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Abstract In order to make 2nd-generation biofuels more competitive, high solid-matter content has to be reached. To progress towards this target, the mechanism for destructuring lignocellulose fibres in semidilute conditions has to be well understood, as this configuration shows the basic mechanism which limits transfers and efficiency. This study aims to delve deeply into the biophysical and transfer limitations occurring during enzymatic hydrolysis. A specific experimental set-up associating in-situ and ex-situ physical (rheometry, chord length analysis) and biochemical analysis was used to expand the knowledge of hydrolysis of extruded softwood paper pulp over 24 h under different substrate concentrations (1%–3%) and enzyme doses (Accellerase 1500, 5 and 25 FPU/g cellulose). Non-Newtonian behaviour associated with pronounced yield stress stand as the major factors limiting process efficiency. A critical time was deduced from viscosity evolution, and the existence of a unique, dimensionless viscosity-time curve was established, suggesting similar mechanisms for fibre degradation. In addition, chord length distribution allowed for the description of population evolution and was discussed in the light of in-situ viscosity and hydrolysis yield. Physical (viscosity, particle size) and biochemical (substrate) kinetics were modelled (second-order) and coefficients identified. A chronology of the encountered phenomenological limitations demonstrates the necessity of optimising bioprocesses by considering physical parameters. A reference feed rate is proposed in order to reach high solid loading under fed-batch strategy. Highlights • An in- & ex-situ multiscale approach was used to study the paper pulp hydrolysis. • The bio-physical and transfer limitations during hydrolysis were investigated. • A non-Newtonian behaviour was the major factor limiting process efficiency. • A unique dimensionless viscosity-time curve was identified. • A reference feed rate is proposed to reach high solid loading with fed-batch mode. [ABSTRACT FROM AUTHOR]

• The pattern formation of morphogens is studied in geometrically-confined microtissues during early embryogenesis. • The microtissue consisted of human stem cells is modeled as a piece of biphasic poroelastic material. • The active contractility is fully-coupled with the reaction-diffusion of the morphogens through the poroelasticity. • Linear stability analysis is performed to determine ranges of parameters that leads to diffusion-induced instability. • A comprehensive parameter study, including the sizes and geometries of the tissues, is carried out in the paper. The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Mechanical cues, such as the cellular stresses and strains, have been found to dictate the pattern formation in human stem cell differentiation. As a result, the traditional reaction-diffusion models are modified by adding mechanically related terms to consider the role played by the mechanical cues during the very early stage of embryogenesis. However, these models either do not consider the activeness of the cellular tissues or neglect their poroelastic nature that biological tissues are made by both cells and interstitial fluid. Here we propose a modified reaction-diffusion model that couples with the active contraction of cellular tissues. The cellular tissue is modelled as a piece of biphasic poroelastic material, where mechanical forces naturally regulate the transport of chemical cues. Such chemical cues direct cell fate and hence yield certain types of pattern formations observed in previous experiments. [ABSTRACT FROM AUTHOR]

This paper presents the methods that have participated in the SHREC 2022 contest on protein–ligand binding site recognition. The prediction of protein- ligand binding regions is an active research domain in computational biophysics and structural biology and plays a relevant role for molecular docking and drug design. The goal of the contest is to assess the effectiveness of computational methods in recognizing ligand binding sites in a protein based on its geometrical structure. Performances of the segmentation algorithms are analyzed according to two evaluation scores describing the capacity of a putative pocket to contact a ligand and to pinpoint the correct binding region. Despite some methods perform remarkably, we show that simple non-machine-learning approaches remain very competitive against data-driven algorithms. In general, the task of pocket detection remains a challenging learning problem which suffers of intrinsic difficulties due to the lack of negative examples (data imbalance problem). [Display omitted] • A new contest for binding site detection in a protein. • Proteins are provided both as molecular surfaces and in anonymized PQR format. • Analysis of computational methods for recognizing ligand binding sites in a protein. • Analysis of the performances of the methods that participated in SHREC 2022. [ABSTRACT FROM AUTHOR]

This paper presents a new approach to guiding coastal stakeholders about making informed decisions about Disaster Risk Reduction (DRR) measures and alternatives. As part of the RISC-KIT project and tool box, the paper presents a holistic DRR measure approach including the biophysical environment, governance aspects and practical examples from coastal areas in Europe and elsewhere. The guide (see: www.coastal-management.eu ) is addressed to a wide variety of coastal stakeholders with a different level of knowledge about DRR measures with the aim to provide guidance and information. The paper gives an overview of the overall structure of the guide. [ABSTRACT FROM AUTHOR]

Adaptive management and related fields have theorized new governance strategies that embrace complexity and are able to respond effectively to changing and unpredictable biophysical dynamics. However, this body of work pays inadequate attention to important on-the-ground realities, including feasibility of implementation and the power dynamics embedded in multi-scalar systems of environmental governance. This paper presents findings from a research project on challenges to adaptive management in the variable wetland ecosystem of the Okavango Delta, Botswana. Many residents of this rural region rely on transitional agricultural practices, shifting between dryland and floodplain farming in response to dynamic precipitation and flooding patterns. Higher than average floods in 2009–2011 inundated many floodplain fields past the point of production, causing farmers to shift to the dryland for multiplem seasons. At the same time, the highly centralized Government of Botswana began to implement stricter regulations over floodplain resources, which stemmed in part from a new adaptive management plan developed for the region. As a result, many farmers felt pressured by the government to abandon transitional livelihood practices and to shift permanently to dryland agriculture even though many preferred to continue floodplain farming. This loss of a responsive livelihood strategy will likely result in decreased long-term adaptive capacity for many residents. Drawing on these findings, this paper advances the argument that if adaptive management is to become a viable option for communities in changing environments, more attention must be given to the role of unequal power relations in multi-scalar systems of environmental governance. [ABSTRACT FROM AUTHOR]

Appropriate integration of remote sensing technologies into ecosystem services concepts and practices leads to potential practical benefits for the protection of biodiversity and the promotion of sustainable use of Earth's natural assets. The last decade has seen the rapid development of research efforts on the topic of ecosystem services, which has led to a significant increase in the number of scientific publications. This systematic review aims to identify, evaluate and synthesise the evidence provided in published peer reviewed studies framing their work in the context of spatially explicit remote sensing assessment and valuation of ecosystem services. Initially, a search through indexed scientific databases found 5920 papers making direct and/or indirect reference to the topic of “ecosystem services” between the years of 1960 and 2013. Among these papers, 211 make direct reference to the use of remote sensing. During the search we aimed at selecting papers that were peer-reviewed publications available through indexed bibliographic databases. For this reason, our literature search did not include books, grey literature, extended abstracts and presentations. We quantitatively present the growth of remote sensing applications in ecosystem services’ research, reviewing the literature to produce a summary of the state of available and feasible remote sensing variables used in the assessment and valuation of ecosystem services. The results provide valuable information on how remotely sensed Earth observation data are used currently to produce spatially-explicit assessments and valuation of ecosystem services. Using examples from the literature we produce a concise summary of what has been done, what can be done and what can be improved upon in the future to integrate remote sensing into ecosystem services research. The reason for doing so is to motivate discussion about methodological challenges, solutions and to encourage an uptake of remote sensing technology and data where it has potential practical applications. [ABSTRACT FROM AUTHOR]

