855 research outputs found
Robust non-adiabatic molecular dynamics for metals and insulators
We present a new formulation of the correlated electron-ion dynamics (CEID)
scheme, which systematically improves Ehrenfest dynamics by including quantum
fluctuations around the mean-field atomic trajectories. We show that the method
can simulate models of non-adiabatic electronic transitions, and test it
against exact integration of the time-dependent Schroedinger equation. Unlike
previous formulations of CEID, the accuracy of this scheme depends on a single
tunable parameter which sets the level of atomic fluctuations included. The
convergence to the exact dynamics by increasing the tunable parameter is
demonstrated for a model two level system. This algorithm provides a smooth
description of the non-adiabatic electronic transitions which satisfies the
kinematic constraints (energy and momentum conservation) and preserves quantum
coherence. The applicability of this algorithm to more complex atomic systems
is discussed.Comment: 36 pages, 5 figures. Accepted for publication in Journal of Chemical
Physic
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
Power dissipation in nanoscale conductors: classical, semi-classical and quantum dynamics
Modelling Joule heating is a difficult problem because of the need to introduce correct correlations between the motions of the ions and the electrons. In this paper we analyse three different models of current induced heating (a purely classical model, a fully quantum model and a hybrid model in which the electrons are treated quantum mechanically and the atoms are treated classically). We find that all three models allow for both heating and cooling processes in the presence of a current, and furthermore the purely classical and purely quantum models show remarkable agreement in the limit of high biases. However, the hybrid model in the Ehrenfest approximation tends to suppress heating. Analysis of the equations of motion reveals that this is a consequence of two things: the electrons are being treated as a continuous fluid and the atoms cannot undergo quantum fluctuations. A means for correcting this is suggested
Efficient electron open boundaries for simulating electrochemical cells
Nonequilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and leave the computational cell. Here we present a limiting form for electron open boundaries that we expect to apply when the magnitude of the electric current is determined by the drift and diffusion of ions in a solution and which is sufficiently computationally efficient to be used with molecular dynamics. We present tight-binding simulations of a parallel-plate capacitor with nothing, a dimer, or an atomic wire situated in the space between the plates. These simulations demonstrate that this scheme can be used to perform molecular dynamics simulations when there is an applied bias between two metal plates with, at most, weak electronic coupling between them. This simple system captures some of the essential features of an electrochemical cell, suggesting this approach might be suitable for simulations of electrochemical cells out of equilibrium
Validity and practical utility of accelerometry for the measurement of in-hand physical activity in horses
Background:
Accelerometers are valid, practical and reliable tools for the measurement of habitual physical activity (PA). Quantification of PA in horses is desirable for use in research and clinical settings. The objective of this study was to evaluate a triaxial accelerometer for objective measurement of PA in the horse by assessment of their practical utility and validity.
Horses were recruited to establish both the optimal site of accelerometer attachment and questionnaire designed to explore owner acceptance. Validity and cut-off values were obtained by assessing PA at various gaits. Validation study- 20 horses wore the accelerometer while being filmed for 10Â min each of rest, walking and trotting and 5 mins of canter work. Practical utility study- five horses wore accelerometers on polls and withers for 18Â h; compliance and relative data losses were quantified.
Results:
Accelerometry output differed significantly between the four PA levels (P <0•001) for both wither and poll placement. For withers placement, ROC analyses found optimal sensitivity and specificity at a cut-off of <47 counts per minute (cpm) for rest (sensitivity 99.5 %, specificity 100 %), 967–2424 cpm for trotting (sensitivity 96.7 %, specificity 100 %) and ≥2425 cpm for cantering (sensitivity 96.0 %, specificity 97.0 %). Attachment at the poll resulted in optimal sensitivity and specificity at a cut-off of <707 counts per minute (cpm) for rest (sensitivity 97.5 %, specificity 99.6 %), 1546–2609 cpm for trotting (sensitivity 90.33 %, specificity 79.25 %) and ≥2610 cpm for cantering (sensitivity 100 %, specificity 100 %) In terms of practical utility, accelerometry was well tolerated and owner acceptance high.
Conclusion:
Accelerometry data correlated well with varying levels of in-hand equine activity. The use of accelerometers is a valid method for objective measurement of controlled PA in the horse
Block bond-order potential as a convergent moments-based method
The theory of a novel bond-order potential, which is based on the block
Lanczos algorithm, is presented within an orthogonal tight-binding
representation. The block scheme handles automatically the very different
character of sigma and pi bonds by introducing block elements, which produces
rapid convergence of the energies and forces within insulators, semiconductors,
metals, and molecules. The method gives the first convergent results for
vacancies in semiconductors using a moments-based method with a low number of
moments. Our use of the Lanczos basis simplifies the calculations of the band
energy and forces, which allows the application of the method to the molecular
dynamics simulations of large systems. As an illustration of this convergent
O(N) method we apply the block bond-order potential to the large scale
simulation of the deformation of a carbon nanotube.Comment: revtex, 43 pages, 11 figures, submitted to Phys. Rev.
