Structure determination from powder data : Mogul and CASTEP

When solving the crystal structure of complex molecules from powder data, accurately locating the global minimum can be challenging, particularly where the number of internal degrees of freedom is large. The program Mogul provides a convenient means to access typical torsion angle ranges for fragments related to the molecule of interest. The impact that the application of modal torsion angle constraints has on the structure determination process of two structure solution attempts using DASH is presented. Once solved, accurate refinement of a molecular structure against powder data can also present challenges. Geometry optimisation using density functional theory in CASTEP is shown to be an effective means to locate hydrogen atom positions reliably and return a more accurate description of molecular conformation and intermolecular interactions than global optimisation and Rietveld refinement alone

Earth materials and earth dynamics

In the project ''Earth Materials and Earth Dynamics'' we linked fundamental and exploratory, experimental, theoretical, and computational research programs to shed light on the current and past states of the dynamic Earth. Our objective was to combine different geological, geochemical, geophysical, and materials science analyses with numerical techniques to illuminate active processes in the Earth. These processes include fluid-rock interactions that form and modify the lithosphere, non-linear wave attenuations in rocks that drive plate tectonics and perturb the earth's surface, dynamic recrystallization of olivine that deforms the upper mantle, development of texture in high-pressure olivine polymorphs that create anisotropic velocity regions in the convecting upper mantle and transition zone, and the intense chemical reactions between the mantle and core. We measured physical properties such as texture and nonlinear elasticity, equation of states at simultaneous pressures and temperatures, magnetic spins and bonding, chemical permeability, and thermal-chemical feedback to better characterize earth materials. We artificially generated seismic waves, numerically modeled fluid flow and transport in rock systems and modified polycrystal plasticity theory to interpret measured physical properties and integrate them into our understanding of the Earth. This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL)

Development of a technology for reducing polycyclic aromatic hydrocarbons in smoked food and smoked ingredients

The popularity of smoked foodstuffs such as sauces, marinades and rubs is on the rise. However, during the traditional smoking process, in addition to the desirable smoky aroma compounds, harmful polycyclic aromatic hydrocarbons (PAHs) are also generated. In this work, a selective filter has been developed which reduces PAH concentrations in a smoke by up to 90%, whilst maintaining a desirable smoky flavor. Preliminary studies using a cocktail of 12 PAHs stirred with a zeolite showed the potential for this zeolite to selectively remove PAHs from a simple solution. However pre-treatment of the smoke prior to application removed the PAHs more efficiently and is more widely applicable to a range of food ingredients. Whilst volatile analysis showed that there was a concomitant reduction in the concentration of the smoky compounds such as 2-methoxyphenol (guaiacol), 2-methylphenol (m-cresol) and the isoeugenols, qualitative descriptive analysis by a sensory panel showed that the difference in perception of flavour was minimal

Strain-induced kinetics of intergrain defects as the mechanism of slow dynamics in the nonlinear resonant response of humid sandstone bars

A closed-form description is proposed to explain nonlinear and slow dynamics effects exhibited by sandstone bars in longitudinal resonance experiments. Along with the fast subsystem of longitudinal nonlinear displacements we examine the strain-dependent slow subsystem of broken intergrain and interlamina cohesive bonds. We show that even the simplest but phenomenologically correct modelling of their mutual feedback elucidates the main experimental findings typical for forced longitudinal oscillations of sandstone bars, namely, (i) hysteretic behavior of a resonance curve on both its up- and down-slopes, (ii) linear softening of resonant frequency with increase of driving level, and (iii) gradual recovery (increase) of resonant frequency at low dynamical strains after the sample was conditioned by high strains. In order to reproduce the highly nonlinear elastic features of sandstone grained structure a realistic non-perturbative form of strain potential energy was adopted. In our theory slow dynamics associated with the experimentally observed memory of peak strain history is attributed to strain-induced kinetic changes in concentration of ruptured inter-grain and inter-lamina cohesive bonds causing a net hysteretic effect on the elastic Young's modulus. Finally, we explain how enhancement of hysteretic phenomena originates from an increase in equilibrium concentration of ruptured cohesive bonds that are due to water saturation.Comment: 5 pages, 3 figure

Nonlinear elastic wave interaction in a sandstone bar: A summary of recent pulse-mode experiments

We have performed nonlinear pulse propagation experiments in a 3.8 cm diameter rod of Berea sandstone 1.8 m long at ambient conditions. Unlike earlier studies, we measured acceleration and not displacement. Moreover, we detected 2nd and 3rd harmonic growth at smaller strain amplitudes than were observed previously (10{sup {minus}7}). Harmonic growth at identical strain amplitudes has also been noted in resonance studies using the same rock type. Current measurements are underway with the rod in vacuum where the wave attenuation is less and the conditions can be carefully controlled. Ultimately, we wish to test the validity of current analytic and numerical models for nonlinear propagation in microcracked materials

Modelling of an imaging beamline at the ISIS pulsed neutron source

A combined neutron imaging and neutron diffraction facility, IMAT, is currently being built at the pulsed neutron spallation source ISIS in the U.K. A supermirror neutron guide is required to combine imaging and diffraction modes at the sample position in order to obtain suitable time of flight resolutions for energy selective imaging and diffraction experiments. IMAT will make use of a straight neutron guide and we consider here the optimization of the supermirror guide dimensions and characterisation of the resulting beam characteristics, including the homogeneity of the flux distribution in space and energy and the average and peak neutron fluxes. These investigations take into account some main design criteria: to maximise the neutron flux, to minimise geometrical artefacts in the open beam image at the sample position and to obtain a good energy resolution whilst retaining a large neutron bandwidth. All of these are desirable beam characteristics for the proposed imaging and diffraction analysis modes of IMAT

Dynamic interaction between WT1 and BASP1 in transcriptional regulation during differentiation

The Wilms’ tumour suppressor protein WT1 plays a central role in the development of the kidney and also other organs. WT1 can act as a transcription factor with highly context-specific activator and repressor functions. We previously identified Brain Acid Soluble Protein 1 (BASP1) as a transcriptional cosuppressor that can block the transcriptional activation function of WT1. WT1 and BASP1 are co-expressed during nephrogenesis and both proteins ultimately become restricted to the podocyte cells of the adult kidney. Here, we have analysed the WT1/BASP1 complex in a podocyte precursor cell line that can be induced to differentiate. Chromatin immunoprecipitation revealed that WT1 and BASP1 occupy the promoters of the Bak, c-myc and podocalyxin genes in podocyte precursor cells. During differentiation-dependent upregulation of podocalyxin expression BASP1 occupancy of the podocalyxin promoter is reduced compared to that of WT1. In contrast, the repressive WT1/BASP1 occupancy of the c-myc and Bak promoters is maintained and these genes are downregulated during the differentiation process. We provide evidence that the regulation of BASP1 promoter occupancy involves the sumoylation of BASP1. Our results reveal a dynamic cooperation between WT1 and BASP1 in the regulation of gene expression during differentiation