This paper presents a biophysical method to characterize single bacterium in water by using an on-chip optofluidic immersion refractometer. Water safety is a major factor in the well-being of people, but the presence of bacteria such as Escherichia coli ( E. coli ), bacillus subtilis , Shigella flexneri and vibrio cholera in drinking water can lead to infectious diseases such as typhoid fever. Hence, it is crucial to detect and identify bacteria to prevent bacterial outbreaks. In this paper, an optofluidic immersion refractometer is developed to measure three biophysical parameters, i.e. size, shape and refractive index. The refractive index of a single bacterium is measured in high sensitivity of 0.005 RIU. This system is an innovative method to allow on-site real-time detection of single bacterium in water. It significantly reduces the amount of detection time and do not require trained personnel or additional chemical and biological reagents. [ABSTRACT FROM AUTHOR]

Abstract: Multifunctional landscapes are characterized by various functions and values that sustain directly or indirectly the quality of human life, through the provision of natural capital flow. Primary production (PP), representing a measure of the solar energy captured by the system and available to drive its functioning, is recognized as a fundamental supporting service. Several biophysical modification and conversion altering the primary production are due to land-use change. Natural protected areas with a sustainable management of land-use could be able to guarantee the persistence of structure and processes (primary production) fundamental for the provision of natural capital. In this context, the aims of this paper are to investigate the spatial–temporal patterns of PP variability (1986–2010) in the Natural Protected Area of “Torre Guaceto” (southern Italy), taking into account land-cover change and climate conditions and looking at PP as a supporting service able to guarantee natural capital flow. In dealing with this issue, this paper aims at testing whether NDVI (Normalized Difference Vegetation Index) integrated with NDII (Normalized Difference Infrared Index) can be suitable surrogates for the assessment of shifts in the spatial–temporal dynamics of PP, useful to explore possible feedbacks related to conservation management choices in supporting natural capital flow. Therefore, the assessment of the complex spatial–temporal dynamics of natural vegetation has been performed by using NDVI and NDII. The results showed that after the establishment of the Natural Protected Area of “Torre Guaceto” in 2000, there has been an increase of NDVI that could represent an increase of PP. However, since PP depends also on water content, measured by NDII, a Pearson correlation analysis between NDII and land Surface Temperature (TS) has been carried out, demonstrating that low level of PP in 2005 was not imputable to climate conditions but to the worse quality of vegetation associated to the wetland due to aging phenomenon. In conclusion, to make the conservation management more effective it is not enough to identify and quantify the major landscape transformations and the underlying causes, but rather to detect the capability of new landscape patterns, in terms of configuration and composition, to sustain ecosystem services. The analysis of conservation management based on NDVI and NDII, used as surrogate to detect the maintenance of PP, appears to be very promising in order to develop better strategies for the adaptive management of natural protected areas. [Copyright &y& Elsevier]

Abstract: Economic analysis of climate scenarios and alternative water policies is critical for development and implementation of appropriate water policies and programs. Mathematical models have been developed to assess water resources policies due to their ability to explicitly represent the biophysical dynamics of natural systems while integrating these within social and economic constraints. These models have been criticised, however, due to the problems of simplification, overspecialisation, plausibility and lack of empirical validation. This paper introduces a mathematical programming model which uses positive mathematical programming method to calibrate and model agriculture and water use in the Murray-Darling Basin of Australia. This paper reviews the theoretical and technical details of the model development including the key steps taken in collating and scaling the biophysical and economic data, and to address model parameterisation issues. The paper summarises results of an application of the model for assessing climate change impacts in the form of reduced rainfall and water allocations and increased crop water use for agricultural production. The results show the degree of variability in gross values under different climate scenarios compared to the base case scenario, especially in very dry years. The results also show how on-farm adaptation options and water markets can mitigate these losses. [Copyright &y& Elsevier]

Abstract: While the recent emergence of a global land rush has initiated large debates and conflicts over the use and access to land, further investigation into the underlying drivers is required to enhance the understanding of the potential trajectories of the land grab phenomenon. This paper takes a biophysical perspective and explores how declining fossil stocks and a global transition towards renewable energies ultimately drive the land rush. The paper addresses, in qualitative terms, how societal needs for land change with different patterns of societal energy metabolism. The potential spatial expansions of renewables are illustrated in quantitative terms, based on the power density concept and energy provision forecasts for the year 2020. The transition from an energy system based on fossils stocks, with high power densities, to one based on renewables, with low power densities, drastically boosts societal demand for land. This drives the land rush directly through land acquisitions for the expansion of energy systems. The energy transition also drives the land rush indirectly, in particular through food security threats motivated by the growing competition over farmland uses and changes in crop supply. Although currently fossil stocks are still relatively abundant, future declines are expected to trigger the demand for land to even greater extents. Given the inevitability of the energy transition, we believe that the land rush will have persistence, bearing long-term consequences for land use and struggles over access to land. [Copyright &y& Elsevier]

