cyclo(L-Ala-Gly) have larger N-H contributions compared to their trans-amide counterparts. Compared to trans-amide II vibrations, cis-amide II vibrations show a considerable decrease in N-H character.

Policy packages as potential routes to urban road pricing in the UK

This paper focuses on urban road pricing as a demand management policy that is often regarded as radical and generally unacceptable. Road pricing often gets delayed or abandoned due to low acceptability. This may be due to the fact that complex interactions and drivers of change affect road transport management and require cooperation within implementation networks. The implementation network is a group of people (referred to as partners and actors) who co-ordinate the introduction of policy tools. The drivers of change include any internal or external influences that have an effect on the time, place, or ‘shape’ of the policy measures being introduced. Demand management measures that focus on 'sustainable transport' usually address a limited set of objectives and are often implemented alone i.e. are not necessarily combined with other policy measures. When combined with other measures, it is not always clear whether the multiple interactions between policy tools and implementation networks have been sufficiently considered. Examples of ongoing implementation of policy package in the UK are the support of road pricing initiatives combined with public transport improvements by the Transport Innovation Fund. The objectives of the paper are twofold. First, we present a review of the UK urban road pricing situation. Second, we contrast the emerging issues against six key implementation factors. The analysis of three existing UK road pricing examples - London, Edinburgh and Durham – shows the importance of combining policy tools. Furthermore, through the above examples and theoretical arguments, we emphasise the additional need of creating and maintaining strong networks when implementing policy packages.