A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters : theory and application to microfilaments

As all-atom molecular dynamics method is limited by its enormous computational cost, various coarse-grained strategies have been developed to extend the length scale of soft matters in the modeling of mechanical behaviors. However, the classical thermostat algorithm in highly coarse-grained molecular dynamics method would underestimate the thermodynamic behaviors of soft matters (e.g. microfilaments in cells), which can weaken the ability of materials to overcome local energy traps in granular modeling. Based on all-atom molecular dynamics modeling of microfilament fragments (G-actin clusters), a new stochastic thermostat algorithm is developed to retain the representation of thermodynamic properties of microfilaments at extra coarse-grained level. The accuracy of this stochastic thermostat algorithm is validated by all-atom MD simulation. This new stochastic thermostat algorithm provides an efficient way to investigate the thermomechanical properties of large-scale soft matters.

A comparative study of the semi-elastic and fully-elastic MapReduce models

MapReduce is a computation model for processing large data sets in parallel on large clusters of machines, in a reliable, fault-tolerant manner. A MapReduce computation is broken down into a number of map tasks and reduce tasks, which are performed by so called mappers and reducers, respectively. The placement of the mappers and reducers on the machines directly affects the performance and cost of the MapReduce computation in cloud computing. From the computational point of view, the mappers/reducers placement problem is a generation of the classical bin packing problem, which is NP-complete. Thus, in this paper we propose a new heuristic algorithm for the mappers/reducers placement problem in cloud computing and evaluate it by comparing with other several heuristics on solution quality and computation time by solving a set of test problems with various characteristics. The computational results show that our heuristic algorithm is much more efficient than the other heuristics and it can obtain a better solution in a reasonable time. Furthermore, we verify the effectiveness of our heuristic algorithm by comparing the mapper/reducer placement for a benchmark problem generated by our heuristic algorithm with a conventional mapper/reducer placement which puts a fixed number of mapper/reducer on each machine. The comparison results show that the computation using our mapper/reducer placement is much cheaper than the computation using the conventional placement while still satisfying the computation deadline.

Performance-driven live migration of multiple virtual machines in datacenters

Live migration of multiple Virtual Machines (VMs) has become an indispensible management activity in datacenters for application performance, load balancing, server consolidation. While state-of-the-art live VM migration strategies focus on the improvement of the migration performance of a single VM, little attention has been given to the case of multiple VMs migration. Moreover, existing works on live VM migration ignore the inter-VM dependencies, and underlying network topology and its bandwidth. Different sequences of migration and different allocations of bandwidth result in different total migration times and total migration downtimes. This paper concentrates on developing a multiple VMs migration scheduling algorithm such that the performance of migration is maximized. We evaluate our proposed algorithm through simulation. The simulation results show that our proposed algorithm can migrate multiple VMs on any datacenter with minimum total migration time and total migration downtime.

Photocatalysis on supported gold and silver nanoparticles under ultraviolet and visible light irradiation

Studies of the optical properties and catalytic capabilities of noble metal nanoparticles (NPs), such as gold (Au) and silver (Ag), have formed the basis for the very recent fast expansion of the field of green photocatalysis: photocatalysis utilizing visible and ultraviolet light, a major part of the solar spectrum. The reason for this growth is the recognition that the localised surface plasmon resonance (LSPR) effect of Au NPs and Ag NPs can couple the light flux to the conduction electrons of metal NPs, and the excited electrons and enhanced electric fields in close proximity to the NPs can contribute to converting the solar energy to chemical energy by photon-driven photocatalytic reactions. Previously the LSPR effect of noble metal NPs was utilized almost exclusively to improve the performance of semiconductor photocatalysts (for example, TiO2 and Ag halides), but recently, a conceptual breakthrough was made: studies on light driven reactions catalysed by NPs of Au or Ag on photocatalytically inactive supports (insulating solids with a very wide band gap) have demonstrated that these materials are a class of efficient photocatalysts working by mechanisms distinct from those of semiconducting photocatalysts. There are several reasons for the significant photocatalytic activity of Au and Ag NPs. (1) The conduction electrons of the particles gain the irradiation energy, resulting in high energy electrons at the NP surface which is desirable for activating molecules on the particles for chemical reactions. (2) In such a photocatalysis system, both light harvesting and the catalysing reaction take place on the nanoparticle, and so charge transfer between the NPs and support is not a prerequisite. (3) The density of the conduction electrons at the NP surface is much higher than that at the surface of any semiconductor, and these electrons can drive the reactions on the catalysts. (4) The metal NPs have much better affinity than semiconductors to many reactants, especially organic molecules. Recent progress in photocatalysis using Au and Ag NPs on insulator supports is reviewed. We focus on the mechanism differences between insulator and semiconductor-supported Au and Ag NPs when applied in photocatalytic processes, and the influence of important factors, light intensity and wavelength, in particular estimations of light irradiation contribution, by calculating the apparent activation energies of photo reactions and thermal reactions.

