Abattoir Factors Influencing the Incidence of Dark Cutting in Australian Grain-Fed Beef.

The aim of this study was to evaluate the effect of carcass traits, lairage time and weather conditions during lairage and abattoir factors that impact the incidence of dark cutting in 142,228 grain-fed carcasses, as defined by Meat Standards Australia (MSA) guidelines. This study was conducted over a 12-month period analysing data from cattle that were supplied from seven feedlots and processed at three abattoirs. Abattoir data indicated that the average incidence of dark cutting within the study was 2.8%. Increased wind speeds (WSs) and rain during lairage at the abattoir was associated with an increased risk of dark cutting, whereas variation in ambient temperature and/or relative humidity did not influence dark cutting. Heavier carcasses with whiter fat, larger hump heights, more rib fat, higher marble scores and lower ossification had lower incidences of dark cutting. The factors abattoir, time in lairage, time to grading and grader within Abattoir had significant effects on the incidence of dark cutting. The results from this study suggest that reducing the time in lairage and increasing the time between slaughter and grading are the two major ways to reduce dark cutting in MSA carcasses.

Insight into the Charge Density Wave Gap from Contrast Inversion in Topographic STM Images.

Charge density waves (CDWs) are understood in great detail in one dimension, but they remain largely enigmatic in two-dimensional systems. In particular, numerous aspects of the associated energy gap and the formation mechanism are not fully understood. Two long-standing riddles are the amplitude and position of the CDW gap with respect to the Fermi level (E_{F}) and the frequent absence of CDW contrast inversion (CI) between opposite bias scanning tunneling microscopy (STM) images. Here, we find compelling evidence that these two issues are intimately related. Combining density functional theory and STM to analyze the CDW pattern and modulation amplitude in 1T-TiSe_{2}, we find that CI takes place at an unexpected negative sample bias because the CDW gap opens away from E_{F}, deep inside the valence band. This bias becomes increasingly negative as the CDW gap shifts to higher binding energy with electron doping. This study shows the importance of CI in STM images to identify periodic modulations with a CDW and to gain valuable insight into the CDW gap, whose measurement is notoriously controversial.

"Older Adults with ASD: The Consequences of Aging." Insights from a series of special interest group meetings held at the International Society for Autism Research 2016-2017.

A special interest group (SIG) entitled "Older Adults with ASD: The Consequences of Aging" was held at the International Society for Autism Research (INSAR) annual meetings in 2016 and 2017. The SIG and subsequent meetings brought together, for the first time, international delegates who were members of the autistic community, researchers, practitioners and service providers. Based on aging autism research that is already underway in UK, Europe, Australia and North America, discussions focussed on conceptualising the parameters of aging when referring to autism, and the measures that are appropriate to use with older adults when considering diagnostic assessment, cognitive factors and quality of life in older age. Thus, the aim of this SIG was to progress the research agenda on current and future directions for autism research in the context of aging. A global issue on how to define 'aging' when referring to ASD was at the forefront of discussions. The 'aging' concept can in principle refer to all developmental transitions. However, in this paper we focus on the cognitive and physical changes that take place from mid-life onwards. Accordingly, it was agreed that aging and ASD research should focus on adults over the age of 50 years, given the high rates of co-occurring physical and mental health concerns and increased risk of premature death in some individuals. Moreover, very little is known about the cognitive change, care needs and outcomes of autistic adults beyond this age. Discussions on the topics of diagnostic and cognitive assessments, and of quality of life and well-being were explored through shared knowledge about which measures are currently being used and which background questions should be asked to obtain comprehensive and informative developmental and medical histories. Accordingly, a survey was completed by SIG delegates who were representatives of international research groups across four continents, and who are currently conducting studies with older autistic adults. Considerable overlap was identified across different research groups in measures of both autism and quality of life, which pointed to combining data and shared learnings as the logical next step. Regarding the background questions that were asked, the different research groups covered similar topics but the groups differed in the way these questions were formulated when working with autistic adults across a range of cognitive abilities. It became clear that continued input from individuals on the autism spectrum is important to ensure that questionnaires used in ongoing and future are accessible and understandable for people across the whole autistic spectrum, including those with limited verbal abilities.

