Multi-Representation Techniques for Multi-Scale Simulation: Reactive Microflows in a Catalytic Converter

Abstract

We describe the basic ideas behind a multi-representation (floating-point and integer) algorithm for the numerical simulation of reactive flows with heat transfer. In particular, we provide some details on the interface connecting the integerized to the floating-point components. An application to catalytic conversion is briefly discussed.     

Discoveries and Explorations of Mode Splitting Phenomenon in Lossy Dielectric Waveguide

We discovered that a specific transmission mode in the fiber waveguide will split into two modes at near cut-off conditions when the fiber is coated with lossy dielectric nanofilms with higher refractive index. One of the two splitting modes is high lossy while the other is slightly lossy. We defined the “mode splitting coefficient” to describe the degree of mode splitting. We found that the biggest mode splitting coefficient was obtained at the mode cut-off wavelength using finite element method. Finally, we put forward an explanation towards the mode splitting phenomenon and expounded the relationship between the mode splitting and mode coupling.

     

Direct Coupling Strategy in Plasmonic Nanocircuits for Low Loss and Easy Fabrication

Plasmonic nanocircuits can deliver light in subwavelength scale, however, require state-of-the-art fabrication process due to the ultra-small footprints. Here, we introduce direct coupling strategy based on metal-insulator-metal (MIM) waveguide systems to reduce the system loss as well as the fabrication difficulty and increase the structural stability. Following this strategy, the coupling between the input waveguide and square ring resonator (SRR) can be realized via an aperture, and for the coupling between SRRs, the metal gap can be removed. The numerical results show that such direct coupling can produce similar effects with conventional indirect coupling in MIM waveguide systems, and the physics mechanism behind as well as influences of geometric parameters on transmission spectrum is also investigated. This work provides a simpler approach to realize on-chip plasmonic nanodevices, such as filters, sensors, and optical delay lines, in practice.

     

National inventories of land occupation and transformation flows in the world for land use impact assessment

Purpose

Land use can cause significant impacts on ecosystems and natural resources. To assess these impacts using life cycle assessment (LCA) and ensure adequate decision-making, comprehensive national inventories of land occupation and transformation flows are required. Here, we aim at developing globally differentiated inventories of land use flows that can be used for primary use in life cycle impact assessment or national land planning.

Methods

Using publicly available data and inventory techniques, national inventories for several land use classes were developed. All land use classes were covered with the highest retrievable level of disaggregation within urban, forestry, agriculture and other land use classes, thus differentiating 21 land use classes. For illustrating the application of this newly developed inventory, two different application settings relevant to life cycle impact assessment were considered: the calculation of global normalisation references for 11 land use impact indicators related to soil quality assessment (adopting the methods recommended by the EU Commission) and the determination of generic globally applicable characterisation factors (CFs) resulting from aggregation of country-level CFs for situations for use when land use location is unknown.

Results and discussion

We built national inventories of 21 land occupation and 17 land transformation flows for 225 countries in the world for the reference year 2010. Cross-comparisons with existing inventories of narrower scopes attested its consistency. Detailed analyses of the calculated global normalisation references for the 11 land use impact categories showed different patterns across the land use impact indicators for each country, thus raising attention on key land use impacts specific to each country. Furthermore, the upscaling of country-level CFs to global generic CFs using the land use inventory revealed discrepancies with other alternative approaches using land use data at different resolutions.

Conclusions

In this study, we made a first attempt at developing national inventories of land use flows with sufficient disaggregation level to enable the calculation of normalisation references and differentiated impacts. However, the findings also demonstrated the need to refine the consistency of the inventory, particularly in the combination of land cover and land use data, which should be harmonised in future studies, and to expand it with differentiated coverage of more land use flows relevant to impact assessment.

