P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Climate change and agricultural adaptation in Sri Lanka: a review

Climate change is inevitable and will continue into the next century. Since the agricultural sector in Sri Lanka is one of the most vulnerable to climate change, a thorough understanding of climate transition is critical for formulating effective adaptation strategies. This paper provides an overview of the status of climate change and adaptation in the agricultural sector in Sri Lanka. The review clearly indicates that climate change is taking place in Sri Lanka in terms of rainfall variability and an increase in climate extremes and warming. A number of planned and reactive adaptation responses stemming from policy and farm-level decisions are reported. These adaptation efforts were fragmented and lacked a coherent connection to the national development policies and strategies. Research efforts are needed to develop and identify adaptation approaches and practices that are feasible for smallholder farmers, particularly in the dry zone where paddy and other food crops are predominately cultivated. To achieve the envisaged growth in the agricultural sector, rigorous efforts are necessary to mainstream climate change adaptation into national development policies and ensure that they are implemented at national, regional and local levels.

Community-based climate change adaptation strategies for integrated prawn-fish-rice farming in Bangladesh to promote social-ecological resilience

Farming freshwater prawns with fish in rice fields is widespread in coastal regions of southwest Bangladesh because of favourable resources and ecological conditions. This article provides an overview of an ecosystem-based approach to integrated prawn-fish-rice farming in southwest Bangladesh. The practice of prawn and fish farming in rice fields is a form of integrated aquaculture-agriculture, which provides a wide range of social, economic and environmental benefits. Integrated prawn-fish-rice farming plays an important role in the economy of Bangladesh, earning foreign exchange and increasing food production. However, this unique farming system in coastal Bangladesh is particularly vulnerable to climatechange. We suggest that community-based adaptation strategies must be developed to cope with the challenges. We propose that integrated prawn-fish-rice farming could be relocated from the coastal region to less vulnerable upland areas, but caution that this will require appropriate adaptation strategies and an enabling institutional environment.

Adaptation-induced collective dynamics of a single-cell protozoan

We investigate the behavior of a single-cell protozoan in a narrow tubular ring. This environment forces them to swim under a one-dimensional periodic boundary condition. Above a critical density, single-cell protozoa aggregate spontaneously without external stimulation. The high-density zone of swimming cells exhibits a characteristic collective dynamics including translation and boundary fluctuation. We analyzed the velocity distribution and turn rate of swimming cells and found that the regulation of the turing rate leads to a stable aggregation and that acceleration of velocity triggers instability of aggregation. These two opposing effects may help to explain the spontaneous dynamics of collective behavior. We also propose a stochastic model for the mechanism underlying the collective behavior of swimming cells.

Determination of tube theory parameters using a simple grid model as an example

Although the tube theory is successful in describing entangled polymers qualitatively, a more quantitative description requires precise and consistent definitions of its parameters. Here we investigate the simplest model of entangled polymers, namely a single Rouse chain in a cubic lattice of line obstacles, and illustrate the typical problems and uncertainties of the tube theory. In particular we show that in general one needs 3 entanglement related parameters, but only 2 combinations of them are relevant for the long-time dynamics. Conversely, the plateau modulus can not be determined from these two parameters and requires a more detailed model of entanglements with explicit entanglement forces, such as the slipsprings model. It is shown that for the grid model the Rouse time within the tube is larger than the Rouse time of the free chain, in contrast to what the standard tube theory assumes.

An investigation of thermal comfort adaptation behaviour in office buildings in the UK

Around 40% of total energy consumption in the UK is consumed by creating comfortable indoor environment for occupants. Occupants’ behaviour in terms of achieving thermal comfort could have a significant impact on a building’s energy consumption. Therefore, understanding the interactions of occupants with their buildings would be essential to provide a thermal comfort environment that is less reliance on energy-intensive heating, ventilation and air-conditioning systems, to meet energysaving and carbon emission targets. This paper presents the findings of a year-long field study conducted in non-air-conditioned office buildings in the UK. Occupants’ adaptive responses in terms of technological and personal dimensions are dynamic processes which could vary with both indoor and outdoor thermal conditions. The adaptive behaviours of occupants in the surveyed building show substantial seasonal and daily variations. Our study shows that non-physical factors such as habit could influence the adaptive responses of occupants. However, occupants sometimes displayed inappropriate adaptive behaviour, which could lead to a misuse of energy. This paper attempts to illustrate how occupants would adapt and interact with their built environment and consequently contribute to development of a guide for future design/refurbishment of buildings and to develop energy management systems for a comfortable built environment.

