Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Planning for Renewable Energy: Lessons from the UK’s Devolved Administrations

The planning system has been put forward as a key element in facilitating the low carbon transition (Bulkeley 2006, While 2008), by reducing carbon footprints through initiatives such as encouraging less-energy intensive development, reducing the need to travel or promoting sustainable forms of transport. It has also played a key role on encouraging a shift to more renewable sources of energy, through establishing the spatial ‘rules’ for its regulation, consenting of specific projects and acting as the key arena for mediating a range of social concerns over the resulting socio-technical shift. Despite having this key facilitative role, planning is also regularly seen as a key impediment to renewables, particularly on-shore wind (Ellis et al 2009). There is however, little known about what makes the ‘best’ approach to planning for renewables and indeed little discussion on how to judge the effectiveness of a planning regime for this issue – is it one that maximises generating capacity, protects or landscapes or biodiversity, or perhaps one that maximises social acceptance of renewable developments?

The UK offers a useful context for exploring these issues, with its four main territories (England, Northern Ireland, Scotland and Wales) having broadly similar institutional arrangements, but autonomy over spatial planning during the period in which renewables expanded across the landscape. Each of these jurisdictions has sought to use their planning system to encourage renewables with subtlety different discourses, regulations and spatial strategies. Such an ‘experiment’ offers some important insight into what ‘works’.

This paper will draw on a two year study funded by the UK’s Economic and Social Research Council (RES-062-23-2526), which has charted the effects of devolved administrations on policy and delivery of renewable energy from 1990 to 2012. Drawing on more than 80 interviews, documentary analysis and secondary data sources it describes the growth of renewable capacity in each jurisdiction, explores the spatial strategies adopted and analyses the way in which the broader institutional frameworks in which planning for renewables has emerged. The paper uses this analysis to consider the lessons that can be drawn from the comparable experience of the devolved administrations in the UK and points to the ways in which we should evaluate the effectiveness of planning regimes for renewable energy.

Editorial

Malone, C.A.T., S.K.F. Stoddart, and N. James, Editorial. Antiquity, (Topics Include Antiquity’s first century, landscapes, textiles, Philip Barker, Barri Jones).

Later Pleistocene evolution of the Exe valley: A chronstratigraphic model of terrace formation and its implications for Palaeolithic archaeology

This paper presents the ?rst systematic chronostratigraphic study of the river terraces of the Exe catchment in South West England and a new conceptual model for terrace formation in unglaciated basins with applicability to terrace staircase sequences elsewhere. The Exe catchment lay beyond the maximum extent of Pleistocene ice sheets and the drainage pattern evolved from the Tertiary to the Middle Pleistocene, by which time the major valley systems were in place and downcutting began to create a staircase of strath terraces. The higher terraces (8-6) typically exhibit altitudinal overlap or appear to be draped over the landscape, whilst the middle terraces show greater altitudinal separation and the lowest terraces are of a cut and ?ll form. The terrace deposits investigated in this study were deposited in cold phases of the glacial-interglacial Milankovitch climatic cycles with the lowest four being deposited in the Devensian Marine Isotope Stages (MIS) 4-2. A new cascade process-response model is proposed of basin terrace evolution in the Exe valley, which emphasises the role of lateral erosion in the creation of strath terraces and the reworking of inherited resistant lithological components down through the staircase. The resultant emergent valley topography and the reworking of artefacts along with gravel clasts, have important implications for the dating of hominin presence and the local landscapes they inhabited. Whilst the terrace chronology suggested here is still not as detailed as that for the Thames or the Solent System it does indicate a Middle Palaeolithic hominin presence in the region, probably prior to the late Wolstonian Complex or MIS 6. This supports existing data from cave sites in South West England.

Determining the response of African biota to climate change: using the past to model the future

Prediction of biotic responses to future climate change in tropical Africa tends to be based on two modelling approaches: bioclimatic species envelope models and dynamic vegetation models. Another complementary but underused approach is to examine biotic responses to similar climatic changes in the past as evidenced in fossil and historical records. This paper reviews these records and highlights the information that they provide in terms of understanding the local- and regional-scale responses of African vegetation to future climate change. A key point that emerges is that a move to warmer and wetter conditions in the past resulted in a large increase in biomass and a range distribution of woody plants up to 400–500 km north of its present location, the so-called greening of the Sahara. By contrast, a transition to warmer and drier conditions resulted in a reduction in woody vegetation in many regions and an increase in grass/savanna-dominated landscapes. The rapid rate of climate warming coming into the current interglacial resulted in a dramatic increase in community turnover, but there is little evidence for widespread extinctions. However, huge variation in biotic response in both space and time is apparent with, in some cases, totally different responses to the same climatic driver. This highlights the importance of local features such as soils, topography and also internal biotic factors in determining responses and resilience of the African biota to climate change, information that is difficult to obtain from modelling but is abundant in palaeoecological records.

