Green's functions perspective on nonequilibrium thermodynamics of open quantum systems strongly coupled to baths

We give nonequilibrium Green's function (NEGF) perspective on thermodynamics formulations for open quantum systems strongly coupled to baths. Scattering approach implying thermodynamic consideration of a super-system (system plus baths) weakly coupled to external super-baths is compared with consideration of thermodynamics of a system strongly coupled to its baths. We analyze both approaches from the NEGF perspective and argue that the latter yields a possibility of thermodynamic formulation consistent with dynamical (quantum transport) description.Comment: 6 page

Revisiting and revitalizing political ecology in the American West

Political ecology, initially conceived to better understand the power relations implicit in management and distribution of natural resources in the developing world, came “home” to the American West in the 1990s and 2000s. This groundswell of research did much to problematize socio-environmental conflicts in the region, long typified by tensions over land and resources, identity and belonging, autonomy and authority. Since first touching down in the West, however, the “big tent” of political ecology has only grown bigger, incorporating new perspectives, epistemologies, and ontologies. At the same time, the nexus of environment and society is perhaps even more salient today, amid a regional conjuncture of populist revolt, climate change, and rapid political economic transformation. Here we reflect on three longstanding regional concerns – energy development, wolf reintroduction, and participatory governance – leveraging the pluralism of contemporary political ecology to better understand their contemporary incarnations. In so doing, we highlight the need to bring together insights from both “traditional” approaches and newer directions to better understand and engage contemporary challenges, with their heightened stakes and complexity. Such an approach demonstrates what we might learn about global processes in this place, as well as what insights regional praxis (often woefully provincial) might gain from elsewhere – new ways of seeing and doing political ecology. Our goal is to generate discussion among and between political ecologists and regional critical scholars, initiating new collaborative engagements that might serve the next wave of political ecology in the 21st century American West

Colloquium: Atomic spin chains on surfaces

In the present Colloquium, we focus on the properties of 1-D magnetic systems on solid surfaces. From the emulation of 1-D quantum phases to the potential realization of Majorana edge states, spin chains are unique systems to study. The advent of scanning tunnelling microscope (STM) based techniques has permitted us to engineer spin chains in an atom-by-atom fashion via atom manipulation and to access their spin states on the ultimate atomic scale. Here, we present the current state of research on spin correlations and dynamics of atomic spin chains as studied by the STM. After a brief review of the main properties of spin chains on solid surfaces, we classify spin chains according to the coupling of their magnetic moments with the holding substrate. This classification scheme takes into account that the nature and lifetimes of the spin-chain excitation intrinsically depend on the holding substrate. We first show the interest of using insulating layers on metals, which generally results in an increase in the spin state's lifetimes such that their quantized nature gets evident and they are individually accessible. Next, we show that the use of semiconductor substrates promises additional control through the tunable electron density via doping. When the coupling to the substrate is increased for spin chains on metals, the substrate conduction electron mediated interactions can lead to emergent exotic phases of the coupled spin chain-substrate conduction electron system. A particularly interesting example is furnished by superconductors. Magnetic impurities induce states in the superconducting gap. Due to the extended nature of the spin chain, the in-gap states develop into bands that can lead to the emergence of 1-D topological superconductivity and, consequently to the appearance of Majorana edge states

Towards an autonomous maintenance, repair and overhaul process: Exemplary holistic data management approach for the regeneration of aero-engine blades

The maintenance, repair and overhaul (MRO) processes of aircraft engines are dominated by a high proportion of manual work and subjective condition assessment of used parts. This leads to inefficiency due to additional, partially not required workload and high scrap rates. Further, there is a lack of knowledge about the effects of the respective repair measures on the performance of the parts. So far, there are no autonomous repair solutions that allow an optimal and individually tailored regeneration. In order to realize such a process, it is necessary to bring together the manufacturing, function-simulating and logistics-oriented disciplines in an integrated system. For this, data management along the process chain is an important success factor. In particular, the provision and linking of the data and data formats required for simulation and the production environment is of fundamental importance. This paper presents a data architecture that can serve as a framework for data integration within a representative process chain for regeneration