Mutual dependency grid for stakeholder mapping: a component-based approach to supply chain participant analysis

Stakeholder analysis plays a critical role in business analysis. However, the majority of the stakeholder identification and analysis methods focus on the activities and processes and ignore the artefacts being processed by human beings. By focusing on the outputs of the organisation, an artefact-centric view helps create a network of artefacts, and a component-based structure of the organisation and its supply chain participants. Since the relationship is based on the components, i.e. after the stakeholders are identified, the interdependency between stakeholders and the focal organisation can be measured. Each stakeholder is associated with two types of dependency, namely the stakeholder’s dependency on the focal organisation and the focal organisation’s dependency on the stakeholder. We identify three factors for each type of dependency and propose the equations that calculate the dependency indexes. Once both types of the dependency indexes are calculated, each stakeholder can be placed and categorised into one of the four groups, namely critical stakeholder, mutual benefits stakeholder, replaceable stakeholder, and easy care stakeholder. The mutual dependency grid and the dependency gap analysis, which further investigates the priority of each stakeholder by calculating the weighted dependency gap between the focal organisation and the stakeholder, subsequently help the focal organisation to better understand its stakeholders and manage its stakeholder relationships.

Climate change adaptation strategies in Sub-Saharan Africa: foundations for the future

Many institutions across sub-Saharan Africa (SSA) and many funding agencies that support them are currently engaged in initiatives that are targeted towards adapting rainfed agriculture to climate change. This does, however, present some very real and complex research and policy challenges. Given to date the generally low impact of agricultural research across SSA on improving the welfare of rainfed farmers under current climatic conditions, a comprehensive strategy is required if the considerably more complex challenge of adapting agriculture to future climate change is to bear fruit. In articulating such a strategy, it is useful to consider the criteria by which current successful initiatives should be judged.

Early metabolic adaptation in C57BL/6 mice resistant to high fat diet induced weight gain involves an activation of mitochondrial oxidative pathways

We investigated the short-term (7 days) and long-term (60 days) metabolic effect of high fat diet induced obesity (DIO) and weight gain in isogenic C57BL/6 mice and examined the specific metabolic differentiation between mice that were either strong-responders (SR), or non-responders (NR) to weight gain. Mice (n = 80) were fed a standard chow diet for 7 days prior to randomization into a high-fat (HF) (n = 56) or a low-fat (LF) (n = 24) diet group. The (1)H NMR urinary metabolic profiles of LF and HF mice were recorded 7 and 60 days after the diet switch. On the basis of the body weight gain (BWG) distribution of HF group, we identified NR mice (n = 10) and SR mice (n = 14) to DIO. Compared with LF, HF feeding increased urinary excretion of glycine conjugates of β-oxidation intermediate (hexanoylglycine), branched chain amino acid (BCAA) catabolism intermediates (isovalerylglycine, α-keto-β-methylvalerate and α-ketoisovalerate) and end-products of nicotinamide adenine dinucleotide (NAD) metabolism (N1-methyl-2-pyridone-5-carboxamide, N1-methyl-4-pyridone-3-carboxamide) suggesting up-regulation of mitochondrial oxidative pathways. In the HF group, NR mice excreted relatively more hexanoylglycine, isovalerylglycine, and fewer tricarboxylic acid (TCA) cycle intermediate (succinate) in comparison to SR mice. Thus, subtle regulation of ketogenic pathways in DIO may alleviate the saturation of the TCA cycle and mitochondrial oxidative metabolism.

A fast two-grid and finite section method for a class of integral equations on the real line with application to an acoustic scattering problem in the half-plane

We consider the numerical treatment of second kind integral equations on the real line of the form ∅(s) = ∫_(-∞)^(+∞)▒〖κ(s-t)z(t)ϕ(t)dt,s=R〗 (abbreviated ϕ= ψ+K_z ϕ) in which K ϵ L_1 (R), z ϵ L_∞ (R) and ψ ϵ BC(R), the space of bounded continuous functions on R, are assumed known and ϕ ϵ BC(R) is to be determined. We first derive sharp error estimates for the finite section approximation (reducing the range of integration to [-A, A]) via bounds on (1-K_z )^(-1)as an operator on spaces of weighted continuous functions. Numerical solution by a simple discrete collocation method on a uniform grid on R is then analysed: in the case when z is compactly supported this leads to a coefficient matrix which allows a rapid matrix-vector multiply via the FFT. To utilise this possibility we propose a modified two-grid iteration, a feature of which is that the coarse grid matrix is approximated by a banded matrix, and analyse convergence and computational cost. In cases where z is not compactly supported a combined finite section and two-grid algorithm can be applied and we extend the analysis to this case. As an application we consider acoustic scattering in the half-plane with a Robin or impedance boundary condition which we formulate as a boundary integral equation of the class studied. Our final result is that if z (related to the boundary impedance in the application) takes values in an appropriate compact subset Q of the complex plane, then the difference between ϕ(s)and its finite section approximation computed numerically using the iterative scheme proposed is ≤C_1 [kh log⁡〖(1⁄kh)+(1-Θ)^((-1)⁄2) (kA)^((-1)⁄2) 〗 ] in the interval [-ΘA,ΘA](Θ<1) for kh sufficiently small, where k is the wavenumber and h the grid spacing. Moreover this numerical approximation can be computed in ≤C_2 N log⁡N operations, where N = 2A/h is the number of degrees of freedom. The values of the constants C1 and C2 depend only on the set Q and not on the wavenumber k or the support of z.