Local Real-Space View of the Achiral 1T-TiSe_{2} 2×2×2 Charge Density Wave.

The transition metal dichalcogenide 1T-TiSe_{2}-two-dimensional layered material undergoing a commensurate 2×2×2 charge density wave (CDW) transition with a weak periodic lattice distortion (PLD) below ≈200 K. Scanning tunneling microscopy (STM) combined with intentionally introduced interstitial Ti atoms allows us to go beyond the usual spatial resolution of STM and to intimately probe the three-dimensional character of the PLD. Furthermore, the inversion-symmetric achiral nature of the CDW in the z direction is revealed, contradicting the claimed existence of helical CDW stacking and associated chiral order. This study paves the way to a simultaneous real-space probing of both charge and structural reconstructions in CDW compounds.

Alane adsorption and dissociation on the Si(0 0 1) surface.

We used DFT to study the energetics of the decomposition of alane, AlH3, on the Si(0 0 1) surface, as the acceptor complement to PH3. Alane forms a dative bond with the raised atoms of silicon surface dimers, via the Si atom lone pair. We calculated the energies of various structures along the pathway of successive dehydrogenation events following adsorption: AlH2, AlH and Al, finding a gradual, significant decrease in energy. For each stage, we analyse the structure and bonding, and present simulated STM images of the lowest energy structures. Finally, we find that the energy of Al atoms incorporated into the surface, ejecting a Si atom, is comparable to Al adatoms. These findings show that Al incorporation is likely to be as precisely controlled as P incorporation, if slightly less easy to achieve.

Stripe and Short Range Order in the Charge Density Wave of 1T-Cu_{x}TiSe_{2}.

We study the impact of Cu intercalation on the charge density wave (CDW) in 1T-Cu_{x}TiSe_{2} by scanning tunneling microscopy and spectroscopy. Cu atoms, identified through density functional theory modeling, are found to intercalate randomly on the octahedral site in the van der Waals gap and to dope delocalized electrons near the Fermi level. While the CDW modulation period does not depend on Cu content, we observe the formation of charge stripe domains at low Cu content (x<0.02) and a breaking up of the commensurate order into 2×2 domains at higher Cu content. The latter shrink with increasing Cu concentration and tend to be phase shifted. These findings invalidate a proposed excitonic pairing as the primary CDW formation mechanism in this material.

Structure of Self-Assembled Mn Atom Chains on Si(001).

Mn has been found to self-assemble into atomic chains running perpendicular to the surface dimer reconstruction on Si(001). They differ from other atomic chains by a striking asymmetric appearance in filled state scanning tunneling microscopy (STM) images. This has prompted complicated structural models involving up to three Mn atoms per chain unit. Combining STM, atomic force microscopy, and density functional theory we find that a simple necklacelike chain of single Mn atoms reproduces all their prominent features, including their asymmetry not captured by current models. The upshot is a remarkably simpler structure for modeling the electronic and magnetic properties of Mn atom chains on Si(001).

Doping nature of native defects in 1T-TiSe2.

The transition-metal dichalcogenide 1T-TiSe2 is a quasi-two-dimensional layered material with a charge density wave (CDW) transition temperature of T(CDW) ≈ 200 K. Self-doping effects for crystals grown at different temperatures introduce structural defects, modify the temperature-dependent resistivity, and strongly perturbate the CDW phase. Here, we study the structural and doping nature of such native defects combining scanning tunneling microscopy or spectroscopy and ab initio calculations. The dominant native single atom dopants we identify in our single crystals are intercalated Ti atoms, Se vacancies, and Se substitutions by residual iodine and oxygen.

DSSC anchoring groups: a surface dependent decision.