Abstract We present SIBIA (Scalable Integrated Biophysics-based Image Analysis), a framework for joint image registration and biophysical inversion and we apply it to analyze MR images of glioblastomas (primary brain tumors). We have two applications in mind. The first one is normal-to-abnormal image registration in the presence of tumor-induced topology differences. The second one is biophysical inversion based on single-time patient data. The underlying optimization problem is highly non-linear and non-convex and has not been solved before with a gradient-based approach. Given the segmentation of a normal brain MRI and the segmentation of a cancer patient MRI, we determine tumor growth parameters and a registration map so that if we "grow a tumor" (using our tumor model) in the normal brain and then register it to the patient image, then the registration mismatch is as small as possible. This " coupled problem " two-way couples the biophysical inversion and the registration problem. In the image registration step we solve a large-deformation diffeomorphic registration problem parameterized by an Eulerian velocity field. In the biophysical inversion step we estimate parameters in a reaction–diffusion tumor growth model that is formulated as a partial differential equation (PDE). In SIBIA, we couple these two sub-components in an iterative manner. We first presented the components of SIBIA in "Gholami et al., Framework for Scalable Biophysics-based Image Analysis, IEEE/ACM Proceedings of the SC2017" , in which we derived parallel distributed memory algorithms and software modules for the decoupled registration and biophysical inverse problems. In this paper, our contributions are the introduction of a PDE-constrained optimization formulation of the coupled problem, and the derivation of a Picard iterative solution scheme. We perform extensive tests to experimentally assess the performance of our method on synthetic and clinical datasets. We demonstrate the convergence of the SIBIA optimization solver in different usage scenarios. We demonstrate that using SIBIA, we can accurately solve the coupled problem in three dimensions (25 6 3 resolution) in a few minutes using 11 dual-x86 nodes. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Ecosystem service accounts are a useful tool to assess changes in the service use. • Spatial models of ecosystem services provide key information for accounting. • Proximity between recreation potential and demand determine the actual flow. • Accounting tables show the monetary value of nature-based recreation. • Linkages between nature-based recreation and components of human wellbeing are shown. Abstract Natural capital accounting aims to measure changes in the stock of natural assets (i.e., soil, air, water and all living things) and to integrate the value of ecosystem services into accounting systems that will contribute to better ecosystems management. This study develops ecosystem services accounts at the European Union level, using nature-based recreation as a case study and following the current international accounting framework: System of Environmental-Economic Accounting – Experimental Ecosystem Accounting (SEEA EEA). We adapt and integrate different biophysical and socio-economic models, illustrating the workflow necessary for ecosystem services accounts: from a biophysical assessment of nature-based recreation to an economic valuation and compilation of the accounting tables. The biophysical assessment of nature-based recreation is based on spatially explicit models for assessing different components of ecosystem services: potential, demand and actual flow. Deriving maps of ecosystem service potential and demand is a key step in quantifying the actual flow of the service used, which is determined by the spatial relationship (i.e., proximity in the case of nature-based recreation) between service potential and demand. The nature-based recreation accounts for 2012 show an actual flow of 40 million potential visits to 'high-quality areas for daily recreation', with a total value of EUR 50 billion. This constitutes an important contribution of ecosystems to people's lives that has increased by 26% since 2000. Practical examples of ecosystem services accounts, as shown in this study, are required to derive recommendations and further develop the conceptual and methodological framework proposed by the SEEA EEA. This paper highlights the importance of using spatially explicit models for ecosystem services accounts. Mapping the different components of ecosystem services allows proper identification of the drivers of changes in the actual service flow derived from ecosystems, socio-economic systems and/or their spatial relationship. This will contribute to achieving one of the main goals of ecosystem accounts, namely measuring changes in natural capital, but it will also support decision-making that targets the enhancement of ecosystems, their services and the benefits they provide. [ABSTRACT FROM AUTHOR]

Abstract: We have developed a new hierarchical European Landscape Classification that can be used as a framework for, e.g., indicator reporting and environmental sampling. Landscapes are ecological meaningful units where many processes and components interact. And as such, landscapes themselves have resulted from long-term interactions of natural abiotic, biotic and anthropogenic processes. A good understanding of landscapes is essential for its assessment, protection, management and planning. An internationally consistent approach is therefore obligatory and the production of landscape classifications and associated maps is an important tool in this context. Although intuitive maps are available there are no consistent quantitative maps of European landscapes. In this paper, landscapes are regarded as forming recognizable parts of the earth''s surface and as showing a characteristic ordering of elements. The complex nature of the underlying scientific concepts, which sometimes overlap and conflict, requires an objective and consistent methodology, as described in the present paper. As there are many regional differences in landscape properties, it is crucial to strike the right balance between reducing the inherent complexity and maintaining an adequate level of detail. Against this background, a European Landscape Map (LANMAP) has been produced, making use of available segmentation and classification techniques on high-resolution spatial data sets. LANMAP is a landscape classification of Pan-Europe with four hierarchical levels; using digital data on climate, altitude, parent material and land use as determinant factors; and has 350 landscape types at the most detailed level. At this level there are 14,000 mapping units with a minimum mapping unit of 11km2. Thus far, LANMAP is limited to a biophysical approach, since there is a lack of consistent and European-wide data on cultural–historical factors. This paper describes the conceptual background of LANMAP, its methodology and results, and shows its potentials and limitations. [Copyright &y& Elsevier]

Abstract: It is the forces between the microscopic constituents of materials which to a large extent determine the macroscopic properties. For example, it is the differences in bonding between the carbon atoms which determines the different physical properties of carbon and graphite. The same is true in colloidal systems. In colloidal systems, there are three common types of long-range interactions between particles: van der Waals forces, electrical double layer forces and steric forces. In this paper, examples as to how these forces can be modified and even manipulated will be given. To convincingly demonstrate these effects, it is necessary to measure these interaction forces. We have achieved this by using the principles of atomic force microscopy (AFM). The principle is simple, a small particle, 5–30 μm, is attached onto a small weak cantilever spring. The interaction between this particle and another particle or a surface is measured by monitoring the deflection of the spring as the two particles are moved together. In this paper, I shall give examples of direct measurements of van der Waals, electrical double layer and steric forces and show how they can be modified and how these modifications affect the properties of bulk suspensions. Similar principles are involved in the interactions of biological materials. However, nature is much cleverer than man such that many of the macromolecules on cell surfaces are able to specifically recognise only one other molecule. An example of this recognition-type interaction, namely, cholera toxin interacting with the glycolipid Gm1, will also be presented. Finally, the adhesion of cells to surfaces of different surface chemistries has been determined; this is of significance in many fields ranging from fouling of filtration membranes on the one hand to the biocompatibility of surgical implants on the other. [Copyright &y& Elsevier]

This paper empirically analyzes the socioeconomic energy metabolism of Austria in the period 1830–1995. During this period Austria underwent a transition from being a largely agricultural society to being an industrial society. We describe the changes associated with this transition in terms of the ‘physical economy,’ or more precisely, in terms of changes in the throughput of energy, assessed in physical units (J per year). In accordance with currently used methods of material flow accounting (MFA), we define the indicators ‘direct input’ and ‘domestic consumption’ with respect to socioeconomic energy flows. Using these indicators, we analyze the transition from 1830, at which time biomass provided more than 99% of Austria''s domestic energy consumption (DEC), to 1995, when biomass accounted for 30% and fossil energy for 60% of DEC. Total DEC in Austria increased by a factor of 6 in this period. The paper discusses the relevance of these changes for processes of interaction between society and its natural environment, focusing on the interrelations between energy metabolism and changes in land use. [Copyright &y& Elsevier]