Adulteration and Poor Quality of Ginkgo biloba Supplements
Adulteration of Ginkgo products sold as unregistered supplements within the very large market of Ginkgo products (reputedly £650 million annually) through the post-extraction addition of cheaper (e.g. buckwheat derived) rutin is suspected to allow sub-standard products to appear satisfactory to third parties, e.g. secondary buyers along the value chain or any regulatory authorities. This study was therefore carried out to identify products that did not conform to their label specification and may have been actively adulterated to enable access to the global markets. 500 MHz Bruker NMR spectroscopy instrumentation combined with Topspin version 3.2 and a CAMAG HPTLC system (HPTLC Association for the analysis of Ginkgo biloba leaf) were used to generate NMR spectra (focusing on the 6–8 ppm region for analysis) and chromatograms, respectively. Out of the 35 samples of Ginkgo biloba analysed, 33 were found to contain elevated levels of rutin and/or quercetin, or low levels of Ginkgo metabolites when compared with the reference samples. Samples with disproportional levels of rutin or quercetin compared with other gingko metabolites are likely to be adulterated, either by accident or intentionally, and those samples with low or non-existent gingko metabolite content may have been produced using poor extraction techniques. Only two of the investigated samples were found to match with the High-Performance Thin-Layer Chromatography (HPTLC) fingerprint of the selected reference material. All others deviated significantly. One product contained a 5-hydroxytryptophan derivative, which is not a natural constituent of Ginkgo biloba. Overall, these examples either suggest a poor extraction technique or deliberate adulteration along the value chain. Investigating the ratio of different flavonoids e.g. quercetin and kaempferol using NMR spectroscopy and HPTLC will provide further evidence as to the degree and kind of adulteration of Gingko supplements. From a consumer perspective the equivalence in identity and overall quality of the products needs to be guaranteed for supplements too and not only for products produced according to a quality standard or pharmacopoeial monograph
spatial normalization and regional assessment of cord atrophy voxel based analysis of cervical cord 3d t1 weighted images
BACKGROUND AND PURPOSE: VBM is widely applied to characterize regional differences in brain volume among groups of subjects. The aim of this study was to develop and validate a method for voxelwise statistical analysis of cord volume and to test, with this method, the correlation between cord tissue loss and aging. MATERIALS AND METHODS: 3D T1-weighted scans of the spinal cord were acquired from 90 healthy subjects spanning several decades of life. Using an AS method, we outlined the cord surface and created output images reformatted with image planes perpendicular to the estimated cord centerline. Unfolded cervical cord images were coregistered into a common standard space, and smoothed cord binary masks, produced by using the cord outlines estimated by the AS approach, were used as input images for spatial statistics. RESULTS: High spatial correlation between normalized images was observed. Averaging of the normalized scans allowed the creation of a cervical cord template and of a standardized region-of-interest atlas. VBM analysis showed some significant associations between a decreased probability of cord tissue and aging. Results were robust across different smoothing levels, but the use of an anisotropic Gaussian kernel gave the optimal trade-off between spatial resolution and the requirements of the Gaussian random field theory. CONCLUSIONS: VBM analysis of the cervical cord was feasible and holds great promise for accurate localization of regional cord atrophy in several neurologic conditions
Optimal branching asymmetry of hydrodynamic pulsatile trees
Most of the studies on optimal transport are done for steady state regime
conditions. Yet, there exists numerous examples in living systems where supply
tree networks have to deliver products in a limited time due to the pulsatile
character of the flow. This is the case for mammals respiration for which air
has to reach the gas exchange units before the start of expiration. We report
here that introducing a systematic branching asymmetry allows to reduce the
average delivery time of the products. It simultaneously increases its
robustness against the unevitable variability of sizes related to
morphogenesis. We then apply this approach to the human tracheobronchial tree.
We show that in this case all extremities are supplied with fresh air, provided
that the asymmetry is smaller than a critical threshold which happens to fit
with the asymmetry measured in the human lung. This could indicate that the
structure is adjusted at the maximum asymmetry level that allows to feed all
terminal units with fresh air.Comment: 4 pages, 4 figure
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