     

Into turbulent air: size-dependent effects of von Kármán vortex streets on hummingbird flight kinematics and energetics

Animal fliers frequently move through a variety of perturbed flows during their daily aerial routines. However, the extent to which these perturbations influence flight control and energetic expenditure is essentially unknown. Here, we evaluate the kinematic and metabolic consequences of flight within variably sized vortex shedding flows using five Anna''s hummingbirds feeding from an artificial flower in steady control flow and within vortex wakes produced behind vertical cylinders. Tests were conducted at three horizontal airspeeds (3, 6 and 9 m s⁻¹) and using three different wake-generating cylinders (with diameters equal to 38, 77 and 173% of birds'' wing length). Only minimal effects on wing and body kinematics were demonstrated for flight behind the smallest cylinder, whereas flight behind the medium-sized cylinder resulted in significant increases in the variances of wingbeat frequency, and variances of body orientation, especially at higher airspeeds. Metabolic rate was, however, unchanged relative to that of unperturbed flight. Hummingbirds flying within the vortex street behind the largest cylinder exhibited highest increases in variances of wingbeat frequency, and of body roll, pitch and yaw amplitudes at all measured airspeeds. Impressively, metabolic rate under this last condition increased by up to 25% compared with control flights. Cylinder wakes sufficiently large to interact with both wings can thus strongly affect stability in flight, eliciting compensatory kinematic changes with a consequent increase in flight metabolic costs. Our findings suggest that vortical flows frequently encountered by aerial taxa in diverse environments may impose substantial energetic costs.     

Resonance Bandwidth Controllable Adjustment of Electromagnetically Induced Transparency-like Using Terahertz Metamaterial

In the fields of communication and sensing, resonance bandwidth is a very critical index. It is very meaningful to implement a broadband resonance device with a simple metamaterial structure in the terahertz band. In this paper, we propose a simple metamaterial structure which consists of one horizontal metal strip and two vertical metal strips. This structure can achieve an electromagnetically induced transparency-like (EIT-like) effect in the frequency range of 0.1~3.0 THz to obtain a transparent window with a resonance bandwidth as high as 1.212 THz. When the relative distance between two vertical metal strips is changed, the bandwidth can be effectively controlled. Furthermore, we found that the EIT-like effect can be actively adjusted by replacing vertical metal strips with photosensitive silicon.

     

Ultrafast Nano-scale Optical Switching in a Plasmonic Interferometer with Enhanced Tunability

An all-optical switch based on plasmonic metal–insulator–metal (MIM) waveguides and the Mach–Zehnder (MZ) interferometer is designed. In order to realize an all-optical and active switch, a nonlinear material with intensity-dependent refractive index is introduced in one arm. Other than studying a typical MZ structure, we also investigate the asymmetric case where unequal thicknesses and distances for MZ arms are proposed. The finite element method (FEM) with a refined triangle mesh is employed for simulations. Results for ON and OFF states are provided with or without employing the pump field. Investigation of the geometrical dispersion reveals tunability of the structure for specific frequencies in the terahertz region. Finally, we show that introducing asymmetric arms provides better tunability in the designed ultrafast nano-scale switch and suggests its potential applications in integrated optical circuits.

     

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri

Background

Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species A. lyrata and the closely related reference model species A. thaliana exhibit merely basal metal tolerance.

Results

For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In A. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease Resistance (R) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes.

Conclusions

Our results provide genome-wide support for a link between evolutionary adaptation and CND in A. halleri as shown previously for Heavy metal ATPase4. Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off.

     

Energy-aware routing considering load balancing for SDN: a minimum graph-based Ant Colony Optimization

Software-Defined Network (SDN) technology is a network management approach that facilitates a high level of programmability and centralized manageability. By leveraging the control and data plane separation, an energy-aware routing model could be easily implemented in the networks. In the present paper, we propose a two-phase SDN-based routing mechanism that aims at minimizing energy consumption while providing a certain level of QoS for the users’ flows and realizing the link load balancing. To reduce the network energy consumption, a minimum graph-based Ant Colony Optimization (ACO) approach is used in the first phase. It prunes and optimizes the network tree by turning unnecessary switches off and providing an energy-minimized sub-graph that is responsible for the network existing flows. In the second phase, an innovative weighted routing approach is developed that guarantees the QoS requirements of the incoming flows and routes them so that to balance the loads on the links. We validated our proposed approach by conducting extensive simulations on different traffic patterns and scenarios with different thresholds. The results indicate that the proposed routing method considerably minimizes the network energy consumption, especially for congested traffics with mice-type flows. It can provide effective link load balancing while satisfying the users’ QoS requirements.