The assessment of Land Uses and Land-use Changes (LULUC) impacts has become increasingly complex. Sophisticated modelling tools such as Life Cycle Assessment (LCA) are employed to capture both direct and indirect damages. However, quantitative assessments are often incomplete, dominated by environmental aspects. Land uses are a multidisciplinary matter and environmental and sustainable development policies intertwine. Yet, LCAs mostly focus on environmental impacts excluding socioeconomic implications of land occupation. This paper investigates the limitations of current LULUC modelling practices in LCA. Common LCA assumptions harbor value choices reflect a post-positivist epistemology that are often non-transparent to e.g. policymakers. They particularly influence the definition of the functional unit, the reference system and system boundaries, among other LCA methodological choices. Consequently, results informing land policies may be biased towards determined development strategies or hide indirect effects and socioeconomic damages caused by large-scale land acquisitions, such as violation of tenure rights, speculation and displacement. Quantitative assessments of LULUC impacts are certainly useful but should holistically encompass both direct and indirect impacts concerning the environmental and the social science dimension of LULUC. An epistemological shift towards a dialectic approach would facilitate the integration of multiple tools and methods and a critical interpretation of results. [ABSTRACT FROM AUTHOR]

Advancing urban sustainability requires an implementation of various measures such as environmental policy, behavioral change, and technological developments, which have to be taken at various spatial scales. However, choosing the right measures demands considering their potential contribution in reducing the environmental impact and advancing urban sustainability. In recent years, some attempts to assess the contribution of implementing various measures have been advanced by various researchers focusing on different components of urban environmental interactions. While these studies make a significant contribution towards the understanding of the impact of various measures taken for a specific environmental issue, they mostly ignore the diversity and complexity of the urban interface with the environment at different spatial scales, as well as the ecological economics perspective, which approaches the city as a system. This paper uses the UBSI index published recently in this journal, to evaluate the urban biophysical sustainability of the city of Tel Aviv-Jaffa (Israel) in 2014. Based on this data, future scenarios are developed, which examine the potential contribution of various policy measures and different technological processes to the city's sustainability. This examination is conducted while considering population growth and changes of consumption patterns as they are expected to occur until 2030. [ABSTRACT FROM AUTHOR]

This paper presents a preliminary attempt to estimate the awareness and value that society gives to the maintenance and protection of marine protected areas, linking the ecological and economic value scale assigned to the study. To accomplish this, we took as illustrative example the Biophysical Interest Zone of Avencas (ZIBA), in Portugal. The ZIBA spans over one ha and its coastal ecosystems present a very rich biodiversity, providing several socio-economic opportunities to society. To estimate the value that society attributes to this area we conducted a contingent valuation exercise, considering two different aspects: 1) the direct economic value that people state to conserve the ecosystem and 2) the willingness to contribute through the allocation of hours of voluntary work to its conservation. The values obtained indicate the dependence and importance of this ecosystem to local population (willing to pay to conserve it of 60 € per household per year and willing to give 3 h of voluntary work per year). The proximity of the local population to the protected area increases the willing to pay for its conservation; this could reveal a good local indicator of ecosystem valuation. This valuation exercise highlights the importance of coastal ecosystem services to society and draws attention to the benefits that local populations derive from those systems. These results have also implications in future governance actions regarding protected areas, as well as to justify for sustainable investments in coastal management efforts, to sustain the flow of coastal ecosystem services for current and future generations. [ABSTRACT FROM AUTHOR]

Recently, molecular representation and property exploration, with the combination of neural network, play a critical role in the field of drug design and discovery for assisting in drug related research. However, previous research in molecular representation relies heavily on artificial extraction of features based on biological experiments which may result in a manually introduced noise of molecular information with high cost in time and money. In this paper, a novel method named Substructural Hierarchical Attention Network (SuHAN) is proposed to discover inherent characteristics of molecules for representation learning. Specifically, SuHAN is composed of the cascaded layer: atom-level layer and substructure-level layer. Molecule in the SMILES format is divided into several substructural fragments by predefined partition rules, and then they are fed into atom-level layer and substructure-level layer successively to obtain feature representation from different perspective: atomic view and substructural view. In this way, the prominent structural features that may be omitted in global extraction are excavated from a fine-grained viewpoint and fused to reconstruct representative pattern in an overall view. Experiments on biophysics and physiology datasets demonstrate that our model is competitive with a significant improvement of both accuracy and stability in performance. We confirmed that the substructural segments and progressive hierarchical networks lead to an effective molecular representation for downstream tasks. These results provide a novel perspective about reconstructing overall pattern through local prominent structure. [Display omitted] • Substructural hierarchical attention network provides a multi-perspective view of molecular. • Predefined partition rules effectively divide SMILES sequence into segmentations for feature extracting. • Atomic view and substructural view are conducive to a precise refine of molecular representation. • GRU-based architecture and attention mechanism contributes to excavating prominent feature and reintegration substructure. [ABSTRACT FROM AUTHOR]

The aim of this study was to develop a bio-economic model to estimate the feasibility and net profit (or net costs) of achieving set water quality targets (sediment, nitrogen, phosphorus and herbicide load reductions) in the Burnett-Mary region within the southern portion of the Great Barrier Reef (GBR), southern Queensland, Australia. Two sets of targets were evaluated, namely (1) Reef Plan Targets (RPTs) representing currently agreed targets, and (2) the more ambitious Ecologically Relevant Targets (ERTs) designed to halt the decline and improve the condition of the GBR. This paper describes the construction of a bio-economic optimisation framework linking field and catchment scale biophysical model results and farm economic analysis to solve for RPTs or ERTs assigned either regionally or within discrete basins. Key outcomes from the study were that RPTs could be achieved whereas ERTs required significant additional investment and were infeasible if individual basins must meet the targets. [ABSTRACT FROM AUTHOR]

While the concept of the Anthropocene reflects the past and present nature, scale and magnitude of human impacts on the Earth System, its true significance lies in how it can be used to guide attitudes, choices, policies and actions that influence the future. Yet, to date much of the research on the Anthropocene has focused on interpreting past and present changes, while saying little about the future. Likewise, many futures studies have been insufficiently rooted in an understanding of past changes, in particular the long-term co-evolution of bio-physical and human systems. The Anthropocene perspective is one that encapsulates a world of intertwined drivers, complex dynamic structures, emergent phenomena and unintended consequences, manifest across different scales and within interlinked biophysical constraints and social conditions. In this paper we discuss the changing role of science and the theoretical, methodological and analytical challenges in considering futures of the Anthropocene. We present three broad groups of research questions on: (1) societal goals for the future; (2) major trends and dynamics that might favor or hinder them; (3) and factors that might propel or impede transformations towards desirable futures. Tackling these questions requires the development of novel approaches integrating natural and social sciences as well as the humanities beyond what is current today. We present three examples, one from each group of questions, illustrating how science might contribute to the identification of desirable and plausible futures and pave the way for transformations towards them. We argue that it is time for debates on the sustainability of the Anthropocene to focus on opportunities for realizing desirable and plausible futures. [ABSTRACT FROM AUTHOR]