Modelling after-the-fact leakage for key exchange

Security models for two-party authenticated key exchange (AKE) protocols have developed over time to prove the security of AKE protocols even when the adversary learns certain secret values. In this work, we address more granular leakage: partial leakage of long-term secrets of protocol principals, even after the session key is established. We introduce a generic key exchange security model, which can be instantiated allowing bounded or continuous leakage, even when the adversary learns certain ephemeral secrets or session keys. Our model is the strongest known partial-leakage-based security model for key exchange protocols. We propose a generic construction of a two-pass leakage-resilient key exchange protocol that is secure in the proposed model, by introducing a new concept: the leakage-resilient NAXOS trick. We identify a special property for public-key cryptosystems: pair generation indistinguishability, and show how to obtain the leakage-resilient NAXOS trick from a pair generation indistinguishable leakage-resilient public-key cryptosystem.

"Candidatus Similichlamydia laticola", a novel Chlamydia-like agent of epitheliocystis in seven consecutive cohorts of farmed Australian barramundi, lates calcarifer (Bloch)

Six consecutively hatched cohorts and one cohort of pre-hatch eggs of farmed barramundi (Lates calcarifer) from south Australia were examined for Chlamydia-like organisms associated with epitheliocystis. To identify and characterise the bacteria, 59 gill samples and three pre-hatch egg samples were processed for histology, in situ hybridisation and 16S rRNA amplification, sequencing and comprehensive phylogenetic analysis. Cases of epitheliocystis were observed microscopically and characterised by membrane-enclosed basophilic cysts filled with a granular material that caused hypertrophy of the epithelial cells. In situ hybridisation with a Chlamydiales-specific probe lead to specific labelling of the epitheliocystis inclusions within the gill epithelium. Two distinct but closely related 16S rRNA chlamydial sequences were amplified from gill DNA across the seven cohorts, including from pre-hatch eggs. These genotype sequences were found to be novel, sharing 97.1 - 97.5% similarity to the next closest 16S rRNA sequence, Ca. Similichlamydia latridicola, from Australian striped trumpeter. Comprehensive phylogenetic analysis of these genotype sequences against representative members of the Chlamydiales order and against other epitheliocystis agents revealed these Chlamydia-like organisms to be novel and taxonomically placed them within the recently proposed genus Ca. Similichlamydia. Following Fredricks and Relman's molecular postulates and based on these observations, we propose the epitheliocystis agents of barramundi to be known as "Candidatus Similichlamydia laticola" (sp. nov.).