     

Tunable Plasmonically Induced Transparency with Asymmetric Multi-rectangle Resonators

Plasmonically induced transparency (PIT) effect in a metal–insulator–metal waveguide coupled to asymmetric multi-rectangle resonators is investigated numerically. By adjusting parameters of resonators, we cannot only realize single, double, or treble PIT peaks in the compact structure, but also induce an off-to-on PIT optical response. Numerical simulation by finite element method was conducted to verify our designs. This proposed structure, hence has potential applications for ultra-compact optoelectronic devices at communication band.

     

Rapid fractionation of wheat leaf protoplasts using membrane filtration : the determination of metabolite levels in the chloroplasts, cytosol, and mitochondria

A technique is presented for measuring the in vivo metabolite levels in the chloroplast stroma, the cytosol, and the mitochondrial matrix of wheat (Triticum aestivum, var `Timmo') leaf protoplasts, in which membrane filtration is used to prepare fractions enriched in the different subcellular fractions within 0.1 seconds after disruption of the protoplasts. By closing a syringe, protoplasts are forced through a net and disrupted, diluting the cytosol into the medium and also releasing intact chloroplasts and mitochondria which can then be immediately removed on membrane filters placed behind the nylon net. By varying the membrane filters, different filtrates are obtained corresponding to (a) mainly cytosol, or (b) cytosol and mitochondria with only low levels of chloroplasts; alternatively, (c) the entire protoplast contents are obtained by omitting the filters. The filtrates are immediately split, half flowing into HClO₄ where they are immediately quenched for subsequent metabolite analyses; the other half flows into detergent and is used to monitor the exact distribution of marker enzymes in each individual fractionation. Using the measured distributions of metabolite and of marker enzymes in the three filtrates, the subcellular distribution of the metabolite can be algebraically calculated. The method is presented using ATP as an example.

The quench time (0.1 second) made possible by membrane filtration is considerably faster than has been possible in the previously developed techniques using silicone oil centrifugation for chloroplasts (1 second) or mitochondria (1 minute). This rapid quench makes it possible to investigate subcellular pools which have a rapid turnover, like the adenine nucleotides.

     

Using a Spread Sheet Program to Model the Interaction of Low-Frequency Electric Fields with Inhomogeneous,Irregularly Shaped Objects

This paper describes the use of an ordinary business spread sheet program to calculate, using a two-stage finite difference method, the electric fields and current densities produced inside irregularly shaped models of the upper arm and forearm. The limb interiors are inhomogeneous, being represented as realistic cross-sections of bone and muscle.

A spread sheet forms a two-dimensional array. Each cell of the sheet can correspond to a physical element of space. Equations entered into the cells then represent the relationships among the potentials of the corresponding spatial elements.

The model is validated for a two-layer, lossy dielectric cylinder. Good agreement is obtained between the numerical and analytical solutions in this case except near the boundaries of the outer layer. The electric field within the limb depends on the shape and orientation of the limb relative to the applied field. The flow of current around the less conductive bones in the forearm can be observed.     

Considering the levels of biological organisation when teaching carbon flows in a terrestrial ecosystem

ABSTRACT

Students often have misconceptions about terrestrial carbon flows and there is a lack of coherence in students’ explanations regarding the different levels of biological organisation at which these processes occur. In this study, problem-based teaching materials on the topic of terrestrial carbon flows were developed and tested with 15 students 18–19 years old (grade 12) using a pre/post-test design. Students focused on specific carbon flows in an ecosystem at the macro level (e.g. CO₂ fixation and heterotrophic respiration) including specific related concepts at the micro level (e.g. photosynthesis and cellular respiration). The findings indicate that the teaching materials improved the students’ understanding of terrestrial carbon flows and their ability to reason across the different levels of biological organisation. On the basis of these findings, implications for teaching terrestrial carbon flows in biological education are discussed.     