In many parts of the humid Tropics, slash and burn shifting cultivation, incorporating a fallow phase, is the most common farming method, encompassing a broad diversity of techniques. The ecological productivity and sustainability of such systems depend upon the crop:fallow time ratio. Farmers often have biophysical criteria by which to match parcels to cropping systems and decide, for example, when to recultivate a fallow. In this paper, we collate reports of indicators used by farmers to aid in fallow choice from across the agronomic, forestry, ecological, and anthropological literature. We found 27 examples of farmers using such biophysical indicators. Examples found were from eight countries across West and Central Africa. The literature review showed that farmers rank fallow age usually first, followed by vegetation composition, the presence of indicator plants, and earthworm casts. 53 indicator plant species were identified across the region of which 37 were said to indicate soil fertility, 13 soil infertility and 3 either fertility or infertility, depending on their growth characteristics. The most exhaustive lists of indicator plants were reported from southern Cameroon, the Ashante region of Ghana and south west Nigeria. Chromolaena odorata was the most frequently mentioned plant indicator species. The trees Triplochiton scleroxylon and Terminalia superba and the grass were each mentioned, generally as soil fertility indicators, in three areas. Other species mentioned multiple times were Aframomum sp., Andropogon gayanus , Ceiba pentandra , Milicia excelsa , Triumfetta cordifolia and Trema guineensis . Farmers in West and Central Africa have identified indicators for selecting which fallow plots to recultivate. Fallow age, vegetation composition, the presence of indicator plants, particularly C. odorata , and earthworm casts all have some logical scientific basis and farmers observations are supported by the results of scientific studies. There is a lack of documentation of farmers’ knowledge and more studies should be conducted. Such knowledge should form the foundation of any suggested interventions in farming systems in the region and provide information to farmers in communities where such knowledge is not currently applied. [ABSTRACT FROM AUTHOR]

Alfred Lotka was one of the founders of modern ecology. This paper explores Lotka's contribution to biophysical economics resulting from the marriage of the three disciplines: biology, physics and economics. Lotka founded the concept of “exosomatic evolution” to characterise the economic activities in their biophysical environment as a continuation of biological processes. Like Vernadsky, he adopted a holistic perspective of planet-system — the biosphere. Georgescu-Roegen was one of the founders of ecological economics. He explained the entropic nature of evolution and adopted Lotka's “exosomatic evolution” concept in his bioeconomic approach. Georgescu-Roegen had several warnings for economists about the irrevocability of the entropic degradation of matter–energy and the pressure on natural resources that goes hand in hand with economic processes in general. This article aims at drawing a parallel between Lotka's contribution and Georgescu-Roegen's bioeconomics, by shedding light not only on their similarities, but also on the divergences that testify the novelty of Georgescu-Roegen's approach. [ABSTRACT FROM AUTHOR]

An ecological economics perspective on urban sustainability embraces a biophysical view which emphasizes the dependence of cities on vast quantities of natural capital from various sources and spatial scales, and the generation of urban wastes which impact the local, regional and global systems. In recent years, several sets of urban sustainability indicators and indices have been developed. However, only a few consider the complex multi-scale interactions between the urban activities and the environment. Furthermore, most existing indices use a relative evaluation approach instead of an absolute approach that is needed when dealing with ecological thresholds. The paper introduces a new urban biophysical sustainability index whose framework includes: the city environmental quality, use of natural resources, and GHG emissions. Each contains topics for assessment related to local, regional and global scales and associated indicators. Standard and optimum values were determined for each indicator and a formula is provided for grading each indicator measurement. The integration of those grades allows for generation of a compound score of each topic, category, spatial scale and the entire urban biophysical sustainability performance. It then demonstrates the index in three major Israeli cities. [ABSTRACT FROM AUTHOR]

The electricity infrastructure in many developed countries requires significant investment to meet ambitious carbon emissions reduction targets, and to bridge the gap between future supply and demand. Perennial energy crops have the potential to deliver electricity generation capacity while reducing carbon emissions, leading to polices supporting the adoption of these crops. In the UK, for example, support has been in place over the past decade, although uptake and the market development have so far been relatively modest. This paper combines biophysical and socio-economic process representations within an agent-based model (ABM), to offer insights into the dynamics of the development of the perennial energy crop market. Against a changing policy landscape, several potential policy scenarios are developed to evaluate the cost-effectiveness of the market in providing a source of low carbon renewable electricity, and to achieve carbon emissions abatement. The results demonstrate the key role of both energy and agricultural policies in stimulating the rate and level of uptake; consequently influencing the cost-effectiveness of these measures. The UK example shows that energy crops have the potential to deliver significant emissions abatement (up to 24 Mt carbon dioxide equivalent year −1 , 4% of 2013 UK total emissions), and renewable electricity (up to 29 TWh year −1 , 8% of UK electricity or 3% of primary energy demand), but a holistic assessment of related policies is needed to ensure that support is cost-effective. However, recent policy developments suggest that domestically grown perennial energy crops will only play a niche role (<0.2%) of the UK energy balance. [ABSTRACT FROM AUTHOR]

Around 9% of global CO 2 emissions originate from land use changes. Often, these emissions are not appropriately addressed in Life Cycle Assessment. The link between demand for crops in one region and impacts in other regions is referred to here as indirect land use change (iLUC) and includes deforestation, intensification and reduced consumption. Existing models for iLUC tend to ignore intensification and reduced consumption, they most often operate with arbitrary amortisation periods to allocate deforestation emissions over time, and the causal link between land occupation and deforestation is generally weakly established. This paper presents the conceptual framework required for a consistent modelling of iLUC in Life Cycle Assessment. It reports on a novel and biophysical iLUC model, in which amortisation is avoided by using discounted Global Warming Potentials (GWPs). The causal link between demand for land and land use changes is established through markets for land's production capacity. The iLUC model presented is generally applicable to all land use types, crops and regions of the world in typical LCA decision-making contexts focusing on the long-term effects of small-scale changes. The model's strengths and weaknesses are discussed. [ABSTRACT FROM AUTHOR]

Addressing the issue of agricultural pollution in water protection areas (WPA) requires assessing the impact of agricultural activities at regional scales. However, current water quality modeling studies often neglect the agronomic concept of a cropping system and interactions with soils. This paper presents a participatory assessment framework involving local experts in building a shared diagnosis of nitrate losses from cropping systems in a WPA. It includes a co-designed typology of landscape units and participatory assessment of nitrate losses with the modeling software Syst'N. Results show that characteristics of cropping systems depended on soils and that nitrate losses were highest in shallow soils. Intercrop periods were identified as critical periods for nitrate leaching, which demonstrates the importance of considering pluri-annual crop rotations rather than individual crops. The framework is generic for a modeling approach based on the involvement of local experts, who define their functional system in an agronomically sound way. [ABSTRACT FROM AUTHOR]