Portrush: Architecture for the North Irish Coast

The North Irish coast resembles one of the unique landscapes that define the scenic character of the place. To understand place you need to engage with stories and histories behind it. The search for Portrush has to start from Ulster. This book offers a journey to explore histories, traditions, festivities and the architecture of the Irish town. Approaching Portrush as a field of experimental architectural studio, the studio at Queen’s University Belfast teamed up to rediscover the Irish coastal condition and have a rethink about the origins and ingredients of Irish architecture and landscape. This book records and discusses this ambitious project and its outcome. Divided into two parts, the book introduces a comprehensive contextual and historical investigation into the heritage, culture and architecture followed by a display of students’ theoretical encounters and designs.

In search of common grounds: Stitching the divided landscape of urban parks in Belfast's interface zones

Political and spatial contestation in divided cities contributes to strategies of self-defense that utilize physical and spatial settings to enable the constitution of social boundaries, borders and territories.
Urban parks that are designed to ease division through an open transitional landscape can instead facilitate further segregation through their spatial order and facility layout. This paper investigates the role of the spatial design and material landscape of integrated parks in Belfast interface areas as instruments of engagement or division. It does so by analyzing the spatial organization of the parks’ facilities and the resultant ‘social voids.’ Space, time and distance were found to be effective tools for the negotiation of privacy, the manifestation of power, and the interplay of dominance and self-confidence. In the context of a divided city, strong community-culture tends to reproduce new boundaries and territories within the shared landscape. Through user interviews and spatial analysis, this paper outlines the design principles that influence spatial behavior in the urban parks of contested urban landscapes. It argues that despite granting equal access to shared public facilities, social voids and physical gaps can instill practices of division that deepen territorial barriers, both psychologically and spatially.

Response of farmland biodiversity to the introduction of bioenergy crops: effects of local factors and surrounding landscape context

The recent growth in bioenergy crop cultivation, stimulated by the need to implement measures to reduce net CO emissions, is driving major land-use changes with consequences for biodiversity and ecosystem service provision. Although the type of bioenergy crop and its associated management is likely to affect biodiversity at the local (field) scale, landscape context and its interaction with crop type may also influence biodiversity on farms. In this study, we assessed the impact of replacing conventional agricultural crops with two model bioenergy crops (either oilseed rape Brassica napus or Miscanthus × giganteus) on vascular plant, bumblebee, solitary bee, hoverfly and carabid beetle richness, diversity and abundance in 50 sites in Ireland. We assessed whether within-field biodiversity was also related to surrounding landscape structure. We found that local- and landscape-scale variables correlated with biodiversity in these agricultural landscapes. Overall, the differences between the bioenergy crops and the conventional crops on farmland biodiversity were mostly positive (e.g. higher vascular plant richness in Miscanthus planted on former conventional tillage, higher solitary bee abundance and richness in Miscanthus and oilseed rape compared with conventional crops) or neutral (e.g. no differences between crop types for hoverflies and bumblebees). We showed that these crop type effects were independent of (i.e. no interactions with) the surrounding landscape composition and configuration. However, surrounding landscape context did relate to biodiversity in these farms, negatively for carabid beetles and positively for hoverflies. Although we conclude that the bioenergy crops compared favourably with conventional crops in terms of biodiversity of the taxa studied at the field scale, the effects of large-scale planting in these landscapes could result in very different impacts. Maintaining ecosystem functioning and the delivery of ecosystem services will require a greater understanding of impacts at the landscape scale to ensure the sustainable development of climate change mitigation measures.

Botanical travel, climate and David Moore’s moral geographies of Europe

During his forty-year curatorship of the Royal Dublin Society's botanical gardens in Glasnevin (1838–1879), David Moore undertook a number of excursions to continental Europe. These served to deepen the networks of plant exchange between Dublin and other botanical institutions and allowed him to examine the relationships between climate, plant survivability and societal development. This paper focuses on two trips taken in the 1860s to Scandinavia and Iberia and charts how Moore situated his experience of these places within a climatic hermeneutic. Moore's understanding of northern and southern Europe was organized around a set of judgments about their relative backwardness or advancement with respect to his experience of home and was seen through the lens of a moral climatology. Moreover, his Scots Presbyterian background and his commitment to natural theology informed his interpretation of the landscapes he encountered in his excursions across Europe.

Business Giving, the Tsunami and Corporates as Rock Stars: Some Implications for Arts Funding?

Financial and cultural aspects of corporate giving by UK and non-UK companies in response to the December 2004 South Asia Tsunami disaster are explored in this article. Literatures on corporate giving rationales, concepts of disaster and donor activity in disasters provide an underpinning. The article seeks to make connections between this high profile if short-lived business giving and the funding of the arts that is sought from business; and to draw tentative lessons for arts funding when seeking business support. The giving accounts in the wake of the Tsunami from a non-probability sample of 56 UK companies and 16 non-UK companies were examined. Reported online to the UK charity Business in the Community, these accounts were accessed in February 2005 and scrutinized thematically. Concurrently, company financial profiles to accompany giving figures were constructed. Although linkages between donation levels and financial performance were lacking, emerging themes included the role of employees, influencing company giving and creating a climate of expectation of firms' contributions. These developments may have important implications for business funding for the arts, where leading philanthropists are prominent as individuals in the giving landscapes; but employees' collective involvement is not marked. Alternatively, cultivation of employees as would-be donors, indirectly via their firms, may be a more secure, if lower level route to funding for some arts organizations than dependence on high profile business leaders. The article considers alternative scenarios for company giving in disaster contexts, including as a sustained and lasting giving theme or as company support as a ‘one-off’ event, rock-star style. The likely development of employee power as a key element in company giving is explored; and its wider meanings for funding in arts settings, (where the giver as rock star heroine/hero is also prominent) are considered.

