Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA's Blue Waters system.

Preliminary investigation of mixed adsorbents for the removal of copper and methylene blue from aqueous solutions

With most recent studies being focused on the development of
advanced chemical adsorbents, this paper investigates the possibility of
using two natural low-cost materials for selective adsorption. Multiadsorbent
systems containing tea waste and dolomite have been tested for
their effectiveness in the removal of copper and methylene blue from
aqueous solutions. The effects of contact time, solution pH and
adsorption isotherms on the sorption behaviour were investigated. The
Langmuir and Freundlich isotherms adequately described the adsorption of
copper ions and methylene blue by both materials in different systems.
The highest adsorption capacities for Cu and MB were calculated as 237.7
at pH 4.5 and 150.44 mg.g‒1 at pH 7 for DO and TW+DO respectively. Tea
waste (TW) and dolomite (DO) were characterized by Fourier transform
infrared spectroscopy, scanning electron microscopy and Energy dispersive
X-ray analysis. The removal of Cu and MB by dolomite was mainly via
surface complexation while physisorption was responsible for most of the
Cu and MB adsorption onto tea waste. Identifying the fundamental mechanisms and behaviour is key to the development of practical multi-adsorbent packed columns.

Chemistry and Mechanism of Alizarin Red S and Methylene Blue Biosorption onto Olive Stone: Equilibrium and Kinetic

The biosorption process of anionic dye Alizarin Red S (ARS) and cationic dye methylene blue (MB) as a function of solution pH, initial concentration and contact time onto olive stone (OS) biomass has been investigated. The main objectives of the current study are to: (i) study the chemistry and the mechanism of ARS and MB biosorption onto olive stone and the type of OS–ARS, MB interactions occurring, (ii) study the biosorption equilibrium and kinetic experimental data required for the design and operation of column reactors. Equilibrium biosorption isotherms and kinetics were also examined. Experimental equilibrium data were fitted to four different isotherms by non-linear regression method, however, the biosorption experimental data for ARS and MB dyes were well interpreted by the Temkin and Langmuir isotherms, respectively. The maximum monolayer adsorption capacity for ARS and MB dyes were 109.0 and 102.6 mg/g, respectively. The kinetic data of the two dyes could be better described by the pseudo second-order model. The data showed that olive stone can be effectively used for removing dyes from wastewater.

The use of a novel compact fluorosensor for in situ monitoring of the photocatalytic destruction of methylene blue dye effluents

The use of TiO 2 photocatalysis for the destruction of dyes such as methylene blue has been extensively reported. One of the challenges faced in both the laboratory and large scale water treatment plants is the fact that the samples have to be removed from the reactor vessel and the catalyst separated prior to analysis being undertaken. In this paper we report the development of a simple fluorimeter instrument and its use in monitoring the photocatalytic destruction of methylene blue dyes in the presence of catalyst suspensions. The results reported show that the instrument provides an effective method for in situ monitoring of the photocatalytic destruction of fluorescent dyes hence allowing more accurate measurement due to the minimisation of sample loss and cross contamination. Furthermore it also provides a method for real time monitoring of the dye pollutant destruction in large scale photocatalytic reactors.

Effect of polyethylenimine, a cell permeabilizer, on the photosensitized destruction of algae by methylene blue and nuclear fast red

The present study reports the effect a cell permeabilizer, polyethylenimine (PEI) has on the photodynamic effect of methylene blue (MB) and nuclear fast red (NFR) in the presence of hydrogen peroxide (H₂O₂). The photosensitized destruction of the algae Chlorella vulgaris under irradiation with visible light is examined. The photodynamic effect was investigated under aerobic and anaerobic conditions. The presence of a permeabilizer during the photosensitized destruction of C. vulgaris does not enhance the activity of the MB, MB/H₂O₂ system or the NFR, NFR/H₂O ₂ system under aerobic conditions. However under anaerobic conditions we have determined that when a cell permeabilizer was added to the MB/H ₂O₂ system, the photosensitized destruction of C. vulgaris proceeded via a combination of Type I and Type II mechanisms. The presence of PEI enforces MB/H₂O₂ to be active toward the destruction of C. vulgaris whether oxygen is present or absent. Under aerobic and anaerobic conditions the activity of NFR was suppressed in the presence of PEI as a result of electrostatic interactions between the photosensitizer and the cell permeabilizer. The decrease in fluorescence recorded is indicative of destruction of the chlorophyll a pigment. 

