Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

Integrated Environmental Modelling Framework for Cumulative Effects Assessment

Global warming and population growth have resulted in an increase in the intensity of natural and anthropogenic stressors. Investigating the complex nature of environmental problems requires the integration of different environmental processes across major components of the environment, including water, climate, ecology, air, and land. Cumulative effects assessment (CEA) not only includes analyzing and modeling environmental changes, but also supports planning alternatives that promote environmental monitoring and management. Disjointed and narrowly focused environmental management approaches have proved dissatisfactory. The adoption of integrated modelling approaches has sparked interests in the development of frameworks which may be used to investigate the processes of individual environmental component and the ways they interact with each other. Integrated modelling systems and frameworks are often the only way to take into account the important environmental processes and interactions, relevant spatial and temporal scales, and feedback mechanisms of complex systems for CEA. This book examines the ways in which interactions and relationships between environmental components are understood, paying special attention to climate, land, water quantity and quality, and both anthropogenic and natural stressors. It reviews modelling approaches for each component and reviews existing integrated modelling systems for CEA. Finally, it proposes an integrated modelling framework and provides perspectives on future research avenues for cumulative effects assessment

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

How to integrate geochemistry at affordable costs into reactive transport for large-scale systems: Abstract Book

This international workshop entitled “How to integrate geochemistry at affordable costs into reac-tive transport for large-scale systems” was organized by the Institute of Resource Ecology of the Helmholtz-Zentrum Dresden Rossendorf in Feb-ruary 2020. A mechanistic understanding and building on that an appropriate modelling of geochemical processes is essential for reliably predicting contaminant transport in groundwater systems, but also in many other cases where migration of hazardous substances is expected and consequently has to be assessed and limited. In case of already present contaminations, such modelling may help to quantify the threads and to support the development and application of suitable remediation measures. Typical application areas are nuclear waste disposal, environmental remediation, mining and milling, carbon capture & storage, or geothermal energy production. Experts from these fields were brought together to discuss large-scale reactive transport modelling (RTM) because the scales covered by such pre-dictions may reach up to one million year and dozens of kilometers. Full-fledged incorporation of geochemical processes, e.g. sorption, precipitation, or redox reactions (to name just a few important basic processes) will thus create inacceptable long computing times. As an effective way to integrate geochemistry at affordable costs into RTM different geochemical concepts (e.g. multidimensional look-up tables, surrogate functions, machine learning, utilization of uncertainty and sensitivity analysis etc.) exist and were extensively discussed throughout the workshop. During the 3-day program of the workshop keynote and regular lectures from experts in the field, a poster session, and a radio lab tour had been offered. In total, 40 scientists from 28 re-search institutes and 8 countries participated

Sources of pesticide losses to surface waters and groundwater at field and landscape scales

Pesticide residues in groundwater and surface waters may harm aquatic ecosystems and result in a deterioration of drinking water quality. EU legislation and policy emphasize risk management and risk reduction for pesticides to ensure long-term, sustainable use of water across Europe. Different tools applicable at scales ranging from farm to national and EU scales are required to meet the needs of the various managers engaged with the task of protecting water resources. The use of computer-based pesticide fate and transport models at such large scales is challenging since models are scale-specific and generally developed for the soil pedon or plot scale. Modelling at larger scales is further complicated by the spatial and temporal variability of agro-environmental conditions and the uncertainty in predictions. The objective of this thesis was to identify the soil processes that dominate diffuse pesticide losses at field and landscape scales and to develop methods that can help identify 'high risk' areas for leaching. The underlying idea was that pesticide pollution of groundwater and surface waters can be mitigated if pesticide application on such areas is reduced. Macropore flow increases the risk of pesticide leaching and was identified as the most important process responsible for spatial variation of diffuse pesticide losses from a 30 ha field and a 9 km² catchment in the south of Sweden. Point-sources caused by careless handling of pesticides when filling or cleaning spraying equipment were also a significant source of contamination at the landscape scale. The research presented in this thesis suggests that the strength of macropore flow due to earthworm burrows and soil aggregation can be predicted from widely available soil survey information such as texture, management practices etc. Thus, a simple classification of soils according to their susceptibility to macropore flow may facilitate the use of process-based models at the landscape scale. Predictions of a meta-model of the MACRO model suggested that, at the field scale, fine-textured soils are high-risk areas for pesticide leaching. Uncertainty in pesticide degradation and sorption did not significantly affect predictions of the spatial extent of these high-risk areas. Thus, site-specific pesticide application seems to be a promising method for mitigating groundwater contamination at this scale

Exploring urban metabolism—Towards an interdisciplinary perspective

© 2017 The Author(s) The discussion on urban metabolism has been long dominated by natural scientists focussing on natural forces shaping the energy and material flows in urban systems. However, in the anthropocene human forces such as industrialization and urbanization are mobilizing people, goods and information at an increasing pace and as such have a large impact on urban energy and material flows. In this white paper, we develop a combined natural and social science perspective on urban metabolism. More specifically, innovative conceptual and methodological interdisciplinary approaches are identified and discussed to enhance the understanding of the forces that shape urban metabolism, and how these forces affect urban living and the environment. A challenging research agenda on urban metabolism is also presented

Research program on exposure dose reconstruction and multimedia simulation tool

Issued as Annual progress report, and Research proposal, Project E-20-X7