10 research outputs found
Magnetic response of carbon nanotubes from ab initio calculations
We present {\it ab initio} calculations of the magnetic susceptibility and of
the C chemical shift for carbon nanotubes, both isolated and in bundles.
These calculations are performed using the recently proposed gauge-including
projector augmented-wave approach for the calculation of magnetic response in
periodic insulating systems. We have focused on the semiconducting zigzag
nanotubes with diameters ranging from 0.6 to 1.6 nm. Both the susceptibility
and the isotropic shift exhibit a dependence with the diameter (D) and the
chirality of the tube (although this dependence is stronger for the
susceptibility). The isotropic shift behaves asymptotically as , where is a different constant for each family of nanotubes.
For a tube diameter of around 1.2 nm, a value normally found in experimental
samples, our results are in excellent agreement with experiments. Moreover, we
calculated the chemical shift of a double-wall tube. We found a diamagnetic
shift of the isotropic lines corresponding to the atoms of the inner tube due
to the effect of the outer tube. This shift is in good agreement with recent
experiments, and can be easily explained by demagnetizing currents circulating
the outer tube.Comment: 7 pages, 4 figure
Robust sparse image reconstruction of radio interferometric observations with purify
Next-generation radio interferometers, such as the Square Kilometre Array
(SKA), will revolutionise our understanding of the universe through their
unprecedented sensitivity and resolution. However, to realise these goals
significant challenges in image and data processing need to be overcome. The
standard methods in radio interferometry for reconstructing images, such as
CLEAN, have served the community well over the last few decades and have
survived largely because they are pragmatic. However, they produce
reconstructed inter\-ferometric images that are limited in quality and
scalability for big data. In this work we apply and evaluate alternative
interferometric reconstruction methods that make use of state-of-the-art sparse
image reconstruction algorithms motivated by compressive sensing, which have
been implemented in the PURIFY software package. In particular, we implement
and apply the proximal alternating direction method of multipliers (P-ADMM)
algorithm presented in a recent article. First, we assess the impact of the
interpolation kernel used to perform gridding and degridding on sparse image
reconstruction. We find that the Kaiser-Bessel interpolation kernel performs as
well as prolate spheroidal wave functions, while providing a computational
saving and an analytic form. Second, we apply PURIFY to real interferometric
observations from the Very Large Array (VLA) and the Australia Telescope
Compact Array (ATCA) and find images recovered by PURIFY are higher quality
than those recovered by CLEAN. Third, we discuss how PURIFY reconstructions
exhibit additional advantages over those recovered by CLEAN. The latest version
of PURIFY, with developments presented in this work, is made publicly
available.Comment: 22 pages, 10 figures, PURIFY code available at
http://basp-group.github.io/purif
Distributed and parallel sparse convex optimization for radio interferometry with PURIFY
Next generation radio interferometric telescopes are entering an era of big
data with extremely large data sets. While these telescopes can observe the sky
in higher sensitivity and resolution than before, computational challenges in
image reconstruction need to be overcome to realize the potential of
forthcoming telescopes. New methods in sparse image reconstruction and convex
optimization techniques (cf. compressive sensing) have shown to produce higher
fidelity reconstructions of simulations and real observations than traditional
methods. This article presents distributed and parallel algorithms and
implementations to perform sparse image reconstruction, with significant
practical considerations that are important for implementing these algorithms
for Big Data. We benchmark the algorithms presented, showing that they are
considerably faster than their serial equivalents. We then pre-sample gridding
kernels to scale the distributed algorithms to larger data sizes, showing
application times for 1 Gb to 2.4 Tb data sets over 25 to 100 nodes for up to
50 billion visibilities, and find that the run-times for the distributed
algorithms range from 100 milliseconds to 3 minutes per iteration. This work
presents an important step in working towards computationally scalable and
efficient algorithms and implementations that are needed to image observations
of both extended and compact sources from next generation radio interferometers