Modeling Metal Flow Systems

Substance flow analysis (SFA) is a frequently used industrial ecology technique for studying societal metal flows, but it is limited in its ability to inform us about future developments in metal flow patterns and how we can affect them. Equation‐based simulation modeling techniques, such as dynamic SFA and system dynamics, can usefully complement static SFA studies in this respect, but they are also restricted in several ways. The objective of this article is to demonstrate the ability of agent‐based modeling to overcome these limitations and its usefulness as a tool for studying societal metal flow systems. The body of the article summarizes the parallel implementation of two models—an agent‐based model and a system dynamics model—both addressing the following research question: What conditions foster the development of a closed‐loop flow network for metals in mobile phones? The results from in silico experimentation with these models highlight three important differences between agent‐based modeling (ABM) and equation‐based modeling (EBM) techniques. An analysis of how these differences affected the insights that could be extracted from the constructed models points to several key advantages of ABM in the study of metal flow systems. In particular, this analysis suggests that a key advantage of the ABM technique is its flexibility to enable the representation of societal metal flow systems in a more native manner. This added flexibility endows modelers with enhanced leverage to identify options for steering metal flows and opens new opportunities for using the metaphor of an ecosystem to understand metal flow systems more fully.     

Chaperone-Mediated Autophagy and Aging: A Novel Regulatory Role of Lipids Revealed

A wide pool of cytosolic proteins is selectively degraded in lysosomes by chaperone-mediated autophagy (CMA). Binding of these proteins to a receptor at the lysosomal membrane is the limiting step in CMA. Levels of this receptor are tightly regulated through changes in its degradation, multimeric organization and dynamic distribution between the lysosomal membrane and lumen. We have now reported that subcompartmentalization of the receptor in discrete lipid microdomains at the lysosomal membrane regulates its engagement in each of these processes — degradation, multimerization and membrane retrieval. Changes in the lipid composition of the membrane thus affect the dynamics of the receptor and, consequently, CMA activity. As an example of CMA dysfunction resulting from perturbation of the lipid composition of the lysosomal membrane, we discuss here a second study in which we analyzed the changes in the dynamics of the receptor during aging. CMA activity decreases with age primarily due to a decrease in the levels of the CMA receptor at the lysosomal membrane. Now we have found that age-related alterations in the lipid composition of the discrete microdomains at the lysosomal membrane are behind the reduced lysosomal levels of the receptor and, consequently, the declined CMA activity that occurs during aging.

Addendum to:

Altered Dynamics of the Lysosomal Receptor for Chaperone-Mediated Autophagy with Age

R. Kiffin, S. Kaushik, M. Zeng, U. Bandyopadhyay, C. Zhang, A.C. Massey, M. Martinez-Vicente and A.M. Cuervo

J Cell Sci 2007; 120:782-91

and

Lysosome Membrane Lipid Microdomains: Novel Regulators of Chaperone-Mediated Autophagy

S. Kaushik, A.C. Massey and A.M. Cuervo

EMBO J 2006; 25:3921-33     

Structural Decomposition Analysis of Raw Material Consumption

The aim of this article is to quantify the drivers for the changes in raw material consumption (domestic material consumption expressed in the form of all materials extracted and used in the production phase) in terms of technology, which refers to the concept of sustainable production; the product structure of final demand, which refers to the concept of sustainable consumption; and the volume of final demand, which is related to economic growth. We also aim to determine to what extent the technological development and a shift in product structure of the final demand compensate for the growth in final consumption volume. Therefore, we apply structural decomposition analysis (SDA) to the change in raw material consumption (RMC) of the Czech Republic between 2000 and 2007. To present the study in a broader context, we also show other material flow indicators for the Czech Republic for 2000 and 2007. Our findings of SDA show that final demand structure has a very limited effect on the change in material flows. The rapid change in final demand volume was not compensated for crude oil, metal ores, construction materials, food crops, and timber. For the material category of non‐iron metal ores, even the change in technology contributes to an increase in material flows. The largest relative increases are reported for non‐iron metal ores (38%) and construction materials (30%). The main changes in material flows related to the Czech Republic are driven by exports and enabled by imports, the main source of these increased material flows. This emphasizes the increasing role of international trade.     

