The conceptual design of SeamFrame

This project deliverable provides the underlying architecture of a concept for linking models and databases and it provides the design of SeamFrame, delivering its architecture to provide an integration framework for models and simulation algorithms, supported by procedures for data handling and spatial representation, quality control, output visualization and documentatio

Affine and toric hyperplane arrangements

We extend the Billera-Ehrenborg-Readdy map between the intersection lattice and face lattice of a central hyperplane arrangement to affine and toric hyperplane arrangements. For arrangements on the torus, we also generalize Zaslavsky's fundamental results on the number of regions.Comment: 32 pages, 4 figure

Direct imaging of changes in aerosol particle viscosity upon hydration and chemical aging

Organic aerosol particles (OA) play major roles in atmospheric chemistry, climate, and public health. Aerosol particle viscosity is highly important since it can determine the ability of chemical species such as oxidants, organics or water to diffuse into the particle bulk. Recent measurements indicate that OA may be present in highly viscous states, however, diffusion rates of small molecules such as water are not limited by these high viscosities. Direct observational evidence of kinetic barriers caused by high viscosity and low diffusivity in aerosol particles were not available until recently; and techniques that are able to dynamically quantify and track viscosity changes during atmospherically relevant processes are still unavailable for atmospheric aerosols. Here we report quantitative, real-time, online observations of microscopic viscosity changes in aerosol particles of atmospherically relevant composition, using fluorescence lifetime imaging (FLIM) of viscosity. We show that microviscosity in ozonated oleic acid droplets and secondary organic aerosol (SOA) particles formed by ozonolysis of myrcene increases substantially with decreasing humidity and atmospheric oxidative aging processes. Furthermore, we found unexpected heterogeneities of microviscosity inside individual aerosol particles. The results of this study enhance our understanding of organic aerosol processes on microscopic scales and may have important implications for the modeling of atmospheric aerosol growth, composition and interactions with trace gases and clouds.Engineering and Physical Sciences Research Council (Career Acceleration Fellowship (Grant ID: EP/I003983/1), Prize studentship), Natural Environment Research Council (Studentship NE/J500070/1), European Research Council (Grant ID: 279405), Max Planck Society, European Union project PEGASOS (Grant ID: 265148

Trade-offs in the design of cross-disciplinary software systems

As researchers we are often faced with the difficult and demanding task of preparing models, and their computer implementations, for decision making, or, more recently, for integrated assessment. Such assessment often involves large scale problems, where the decisions to be made can deeply affect the environment, the social context and the economic background of regions and even nations. Yet, we face the grim reality that a model is a focused representation of the world, and it is always a result of several compromises in terms of details and structure, leading to trade-offs in terms of complexity, flexibility and performance. This trade-off becomes an essential design property. We often wish our models to be as simple as possible, balancing transparency, understandability and level of detail. Now, we are involved in the SEAMLESS project, an EU FP6 Integrated Project, aims at generating an integrated framework of computer models. This framework can be used for assessment of how future alternative agricultural and environmental polices affect sustainable development in Europe. Thus, we are designing a cross disciplinary software system to deal with different simulation domains. In this, we need to take care of many differences between the different modeling societies. We decided to apply an architecture centric development method and evaluated this with stakeholders based on a so-called Architecture Trade-off Analysis method. When prioritizing the requirements we used a cost-benefit analysis as a weighting factor for deciding what to do first. Requirements were grouped in user-roles, that appeal to differences in user-interface options. The resulting software architecture identified the necessity to identify two major blocks: the modeling environment, to be used by a number of user roles, mostly modelers and coders, and the processing environment, which is oriented towards the needs of those user roles more focused on system analysis, rather than design and implementation. Another key factor of our architecture is the knowledge base, which provides a common repository for all knowledge, data, model sources which are shared by the two environments. When moving on from architecture to design and implementation, we tried to steer clear of the risk of inventing another modelling framework, and therefore in our prototype we use different existing frameworks for different tasks in the overall design. This means that we discussed the view that 'one tool fixes everything', and we chose to rely on specific frameworks for specific needs. We chose a modelling framework with a track record in crop modeling, to target our biophysical modeling needs, and we selected a de facto standard framework for economic modeling to solve agri-economic modelling problems. All of this comes at a price, that is the extra effort required to integrate different frameworks. We chose therefore to develop an evolution of the OpenMI integration framework to target this issue. In this article we describe all the risks we have identified as associated to our architecture centric approach and how we dealt with them. This article describes the design of the modeling framework for SEAMLESS. A first prototype is ready in January 2006

Lyashko-Looijenga morphisms and submaximal factorisations of a Coxeter element

When W is a finite reflection group, the noncrossing partition lattice NCP_W of type W is a rich combinatorial object, extending the notion of noncrossing partitions of an n-gon. A formula (for which the only known proofs are case-by-case) expresses the number of multichains of a given length in NCP_W as a generalised Fuss-Catalan number, depending on the invariant degrees of W. We describe how to understand some specifications of this formula in a case-free way, using an interpretation of the chains of NCP_W as fibers of a Lyashko-Looijenga covering (LL), constructed from the geometry of the discriminant hypersurface of W. We study algebraically the map LL, describing the factorisations of its discriminant and its Jacobian. As byproducts, we generalise a formula stated by K. Saito for real reflection groups, and we deduce new enumeration formulas for certain factorisations of a Coxeter element of W.Comment: 18 pages. Version 2 : corrected typos and improved presentation. Version 3 : corrected typos, added illustrated example. To appear in Journal of Algebraic Combinatoric