such as the SKA. The algorithms are implemented in the latest versions of the
SOPT (https://github.com/astro-informatics/sopt) and PURIFY
(https://github.com/astro-informatics/purify) software packages {(Versions
3.1.0)}, which have been released alongside of this article.Comment: 25 pages, 5 figure
Abnormal morphology biases haematocrit distribution in tumour vasculature and contributes to heterogeneity in tissue oxygenation
Oxygen heterogeneity in solid tumors is recognized as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal vascular structure of the tumor, but the precise mechanisms linking abnormal structure and compromised oxygen transport are only partially understood. In this paper, we investigate the role that red blood cell (RBC) transport plays in establishing oxygen heterogeneity in tumor tissue. We focus on heterogeneity driven by network effects, which are challenging to observe experimentally due to the reduced fields of view typically considered. Motivated by our findings of abnormal vascular patterns linked to deviations from current RBC transport theory, we calculated average vessel lengths L⎯⎯
and diameters d⎯⎯
from tumor allografts of three cancer cell lines and observed a substantial reduction in the ratio λ=L⎯⎯/d⎯⎯
compared to physiological conditions. Mathematical modeling reveals that small values of the ratio λ (i.e., λ<6
) can bias hematocrit distribution in tumor vascular networks and drive heterogeneous oxygenation of tumor tissue. Finally, we show an increase in the value of λ in tumor vascular networks following treatment with the antiangiogenic cancer agent DC101. Based on our findings, we propose λ as an effective way of monitoring the efficacy of antiangiogenic agents and as a proxy measure of perfusion and oxygenation in tumor tissue undergoing antiangiogenic treatment
Spin and orbital magnetic response in metals: Susceptibility and NMR shifts
A DFT-based method is presented which allows the computation of all-electron NMR shifts of metallic compounds with periodic boundary conditions. NMR shifts in metals measure two competing physical phenomena. Electrons interact with the applied magnetic field (i) as magnetic dipoles (or spins), resulting in the Knight shift, and (ii) as moving electric charges, resulting in the chemical (or orbital) shift. The latter is treated through an extension to metals of the gauge-invariant projector augmented wave developed for insulators. The former is modeled as the hyperfine interaction between the electronic spin polarization and the nuclear dipoles. NMR shifts are obtained with respect to the computed shieldings of reference compounds, yielding fully ab initio quantities which are directly comparable to experiment. The method is validated by comparing the magnetic susceptibility of interacting and noninteracting homogeneous gas with known analytical results, and by comparing the computed NMR shifts of simple metals with experiment
Distributed and parallel sparse convex optimization for radio interferometry with PURIFY
Next generation radio interferometric telescopes are entering an era of big data with extremely large data sets. While these telescopes can observe the sky in higher sensitivity and resolution than before, computational challenges in image reconstruction need to be overcome to realize the potential of forthcoming telescopes. New methods in sparse image reconstruction and convex optimization techniques (cf. compressive sensing) have shown to produce higher fidelity reconstructions of simulations and real observations than traditional methods. This article presents distributed and parallel algorithms and implementations to perform sparse image reconstruction, with significant practical considerations that are important for implementing these algorithms for Big Data. We benchmark the algorithms presented, showing that they are considerably faster than their serial equivalents. We then pre-sample gridding kernels to scale the distributed algorithms to larger data sizes, showing application times for 1 Gb to 2.4 Tb data sets over 25 to 100 nodes for up to 50 billion visibilities, and find that the run-times for the distributed algorithms range from 100 milliseconds to 3 minutes per iteration. This work presents an important step in working towards computationally scalable and efficient algorithms and implementations that are needed to image observations of both extended and compact sources from next generation radio interferometers such as the SKA. The algorithms are implemented in the latest versions of the SOPT (https://github.com/astro-informatics/sopt) and PURIFY (https://github.com/astro-informatics/purify) software packages {(Versions 3.1.0)}, which have been released alongside of this article