Radiative decay engineering 5: metal-enhanced fluorescence and plasmon emission

Metallic particles and surfaces display diverse and complex optical properties. Examples include the intense colors of noble metal colloids, surface plasmon resonance absorption by thin metal films, and quenching of excited fluorophores near the metal surfaces. Recently, the interactions of fluorophores with metallic particles and surfaces (metals) have been used to obtain increased fluorescence intensities, to develop assays based on fluorescence quenching by gold colloids, and to obtain directional radiation from fluorophores near thin metal films. For metal-enhanced fluorescence it is difficult to predict whether a particular metal structure, such as a colloid, fractal, or continuous surface, will quench or enhance fluorescence. In the present report we suggest how the effects of metals on fluorescence can be explained using a simple concept, based on radiating plasmons (RPs). The underlying physics may be complex but the concept is simple to understand. According to the RP model, the emission or quenching of a fluorophore near the metal can be predicted from the optical properties of the metal structures as calculated from electrodynamics, Mie theory, and/or Maxwell's equations. For example, according to Mie theory and the size and shape of the particle, the extinction of metal colloids can be due to either absorption or scattering. Incident energy is dissipated by absorption. Far-field radiation is created by scattering. Based on our model small colloids are expected to quench fluorescence because absorption is dominant over scattering. Larger colloids are expected to enhance fluorescence because the scattering component is dominant over absorption. The ability of a metal's surface to absorb or reflect light is due to wavenumber matching requirements at the metal-sample interface. Wavenumber matching considerations can also be used to predict whether fluorophores at a given distance from a continuous planar surface will be emitted or quenched. These considerations suggest that the so called "lossy surface waves" which quench fluorescence are due to induced electron oscillations which cannot radiate to the far-field because wavevector matching is not possible. We suggest that the energy from the fluorophores thought to be lost by lossy surface waves can be recovered as emission by adjustment of the sample to allow wavevector matching. The RP model provides a rational approach for designing fluorophore-metal configurations with the desired emissive properties and a basis for nanophotonic fluorophore technology.     

Suitability of aromatic plants for phytoremediation of heavy metal contaminated areas: a review

Abstract

This review briefly elucidates the research undertaken and benefits of using aromatic plants for remediation of heavy metal polluted sites. A sustainable approach to mitigate heavy metal contamination of environment is need of the hour. Phytoremediation has emerged to be one of the most preferable choices for combating the metal pollution problem. Aromatic plants can be used for remediation of contaminated sites as they are non-food crops thus minimizing the risk of food chain contamination. Most promising aromatic plants for phytoremediation of heavy metal contaminated sites have been identified from families – Poaceae, Lamiaceae, Asteraceae, and Geraniaceae. They act as potential phytostabilisers, hyper accumulators, bio-monitors, and facultative metallophytes. Being high value economic crops, monetary benefits can be obtained by growing them in tainted areas instead of food crops. It has been observed that heavy metal stress enhances the essential oil percentage of certain aromatic crops. Research conducted on some major aromatic plants in this context has been highlighted in the present review which suggests that aromatic plants hold a great potential for phytoremediation. It has been reported that essential oil from aromatic crops is not contaminated by heavy metals significantly. Thus, aromatic plants are emerging as an ideal candidate for phytoremediation.

Highlights

? Aromatic plants hold a great potential for phytoremediation of heavy metal contaminated sites.

? Being high value economic crops, monetary benefits can be obtained by growing them in contaminated areas instead of food crops.

? Research done on some major aromatic plants in this context has been highlighted in the present review.     

Ascorbic Acid Oxidation and DNA Scission Catalyzed by Iron and Copper Chelates

The asorbic acid (AH^?) auto-oxidation rates catalyzed by copper chelates of 1,10-phenanthroline (OP) or by iron chelates of bleomycin (BLM) are only slightly higher than the oxidation rates catalyzed by the metal ions. AH^? oxidation in the presence of DNA is accompanied by degradation of the DNA. The rates of DNA scission by the metal chelates are markedly higher than the rates induced by the free metal ions. AH^? oxidation is slowed down in the presence of DNA which forms ternary complexes with the chelates. The ternary complexes react slowly with AH^? but induce DNA double strand breaks more efficiently than the free metal chelates. With OP, DNA is degraded by the reaction of the ternary complex, DNA-(OP)₂Cu(I), withH₂O₂

AH^? oxidation in the presence of DNA was biphasic, showing a marked rate increase after DNA was cleaved. We suggest that this sigmoidal pattern of the oxidation curves reflects the low initial oxidative activity of the ternary complexes, accelerating as DNA is degraded.

Using O₂^?produced by pulse radiolysis as a reductant, we found that AH^? oxidation with (OP)₂Cu(II) induced more DNA double strand breaks per single strand break than bipyridine-copper.

The site specific DNA damaging reactions indicated by these results are relevant to the mechanism of cytotoxic activities of bleomycin and similar antibiotics or cytotoxic agents.