The GeoClaw software for depth-averaged flows with adaptive refinement

Many geophysical flow or wave propagation problems can be modeled with two-dimensional depth-averaged equations, of which the shallow water equations are the simplest example. We describe the GeoClaw software that has been designed to solve problems of this nature, consisting of open source Fortran programs together with Python tools for the user interface and flow visualization. This software uses high-resolution shock-capturing finite volume methods on logically rectangular grids, including latitude--longitude grids on the sphere. Dry states are handled automatically to model inundation. The code incorporates adaptive mesh refinement to allow the efficient solution of large-scale geophysical problems. Examples are given illustrating its use for modeling tsunamis, dam break problems, and storm surge. Documentation and download information is available at www.clawpack.org/geoclawComment: 18 pages, 11 figures, Animations and source code for some examples at http://www.clawpack.org/links/awr10 Significantly modified from original posting to incorporate suggestions of referee

Electronic Properties of Two-Dimensional Carbon

We present a theoretical description of the electronic properties of graphene in the presence of disorder, electron-electron interactions, and particle-hole symmetry breaking. We show that while particle-hole asymmetry, long-range Coulomb interactions, and extended defects lead to the phenomenon of self-doping, local defects determine the transport and spectroscopic properties. Our results explain recent experiments in graphitic devices and predict new electronic behavior.Comment: 4 pages, 5 figures. The paper was originally submitted on May, 12th, 200

Acoustic Events in the Solar Atmosphere from Hinode/SOT NFI observations

We investigate the properties of acoustic events (AEs), defined as spatially concentrated and short duration energy flux, in the quiet sun using observations of a 2D field of view (FOV) with high spatial and temporal resolution provided by the Solar Optical Telescope (SOT) onboard \textit{Hinode}. Line profiles of Fe \textsc{i} 557.6 nm were recorded by the Narrow band Filter Imager (NFI) on a $82" \times 82"$ FOV during 75 min with a time step of 28.75 s and 0.08$"$ pixel size. Vertical velocities were computed at three atmospheric levels (80, 130 and 180 km) using the bisector technique allowing the determination of energy flux in the range 3-10 mHz using two complementary methods (Hilbert transform and Fourier power spectra). Horizontal velocities were computed using local correlation tracking (LCT) of continuum intensities providing divergences. The net energy flux is upward. In the range 3-10 mHz, a full FOV space and time averaged flux of 2700 W m$^{-2}$ (lower layer 80-130 km) and 2000 W m$^{-2}$ (upper layer 130-180 km) is concentrated in less than 1% of the solar surface in the form of narrow (0.3$"$) AE. Their total duration (including rise and decay) is of the order of $10^{3}$ s. Inside each AE, the mean flux is $1.6 10^{5}$ W m$^{-2}$ (lower layer) and $1.2 10^{5}$ W m$^{-2}$ (upper). Each event carries an average energy (flux integrated over space and time) of $2.5 10^{19}$ J (lower layer) to $1.9 10^{19}$ J (upper). More than $10^{6}$ events could exist permanently on the Sun, with a birth and decay rate of 3500 s$^{-1}$. Most events occur in intergranular lanes, downward velocity regions, and areas of converging motions.Comment: 18 pages, 10 figure

Stokes imaging polarimetry using image restoration at the Swedish 1-m Solar Telescope

Aims: We aim to achieve high spatial resolution as well as high polarimetric sensitivity, using an earth-based 1m-class solar telescope, for the study of magnetic fine structure on the Sun. Methods: We use a setup with 3 high-speed, low-noise cameras to construct datasets with interleaved polarimetric states, particularly suitable for Multi-Object Multi-Frame Blind Deconvolution image restorations. We discuss the polarimetric calibration routine as well as various potential sources of error in the results. Results: We obtained near diffraction limited images, with a noise level of approximately 10^(-3) I(cont). We confirm that dark-cores have a weaker magnetic field and at a lower inclination angle with respect to the solar surface than the edges of the penumbral filament. We show that the magnetic field strength in faculae-striations is significantly lower than in other nearby parts of the faculae.Comment: Accepted for publication in Astronomy & Astrophysics, 12 pages, 11 figure

Relationships that Heal: Beyond the Patient-Healer Dyad in Mayan Therapy

Biomedicine fosters particular styles of interaction and behaviors, with the therapeutic relationship seen as occurring between a doctor and patient. In contrast, where alternative modalities of healing are practiced, relationships go beyond a dyadic interaction and include wider social networks. In this article, we propose the existence of a ‘therapeutic unit’ in Maya healing practices in Guatemala that binds healer, wellness seeker, family, and community members, along with the spiritual and natural realms, into a coherent system requiring all of these elements to achieve success. Drawing on interviews with 67 Maya healers, we describe healers’ understanding of raxnaq’il nuk’aslemal (well-being), and show how these interactions activate wider networks that play crucial roles during treatments. We highlight how holism is expressed in relationships typical of indigenous healing systems, and how an appreciation of this is important for developing culturally appropriate health care provision systems