What (science for) adaptation to climate change in Colombian agriculture? A commentary on “A way forward on adaptation to climate change in Colombian agriculture: perspectives towards 2050” by J. Ramirez-Villegas, M. Salazar, A. Jarvis, C. E. Navarro-Valcines.

Climate change is putting Colombian agriculture under significant stress and, if no adaptation is made, the latter will be severely impacted during the next decades. Ramirez-Villegas et al. (2012) set out a government-led, top-down, techno-scientific proposal for a way forward by which Colombian agriculture could adapt to climate change. However, this proposal largely overlooks the root causes of vulnerability of Colombian agriculture, and of smallholders in particular. I discuss some of the hidden assumptions underpinning this proposal and of the arguments employed by Ramirez-Villegas et al., based on existing literature on Colombian agriculture and the wider scientific debate on adaptation to climate change. While technical measures may play an important role in the adaptation of Colombian agriculture to climate change, I question whether the actions listed in the proposal alone and specifically for smallholders, truly represent priority issues. I suggest that by i) looking at vulnerability before adaptation, ii) contextualising climate change as one of multiple exposures, and iii) truly putting smallholders at the centre of adaptation, i.e. to learn about and with them, different and perhaps more urgent priorities for action can be identified. Ultimately, I argue that what is at stake is not only a list of adaptation measures but, more importantly, the scientific approach from which priorities for action are identified. In this respect, I propose that transformative rather than technical fix adaptation represents a better approach for Colombian agriculture and smallholders in particular, in the face of climate change.

Changing European storm loss potentials under modified climate conditions according to ensemble simulations of the ECHAM5/MPI-OM1 GMC

A simple storm loss model is applied to an ensemble of ECHAM5/MPI-OM1 GCM simulations in order to estimate changes of insured loss potentials over Europe in the 21st century. Losses are computed based on the daily maximum wind speed for each grid point. The calibration of the loss model is performed using wind data from the ERA40-Reanalysis and German loss data. The obtained annual losses for the present climate conditions (20C, three realisations) reproduce the statistical features of the historical insurance loss data for Germany. The climate change experiments correspond to the SRES-Scenarios A1B and A2, and for each of them three realisations are considered. On average, insured loss potentials increase for all analysed European regions at the end of the 21st century. Changes are largest for Germany and France, and lowest for Portugal/Spain. Additionally, the spread between the single realisations is large, ranging e.g. for Germany from −4% to +43% in terms of mean annual loss. Moreover, almost all simulations show an increasing interannual variability of storm damage. This assessment is even more pronounced if no adaptation of building structure to climate change is considered. The increased loss potentials are linked with enhanced values for the high percentiles of surface wind maxima over Western and Central Europe, which in turn are associated with an enhanced number and increased intensity of extreme cyclones over the British Isles and the North Sea.

Addressing uncertainty in adaptation planning for agriculture

We present a framework for prioritizing adaptation approaches at a range of timeframes. The framework is illustrated by four case studies from developing countries, each with associated characterization of uncertainty. Two cases on near-term adaptation planning in Sri Lanka and on stakeholder scenario exercises in East Africa show how the relative utility of capacity vs. impact approaches to adaptation planning differ with level of uncertainty and associated lead time. An additional two cases demonstrate that it is possible to identify uncertainties that are relevant to decision making in specific timeframes and circumstances. The case on coffee in Latin America identifies altitudinal thresholds at which incremental vs. transformative adaptation pathways are robust options. The final case uses three crop–climate simulation studies to demonstrate how uncertainty can be characterized at different time horizons to discriminate where robust adaptation options are possible. We find that impact approaches, which use predictive models, are increasingly useful over longer lead times and at higher levels of greenhouse gas emissions. We also find that extreme events are important in determining predictability across a broad range of timescales. The results demonstrate the potential for robust knowledge and actions in the face of uncertainty.