Setting water quality objectives for the health of freshwater fish

An important responsibility of the Environment Protection Authority, Victoria, is to set objectives for levels of environmental contaminants. To support the development of environmental objectives for water quality, a need has been identified to understand the dual impacts of concentration and duration of a contaminant on biota in freshwater streams. For suspended solids contamination, information reported by Newcombe and Jensen [ North American Journal of Fisheries Management , 16(4):693--727, 1996] study of freshwater fish and the daily suspended solids data from the United States Geological Survey stream monitoring network is utilised. The study group was requested to examine both the utility of the Newcombe and Jensen and the USA data, as well as the formulation of a procedure for use by the Environment Protection Authority Victoria that takes concentration and duration of harmful episodes into account when assessing water quality. The extent to which the impact of a toxic event on fish health could be modelled deterministically was also considered. It was found that concentration and exposure duration were the main compounding factors on the severity of effects of suspended solids on freshwater fish. A protocol for assessing the cumulative effect on fish health and a simple deterministic model, based on the biology of gill harm and recovery, was proposed. References D. W. T. Au, C. A. Pollino, R. S. S Wu, P. K. S. Shin, S. T. F. Lau, and J. Y. M. Tang. Chronic effects of suspended solids on gill structure, osmoregulation, growth, and triiodothyronine in juvenile green grouper epinephelus coioides . Marine Ecology Press Series , 266:255--264, 2004. J.C. Bezdek, S.K. Chuah, and D. Leep. Generalized k-nearest neighbor rules. Fuzzy Sets and Systems , 18:237--26, 1986. E. T. Champagne, K. L. Bett-Garber, A. M. McClung, and C. Bergman. {Sensory characteristics of diverse rice cultivars as influenced by genetic and environmental factors}. Cereal Chem. , {81}:{237--243}, {2004}. S. G. Cheung and P. K. S. Shin. Size effects of suspended particles on gill damage in green-lipped mussel perna viridis. Marine Pollution Bulletin , 51(8--12):801--810, 2005. D. H. Evans. The fish gill: site of action and model for toxic effects of environmental pollutants. Environmental Health Perspectives , 71:44--58, 1987. G. C. Grigg. The failure of oxygen transport in a fish at low levels of ambient oxygen. Comp. Biochem. Physiol. , 29:1253--1257, 1969. G. Holmes, A. Donkin, and I.H. Witten. {Weka: A machine learning workbench}. In Proceedings of the Second Australia and New Zealand Conference on Intelligent Information Systems , volume {24}, pages {357--361}, {Brisbane, Australia}, {1994}. {IEEE Computer Society}. D. D. Macdonald and C. P. Newcombe. Utility of the stress index for predicting suspended sediment effects: response to comments. North American Journal of Fisheries Management , 13:873--876, 1993. C. P. Newcombe. Suspended sediment in aquatic ecosystems: ill effects as a function of concentration and duration of exposure. Technical report, British Columbia Ministry of Environment, Lands and Parks, Habitat Protection branch, Victoria, 1994. C. P. Newcombe and J. O. T. Jensen. Channel suspended sediment and fisheries: A synthesis for quantitative assessment of risk and impact. North American Journal of Fisheries Management , 16(4):693--727, 1996. C. P. Newcombe and D. D. Macdonald. Effects of suspended sediments on aquatic ecosystems. North American Journal of Fisheries Management , 11(1):72--82, 1991. K. Schmidt-Nielsen. Scaling. Why is animal size so important? Cambridge University Press, NY, 1984. J. S. Schwartz, A. Simon, and L. Klimetz. Use of fish functional traits to associate in-stream suspended sediment transport metrics with biological impairment. Environmental Monitoring and Assessment , 179(1--4):347--369, 2011. E. Al Shaw and J. S. Richardson. Direct and indirect effects of sediment pulse duration on stream invertebrate assemb ages and rainbow trout ( Oncorhynchus mykiss ) growth and survival. Canadian Journal of Fish and Aquatic Science , 58:2213--2221, 2001. P. Tiwari and H. Hasegawa. {Demand for housing in Tokyo: A discrete choice analysis}. Regional Studies , {38}:{27--42}, {2004}. Y. Tramblay, A. Saint-Hilaire, T. B. M. J. Ouarda, F. Moatar, and B Hecht. Estimation of local extreme suspended sediment concentrations in california rivers. Science of the Total Environment , 408:4221--

Assessment of recycled concrete aggregates as a pavement material

Population increase and economic developments can lead to construction as well as demolition of infrastructures such as buildings, bridges, roads, etc resulting in used concrete as a primary waste product. Recycling of waste concrete to obtain the recycled concrete aggregates (RCA) for base and/or sub-base materials in road construction is a foremost application to be promoted to gain economical and sustainability benefits. As the mortar, bricks, glass and reclaimed asphalt pavement (RAP) present as constituents in RCA, it exhibits inconsistent properties and performance. In this study, six different types of RCA samples were subjected classification tests such as particle size distribution, plasticity, compaction test, unconfined compressive strength (UCS) and California bearing ratio (CBR) tests. Results were compared with those of the standard road materials used in Queensland, Australia. It was found that material type ‘RM1-100/RM3-0’ and ‘RM1-80/RM3-20’ samples are in the margin of the minimum required specifications of base materials used for high volume unbound granular roads while others are lower than that the minimum requirement.