Electrodes in dye sensitised solar cells are typically nanocrystalline anatase TiO2 with a majority (1 0 1) surface exposed. Generally the sensitising dye employs a carboxylic anchoring moiety through which it adheres to the TiO2 surface. Recent interest in exploiting the properties of differing TiO2 electrode morphologies, such as rutile nanorods exposing the (1 1 0) surface and anatase electrodes with high percentages of the (0 0 1) surface exposed, begs the question of whether this anchoring strategy is best, irrespective of the majority surface exposed. Here we address this question by presenting density functional theory calculations contrasting the binding properties of two promising anchoring groups, phosphonic acid and boronic acid, to that of carboxylic acid. Anchor-electrode interactions are studied for the prototypical anatase (1 0 1) surface, along with the anatase (0 0 1) and rutile (1 1 0) surfaces. Finally the effect of using these alternative anchoring groups to bind a typical coumarin dye (NKX-2311) to these TiO2 substrates is examined. Significant differences in the binding properties are found depending on both the anchor and surface, illustrating that the choice of anchor is necessarily dependent upon the surface exposed in the electrode. In particular the boronic acid is found to show the potential to be an excellent anchor choice for electrodes exposing the anatase (0 0 1) surface.

Quantum engineering at the silicon surface using dangling bonds.

Individual atoms and ions are now routinely manipulated using scanning tunnelling microscopes or electromagnetic traps for the creation and control of artificial quantum states. For applications such as quantum information processing, the ability to introduce multiple atomic-scale defects deterministically in a semiconductor is highly desirable. Here we use a scanning tunnelling microscope to fabricate interacting chains of dangling bond defects on the hydrogen-passivated silicon (001) surface. We image both the ground-state and the excited-state probability distributions of the resulting artificial molecular orbitals, using the scanning tunnelling microscope tip bias and tip-sample separation as gates to control which states contribute to the image. Our results demonstrate that atomically precise quantum states can be fabricated on silicon, and suggest a general model of quantum-state fabrication using other chemically passivated semiconductor surfaces where single-atom depassivation can be achieved using scanning tunnelling microscopy.

Δ Self-Consistent Field Method for Natural Anthocyanidin Dyes.

We present an application of the Δ self-consistent field (ΔSCF) method, which we have implemented and tested in the DFT code CONQUEST, on the study of excited states of natural anthocyanidin dyes. We show that ΔSCF allows relaxation of the atomic structure for systems in excited states by following gradients on the excited Born-Oppenheimer surface. We compare the vertical excitation energies of some anthocyanidins in gas-phase to results from time-dependent density functional theory (TDDFT) and experiments. To reproduce a typical dye-sensitized solar cell interface, we adsorb cyanidin on TiO2 anatase (101), focusing on the shift of the lowest excitation energy due to the adsorption. We have found that important modifications occur in the excited state geometry of the adsorbed cyanidin.

O(N) methods in electronic structure calculations.

Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.

Non-adiabatic simulations of current-related structural transformations in metallic nanodevices.

One of the less explored aspects of molecular electronics is the effect of current on the mechanical stability of the conducting molecule: charge flow can alter both the geometry and electronic properties of the device, modifying the conductance and giving rise to nonlinear conduction characteristics or conductance switching. We performed a fundamental study on the correlation between the geometry and evolving electronic structure of small Au clusters that were embedded in finite Au wires and subjected to periodic transient currents. Both the current-carrying electronic states and the local electronic structure of the model system were described away from the ground state within a time-dependent Ehrenfest formalism. Non-adiabatic molecular dynamics simulations revealed that clusters undergo structural transformations between several representative geometries that coincide with patterns in cluster charging. The shape changes were enabled by the fluctuations in cluster band filling associated with the current and assisted by current-related forces. Metastable configurations of stable clusters were linked to events of charge trapping on the cluster.

Spatially local parallel tempering for thermal-equilibrium sampling.

