Diagnosing numerical Cherenkov instabilities in relativistic plasma simulations based on general meshes

Numerical Cherenkov radiation (NCR) or instability is a detrimental effect frequently found in electromagnetic particle-in-cell (EM-PIC) simulations involving relativistic plasma beams. NCR is caused by spurious coupling between electromagnetic-field modes and multiple beam resonances. This coupling may result from the slow down of poorly-resolved waves due to numerical (grid) dispersion and from aliasing mechanisms. NCR has been studied in the past for finite-difference-based EM-PIC algorithms on regular (structured) meshes with rectangular elements. In this work, we extend the analysis of NCR to finite-element-based EM-PIC algorithms implemented on unstructured meshes. The influence of different mesh element shapes and mesh layouts on NCR is studied. Analytic predictions are compared against results from finite-element-based EM-PIC simulations of relativistic plasma beams on various mesh types.Comment: 31 pages, 20 figure

Finite Element Time-Domain Body-of-Revolution Maxwell Solver based on Discrete Exterior Calculus

We present a finite-element time-domain (FETD) Maxwell solver for the analysis of body-of-revolution (BOR) geometries based on discrete exterior calculus (DEC) of differential forms and transformation optics (TO) concepts. We explore TO principles to map the original 3-D BOR problem to a 2-D one in the meridian plane based on a Cartesian coordinate system where the cylindrical metric is fully embedded into the constitutive properties of an effective inhomogeneous and anisotropic medium that fills the domain. The proposed solver uses a TE/TM field decomposition and an appropriate set of DEC-based basis functions on an irregular grid discretizing the meridian plane. A symplectic time discretization based on a leap-frog scheme is applied to obtain the full-discrete marching-on-time algorithm. We validate the algorithm by comparing the numerical results against analytical solutions for resonant fields in cylindrical cavities and against pseudo-analytical solutions for fields radiated by cylindrically symmetric antennas in layered media. We also illustrate the application of the algorithm for a particle-in-cell (PIC) simulation of beam-wave interactions inside a high-power backward-wave oscillator.Comment: 42 pages, 19 figure

Quantum Information Propagation Preserving Computational Electromagnetics

We propose a new methodology, called numerical canonical quantization, to solve quantum Maxwell's equations useful for mathematical modeling of quantum optics physics, and numerical experiments on arbitrary passive and lossless quantum-optical systems. It is based on: (1) the macroscopic (phenomenological) electromagnetic theory on quantum electrodynamics (QED), and (2) concepts borrowed from computational electromagnetics. It was shown that canonical quantization in inhomogeneous dielectric media required definite and proper normal modes. Here, instead of ad-hoc analytic normal modes, we numerically construct complete and time-reversible normal modes in the form of traveling waves to diagonalize the Hamiltonian. Specifically, we directly solve the Helmholtz wave equations for a general linear, reciprocal, isotropic, non-dispersive, and inhomogeneous dielectric media by using either finite-element or finite-difference methods. To convert a scattering problem with infinite number of modes into one with a finite number of modes, we impose Bloch-periodic boundary conditions. This will sparsely sample the normal modes with numerical Bloch-Floquet-like normal modes. Subsequent procedure of numerical canonical quantization is straightforward using linear algebra. We provide relevant numerical recipes in detail and show an important numerical example of indistinguishable two-photon interference in quantum beam splitters, exhibiting Hong-Ou-Mandel effect, which is purely a quantum effect. Also, the present methodology provides a way of numerically investigating existing or new macroscopic QED theories. It will eventually allow quantum-optical numerical experiments of high fidelity to replace many real experiments as in classical electromagnetics.Comment: 17 pages, 11 figures, journal article submitted to Physical review A (under review

Accelerating Particle-in-Cell Kinetic Plasma Simulations via Reduced-Order Modeling of Space-Charge Dynamics using Dynamic Mode Decomposition

We present a data-driven reduced-order modeling of the space-charge dynamics for electromagnetic particle-in-cell (EMPIC) plasma simulations based on dynamic mode decomposition (DMD). The dynamics of the charged particles in kinetic plasma simulations such as EMPIC is manifested through the plasma current density defined on the edges of the spatial mesh. We showcase the efficacy of DMD in modeling the time evolution of current density through a low-dimensional feature space. Not only do such DMD-based predictive reduced-order models help accelerate EMPIC simulations, they also have the potential to facilitate investigative analysis and control applications. We demonstrate the proposed DMD-EMPIC scheme for reduced-order modeling of current density, and speed-up in EMPIC simulations involving electron beams under the influence of magnetic fields and virtual cathode oscillations

