Efficient simulations with electronic open boundaries

We present a reformulation of the Hairy Probe method for introducing electronic open boundaries that is appropriate for steady state calculations involving non-orthogonal atomic basis sets. As a check on the correctness of the method we investigate a perfect atomic wire of Cu atoms, and a perfect non-orthogonal chain of H atoms. For both atom chains we find that the conductance has a value of exactly one quantum unit, and that this is rather insensitive to the strength of coupling of the probes to the system, provided values of the coupling are of the same order as the mean inter-level spacing of the system without probes. For the Cu atom chain we find in addition that away from the regions with probes attached, the potential in the wire is uniform, while within them it follows a predicted exponential variation with position. We then apply the method to an initial investigation of the suitability of graphene as a contact material for molecular electronics. We perform calculations on a carbon nanoribbon to determine the correct coupling strength of the probes to the graphene, and obtain a conductance of about two quantum units corresponding to two bands crossing the Fermi surface. We then compute the current through a benzene molecule attached to two graphene contacts and find only a very weak current because of the disruption of the π-conjugation by the covalent bond between the benzene and the graphene. In all cases we find that very strong or weak probe couplings suppress the current

Using drones and sirens to elicit avoidance behaviour in white rhinoceros as an anti-poaching tactic.

Poaching fuelled by international trade in horn caused the deaths of over 1000 African rhinoceros (Ceratotherium simum and Diceros bicornis) per year between 2013 and 2017. Deterrents, which act to establish avoidance behaviours in animals, have the potential to aid anti-poaching efforts by moving at-risk rhinos away from areas of danger (e.g. near perimeter fences). To evaluate the efficacy of deterrents, we exposed a population of southern white rhinos (C. simum simum) to acoustic- (honeybee, siren, turtle dove), olfactory- (chilli, sunflower), and drone-based stimuli on a game reserve in South Africa. We exposed rhinos to each stimulus up to four times. Stimuli were considered effective deterrents if they repeatedly elicited avoidance behaviour (locomotion away from the deterrent). Rhinos travelled significantly further in response to the siren than to the honeybee or turtle dove stimulus, and to low-altitude drone flights than to higher altitude flights. We found the drone to be superior at manipulating rhino movement than the siren owing to its longer transmission range and capability of pursuit. By contrast, the scent stimuli were ineffective at inciting avoidance behaviour. Our findings indicate that deterrents are a prospective low-cost and in situ method to manage rhino movement in game reserves

An efficient and locking-free material point method for three dimensional analysis with simplex elements

The Material Point Method is a relative newcomer to the world of solid mechanicsmodelling. Its key advantage is the ability to model problems having large defor-mations while being relatively close to standard nite element methods, howeverits use for realistic engineering applications will happen only if the material pointcan be shown to be both ecient and accurate (compared to standard nite elementmethods), when modelling complex geometries with a range of material models. Inthis paper we present developments of the standard material point method aimed atrealising these goals. The key contribution provided here is the development of amaterial point method that avoids volumetric locking (arising from elastic or elasto-plastic material behaviour) whilst using low order tetrahedral nite elements forthe background computational mesh, hence allowing unstructured background gridsto be used for complex geometries. We also show that these developments can beeectively parallelised to improve computational ecienc

Influences of Excluded Volume of Molecules on Signaling Processes on Biomembrane

We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by i) monotonically increasing; ii) increasing then decreasing in a bell-shaped curve; or iii) increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor.Comment: 31 pages, 10 figure

Predicting participation in group parenting education in an Australian sample: The role of attitudes, norms, and control factors

We examined the theory of planned behavior (TPB) in predicting intentions to participate in group parenting education. One hundred and seventy-six parents (138 mothers and 38 fathers) with a child under 12 years completed TPB items assessing attitude, subjective norms, perceived behavioral control (PBC), and two additional social influence variables (self-identity and group norm). Regression analyses supported the TPB predictors of participation intentions with self-identity and group norm also significantly predicting intentions. These findings offer preliminary support for the TPB, along with additional sources of social influence, as a useful predictive model of participation in parenting education

Inward Rectifier Current Downregulation Promotes Spontaneous Calcium Release in a Novel Model of Rat Ventricular Electrophysiology

