74 research outputs found
A parallel Heap-Cell Method for Eikonal equations
Numerous applications of Eikonal equations prompted the development of many
efficient numerical algorithms. The Heap-Cell Method (HCM) is a recent serial
two-scale technique that has been shown to have advantages over other serial
state-of-the-art solvers for a wide range of problems. This paper presents a
parallelization of HCM for a shared memory architecture. The numerical
experiments in show that the parallel HCM exhibits good algorithmic
behavior and scales well, resulting in a very fast and practical solver.
We further explore the influence on performance and scaling of data
precision, early termination criteria, and the hardware architecture. A shorter
version of this manuscript (omitting these more detailed tests) has been
submitted to SIAM Journal on Scientific Computing in 2012.Comment: (a minor update to address the reviewers' comments) 31 pages; 15
figures; this is an expanded version of a paper accepted by SIAM Journal on
Scientific Computin
Wavelet Methods for Studying the Onset of Strong Plasma Turbulence
Wavelet basis functions are a natural tool for analyzing turbulent flows
containing localized coherent structures of different spatial scales. Here,
wavelets are used to study the onset and subsequent transition to fully
developed turbulence from a laminar state. Originally applied to neutral fluid
turbulence, an iterative wavelet technique decomposes the field into coherent
and incoherent contributions. In contrast to Fourier power spectra, finite time
Lyapunov exponents (FTLE), and simple measures of intermittency such as
non-Gaussian statistics of field increments, the wavelet technique is found to
provide a quantitative measure for the onset of turbulence and to track the
transition to fully developed turbulence. The wavelet method makes no
assumptions about the structure of the coherent current sheets or the
underlying plasma model. Temporal evolution of the coherent and incoherent
wavelet fluctuations is found to be highly correlated with the magnetic field
energy and plasma thermal energy, respectively. The onset of turbulence is
identified with the rapid growth of a background of incoherent fluctuations
spreading across a range of scales and a corresponding drop in the coherent
components. This is suggestive of the interpretation of the coherent and
incoherent wavelet fluctuations as measures of coherent structures (e.g.,
current sheets) and dissipation, respectively. The ratio of the incoherent to
coherent fluctuations is found to be fairly uniform across different
plasma models and provides an empirical threshold for turbulence onset. The
technique is illustrated through examples. First, it is applied to the
Kelvin--Helmholtz instability from different simulation models including fully
kinetic, hybrid (kinetic ion/fluid electron), and Hall MHD simulations. Second,
it is applied to the development of turbulence downstream of the bowshock in a
magnetosphere simulation
Droplets I: Pressure-Dominated Sub-0.1 pc Coherent Structures in L1688 and B18
We present the observation and analysis of newly discovered coherent
structures in the L1688 region of Ophiuchus and the B18 region of Taurus. Using
data from the Green Bank Ammonia Survey (GAS), we identify regions of high
density and near-constant, almost-thermal, velocity dispersion. Eighteen
coherent structures are revealed, twelve in L1688 and six in B18, each of which
shows a sharp "transition to coherence" in velocity dispersion around its
periphery. The identification of these structures provides a chance to study
the coherent structures in molecular clouds statistically. The identified
coherent structures have a typical radius of 0.04 pc and a typical mass of 0.4
Msun, generally smaller than previously known coherent cores identified by
Goodman et al. (1998), Caselli et al. (2002), and Pineda et al. (2010). We call
these structures "droplets." We find that unlike previously known coherent
cores, these structures are not virially bound by self-gravity and are instead
predominantly confined by ambient pressure. The droplets have density profiles
shallower than a critical Bonnor-Ebert sphere, and they have a velocity (VLSR)
distribution consistent with the dense gas motions traced by NH3 emission.
These results point to a potential formation mechanism through pressure
compression and turbulent processes in the dense gas. We present a comparison
with a magnetohydrodynamic simulation of a star-forming region, and we
speculate on the relationship of droplets with larger, gravitationally bound
coherent cores, as well as on the role that droplets and other coherent
structures play in the star formation process.Comment: Accepted by ApJ in April, 201
N1-acetylspermidine is a determinant of hair follicle stem cell fate
Stem cell differentiation is accompanied by increased mRNA translation. The rate of protein biosynthesis is influenced by the polyamines putrescine, spermidine and spermine, which are essential for cell growth and stem cell maintenance. However, the role of polyamines as endogenous effectors of stem cell fate and whether they act through translational control remains obscure. Here, we investigate the function of polyamines in stem cell fate decisions using hair follicle stem cell (HFSC) organoids. Compared to progenitor cells, HFSCs showed lower translation rates, correlating with reduced polyamine levels. Surprisingly, overall polyamine depletion decreased translation but did not affect cell fate. In contrast, specific depletion of natural polyamines mediated by spermidine/spermine N1-acetyltransferase (SSAT; also known as SAT1) activation did not reduce translation but enhanced stemness. These results suggest a translation-independent role of polyamines in cell fate regulation. Indeed, we identified N1-acetylspermidine as a determinant of cell fate that acted through increasing self-renewal, and observed elevated N1-acetylspermidine levels upon depilation-mediated HFSC proliferation and differentiation in vivo. Overall, this study delineates the diverse routes of polyamine metabolism-mediated regulation of stem cell fate decisions. This article has an associated First Person interview with the first author of the paper.Peer reviewe
Standard Model Handles and Candles Working Group: Tools and Jets Summary Report
This report summarizes the activity on comparisons of existings tools for the
standard model and on issues in jet physics by the SMHC working group during
and subsequent to the Workshop "Physics at TeV Colliders", Les Houches, France,
11-29 June, 2007.Comment: 94 pages, LaTeX, many figures. Summary report of the tools and jets
parts of the SMHC working group of the Les Houches 2007 workshop "Physics at
TeV Colliders", Les Houches, France, 11-29 June, 200
Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study
Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised
Eikonal Equations: New Two-Scale Algorithms And Error Analysis
Hamilton-Jacobi equations arise in a number of seemingly disparate applications, from front propagation to photolithography to robotic navigation. Eikonal equations fall into an important subset representing isotropic optimal control and often are used as a first benchmark for numerical methods. Many of the interesting geometrical properties of Eikonal and related equations are exploited in two families of popular algorithms: the single-pass Fast Marching Methods and the iterative Fast Sweeping Methods. We start by developing a class of two-scale hybrid algorithms that combine the ideas of these prior methods on different scales. These hybrid methods are shown to have a clear advantage compared to other serial algorithms, but more importantly, one of them ("HCM") is very suitable for parallelization on a shared memory architecture. Our extensive numerical experiments benchmark this parallel HCM against current serial methods and another parallel state-of-the-art solver for the same computer architecture. We demonstrate the robustness of the parallel HCM on a wide range of problems, its good scaling in the number of processors, and its efficiency in solving a problem from exploratory geophysics. In the last part, we focus on estimating the error committed by fast approximate methods that introduce boundary data pollution. Examples include domain restriction methods for recovering only a single optimal path between a source/target pair and a domain decomposition method that creates subdomains whose boundaries are approximately characteristic. In simple cases we use a novel technique to estimate the sensitivity of a gridpoint to other gridpoints in its computational domain of dependence and use this to bound the error
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