Novel hydrogel obtained by chitosan and dextrin-VA co-polymerization

A novel hydrogel was obtained by reticulation of chitosan with dextrin enzymatically linked to vinyl acrylate (dextrin-VA), without cross-linking agents. The hydrogel had a solid-like behaviour with G′ (storage modulus) >> G″ (loss modulus). Glucose diffusion coefficients of 3.9 × 10−6 ± 1.3 × 10−6 cm2/s and 2.9 × 10−6 ± 0.5 × 10−6 cm2/s were obtained for different substitution degrees of the dextrin-VA (20% and 70% respectively). SEM observation revealed a porous structure, with pores ranging from 50 µm to 150 µm

Principles and process for developing participatory adaptation pathways in the primary industries

Adaptation pathways is an approach to identify, assess, and sequence climate change adaptation options over time, linking decisions to critical signals and triggers derived from scenarios of future conditions. However, conceptual differences in their development can hinder methodological advance and create a disconnect between those applying pathways approaches and the wider community of practitioners undertaking vulnerability, impacts, and adaptation assessments. Here, we contribute to close these gaps, advancing principles, and processes that may be used to guide the trajectory for adaptation pathways, without having to rely on data-rich or resource-intensive methods. To achieve this, concepts and practices from the broad pathways literature is combined with our own experience in developing adaptation pathways for primary industries facing the combined impacts of climate change and other, nonclimatic stressors. Each stage is guided by a goal and tools to facilitate discussions and produce feasible pathways. We illustrate the process with a case study from Hawke’s Bay, New Zealand, involving multiple data sources and methods in two catchments. Resulting guidelines and empirical examples are consistent with principles of adaptive management and planning and can provide a template for developing local-, regional- or issue-specific pathways elsewhere and enrich the diversity of vulnerability, impacts, and adaptation assessment practice

Cell migration leads to spatially distinct but clonally related airway cancer precursors

Background Squamous cell carcinoma of the lung is a common cancer with 95% mortality at 5 years. These cancers arise from preinvasive lesions, which have a natural history of development progressing through increasing severity of dysplasia to carcinoma in situ (CIS), and in some cases, ending in transformation to invasive carcinoma. Synchronous preinvasive lesions identified at autopsy have been previously shown to be clonally related. Methods Using autofluorescence bronchoscopy that allows visual observation of preinvasive lesions within the upper airways, together with molecular profiling of biopsies using gene sequencing and loss-of-heterozygosity analysis from both preinvasive lesions and from intervening normal tissue, we have monitored individual lesions longitudinally and documented their visual, histological and molecular relationship. Results We demonstrate that rather than forming a contiguous field of abnormal tissue, clonal CIS lesions can develop at multiple anatomically discrete sites over time. Further, we demonstrate that patients with CIS in the trachea have invariably had previous lesions that have migrated proximally, and in one case, into the other lung over a period of 12 years. Conclusions Molecular information from these unique biopsies provides for the first time evidence that field cancerisation of the upper airways can occur through cell migration rather than via local contiguous cellular expansion as previously thought. Our findings urge a clinical strategy of ablating high-grade premalignant airway lesions with subsequent attentive surveillance for recurrence in the bronchial tree

Cytokine Production but Lack of Proliferation in Peripheral Blood Mononuclear Cells from Chronic Chagas' Disease Cardiomyopathy Patients in Response to T. cruzi Ribosomal P Proteins