The three-dimensional structure of salt marsh plant canopies, amongst other marsh surface characteristics, is of critical importance to the functioning and persistence of coastal salt marshes. Together with plant flexibility it controls the contribution of vegetation to the tidal flow and wave energy dissipation potential of marshes. However detailed information on these two key biophysical properties of salt marsh canopies is scarce. In this paper we present biophysical properties of four plants commonly occurring in NW European salt marshes. We measured stem flexibility, diameter and height of the grasses Spartina anglica , Puccinellia maritima and Elymus athericus and above ground biomass and canopy height in stands of Elymus athericus and the dwarf shrub Atriplex portulacoides . Further we compared the performance of two methods for the non-destructive assessment of above ground biomass, such that they may be used during field assessments of marsh surface vegetation structure (i) measurement of light availability within the canopy and (ii) side-on photography of vegetation. All data were collected on a salt marsh on the Dengie Peninsula, eastern England, UK, in summer (July). We found significant differences in stem flexibility both between species and between the different parts of their stems. P. maritima was found to be the species with the most flexible stems, and, as a result of their relatively large stem diameter, S. anglica the species with the stiffest stems. Above ground biomass and hence potential canopy resistance to water flow could be estimated more accurately by side-on photography of vegetation than from measurement of light availability within the canopy. Our results extend the existing knowledge base on plant properties with relevance to studies of habitat structure and ecosystem functioning as well as wave energy dissipation in salt marsh environments and can be used for the development of a more realistic representation of vegetation in numerical models and laboratory flume studies of plant–flow interactions. [ABSTRACT FROM AUTHOR]

This paper examines vulnerability to climate change in the context of multiple stressors through a case study of Funafuti, Tuvalu. Climate change research in Pacific Islands has largely focused on biophysical changes such as sea-level rise. Less is known about how livelihoods are affected and what adaptation options are realistic. The research employs a vulnerability framework to identify where climate fits in the suite of forces (socioeconomic, cultural, environmental) already affecting livelihoods. The participatory approach includes semi-structured interviews with community members, initially without reference to climate. Key areas of concern to people in Funafuti are economic, food, water and overcrowding, rather than climate change. Vulnerability to changing climatic conditions is evident in water, land, and food through the interaction of non-climatic forces (e.g. overcrowding, urbanization, few economic opportunities, changing land use, and shifting cultural norms), and climatic forces (e.g. dry spells, extreme sea-levels, strong winds and changing marine conditions). Adaptations, beyond bearing the effects and sharing the burden, are mainly reactive and short-term. Future changes in climate will be experienced in the context of these multiple, interacting forces, and adaptation initiatives will need to be designed in light of these. [ABSTRACT FROM AUTHOR]

Adaptive governance focuses our attention on the relationships between science and management, whereby the so-called ‘gaps’ between these groups are seen to hinder effective adaptive responses to biophysical change. Yet the relationships between science and governance, knowledge and action, remain under theorized in discussions of adaptive governance, which largely focuses on abstract design principles or preferred institutional arrangements. In contrast, the metaphor of co-production highlights the social and political processes through which science, policy, and practice co-evolve. Co-production is invoked as a normative goal ( Mitchell et al., 2004 ) and analytical lens ( Jasanoff, 2004a,b ), both of which provide useful insight into the processes underpinning adaptive governance. This paper builds on and integrates these disparate views to reconceptualize adaptive governance as a process of co-production. I outline an alternative conceptual framing, ‘co-productive governance’, that articulates the context, knowledge, process, and vision of governance. I explore these ideas through two cases of connectivity conservation, which draws on conservation science to promote collaborative cross-scale governance. This analysis highlights the ways in which the different contexts of these cases produced very different framings and responses to the same propositions of science and governance. Drawing on theoretical and empirical material, co-productive governance moves beyond long standing debates that institutions can be rationally crafted or must emerge from context resituate adaptive governance in a more critical and contextualized space. This reframing focuses on the process of governance through an explicit consideration of how normative considerations shape the interactions between knowledge and power, science and governance. [ABSTRACT FROM AUTHOR]

Highlights: [•] Theory solves the case of droplet breakup in T-junctions in the obstructed regime. [•] New dynamical behaviors are obtained in microfluidic droplet populations. [•] The quenching of mixing in a chip with an external laser is demonstrated. [•] Streamline patterns have been ‘sculpted’ with inertial microfluidics. [•] Porous media transport laws have been shown to apply in paper microfluidic chips. [Copyright &y& Elsevier]

Abstract: Mapping and assessment of ecosystem services is essential to provide scientific support to global and EU biodiversity policy. Coastal protection has been mostly analysed in the frame of coastal vulnerability studies or in local, habitat-specific assessments. This paper provides a conceptual and methodological approach to assess coastal protection as an ecosystem service at different spatial–temporal scales, and applies it to the entire EU coastal zone. The assessment of coastal protection incorporates 14 biophysical and socio-economic variables from both terrestrial and marine datasets. Those variables define three indicators: coastal protection capacity, coastal exposure and human demand for protection. A questionnaire filled by coastal researchers helped assign ranks to categorical parameters and weights to the individual variables. The three indicators are then framed into the ecosystem services cascade model to estimate how coastal ecosystems provide protection, in particular describing the service function, flow and benefit. The results are comparative and aim to support integrated land and marine spatial planning. The main drivers of change for the provision of coastal protection come from the widespread anthropogenic pressures in the European coastal zone, for which a short quantitative analysis is provided. [Copyright &y& Elsevier]

Abstract: International environmental regimes are considered key factors in dealing with global environmental change problems. It is important to understand if and how regimes are effective in tackling these problems, which requires knowledge on their potential impact on these problems as well as on their political feasibility. Integrated assessments of global environmental change, which are mainly bio-physical and technology-economic oriented, barely address knowledge on environmental regimes, due to problems in drawing general and policy relevant lessons on regime effectiveness and inherent difficulties in modelling human and social dimensions. This paper presents an innovative approach to formalize knowledge on the effectiveness of environmental regimes, so that scientists from both the political science and integrated assessment domain can understand it, discuss it and contribute to it. We constructed a conceptual framework for the systematic analysis of conditions that influence regime effectiveness and implemented it in a computer model using fuzzy logic methodology. We evaluated the fuzzy model in an ex post case study on four existing international environmental regimes. The model can be used as an aid in analysing the effectiveness of existing or future regimes, highlighting which determinants contribute to success or failure, and it enables systematic and meaningful comparisons between regimes and policy measures. We discovered that formalizing knowledge on environmental regimes in a framework and model enhanced its transparency and deductive power as it forced us to be explicit about our choices and assumptions. Developing and using the framework and model also revealed the lacunae in knowledge in environmental regime theory which may inform regime researchers to further structure and increase their knowledge. By making knowledge on environmental regimes explicit and understandable we have taken an important step towards a better integration of political science in integrated assessments. We believe, however, that this integration is still in its early days and requires further attention in the future. [Copyright &y& Elsevier]