Photo-dynamic biocidal action of methylene blue and hydrogen peroxide on the cyanobacterium Synechococcus leopoliensis under visible light irradiation

Biofilm growth on stone surfaces is a significant contributing factor to stone biodeterioration. Current market based biocides are hazardous to the environment and to public health. We have investigated the photo-dynamic effect of methylene blue (MB) in the presence of hydrogen peroxide (H₂O₂) on the destruction of the cyanobacterium Synechococcus leopoliensis (S. leopoliensis) under irradiation with visible light. Data presented in this paper illustrate that illumination of S. leopoliensis in the presence of a photosensitiser (MB) and H₂O₂ results in the decomposition of both the cyanobacterium and the photosensitiser. The presence of MB and H₂O₂ affects the viability of the photosensitiser and the cyanobacterium with the fluorescence of both decreasing by 80% over the irradiation time investigated. The photo-dynamic effect was observed under aerobic and anaerobic conditions indicating that oxygen was not necessary for the process. This novel combination could be effective for the remediation of biofilm colonised stone surfaces

Photosensitized destruction of Chlorella vulgaris by methylene blue or nuclear fast red combined with hydrogen peroxide under visible light irradiation

A considerable number of investigations have started to elucidate the essential roles biological agents play in the biodeterioration of stone. Chemical biocides are becoming increasingly banned because of the environmental and health hazards associated with these toxic substances. The present study reports the photodynamic effect of Methylene Blue (MB) and Nuclear Fast Red (NFR) in the presence of hydrogen peroxide (H₂O₂) on the destruction of the algae Chlorella vulgaris (C. vulgaris) under irradiation with visible light. Illumination of C. vulgaris in the presence of MB or NFR combined with H₂O₂ results in the decomposition of both the algal species and the photosensitizer. The photodynamic effect was investigated under aerobic and anaerobic conditions. Differences in mechanism type are reported and are dependent on both the presence and the absence of oxygen. The behavior of each photosensitizer leads to a Type II mechanism and a Type I/Type II combination for MB and NFR, respectively, being concluded. This novel combination could be effective for the remediation of biofilm-colonized stone surfaces.

Simultaneous biosorption of methylene blue and trivalent chromium onto olive stone

In this work, olive stone (OS) was utilized to investigate its capacity as biosorbent for methylene blue (MB) and Cr(III), which are usually present in textile industry effluents. Equilibrium and kinetic experiments were performed in batch experiments. The biosorption process followed pseudo-second-order kinetics. The equilibrium data were fitted with several models, but Langmuir and Sips models best reproduced the experimental results. Maximum biosorption capacities were 3.296 mg/g (0.0116 mmol/g) and 4.990 mg/g (0.0960 mmol/g) for MB and Cr(III), respectively. Several operation variables, such as
biosorbent mass, flow rate, and initial concentration on the removal of dye and metal, were evaluated in column system. The removal efficiency improved as OS mass increased and decreased when flow rate and initial concentration increased. Also, MB uptake was substantially decreased by increasing the initial concentration of Cr(III), ranging from 6.09 to 2.75 mg/g. These results show that the presence of Cr(III) significantly modifies the biosorption capacity of MB by the OS. These results suggest that OS is a potential low-cost food industry waste for textile industry wastewater treatment.

Mechanism of Alizarin Red S and Methylene Blue Biosorption onto Olive Stone: Isotherm study in Single and Binary Systems

The biosorption process of anionic dye Alizarin Red S (ARS) and cationic dye methylene blue (MB) as a function of contact time, initial concentration and solution pH onto olive stone (OS) biomass has been investigated. Equilibrium biosorption isotherms in single and binary systems and kinetics in batch mode were also examined. The kinetic data of the two dyes were better described by the pseudo second-order model. At low concentration, ARS dye appeared to follow a two-step diffusion process, while MB dye followed a three-step diffusion process. The biosorption experimental data for ARS and MB dyes were well suited to the Redlich-Peterson isotherm. The maximum biosorption of ARS dye, qmax = 16.10 mg/g, was obtained at pH 3.28 and the maximum biosorption of MB dye, qmax = 13.20 mg/g, was observed at basic pH values. In the binary system, it was indicated that the MB dye diffuses firstly inside the biosorbent particle and occupies the biosorption sites forming a monodentate complex and then the ARS dye enters and can only bind to untaken sites; forms a tridentate complex with OS active sites.

Breaking and Entering: Examining the role of stress and aerial exposure in predator-prey relationships between the common shore crab (Carcinus maenas) and cultivated blue mussels (Mytilus edulis).

During benthic cultivation Mytilus edulis (blue mussels) are subject to predation pressure from a number of predators including Carcinus maenas (shore crabs). This predator can be responsible for substantial losses of mussels from the fishery and a full understanding of the predator–prey relationship between M. edulis and C. maenas is required to ensure attempts that reduce predatory pressure and subsequent commercial loss are successful. Whilst much work has examined the prey–predator size relationships between C. maenas and M. edulis, far less research has investigated how stress, such as periods of extended aerial exposure, may affect these relationships. We tested whether profit in terms of calories gained by crabs consuming mussels stressed by aerial exposure for 48 h differed from that of mussels at ambient conditions and whether being stressed affected the mussel's likelihood of predation. We also tested whether the size relationship between predators and their prey differed when mussels were stressed. We found that the profitability of prey (calories gained per second of handling time) did not vary between stressed and unstressed mussels. Handling times for stressed and unstressed mussels were similar, even when crabs were presented with mussels of the maximum size that they are able to consume. Small crabs were more likely to reject a mussel of preferred size if it was unstressed, suggesting that crabs may be able to assess that these mussels would require extra effort to break into and consume. Our findings suggest that the predator–prey relationship between mussels and crabs is not altered when mussels are stressed. C. maenas remains a voracious predator and regardless of the condition of mussels laid on commercial beds there is a need to control this predator in attempt to reduce losses in the benthic fishery.