Islands: Nature and Culture

Islands are contradictory places: they can be remote, mysterious spots, or lively centres of holiday revelry. They are associated alternately with escape, imprisonment, holiday and exile, and their exotic, otherworldly beauty has inspired artists and writers across the centuries. Islands have been sites of immense political, creative and scientific importance from Charles Darwin's enlightening voyage to the Gálapagos Islands, which resulted in his groundbreaking theory of evolution, to the moat-encased prisons incarcerating the world's most dangerous convicts.
Despite the common view of islands as earthly paradises, their often small size means they have restricted resources and limited opportunities for their inhabitants to thrive. In response, islanders have welcomed or sternly rejected, the fresh opportunities offered by turning their homes into tourist destinations. For people seeking beautiful landscapes, solitude or exciting adventure, islands are the most popular holiday spots in the world. They entice the rich and famous, and their allure has provided refuge and inspiration for artists and writers, from Paul Gauguin in Tahiti to George Orwell on Jura in the Hebrides, and general visitors alike.
Filled with illustrations, Islands is a comprehensive exploration of the geographical and cultural aspects of island life – their habitations and environments, their permanent residents and vast transitional populace, their colonial history and their enduring appeal to people around then world.

Fleuve glauque : les départements de la Seine, banlieue des romans « Spécial Police » de Frédéric Dard

This paper studies the representation of suburbs as a place of anguish in the “Special Police” novels (Fleuve Noir publisher, Paris) by Frédéric Dard. This anxiety, it is argued, is what lends this collection of 25 novels some of their essential qualities, their unhealthy climate and absolute darkness. Dard’s suburbs fit into the traditions of realism; but the atmosphere, characters and plots owe to the American hardboiled school and like in film noir, space is stylized and dramatized, and often used to express a judgment of moral nature. Spatial representations in these novels are part of a critique of civilization and constitute a comment on the social modernization and public intervention in the development of the French territory in the postwar period. The novels written by Frédéric Dard from the mid-1950s to mid-1960s offer a profoundly original representation of suburban angst and what was not yet known at the time as the suburban malaise. Avoiding clichés and excessively connoted referential spaces, Dard anchor these noir novels he called “novels of the night” in landscapes that are both biographical and intertextual. The West Suburbs of Paris and what was
to become the Yvelines department are at the centre of Dard’s novelistic geography, turning into a mythical and deadly space in which is negotiated an acculturation in France of the evil and ruined world described in American noir.

Urban planning after the Black Death: townscape transformations in later-medieval England (1350-1530)

This article offers a reconsideration of planning and development in
English towns and cities after the Black Death (1348). Conventional historical
accounts have stressed the occurrence of urban ‘decay’ in the later fourteenth and fifteenth centuries. Here, instead, a case is made that after 1350 urban planning continued to influence towns and cities in England through the transformation of their townscapes. Using the conceptual approaches of urban morphologists in particular, the article demonstrates that not only did the foundation of new towns and creation of new suburbs characterize the period 1350–1530, but so too did the redevelopment of existing urban landscapes through civic improvements and public works. These reveal evidence for the particular ‘agents of change’ involved in the planning and development process, such as surveyors, officials, patrons and architects, and also the role played by maps and drawn surveys. In this reappraisal, England’s urban experiences can be seen to have been closely connected with those instances of urban planning after the Black Death occurring elsewhere in contemporary continental Europe.

Supplementary feeding increases Common Buzzard Buteo buteo productivity but only in poor-quality habitat

Temporal heterogeneity in the effects of food supply during the breeding season on the productivity of the Common Buzzard Buteo buteo was investigated in a supplementary feeding experiment. Pairs were fed artificially (1) before egg-laying, (2) after chicks hatched and (3) continuously throughout the season, and compared with (4) unfed controls. Pairs fed before egg-laying had marginally larger clutches than those not fed, but lay date, egg volume and weight, brood size and hatching success were unaffected. Territorial quality had far greater effects, with pairs nesting in low-quality habitats (bog, scrub and semi-natural grassland) laying later and having lower hatching success, smaller broods and fewer fledglings than those in more productive agricultural landscapes. Supplementary feeding after egg hatching neutralized the negative effect of poor habitat, resulting in fed birds having significantly more fledglings. This study emphasizes the importance of food availability when provisioning chicks in suboptimal habitats and has implications for the success of diversionary feeding in reducing game losses to Buzzards.