Abstract: This paper aims to advance two objectives: (1) identify and explore greenhouse gas emissions from urban areas in Asia at the regional level; and (2) explore covariates of urban greenhouse gas emissions. We use the Emissions Database for Global Atmospheric Research estimates for carbon dioxide, methane, nitrous oxide, and sulfur hexafluoride from 14 source activities for the year 2000, which are allocated on a 1/10° global grid. We extract emissions for 3535 urban extents all with populations over 50,000, accounting for approximately 91% of the region''s urban population. We use regression analysis to associate emissions with urban area and growth, economic, and biophysical characteristics. Our findings suggest that urban areas account for between 30 and 38% of total anthropogenic greenhouse gas emissions for the region and that emission per capita averages from urban areas are lower than those at the national level. Important covariates for total urban greenhouse gas emissions include population size, density and growth rate, income per capita, development status and elevation. This is a first and preliminary assessment of regional baseline trends using these data and this top-down analysis. [Copyright &y& Elsevier]

Abstract: India''s economic growth in the last decade has raised several concerns in terms of its present and future resource demands for materials and energy. While per capita resource consumption is still extremely modest but on the rise, its sheer population qualifies India as a fast growing giant with material and energy throughput that is growing rapidly . If such national and local trends continue, the challenges for regional, national as well as global sustainability are immense in terms of future resource availability, social conflicts, pressure on land and ecosystems and atmospheric emissions. Using the concepts of social metabolism and material flow analysis, this paper presents an original study quantifying resource use trajectories for India from 1961 up to 2008. We argue for India''s need to grow in order to be able to provide a reasonable material standard of living for its vast population. To this end, the challenge is in avoiding the precarious path so far followed by industrialised countries in Europe and Asia, but to opt for a regime shift towards sustainability in terms of resource use by building on a host of promising examples and taking opportunities of existing niches to make India a trendsetter. [Copyright &y& Elsevier]

Abstract: The technical, economic, and ecological aspects of rainwater management are interlinked and spatially bounded. Developing, scaling-out, and targeting rainwater management innovations as adaptive strategies to upgrade rainfed agriculture are therefore preferably best approached through integrated innovations and recommendation domains as a paradigm. At the level of scenario development, the integrated innovations paradigm helps to understand and address integrity between technical, economic, and ecological issues that affect technology adoption, impact, and sustained use. At the level of scaling-out and targeting, recommendation domains provide the spatial dimension that embraces the economic, institutional, biophysical, and agro-ecological conditions in which integrated rainwater management innovations can be accommodated to address heterogeneity. This paper reviews Ethiopia''s experience in rainwater management (adoption, performance, and impact) to get insights about the proposed paradigm and the factors entering the paradigm. The findings suggest that integrated innovations and the conditions of success embraced in a recommendation domain provide the necessary and sufficient conditions for a successful rainwater management intervention at a landscape level. [Copyright &y& Elsevier]

Abstract: Statistical–mechanical, 3D-RISM-KH molecular theory of solvation is an integral equation theory of molecular liquids capable of describing, from the first principles, solvation structure and thermodynamics in complex nanoscale systems. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as chaperonins and ion channels. It predicts 3D maps of ligand binding affinity at once without using empirical scoring functions, and has significant potential for computer-aided drug design. Recently, the 3D-RISM-KH theory was coupled with MD simulations by contracting solvent degrees of freedom to treat solvated biomolecules, and the MD/3D-RISM-KH multiscale method was implemented in the Amber molecular dynamics package [T. Luchko et al., 2010, []]. The MD/3D-RISM-KH method allows one to study biomolecular processes on extremely long timescales, as the statistics of rare solvent and ligand events is accounted for analytically. We further replaced the MM/GB(PB)SA post-processing which evaluates the free energy by empirical treatment of non-polar solvation effects with the MM/3D-RISM-KH method which employs 3D-RISM-KH to evaluate the solvation thermodynamics. In this paper, we briefly review the 3D-RISM-KH theory as well as the MD/3D-RISM-KH multiscale method implemented in the Amber package. We illustrate the MM/3D-RISM-KH method on binding of thiamine (vitamin of group B) to extracytoplasmic thiamine-binding lipoprotein MG289, and on the microscopic solvation properties of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) homologue. [Copyright &y& Elsevier]

Abstract: The modeling of the electrical activity of the heart is of great medical and scientific interest as it provides a way to better understand the underlying biophysical phenomena, supports the development of new techniques for diagnoses and serves as a platform for drug tests. At cellular level, the electrical activity of cardiac myocytes may be simulated by solving a system of ordinary di_erential equations (ODEs) describing the electrical behavior of the cell membrane. Because the biophysical processes underlying this phenomenon are non-linear and change very rapidly, the ODE system is challenging to solve numerically. Furthermore, the implementation of these models is a hard task. This paper presents a tool to describe models using Ordinary Differential Equations. It is based on CellML standard and automatically generates C++ source-code, with numerical methods to solve the model''s equations. The aim of this work is to present a numerical method with adaptive time step based on the Euler Method and Second Order Runge-Kutta method. The proposed method accelerated the execution and kept numerical errors under control. Preliminary results suggest this adaptive method is up to 25 times faster than the explicit Euler method with fixed time step. [Copyright &y& Elsevier]

Abstract: Monitoring and maximization of bioenergy yield from biomass feedstock has recently become a critically important goal for researchers. Remote sensing represents a potential method to monitor and estimate biomass so as to increase biomass feedstock production from energy crops. This paper reviews the biophysical properties of biomass and remote sensing methods for monitoring energy crops for site-specific management. While several research studies have addressed the agronomic dimensions of this approach, more research is required on perennial energy crops in order to maximize the yield of biomass feedstock. Assessment of established methods could lead to a new strategy to monitor energy crops for the adoption of site-specific management in biomass feedstock production. In this article, satellite, aerial and ground-based remote sensing’s were reviewed and focused on the spatial and temporal resolutions of imagery to adopt for site-specific management. We have concluded that the biomass yield prediction, the ground-based sensing is the most suitable to establish the calibration model and reference for aerial and satellite remote sensing. The aerial and satellite remote sensing are required for wide converge of planning and policy implementations of biomass feedstock production systems. [Copyright &y& Elsevier]