Accessibility of pores in coal to methane and carbon dioxide

Fluid–solid interactions in natural and engineered porous solids underlie a variety of technological processes, including geological storage of anthropogenic greenhouse gases, enhanced coal bed methane recovery, membrane separation, and heterogeneous catalysis. The size, distribution and interconnectivity of pores, the chemical and physical properties of the solid and fluid phases collectively dictate how fluid molecules migrate into and through the micro- and meso-porous media, adsorb and ultimately react with the solid surfaces. Due to the high penetration power and relatively short wavelength of neutrons, smallangle neutron scattering (SANS) as well as ultra small-angle scattering (USANS) techniques are ideally suited for assessing the phase behavior of confined fluids under pressure as well as for evaluating the total porosity in engineered and natural porous systems including coal. Here we demonstrate that SANS and USANS can be also used for determining the fraction of the pore volume that is actually accessible to fluids as a function of pore sizes and study the fraction of inaccessible pores as a function of pore size in three coals from the Illinois Basin (USA) and Bowen Basin (Australia). Experiments were performed at CO2 and methane pressures up to 780 bar, including pressures corresponding to zero average contrast condition (ZAC), which is the pressure where no scattering from the accessible pores occurs. Scattering curves at the ZAC were compared with the scattering from same coals under vacuum and analysed using a newly developed approach that shows that the volume fraction of accessible pores in these coals varies between �90% in the macropore region to �30% in the mesopore region and the variation is distinctive for each of the examined coals. The developed methodology may be also applied for assessing the volume of accessible pores in other natural underground formations of interest for CO2 sequestration, such as saline aquifers as well as for estimating closed porosity in engineered porous solids of technological importance.

Continuous after-the-fact leakage-resilient key exchange

Security models for two-party authenticated key exchange (AKE) protocols have developed over time to provide security even when the adversary learns certain secret keys. In this work, we advance the modelling of AKE protocols by considering more granular, continuous leakage of long-term secrets of protocol participants: the adversary can adaptively request arbitrary leakage of long-term secrets even after the test session is activated, with limits on the amount of leakage per query but no bounds on the total leakage. We present a security model supporting continuous leakage even when the adversary learns certain ephemeral secrets or session keys, and give a generic construction of a two-pass leakage-resilient key exchange protocol that is secure in the model; our protocol achieves continuous, after-the-fact leakage resilience with not much more cost than a previous protocol with only bounded, non-after-the-fact leakage.

Handmade clay balls and recycled crush glass as alternative media in water filtration

For many years materials such as quarried sand, anthracite, and granular activated carbon have been the principal media-products traditionally used in water and wastewater filtration plants. Pebble Matrix Filtration (PMF) is a novel non-chemical, sustainable pre-treatment method of protecting Slow Sand Filters (SSF) from high turbidity during heavy monsoon periods. PMF uses sand and pebbles as the filter media and the sustainability of this new technology might depend on availability and supply of pebbles and sand, both finite resources. In many countries there are two principal methods of obtaining pebbles and sand, namely dredging from rivers and beaches, and due to the scarcity of these resources in some countries the cost of pebbles is often 4-5 times higher than that of sand. In search for an alternative medium to pebbles after some preliminary laboratory tests conducted in Colombo-Sri Lanka, Poznan-Poland and Cambridge-UK, a 100-year-old brick factory near Sudbury, Suffolk, has produced hand-made clay pebbles satisfying the PMF quality requirements. As an alternative to sand, crushed recycled glass from a UK supplier was used and the PMF system was operated together with hand-made clay balls in the laboratory for high turbidity removal effectively. The results of laboratory experiments with alternative media are presented in this paper. There are potential opportunities for recycled crushed glass and clay ball manufacturing processes in some countries where they can be used as filter media.