Aberrant intracellular calcium handling, as observed in diseases such as heart failure, promotes lethal ventricular arrhythmias and sudden cardiac death. Recent data from our laboratory suggests that reduced expression of the inward rectifier current in failing rat myocytes increases spontaneous calcium release, however existing computational models are unable to reproduce the underlying stochastic calcium cycling dynamics and so we have been unable to use simulation approaches to explore the cause of this pro-arrhythmic behaviour. Here, we develop a novel model of rat ventricular electrophysiology that reproduces normal spatio-temporal calcium dynamics. Simulations implementing a similar reduction in inward rectifier current to that observed experimentally show that spontaneous calcium release is promoted by action potential prolongation and sarcoplasmic reticulum loading in the presence of a depolarised resting membrane potential. Combined, these effects can result in triggered activity. The model therefore provides insight into arrhythmogenic mechanisms in failing ventricular myocytes and can be utilised to further explore pro-arrhythmic behaviour caused by abnormal calcium handling

Negligible hormonal response following dehorning in free-ranging white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) is experiencing unsustainable poaching losses fuelled by a demand for horn. Increasingly, private and state reserves are dehorning their rhinoceros populations in an attempt to reduce poaching pressure. Rhinoceroses use their horns in social interactions as well as during resource access and so its partial removal as part of reserve management practices may adversely influence these behaviours. Physiological stress can correlate with animal welfare, reproductive state and health and thus acts as a useful indicator of these parameters. To establish whether dehorning causes a physiological stress response, glucocorticoid and gonadal steroid profiles of free-ranging white rhinoceroses were determined through the collection and analysis of faecal steroid metabolites before and after dehorning. Faecal corticoid profiles were not influenced by the number of occasions a rhinoceros had been dehorned or by the number of days that had elapsed since dehorning. Furthermore, there was no apparent suppression in the concentrations of testosterone or progesterone metabolites in males and females, respectively, after exposure to multiple dehorning procedures. These findings should increase wildlife managers' confidence that dehorning does not negatively impact white rhinoceros physiology as measured hormonally

Multi-scale approaches for the simulation of cardiac electrophysiology: II - tissue-level structure and function

Computational models of the heart, from cell-level models, through one-, two- and three-dimensional tissue-level simplifications, to biophysically-detailed three-dimensional models of the ventricles, atria or whole heart, allow the simulation of excitation and propagation of this excitation, and have provided remarkable insight into the normal and pathological functioning of the heart. In this article we present equations for modelling cellular excitation (i.e. the cell action potential) from both a phenomenological and a biophysical perspective. Hodgkin-Huxley formalism is discussed, along with the current generation of biophysically-detailed cardiac cell models. Alternative Markovian formulations for modelling ionic currents are also presented. Equations describing propagation of this cellular excitation, through one-, two- and three-dimensional idealised or realistic tissues, are then presented. For all types of model, from cell to tissue, methods for discretisation and integration of the underlying equations are discussed. The article finishes with a discussion of two tissue-level experimental imaging techniques – diffusion tensor magnetic resonance imaging and optical imaging – that can be used to provide data for parameterisation and validation of cell- and tissue-level cardiac models

Electronic transport in polycrystalline graphene

Most materials in available macroscopic quantities are polycrystalline. Graphene, a recently discovered two-dimensional form of carbon with strong potential for replacing silicon in future electronics, is no exception. There is growing evidence of the polycrystalline nature of graphene samples obtained using various techniques. Grain boundaries, intrinsic topological defects of polycrystalline materials, are expected to dramatically alter the electronic transport in graphene. Here, we develop a theory of charge carrier transmission through grain boundaries composed of a periodic array of dislocations in graphene based on the momentum conservation principle. Depending on the grain boundary structure we find two distinct transport behaviours - either high transparency, or perfect reflection of charge carriers over remarkably large energy ranges. First-principles quantum transport calculations are used to verify and further investigate this striking behaviour. Our study sheds light on the transport properties of large-area graphene samples. Furthermore, purposeful engineering of periodic grain boundaries with tunable transport gaps would allow for controlling charge currents without the need of introducing bulk band gaps in otherwise semimetallic graphene. The proposed approach can be regarded as a means towards building practical graphene electronics.Comment: accepted in Nature Material