Background:Trypanosoma cruzi ribosomal P proteins, P2β and P0, induce high levels of antibodies in patients with chronic Chagas' disease Cardiomyopathy (CCC). It is well known that these antibodies alter the beating rate of cardiomyocytes and provoke apoptosis by their interaction with β1-adrenergic and M2-muscarinic cardiac receptors. Based on these findings, we decided to study the cellular immune response to these proteins in CCC patients compared to non-infected individuals.Methodology/Principal findings:We evaluated proliferation, presence of surface activation markers and cytokine production in peripheral blood mononuclear cells (PBMC) stimulated with P2β, the C-terminal portion of P0 (CP0) proteins and T. cruzi lysate from CCC patients predominantly infected with TcVI lineage. PBMC from CCC patients cultured with P2β or CP0 proteins, failed to proliferate and express CD25 and HLA-DR on T cell populations. However, multiplex cytokine assays showed that these antigens triggered higher secretion of IL-10, TNF-α and GM-CSF by PBMC as well as both CD4+ and CD8+ T cells subsets of CCC subjects. Upon T. cruzi lysate stimulation, PBMC from CCC patients not only proliferated but also became activated within the context of Th1 response. Interestingly, T. cruzi lysate was also able to induce the secretion of GM-CSF by CD4+ or CD8+ T cells.Conclusions/Significance:Our results showed that although the lack of PBMC proliferation in CCC patients in response to ribosomal P proteins, the detection of IL-10, TNF-α and GM-CSF suggests that specific T cells could have both immunoregulatory and pro-inflammatory potential, which might modulate the immune response in Chagas' disease. Furthermore, it was possible to demonstrate for the first time that GM-CSF was produced by PBMC of CCC patients in response not only to recombinant ribosomal P proteins but also to parasite lysate, suggesting the value of this cytokine to evaluate T cells responses in T. cruzi infection.Fil: Longhi, Silvia Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; ArgentinaFil: Atienza, Augusto. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Perez Prados, Graciela. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Juan A. Fernández"; ArgentinaFil: Buying, Alcinette. Torrey Pines Institute for Molecular Studies; Estados UnidosFil: Balouz, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Buscaglia, Carlos Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Santos, Radleigh. Torrey Pines Institute for Molecular Studies; Estados UnidosFil: Tasso, Laura Mónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Bonato, Ricardo. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Chiale, Pablo. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Ramos Mejía"; ArgentinaFil: Pinilla, Clemencia. Torrey Pines Institute for Molecular Studies; Estados UnidosFil: Judkowski, Valeria A.. Torrey Pines Institute for Molecular Studies; Estados UnidosFil: Gomez, Karina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentin

Methods for in vitro evaluating antimicrobial activity of medicinal plants : the need for standardization.

A crescente incid?ncia de pat?genos resistentes aos medicamentos atuais incentiva a busca de novos agentes antimicrobianos. Neste contexto, as plantas medicinais se destacam, sendo uma importante fonte de novos f?rmacos. Existem diversos m?todos para avaliar a atividade antibacteriana e antif?ngica de extratos, fra??es, ?leos essenciais e subst?ncias isoladas de vegetais. Os mais conhecidos incluem m?todos de difus?o, dilui??o e bioautografia. A proposta desse trabalho ? apresentar os m?todos mais utilizados atualmente, juntamente com suas vantagens, desvantagens e fatores interferentes. Entre os artigos indexados na biblioteca SciELO, abrangendo os ?ltimos dez anos, somente 4,4% das pesquisas com plantas medicinais est?o relacionadas com atividade antimicrobiana. O m?todo mais utilizado foi a microdilui??o (57,9%), o mais recomendado devido ? alta sensibilidade, ? quantidade m?nima de reagentes e amostra e ? possibilidade de um maior n?mero de r?plicas. Nos trabalhos que utilizaram esse m?todo, foram verificadas diverg?ncias de fatores que podem interferir nos resultados. A fim de facilitar a obten??o de resultados compar?veis e reprodut?veis, destaca-se a necessidade da padroniza??o dos m?todos utilizadas pelos pesquisadores. Recomenda-se utilizar como refer?ncia as normas estabelecidas pelo CLSI para meio de cultura e concentra??o de in?culo nos testes. Al?m disso, tamb?m recomenda-se a inclus?o de um controle negativo da forma de solubiliza??o das amostras, com quantifica??o do crescimento microbiano, para evitar a interfer?ncia nos resultados.The increasing incidence of resistant pathogens to current drugs encourages the search for new antimicrobial agents. In this context, medicinal plants are an important source of new drugs. There are several methods for evaluating the antibacterial and antifungal activity of extracts, fractions, essential oils and isolated substances from the plant. The most known include diffusion, dilution and bioautography methods. The purpose of this paper is to present the most used methods currently, along with their advantages, disadvantages and interfering factors. Among the works available in the SciELO database, covering the last ten years, only 4,4% of research on medicinal plants are related to the antimicrobial activity. The most used method is microdilution (57,9%), the best recommended due to high sensitivity, the minimum quantity of reagents and sample and the possibility of a more significant number of replicates. In articles that used this method, differences were observed in factors that may affect the results. Thereby, there is the need for standardization of methods used by researchers to facilitate obtaining comparable and reproducible results. To achieve comparable and reproducible results, there is the need to standardize the methods used by the researchers. It is recommended to use as reference the standards established by CLSI for culture medium and inoculum concentration in the tests. It also recommended the inclusion of negative control of the solubilization of the samples with quantification of microbial growth to avoid interference with the results