Dynamic Modelling of Material Flows and Sustainable Resource Use: Case Studies in Regional Metabolism and Space Life Support Systems

Sustainable resource use is one of the most important environmental issues of our times. It is closely related to discussions on the 'peaking' of various natural resources serving as energy sources, agricultural nutrients, or metals indispensable in high-technology applications. Although the peaking theory remains controversial, it is commonly recognized that a more sustainable use of resources would alleviate negative environmental impacts related to resource use. In this thesis, sustainable resource use is analysed from a practical standpoint, through several different case studies. Four of these case studies relate to resource metabolism in the Canton of Geneva in Switzerland: the aim was to model the evolution of chosen resource stocks and flows in the coming decades. The studied resources were copper (a bulk metal), phosphorus (a vital agricultural nutrient), and wood (a renewable resource). In addition, the case of lithium (a critical metal) was analysed briefly in a qualitative manner and in an electric mobility perspective. In addition to the Geneva case studies, this thesis includes a case study on the sustainability of space life support systems. Space life support systems are systems whose aim is to provide the crew of a spacecraft with the necessary metabolic consumables over the course of a mission. Sustainability was again analysed from a resource use perspective. In this case study, the functioning of two different types of life support systems, ARES and BIORAT, were evaluated and compared; these systems represent, respectively, physico-chemical and biological life support systems. Space life support systems could in fact be used as a kind of 'laboratory of sustainability' given that they represent closed and relatively simple systems compared to complex and open terrestrial systems such as the Canton of Geneva. The chosen analysis method used in the Geneva case studies was dynamic material flow analysis: dynamic material flow models were constructed for the resources copper, phosphorus, and wood. Besides a baseline scenario, various alternative scenarios (notably involving increased recycling) were also examined. In the case of space life support systems, the methodology of material flow analysis was also employed, but as the data available on the dynamic behaviour of the systems was insufficient, only static simulations could be performed. The results of the case studies in the Canton of Geneva show the following: were resource use to follow population growth, resource consumption would be multiplied by nearly 1.2 by 2030 and by 1.5 by 2080. A complete transition to electric mobility would be expected to only slightly (+5%) increase the copper consumption per capita while the lithium demand in cars would increase 350 fold. For example, phosphorus imports could be decreased by recycling sewage sludge or human urine; however, the health and environmental impacts of these options have yet to be studied. Increasing the wood production in the Canton would not significantly decrease the dependence on wood imports as the Canton's production represents only 5% of total consumption. In the comparison of space life support systems ARES and BIORAT, BIORAT outperforms ARES in resource use but not in energy use. However, as the systems are dimensioned very differently, it remains questionable whether they can be compared outright. In conclusion, the use of dynamic material flow analysis can provide useful information for policy makers and strategic decision-making; however, uncertainty in reference data greatly influences the precision of the results. Space life support systems constitute an extreme case of resource-using systems; nevertheless, it is not clear how their example could be of immediate use to terrestrial systems.

Stand dynamics modelling approaches for multicohort management of eastern Canadian boreal forests

Abstract

Analysis of sensitivity with respect to a compositional parameter : A comment on 'Local sensitivity analysis for compositional data with application to soil texture in hydrologic modelling' by L. Loosvelt and co-authors

A comment about the article “Local sensitivity analysis for compositional data with application to soil texture in hydrologic modelling” writen by L. Loosvelt and co-authors. The present comment is centered in three specific points. The first one is related to the fact that the authors avoid the use of ilr-coordinates. The second one refers to some generalization of sensitivity analysis when input parameters are compositional. The third tries to show that the role of the Dirichlet distribution in the sensitivity analysis is irrelevant

Modelling variation of needle density of Scots pine at high latitudes

[Abstract]

Collective symbolic coping with disease threat and othering: A case study of avian influenza

Much research studies how individuals cope with disease threat by blaming out-groups and protecting the in-group. The model of collective symbolic coping (CSC) describes four stages by which representations of a threatening event are elaborated in the mass media: awareness, divergence, convergence, and normalization. We used the CSC model to predict when symbolic in-group protection (othering) would occur in the case of the avian influenza (AI) outbreak. Two studies documented CSC stages and showed that othering occurred during the divergence stage, characterized by an uncertain symbolic environment. Study 1 analysed media coverage of AI over time, documenting CSC stages of awareness and divergence. In Study 2, a two-wave repeated cross-sectional survey was conducted just after the divergence stage and a year later. Othering was measured by the number of foreign countries erroneously ticked by participants as having human victims. Individual differences in germ aversion and social dominance orientation interacted to predict othering during the divergence stage but not a year later. Implications for research on CSC and symbolic in-group protection strategies resulting from disease threat are discussed.

Modelling the effect of temperature on height increment of Scots pine at high latitudes

Abstract

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes.

Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid.

Linear prediction application for modelling the relationships between a large number of stand characteristics of Norway spruce stands

Abstract

Individual-based modelling and simulation: towards a better understanding of growth dynamics from small inocula

Postprint (published version)

Energy-based modelling and simulation of the interconnection of a back-to-back converter and a doubly-fed induction machine

This paper describes the port interconnection of two subsystems: a power electronics subsystem (a back-to-back AC/CA converter (B2B), coupled to a phase of the power grid), and an electromechanical subsystem (a doubly-fed induction machine (DFIM). The B2B is a variable structure system (VSS), due to presence of control-actuated switches: however, from a modelling simulation, as well as a control-design, point of view, it is sensible to consider modulated transformers (MTF in the bond graph language) instead of the pairs of complementary switches. The port-Hamiltonian models of both subsystems are presented and, using a power-preserving interconnection, the Hamiltonian description of the whole system is obtained; detailed bond graphs of all subsystems and the complete system are also provided. Using passivity-based controllers computed in the Hamiltonian formalism for both subsystems, the whole model is simulated; simulations are run to rest the correctness and efficiency of the Hamiltonian network modelling approach used in this work.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

The Arcuated Lintel and the "Serlian Motif". Imperial Identity, Architectural and Symbolic Interactions in Ancient Rome

Essay on the origin, use and development of the arcuated lintel in ancient Rome and the configuration of the so– called ‘Serlian motif’. These architectural elements will be related to the architecture of prestige on its technical, functional, visual and symbolic sphere. Its depictions, in addition to buildings, can offer a rich repertory of images that speak about the relations between visual culture, religion and power. Furthermore, the analyzed motifs will become important elements of the Western cultural legacy for centuries. The analysis of these events will contribute to the comprehension of the role played by some resources of ancient Rome architecture of prestige and its success