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined

Observation of a non-adiabatic geometric phase for elastic waves

We report the experimental observation of a geometric phase for elastic waves in a waveguide with helical shape. The setup reproduces the experiment by Tomita and Chiao [A. Tomita, R.Y. Chiao, Phys. Rev. Lett. 57 (1986) 937-940, 2471] that showed first evidence of a Berry phase, a geometric phase for adiabatic time evolution, in optics. Experimental evidence of a non-adiabatic geometric phase has been reported in quantum mechanics. We have performed an experiment to observe the polarization transport of classical elastic waves. In a waveguide, these waves are polarized and dispersive. Whereas the wavelength is of the same order of magnitude as the helix's radius, no frequency dependent correction is necessary to account for the theoretical prediction. This shows that in this regime, the geometric phase results directly from geometry and not from a correction to an adiabatic phase.Comment: 13 figure

Yellow fever virus envelope protein expressed in insect cells is capable of syncytium formation in lepidopteran cells and could be used for immunodetection of YFV in human sera

<p>Abstract</p> <p>Background</p> <p>Yellow fever is an haemorrhagic disease caused by a virus that belongs to the genus Flavivirus (Flaviviridae family) and is transmitted by mosquitoes. Among the viral proteins, the envelope protein (E) is the most studied one, due to its high antigenic potencial. Baculovirus are one of the most popular and efficient eukaryotic expression system. In this study a recombinant baculovirus (vSynYFE) containing the envelope gene (<it>env</it>) of the 17D vaccine strain of yellow fever virus was constructed and the recombinant protein antigenicity was tested.</p> <p>Results</p> <p>Insect cells infected with vSynYFE showed syncytium formation, which is a cytopathic effect characteristic of flavivirus infection and expressed a polypeptide of around 54 kDa, which corresponds to the expected size of the recombinant E protein. Furthermore, the recombinant E protein expression was also confirmed by fluorescence microscopy of vSynYFE-infected insect cells. Total vSynYFE-infected insect extracts used as antigens detected the presence of antibodies for yellow fever virus in human sera derived from yellow fever-infected patients in an immunoassay and did not cross react with sera from dengue virus-infected patients.</p> <p>Conclusions</p> <p>The E protein expressed by the recombinant baculovirus in insect cells is antigenically similar to the wild protein and it may be useful for different medical applications, from improved diagnosis of the disease to source of antigens for the development of a subunit vaccine.</p

The first 62 AGN observed with SDSS-IV MaNGA -- III: stellar and gas kinematics

We investigate the effects of Active Galactic Nuclei (AGN) on the gas kinematics of their host galaxies, using MaNGA data for a sample of 62 AGN hosts and 109 control galaxies (inactive galaxies). We compare orientation of the line of nodes (kinematic Position Angle - PA) measured from the gas and stellar velocity fields for the two samples. We found that AGN hosts and control galaxies display similar kinematic PA offsets between gas and stars. However, we note that AGN have larger fractional velocity dispersion $\sigma$ differences between gas and stars [$\sigma_{frac}=(\sigma_{\rm gas}-\sigma_{stars})/\sigma_{\rm stars}$] when compared to their controls, as obtained from the velocity dispersion values of the central (nuclear) pixel (2.5" diameter). The AGN have a median value of $\sigma_{\rm frac}$ of $_{\rm AGN}=0.04$, while the the median value for the control galaxies is $_{\rm CTR}=-0.23$. 75% of the AGN show $\sigma_{frac}>-0.13$, while 75% of the normal galaxies show $\sigma_{\rm frac}<-0.04$, thus we suggest that the parameter $\sigma_{\rm frac}$ can be used as an indicative of AGN activity. We find a correlation between the [OIII]$\lambda$5007 luminosity and $\sigma_{frac}$ for our sample. Our main conclusion is that the AGN already observed with MaNGA are not powerful enough to produce important outflows at galactic scales, but at 1-2 kpc scales, AGN feedback signatures are always present on their host galaxies.Comment: 19 pages, 8 figures, published in MNRA

Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.

In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in Caenorhabditis elegans. Sampling several time points from young adulthood until early old age, our study covers the full duration of aging and include transcriptomics, and targeted MS-based metabolomics. In order to focus on the metabolic changes due to age we used two strains that are metabolically close to wild-type, yet are conditionally non-reproductive. Using these data in combination with a whole-genome model of the metabolism of C. elegans and mathematical modeling, we predicted metabolic fluxes during early aging. We find that standard Flux Balance Analysis does not accurately predict in vivo measured fluxes nor age-related changes associated with the Citric Acid cycle. We present a novel Flux Balance Analysis method where we combined biomass production and targeted metabolomics information to generate an objective function that is more suitable for aging studies. We validated this approach with a detailed case study of the age-associated changes in the Citric Acid cycle. Our approach provides a comprehensive time-resolved multi-omics and modeling resource for studying the metabolic changes during normal aging in C. elegans