Feynman diagrams with the effective action

A derivation is given of the Feynman rules to be used in the perturbative computation of the Green's functions of a generic quantum many-body theory when the action which is being perturbed is not necessarily quadratic. Some applications are discussed.Comment: Extended revised version. RevTex, 19 pages, 10 figure

Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor

FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95% of the peak random access bandwidth limit when executed on the KNL and almost all the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature. IEE

On the parallelization of molecular dynamics codes

Abstract Molecular dynamics (MD) codes present a high degree of spatial data locality and a significant amount of independent computations. However, most of the parallelization strategies are usually based on the manual transformation of sequential programs either by completely rewriting the code with message passing routines or using specific libraries intended for writing new MD programs. In this paper we propose a new library-based approach (DDLY) which supports parallelization of existing short-range MD sequential codes. The novelty of this approach is that it can directly handle the distribution of common data structures used in MD codes to represent data (arrays, Verlet lists, link cells), using domain decomposition. Thus, the insertion of run-time support for distribution and communication in a MD program does not imply significant changes to its structure. The method is simple, efficient and portable. It may be also used to extend existing parallel programming languages, such as HPF

Contribution of phytochelatins to cadmium tolerance in peanut plants

Cadmium (Cd) is a well known heavy metal considered as one of the most toxic metals on Earth, affecting all viable cells that are exposed even at low concentration. It is introduced to agricultural soils mainly by phosphate fertilizers and causes many toxic symptoms in cells. Phytochelatins (PCs) are non-protein thiols which are involved in oxidative stress protection and are strongly induced by Cd. In this work, we analyzed metal toxicity as well as PCs implication on protection of peanut plants exposed to Cd. Results showed that Cd exposure induced a reduction of peanut growth and produced changes in the histological structure with a deposit of unknown material on the epidermal and endodermal cells. When plants were exposed to 10 μM Cd, no modification of chlorophyll, lipid peroxides, carbonyl groups, or hydrogen peroxide (H2O2) content was observed. At this concentration, peanut leaves and roots glutathione (GSH) content decreased. However, peanut roots were able to synthesize different types of PCs (PC2, PC3, PC4). In conclusion, PC synthesis could prevent metal disturbance on cellular redox balance, avoiding oxidative damage to macromolecules.Fil: Bianucci, Eliana Carolina. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Sobrino Plata, Juan. No especifíca;Fil: Carpena Ruiz, Ramón O.. Universidad Autónoma de Madrid; EspañaFil: Del Carmen Tordable, María. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; ArgentinaFil: Fabra, Adriana Isidora. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Hernández, Luis E.. No especifíca;Fil: Castro, Stella Maris. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentin

The AFLOW Fleet for Materials Discovery

The traditional paradigm for materials discovery has been recently expanded to incorporate substantial data driven research. With the intent to accelerate the development and the deployment of new technologies, the AFLOW Fleet for computational materials design automates high-throughput first principles calculations, and provides tools for data verification and dissemination for a broad community of users. AFLOW incorporates different computational modules to robustly determine thermodynamic stability, electronic band structures, vibrational dispersions, thermo-mechanical properties and more. The AFLOW data repository is publicly accessible online at aflow.org, with more than 1.7 million materials entries and a panoply of queryable computed properties. Tools to programmatically search and process the data, as well as to perform online machine learning predictions, are also available.Comment: 14 pages, 8 figure

Mononuclear Phagocytes and Airway Epithelial Cells: Novel Sources of Matrix Metalloproteinase-8 (MMP-8) in Patients with Idiopathic Pulmonary Fibrosis

Objectives: Matrix metalloproteinase-8 (MMP-8) promotes lung fibrotic responses to bleomycin in mice. Although prior studies reported that MMP-8 levels are increased in plasma and bronchoalveolar lavage fluid (BALF) samples from IPF patients, neither the bioactive forms nor the cellular sources of MMP-8 in idiopathic pulmonary fibrosis (IPF) patients have been identified. It is not known whether MMP-8 expression is dys-regulated in IPF leukocytes or whether MMP-8 plasma levels correlate with IPF outcomes. Our goal was to address these knowledge gaps. Methods: We measured MMP-8 levels and forms in blood and lung samples from IPF patients versus controls using ELISAs, western blotting, and qPCR, and assessed whether MMP-8 plasma levels in 73 IPF patients correlate with rate of lung function decline and mortality. We used immunostaining to localize MMP-8 expression in IPF lungs. We quantified MMP-8 levels and forms in blood leukocytes from IPF patients versus controls. Results: IPF patients have increased BALF, whole lung, and plasma levels of soluble MMP-8 protein. Active MMP-8 is the main form elevated in IPF lungs. MMP-8 mRNA levels are increased in monocytes from IPF patients, but IPF patients and controls have similar levels of MMP-8 in PMNs. Surprisingly, macrophages and airway epithelial cells are the main cells expressing MMP-8 in IPF lungs. Plasma and BALF MMP-8 levels do not correlate with decline in lung function and/or mortality in IPF patients. Conclusion: Blood and lung MMP-8 levels are increased in IPF patients. Active MMP-8 is the main form elevated in IPF lungs. Surprisingly, blood monocytes, lung macrophages, and airway epithelial cells are the main cells in which MMP-8 is upregulated in IPF patients. Plasma and BALF MMP-8 levels are unlikely to serve as a prognostic biomarker for IPF patients. These results provide new information about the expression patterns of MMP-8 in IPF patients

Sex differences in mortality in patients with COPD

Little is known about survival and clinical prognostic factors in females with chronic obstructive pulmonary disease (COPD). The aim of the present study was to determine the survival difference between males and females with COPD and to compare the value of the different prognostic factors for the disease. In total, 265 females and 272 males with COPD matched at baseline by BODE (body mass index, airflow obstruction, dyspnoea, exercise capacity) and American Thoracic Society/European Respiratory Society/Global Initiative of Chronic Obstructive Lung Disease criteria were prospectively followed. Demographics, lung function, St George’s Respiratory Questionnaire, BODE index, the components of the BODE index and comorbidity were determined. Survival was documented and sex differences were determined using Kaplan–Meier analysis. The strength of the association of the studied variables with mortality was determined using multivariate and receiver operating curves analysis. All-cause (40 versus 18%) and respiratory mortality (24 versus 10%) were higher in males than females. Multivariate analysis identified the BODE index in females and the BODE index and Charlson comorbidity score in males as the best predictors of mortality. The area under the curve of the BODE index was a better predictor of mortality than the forced expiratory volume in one second for both sexes. At similar chronic obstructive pulmonary disease severity by BODE index and forced expiratory volume in one second, females have significantly better survival than males. For both sexes the BODE index is a better predictor of survival than the forced expiratory volume in one second

Ionization via Chaos Assisted Tunneling

A simple example of quantum transport in a classically chaotic system is studied. It consists in a single state lying on a regular island (a stable primary resonance island) which may tunnel into a chaotic sea and further escape to infinity via chaotic diffusion. The specific system is realistic : it is the hydrogen atom exposed to either linearly or circularly polarized microwaves. We show that the combination of tunneling followed by chaotic diffusion leads to peculiar statistical fluctuation properties of the energy and the ionization rate, especially to enhanced fluctuations compared to the purely chaotic case. An appropriate random matrix model, whose predictions are analytically derived, describes accurately these statistical properties.Comment: 30 pages, 11 figures, RevTeX and postscript, Physical Review E in pres