Abstract: This paper describes an agent-based software package, called Mathematical Programming-based Multi Agent Systems (MP-MAS), which builds on a tradition of using constrained optimization to simulate farm decision-making in agricultural systems. The purpose of MP-MAS is to understand how agricultural technology, market dynamics, environmental change, and policy intervention affect a heterogeneous population of farm households and the agro-ecological resources these households command. The software is presented using the Overview, Design concepts, and Details (ODD) protocol. Modeling features are demonstrated with empirical applications to study sites in Chile, Germany, Ghana, Thailand, Uganda, and Vietnam. We compare MP-MAS with eight other simulators of human–environment interactions (ABSTRACT, CATCHSCAPE, ECECMOD, IMT, LUDAS, PALM, SAM, and SIM). The comparison shows that the uniqueness of MP-MAS lies in its combination of a microeconomic modeling approach and a choice of alternative biophysical modules that are either coded as part of the software or coupled with it using the Typed Data Transfer (TDT) library. [Copyright &y& Elsevier]

Abstract: Rural landscapes are often multifunctional, meaning that at one single location different goods and services are being provided. Multifunctionality is spatially heterogeneous as not all areas are equally suitable to supply multiple goods and services. This suitability depends on favourable biophysical and socio-economic conditions and interactions among landscape functions. The objective of this paper is to identify and quantify interactions among landscape functions in a diverse and dynamic rural region, the Gelderse Vallei in the Netherlands. To be able to study these interactions first seven landscape functions (residential, intensive livestock, cultural heritage, tourism, plant habitat, arable production, and leisure cycling) are quantified and mapped using landscape indicators. These landscape function maps are subsequently aggregated to identify and quantify multifunctionality. The results of these analyses are used to study three aspects of landscape function interactions (a) influence of landscape characteristics on function interactions, (b) interrelations among landscape functions and (c) effect of multifunctionality on the different landscape functions. Landscape functions do not equally interact with one another, some landscape functions are affected negatively by the presence of other functions while other landscape functions benefit from multifunctionality. At multifunctionality hot spots different landscape functions are present that are enhancing one another. Additionally, in our study area it appears that mainly locations with landscape functions that sub-optimally provide goods and services are strongly multifunctional. Quantification and an improved understanding of landscape interactions will help to design and evaluate spatial policies related to the provision of multiple goods and services by the landscape. [Copyright &y& Elsevier]

Abstract: This paper shows the utility of multibody dynamics in evaluating changes in injury related parameters of the head and lower limbs of children following falls from playground climbing frames. A particular fall case was used as a starting point to analyze the influence of surface properties, posture of the body at impact, and intermediate collisions against the climbing frame before impacting the ground. Simulations were made using the 6-year-old pedestrian MADYMO rigid body model and scaled head contact characteristics. Energy absorbing surfaces were shown to reduce injury severity parameters by up to 30–80% of those of rigid surfaces, depending on impact posture and surface. Collisions against components of a climbing frame during a fall can increase injury severity of the final impact of the head with the ground by more than 90%. Negligible changes are associated with lower limb injury risks when different surfacing materials are used. Computer reconstructions of actual falls that are intended to quantify the severity of physical injuries rely on accurate knowledge of initial conditions prior to falling, intermediate kinematics of the fall and the orientation of the body when it impacts against the ground. Multibody modelling proved to be a valuable tool to analyze the quality of eyewitness information and analyze the relative injury risk associated with changes in components influencing fall injuries from playground climbing frames. Such simulations can also support forensic investigations by evaluating alternative hypotheses for the sequence of kinematic motion of falls which result in known injuries. [Copyright &y& Elsevier]

Abstract: The amount of land consumption required for housing and transport severely conflicts with both the necessity and the legal obligation to maintain the ecological potential afforded by open spaces to meet the needs of current and future generations with regards to the protection of resources and climate change. Owing to an increasing intensity of soil use, soil conditions appear to have deteriorated in most city regions around the world, namely their filter and runoff regulating functions are impaired by land surfacing. As such soil functions depend on the soil''s biophysical properties and the degree of imperviousness, the impact on the water balance caused by urban growth varies considerably. In response to the demand for sustainably secure urban water resources, it needs to be assessed exactly how land surfacing affects the functions concerned. Analysing and evaluating urban land use change on the long-term water balance should improve our understanding of the impact of urbanisation on the water household. Therefore, this paper analyses the impact of urban land use change and land surfacing on the long-term urban water balance over a 130-year trajectory by using simple model approaches that are based on data available to the public. The test site is the city of Leipzig. In particular, attention is to be paid to estimating changes of evapotranspiration, direct runoff and groundwater recharge. [Copyright &y& Elsevier]

Abstract: We describe in this paper two applications of Eulerian level set methods to fluid-structure problems arising in biophysics. The first one is concerned with three-dimensional equilibrium shapes of phospholipidic vesicles. This is a complex problem, which can be recast as the minimization of the curvature energy of an immersed elastic membrane, under a constant area constraint. The second deals with isolated cardiomyocyte contraction. This problem corresponds to a generic incompressible fluid-structure coupling between an elastic body and a fluid. By the choice of these two quite different situations, we aim to bring evidence that Eulerian methods provide efficient and flexible computational tools in biophysics applications. [Copyright &y& Elsevier]

Abstract: To understand the stochastic behavior of biological systems, we adopt an “in silico” stochastic event based simulation methodology that can determine the temporal dynamics of different molecules. The main requirement for this technique is the event execution time models for the different biological functions of the system. This paper presents a parametric model to determine the execution time of one such biological function: protein–DNA binding. This biological function is modeled as a combination of microlevel biological events using a coarse-grained probability measure to estimate the stochastic parameters of the function. Our model considers the actual binding mechanism along with some approximated protein and DNA structural information. We use a collision theory based approach to transform the thermal and concentration gradients of this biological function into their corresponding probability measure. This information theoretic approach significantly removes the complexity of the classical protein sliding along the DNA model, improves the speed of computation and can bypass the speed-stability paradox. This model can produce acceptable estimates of DNA–protein binding time necessary for our event based stochastic system simulator where the higher order (more than second order statistics) uncertainties can be ignored. The results show good correspondence with available experimental estimates. The model depends very little on experimentally generated rate constants and brings the important biological parameters and functions into consideration. We also present some “in silico” results showing the effects of protein–DNA binding on gene expression in prokaryotic cells. [Copyright &y& Elsevier]

Land use patterns influence the long-term productivity of agro-ecosystems and result from socio-economic as well as biophysical and climatic drivers. This paper qualitatively examines how past demographic and political-economic changes in southern Romania twice led to vulnerable socio-economic and agro-ecological systems. Drawing on this case study, we establish broad-brush hypotheses identifying some of the potential causes of vulnerability. We suggest that vulnerable systems appear more likely to occur when socio-political uncertainty combines with a lack of off-farm employment in regions where there are abundant natural capital stocks that can be quickly liquidated. [Copyright &y& Elsevier]