Parallel tempering (PT) is a set of techniques for accelerating thermal-equilibrium sampling in systems where the exploration of configuration space is hindered by energy barriers. With standard PT algorithms, the computational effort scales unfavorably with system size, so that it is difficult to apply them to large systems. We propose local PT algorithms, for which the computational effort is proportional to the number of degrees of freedom. We demonstrate the effectiveness of the new algorithms on two one-dimensional model systems, showing that results for selected observables are correctly reproduced, and that practical linear scaling is achieved. We show also that the algorithms are readily applied to systems in higher dimensions. We note the prospects for studying large extended systems, including surfaces and interfaces.

Calculations for millions of atoms with density functional theory: linear scaling shows its potential.

An overview of the CONQUEST linear scaling density functional theory (DFT) code is given, focusing particularly on the scaling behaviour on modern high-performance computing platforms. We demonstrate that essentially perfect linear scaling and weak parallel scaling (with fixed number of atoms per processor core) can be achieved, and that DFT calculations on millions of atoms are now possible.

The interaction of Cu with Bi nanolines on H-passivated Si(001): an ab initio analysis.

In spite of the known tendency for Cu to be a fast diffuser inside bulk Si, it was recently shown that it presents a clear preference for migrating towards a hydrogen terminated Si(001) surface along the dimer rows; on a surface with Bi nanolines, this will drive the Cu towards the Bi nanolines. In this paper, we present a density functional theory study of the behaviour of Cu atoms near self-assembled Bi nanolines on the hydrogen-passivated Si(001) surface, predicting that Cu will attack the nanolines and insert in the Bi-Si bonds. The migration routes from subsurface locations and surface deposition are found and the pairing tendency for Cu is examined and compared to that for Ag on Bi nanolines.

Atomic structure of misfit dislocations at InAs/GaAs(110).

Heteroepitaxy of InAs on GaAs(110) leads to the formation of subsurface misfit dislocations to relieve strain. These dislocations have been observed both with transmission electron microscopy (TEM) and scanning tunnelling microscopy (STM), and show regular spacing. Electronic structure calculations of the structure of the core of the dislocations, as well as their location within the epitaxial layer, are presented. The most stable location is found to be at the interface, with the core centred over In. Calculated strain profiles and the thickness at which dislocations should form are in good agreement with available experimental data.

Automatic data distribution and load balancing with space-filling curves: implementation in CONQUEST.

We present an automatic, spatially local data distribution and load balancing scheme applicable to many-body problems running on parallel architectures. The particle distribution is based on spatial decomposition of the simulation cell. A one-dimensional Hilbert curve is mapped onto the three-dimensional real space cell, which reduces the dimensionality of the problem and provides a way to assign different spatially local parts of the cell to each processor. The scheme is independent of the number of processors. It can be used for both ordered and disordered structures and does not depend on the dimensionality or shape of the system. Details of implementation in the linear-scaling density functional code CONQUEST, as well as several case studies of systems of various complexity, containing up to 55 755 particles, are given.

Factor V Leiden: prevalence and thromboembolic complications after total hip replacement in Ireland.

BACKGROUND: The Factor V Leiden (FVL) mutation is the commonest genetic abnormality associated with venous thromboembolism. AIMS: To determine the prevalence of the FVL mutation in Irish patients undergoing total hip replacement and whether it has an increased risk of deep venous thrombosis or pulmonary embolism (DVT/PE). METHODS: Prospective screening of 113 patients over 2 years. All had prophylaxis against thrombosis. Symptomatic DVT and PE were diagnosed with venography and ventilation-perfusion scans, respectively. RESULTS: The prevalence of the FVL mutation was 2%. Six patients (5.3%) developed a DVT/PE. Half of these had a history of venous thromboembolism (resulting in a higher risk of post operative DVT/PE (P = 0.04, Fischer's exact test) but none had the FVL mutation. Of the remaining 107 patients not developing DVT/PE, 2 had the FVL mutation (heterozygotes). CONCLUSIONS: The prevalence of the FVL mutation was 2% but was not a risk factor for acute symptomatic DVT/PE.