Synthesis and characterization of titanium sol–gels in varied gravity

Two unique test systems were designed and built to allow the effects of varied gravity (high, normal, reduced) during synthesis of titanium sol–gels to be studied. A centrifuge capable of providing high gravity environments of up to 70 g for extended periods while applying a 100 mbar vacuum and a temperature of 40–50 °C to the reaction chambers was developed. The second system was used in the QUT Microgravity Drop Tower Facility also provided the same thermal and vacuum conditions used in the centrifuge, but was required to operate autonomously during free fall. Through the use of post synthesis instrumental characterization, it was found that increased gravity levels during synthesis, had the greatest effect on the final products. Samples produced in reduced and normal gravity appeared to form amorphous gels containing very small particles with moderate surface areas. Whereas crystalline anatase (TiO2), was found to form in samples synthesized above 5 g with significant increases in crystallinity, particle size and surface area observed when samples were produced at gravity levels up to 70 g. It is proposed that for samples produced in higher gravity, an increased concentration gradient of water is forms at the bottom of the reacting film due to forced convection. The particles formed in higher gravity diffuse downward toward this excess of water, which favors the condensation reaction of remaining sol–gel precursors with the particles promoting increased particle growth. Due to the removal of downward convection in reduced gravity, particle growth due to condensation reaction processes are physically hindered hydrolysis reactions favored instead. Another significant finding from this work was that anatase could be produced at relatively low temperatures of 40–50 °C instead of the conventional method of calcination above 450 °C solely through sol–gel synthesis at higher gravity levels.

A comparison of stability and bifurcation criteria for inflated spherical elastic shells

The nonlinear stability analysis introduced by Chen and Haughton [1] is employed to study the full nonlinear stability of the non-homogeneous spherically symmetric deformation of an elastic thick-walled sphere. The shell is composed of an arbitrary homogeneous, incompressible elastic material. The stability criterion ultimately requires the solution of a third-order nonlinear ordinary differential equation. Numerical calculations performed for a wide variety of well-known incompressible materials are then compared with existing bifurcation results and are found to be identical. Further analysis and comparison between stability and bifurcation are conducted for the case of thin shells and we prove by direct calculation that the two criteria are identical for all modes and all materials.

On extension and torsion of a compressible elastic circular cylinder

In this paper we examine the combined extension and torsion of a compressible isotropic elastic cylinder of finite extent. The equilibrium equations are formulated in terms of the principal stretches and then applied to the special case of pure torsion superimposed on a uniform extension (an isochoric deformation). Explicit necessary and sufficient conditions on the strain-energy function for the material to support this deformation with vanishing traction on the lateral surfaces of the cylinder are obtained. Some strain-energy functions satisfying these conditions are considered, existing results are recovered as special cases and new results are obtained. We also point out how the strain-energy functions generated from the considered isochoric deformation considered (of a compressible material) can be used to generate energy functions and corresponding solutions for the incompressible theory.

Plasmas meet plasmonics

The term ‘plasmon’ was first coined in 1956 to describe collective electronic oscillations in solids which were very similar to electronic oscillations/surface waves in a plasma discharge (effectively the same formulae can be used to describe the frequencies of these physical phenomena). Surface waves originating in a plasma were initially considered to be just a tool for basic research, until they were successfully used for the generation of large-area plasmas for nanoscale materials synthesis and processing. To demonstrate the synergies between ‘plasmons’ and ‘plasmas’, these large-area plasmas can be used to make plasmonic nanostructures which functionally enhance a range of emerging devices. The incorporation of plasma-fabricated metal-based nanostructures into plasmonic devices is the missing link needed to bridge not only surface waves from traditional plasma physics and surface plasmons from optics, but also, more topically, macroscopic gaseous and nanoscale metal plasmas. This article first presents a brief review of surface waves and surface plasmons, then describe how these areas of research may be linked through Plasma Nanoscience showing, by closely looking at the essential physics as well as current and future applications, how everything old, is new, once again.