Traditional herbal medicine in Mesoamerica: toward its evidence base for improving universal health coverage

The quality of health care in Mesoamerica is influenced by its rich cultural diversity and characterized by social inequalities. Especially indigenous and rural communities confront diverse barriers to accessing formal health services, leading to often conflicting plurimedical systems. Fostering integrative medicine is a fundamental pillar for achieving universal health coverage (UHC) for marginalized populations. Recent developments toward health sovereignty in the region are concerned with assessing the role of traditional medicines, and particularly herbal medicines, to foster accessible and culturally pertinent healthcare provision models. In Mesoamerica, as in most regions of the world, a wealth of information on traditional and complementary medicine has been recorded. Yet these data are often scattered, making it difficult for policy makers to regulate and integrate traditionally used botanical products into primary health care. This critical review is based on a quantitative analysis of 28 survey papers focusing on the traditional use of botanical drugs in Mesoamerica used for the compilation of the "Mesoamerican Medicinal Plant Database" (MAMPDB), which includes a total of 12,537 use-records for 2188 plant taxa. Our approach presents a fundamental step toward UHC by presenting a pharmacological and toxicological review of the cross-culturally salient plant taxa and associated botanical drugs used in traditional medicine in Mesoamerica. Especially for native herbal drugs, data about safety and effectiveness are limited. Commonly used cross-culturally salient botanical drugs, which are considered safe but for which data on effectiveness is lacking constitute ideal candidates for treatment outcome studies

Dynamic optical coherence tomography of chronic venous ulcers

Background Chronic ulcers, especially venous leg ulcers, are a major burden on the healthcare system. To date there are only few non-invasive established procedures for evaluation of blood perfusion in wounds. Dynamic optical coherence tomography (D-OCT) provides images of the skin's superficial vascularisation. Objectives This study aims to investigate if and how the D-OCT measurement of chronic wounds can provide new information about the vascularisation during the healing process. Methods We examined 16 venous ulcers over 16 weeks and evaluated the vessel morphology and density using D-OCT at the wound bed, borders, two centimetres adjacent to the wound und at non-ulcerated skin on the contralateral leg. Results In D-OCT scans clumps were unique and the most common vessel type in the wound area of venous ulcers, whereas lines and serpiginous vessels were the most common in non-ulcerated skin. At the wound border mottle and cluster patterns occurred more frequently. Healthy skin showed a significant increase of mesh pattern. Vessel density significantly increased at the wound area compared to non-ulcerated skin. During the healing process the wound border showed the most vascular changes while only an increase in curves was observed in the wound centre. Non-healing wounds had fewer dots and blobs at the borders, fewer dots, coils, clumps, lines and serpiginous vessels at the centre and fewer dots in adjacent skin. Temperature analysis showed higher temperatures in non-ulcerated skin, followed by the wound margin and centre. Non-healing wounds showed the lowest temperatures in the wound centre. Conclusions These results highlight the non-invasive use of D-OCT for the examination and monitoring of wound healing in chronic venous ulcers. D-OCT imaging of blood vessels may offer the potential to detect disorders of wound healing at an early stage, differentiate ulcers of different genesis and to tailor more individualized, patient-oriented therapy

Models of electron transport in single layer graphene

The main features of the conductivity of doped single layer graphene are analyzed, and models for different scattering mechanisms are presented.Comment: 15 pages. Submitted to the Proceedings of the ULTI symposium on Quantum Phenomena and Devices at Low Temperatures, Espoo, Finland, to be published in the Journ. of Low. Temp. Phy

Transport properties of ybco thin films near the critical state with no applied field

Transport measurements carried out on twinned ybco films are compared to the predictions of a previously proposed model suggesting that the vortices move along the films twin boundaries that behave as rows of Josephson weak links [P.Bernstein and J.F.Hamet, J.Appl.Phys.95 (2004) 2569]. The obtained results suggest that, except if the films are very thin, the twin boundaries consist of superimposed rows of weak links with mean height,ds, whose mean length along the TBs is an universal function of T/Tc, the reduced temperature. This conclusion yields a general expression for the critical surface current density of the films as a function of T/Tc and of the number of superimposed weak links rows, while the critical current density depends on ds. A comparison of the measurements reported by various authors shows that the nature of the substrate and the growth technique have both a strong effect on ds . The existence of superimposed weak links rows is attributed to extended defects generated by y2o3 inclusions.Comment: 33 pages, 13 figures; accepted for publication in Physica