Observing superluminous supernovae and long gamma ray bursts as potential birthplaces of repeating fast radio bursts

Superluminous supernovae (SLSNe) and long gamma ray bursts (LGRBs) have been proposed as progenitors of repeating Fast Radio Bursts (FRBs). In this scenario, bursts originate from the interaction between a young magnetar and its surrounding supernova remnant (SNR). Such a model could explain the repeating, apparently non-Poissonian nature of FRB121102, which appears to display quiescent and active phases. This bursting behaviour is better explained with a Weibull distribution, which includes parametrisation for clustering. We observed 10 SLSNe/LGRBs for 63 hours, looking for repeating FRBs with the Effelsberg-100 m radio telescope, but have not detected any bursts. We scale the burst rate of FRB121102 to an FRB121102-like source inhabiting each of our observed targets, and compare this rate to our upper burst rate limit on a source by source basis. By adopting a fiducial beaming fraction of 0.6, we obtain 99.99\% and 83.4\% probabilities that at least one, and at least half of our observed sources are beamed towards us respectively. One of our SLSN targets, PTF10hgi, is coincident with a persistent radio source, making it a possible analogue to FRB121102. We performed further observations on this source using the Effelsberg-100~m and Parkes-64~m radio telescopes. Assuming that PTF10hgi contains an FRB121102-like source, the probabilities of not detecting any bursts from a Weibull distribution during our observations are 14\% and 16\% for Effelsberg and Parkes respectively. We conclude by showing that a survey of many short observations increases burst detection probability for a source with Weibull distributed bursting activity.Comment: 11 pages, 5 figure

Unimodality Problems in Ehrhart Theory

Ehrhart theory is the study of sequences recording the number of integer points in non-negative integral dilates of rational polytopes. For a given lattice polytope, this sequence is encoded in a finite vector called the Ehrhart $h^*$-vector. Ehrhart $h^*$-vectors have connections to many areas of mathematics, including commutative algebra and enumerative combinatorics. In this survey we discuss what is known about unimodality for Ehrhart $h^*$-vectors and highlight open questions and problems.Comment: Published in Recent Trends in Combinatorics, Beveridge, A., et al. (eds), Springer, 2016, pp 687-711, doi 10.1007/978-3-319-24298-9_27. This version updated October 2017 to correct an error in the original versio

RNA editing signature during myeloid leukemia cell differentiation

Adenosine deaminases acting on RNA (ADARs) are key proteins for hematopoietic stem cell self-renewal and for survival of differentiating progenitor cells. However, their specific role in myeloid cell maturation has been poorly investigated. Here we show that ADAR1 is present at basal level in the primary myeloid leukemia cells obtained from patients at diagnosis as well as in myeloid U-937 and THP1 cell lines and its expression correlates with the editing levels. Upon phorbol-myristate acetate or Vitamin D3/granulocyte macrophage colony-stimulating factor (GM-CSF)-driven differentiation, both ADAR1 and ADAR2 enzymes are upregulated, with a concomitant global increase of A-to-I RNA editing. ADAR1 silencing caused an editing decrease at specific ADAR1 target genes, without, however, interfering with cell differentiation or with ADAR2 activity. Remarkably, ADAR2 is absent in the undifferentiated cell stage, due to its elimination through the ubiquitin–proteasome pathway, being strongly upregulated at the end of the differentiation process. Of note, peripheral blood monocytes display editing events at the selected targets similar to those found in differentiated cell lines. Taken together, the data indicate that ADAR enzymes play important and distinct roles in myeloid cells

Comparative study of the biochemical changes and volatile compound formations during the production of novel whey-based kefir beverages and traditional milk kefir

Cheese whey (CW) and deproteinised cheese whey (DCW) were investigated for their suitability as novel substrates for the production of kefir-like beverages. Lactose consumption, ethanol production, as well as organic acids and volatile compounds formation, were determined during CW and DCW fermentation by kefir grains and compared with values obtained during the production of traditional milk kefir. The results showed that kefir grains were able to utilise lactose from CW and DCW and produce similar amounts of ethanol (7.8–8.3 g/l), lactic acid (5.0 g/l) and acetic acid (0.7 g/l) to those obtained during milk fermentation. In addition, the concentration of higher alcohols (2-methyl-1-butanol, 3-methyl-1-butanol, 1-hexanol, 2-methyl-1-propanol, and 1-propanol), ester (ethyl acetate) and aldehyde (acetaldehyde) in cheese whey-based kefir and milk kefir beverages were also produced in similar amounts. Cheese whey and deproteinised cheese whey may therefore serve as substrates for the production of kefir-like beverages similar to milk kefir.The authors acknowledge the financial support from Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES), CAPES-GRICES and Lactogal for supplying cheese whey powder