Parallel simulation of Population Dynamics P systems: updates and roadmap

Population Dynamics P systems are a type of multienvironment P systems that serve as a formal modeling framework for real ecosystems. The accurate simulation of these probabilistic models, e.g. with Direct distribution based on Consistent Blocks Algorithm, entails large run times. Hence, parallel platforms such as GPUs have been employed to speedup the simulation. In 2012, the first GPU simulator of PDP systems was presented. However, it was able to run only randomly generated PDP systems. In this paper, we present current updates made on this simulator, involving an input modu le for binary files and an output module for CSV files. Finally, the simulator has been experimentally validated with a real ecosystem model, and its performance has been tested with two high-end GPUs: Tesla C1060 and K40.     

The natural history and fisheries ecology of Lake Chilwa,southern Malawi

Lake Chilwa produces between zero and 24,000 metric tons of fish per year, making it one of the most productive but variable lakes in Africa. The size of the lake varies seasonally and among years, sometimes drying completely. Its surrounding wetland and floodplain provide habitat for a diversity of birds and economically valuable grasses and reeds. When the lake has water, there is considerable activity on its shores and temporary fishing villages spring up. People move in and out of the lake basin in concert with these seasonal and longer term changes. This paper examines the environmental dynamics of Lake Chilwa and its surrounding wetlands, presents an overview of the socio-economic context of the area and discusses threats to this resilient system that might occur as a result of climate change. We conclude that management of Lake Chilwa must place the lake in the wider economic and ecological system in which it is situated. Ultimately, land-use practices within the basin present more of a threat to the resilience of the fishery and people's livelihoods than overfishing or a strict focus on the lake's resources. These perspectives present significant challenges to conventional fisheries governance.     

Adiabatic quantum optimization with qudits

Most realistic solid state devices considered as qubits are not true two-state systems. If the energy separation of the upper energy levels from the lowest two levels is not large, then these upper states may affect the evolution of the ground state over time and therefore cannot be neglected. In this work, we study the effect of energy levels beyond the lowest two energy levels on adiabatic quantum optimization in a device with a double-well potential as the basic logical element. We show that the extra levels can be modeled by adding additional ancilla qubits coupled to the original logical qubits, and that the presence of upper levels has no effect on the final ground state. We also study the influence of upper energy levels on the minimum gap for a set of 8-qubit spin glass instances.     

Scenario analysis and management options for sustainable river basin management: Application of the Elbe DSS

We developed a decision support system (DSS) for sustainable river basin management in the German Elbe catchment (～100,000 km²), called Elbe-DSS. The system integrates georeferenced simulation models and related data sets with a user friendly interface and includes a library function. Design and content of the DSS have been developed in close cooperation with end users and stakeholders. The user can evaluate effectiveness of management actions like reforestation, improvement of treatment plant technology or the application of buffer strips under the influence of external constraints on climate, demographic and agro-economic changes to meet water management objectives such as water quality standards and discharge control. The paper (i) describes the conceptual design of the Elbe-DSS, (ii) demonstrates the applicability of the integrated catchment model by running three different management options for phosphate discharge reduction (reforestation, erosion control and ecological-farming) under the assumption of regional climate change based on IPCC scenarios, (iii) evaluates the effectiveness of the management options, and (iv) provides some lessons for the DSS-development in similar settings. The georeferenced approach allows the identification of local inputs in sub-catchments and their impact on the overall water quality, which helps the user to prioritize his management actions in terms of spatial distribution and effectiveness.     

A principled approach to programming with nested types in Haskell

Initial algebra semantics is one of the cornerstones of the theory of modern functional programming languages. For each inductive data type, it provides a Church encoding for that type, a build combinator which constructs data of that type, a fold combinator which encapsulates structured recursion over data of that type, and a fold/build rule which optimises modular programs by eliminating from them data constructed using the buildcombinator, and immediately consumed using the foldcombinator, for that type. It has long been thought that initial algebra semantics is not expressive enough to provide a similar foundation for programming with nested types in Haskell. Specifically, the standard folds derived from initial algebra semantics have been considered too weak to capture commonly occurring patterns of recursion over data of nested types in Haskell, and no build combinators or fold/build rules have until now been defined for nested types. This paper shows that standard folds are, in fact, sufficiently expressive for programming with nested types in Haskell. It also defines buildcombinators and fold/build fusion rules for nested types. It thus shows how initial algebra semantics provides a principled, expressive, and elegant foundation for programming with nested types in Haskell.     

Characterisation of flucloxacillin and 5-hydroxymethyl flucloxacillin haptenated HSA in vitro and in vivo

Flucloxacillin is a synthetic penicillin used in the treatment of Staphylococcal infections. Adverse reactions to the drug are believed to arise through covalent modification of proteins, with tissue damage occurring secondary to an immune reaction. Serum proteins have been shown by adduct-specific antibodies to be modified by flucloxacillin, but the nature and sites of modification have not been characterised. Here, in vitro studies on HSA have shown by MS that the modification of protein lysine residues occurs in a dose-, time- and site-dependent manner. Affinity, cation exchange and reversed phase chromatography prior to MS revealed in vivo modification of HSA with flucloxacillin in tolerant patients, with up to nine modified lysine residues being detected in each patient, and with modification of Lys190 and Lys212 being detected in 8/8 patients. It was also revealed for the first time that plasma proteins could be modified with the 5-hydroxymethyl metabolite of flucloxacillin, and that essentially the same Lys residues were targeted by both the parent drug and its metabolite. This study provides a detailed characterisation of sites of chemical modification of an endogenous target and reveals candidate peptides for T-cell and antibody assays of flucloxacillin hypersensitivity.     

Persistent ocean monitoring with underwater gliders: Adapting sampling resolution

Ocean processes are dynamic and complex and occur on multiple spatial and temporal scales. To obtain a synoptic view of such processes, ocean scientists collect data over long time periods. Historically, measurements were continually provided by fixed sensors, e.g., moorings, or gathered from ships. Recently, an increase in the utilization of autonomous underwater vehicles has enabled a more dynamic data acquisition approach. However, we still do not utilize the full capabilities of these vehicles. Here we present algorithms that produce persistent monitoring missions for underwater vehicles by balancing path following accuracy and sampling resolution for a given region of interest, which addresses a pressing need among ocean scientists to efficiently and effectively collect high‐value data. More specifically, this paper proposes a path planning algorithm and a speed control algorithm for underwater gliders, which together give informative trajectories for the glider to persistently monitor a patch of ocean. We optimize a cost function that blends two competing factors: maximize the information value along the path while minimizing deviation from the planned path due to ocean currents. Speed is controlled along the planned path by adjusting the pitch angle of the underwater glider, so that higher resolution samples are collected in areas of higher information value. The resulting paths are closed circuits that can be repeatedly traversed to collect long‐term ocean data in dynamic environments. The algorithms were tested during sea trials on an underwater glider operating off the coast of southern California, as well as in Monterey Bay, California. The experimental results show improvements in both data resolution and path reliability compared to previously executed sampling paths used in the respective regions. © 2011 Wiley Periodicals, Inc.