Refine
Year of publication
- 2014 (222) (remove)
Document Type
- Doctoral Thesis (222) (remove)
Keywords
- Gammastrahlungsastronomie (4)
- data analysis (4)
- gamma-ray astronomy (4)
- Crab Nebula (3)
- Datenanalyse (3)
- Krebsnebel (3)
- Synchronisation (3)
- Systembiologie (3)
- synchronization (3)
- systems biology (3)
Institute
- Institut für Biochemie und Biologie (37)
- Institut für Physik und Astronomie (25)
- Institut für Geowissenschaften (19)
- Wirtschaftswissenschaften (15)
- Institut für Chemie (13)
- Historisches Institut (12)
- Institut für Informatik und Computational Science (10)
- Department Psychologie (9)
- Hasso-Plattner-Institut für Digital Engineering gGmbH (9)
- Institut für Ernährungswissenschaft (8)
The quantitative descriptions of the state of stress in the Earth’s crust, and spatial-temporal stress changes are of great importance in terms of scientific questions as well as applied geotechnical issues. Human activities in the underground (boreholes, tunnels, caverns, reservoir management, etc.) have a large impact on the stress state. It is important to assess, whether these activities may lead to (unpredictable) hazards, such as induced seismicity. Equally important is the understanding of the in situ stress state in the Earth’s crust, as it allows the determination of safe well paths, already during well planning. The same goes for the optimal configuration of the injection- and production wells, where stimulation for artificial fluid path ways is necessary.
The here presented cumulative dissertation consists of four separate manuscripts, which are already published, submitted or will be submitted for peer review within the next weeks. The main focus is on the investigation of the possible usage of geothermal energy in the province Alberta (Canada). A 3-D geomechanical–numerical model was designed to quantify the contemporary 3-D stress tensor in the upper crust. For the calibration of the regional model, 321 stress orientation data and 2714 stress magnitude data were collected, whereby the size and diversity of the database is unique. A calibration scheme was developed, where the model is calibrated versus the in situ stress data stepwise for each data type and gradually optimized using statistically test methods. The optimum displacement on the model boundaries can be determined by bivariate linear regression, based on only three model runs with varying deformation ratio. The best-fit model is able to predict most of the in situ stress data quite well. Thus, the model can provide the full stress tensor along any chosen virtual well paths. This can be used to optimize the orientation of horizontal wells, which e.g. can be used for reservoir stimulation. The model confirms regional deviations from the average stress orientation trend, such as in the region of the Peace River Arch and the Bow Island Arch.
In the context of data compilation for the Alberta stress model, the Canadian database of the World Stress Map (WSM) could be expanded by including 514 new data records. This publication of an update of the Canadian stress map after ~20 years with a specific focus on Alberta shows, that the maximum horizontal stress (SHmax) is oriented southwest to northeast over large areas in Northern America. The SHmax orientation in Alberta is very homogeneous, with an average of about 47°. In order to calculate the average SHmax orientation on a regular grid as well as to estimate the wave-length of stress orientation, an existing algorithm has been improved and is applied to the Canadian data. The newly introduced quasi interquartile range on the circle (QIROC) improves the variance estimation of periodic data, as it is less susceptible to its outliers.
Another geomechanical–numerical model was built to estimate the 3D stress tensor in the target area ”Nördlich Lägern” in Northern Switzerland. This location, with Opalinus clay as a host rock, is a potential repository site for high-level radioactive waste. The performed modelling aims to investigate the sensitivity of the stress tensor on tectonic shortening, topography, faults and variable rock properties within the Mesozoic sedimentary stack, according to the required stability needed for a suitable radioactive waste disposal site. The majority of the tectonic stresses caused by the far-field shortening from the South are admitted by the competent rock units in the footwall and hanging wall of the argillaceous target horizon, the Upper Malm and Upper Muschelkalk. Thus, the differential stress within the host rock remains relatively low. East-west striking faults release stresses driven by tectonic shortening. The purely gravitational influence by the topography is low; higher SHmax magnitudes below topographical depression and lower values below hills are mainly observed near the surface. A complete calibration of the model is not possible, as no stress magnitude data are available for calibration, yet. The collection of this data will begin in 2015; subsequently they will be used to adjust the geomechanical–numerical model again.
The third geomechanical–numerical model investigates the stress variation in an ultra-deep gold mine in South Africa. This reservoir model is spatially one order of magnitude smaller than the previous local model from Northern Switzerland. Here, the primary focus is to investigate the hypothesis that the Mw 1.9 earthquake on 27 December 2007 was induced by stress changes due to the mining process. The Coulomb failure stress change (DeltaCFS) was used to analyse the stress change. It confirmed that the seismic event was induced by static stress transfer due to the mining progress. The rock was brought closer to failure on the derived rupture plane by stress changes of up to 1.5–15MPa, in dependence of the DeltaCFS analysis type. A forward modelling of a generic excavation scheme reveals that with decreasing distance to the dyke the DeltaCFS values increase significantly. Hence, even small changes in the mining progress can have a significant impact on the seismic hazard risk, i.e. the change of the occurrence probability to induce a seismic event of economic concern.
Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data
(2014)
The Epoch of Reionization marks after recombination the second major change in the ionization state of the universe, going from a neutral to an ionized state. It starts with the appearance of the first stars and galaxies; a fraction of high-energy photons emitted from galaxies permeate into the intergalactic medium (IGM) and gradually ionize the hydrogen, until the IGM is completely ionized at z~6 (Fan et al., 2006). While the progress of reionization is driven by galaxy evolution, it changes the ionization and thermal state of the IGM substantially and affects subsequent structure and galaxy formation by various feedback mechanisms.
Understanding this interaction between reionization and galaxy formation is further impeded by a lack of understanding of the high-redshift galactic properties such as the dust distribution and the escape fraction of ionizing photons. Lyman Alpha Emitters (LAEs) represent a sample of high-redshift galaxies that are sensitive to all these galactic properties and the effects of reionization.
In this thesis we aim to understand the progress of reionization by performing cosmological simulations, which allows us to investigate the limits of constraining reionization by high-redshift galaxies as LAEs, and examine how galactic properties and the ionization state of the IGM affect the visibility and observed quantities of LAEs and Lyman Break galaxies (LBGs).
In the first part of this thesis we focus on performing radiative transfer calculations to simulate reionization. We have developed a mapping-sphere-scheme, which, starting from spherically averaged temperature and density fields, uses our 1D radiative transfer code and computes the effect of each source on the IGM temperature and ionization (HII, HeII, HeIII) profiles, which are subsequently mapped onto a grid. Furthermore we have updated the 3D Monte-Carlo radiative transfer pCRASH, enabling detailed reionization simulations which take individual source characteristics into account.
In the second part of this thesis we perform a reionization simulation by post-processing a smoothed-particle hydrodynamical (SPH) simulation (GADGET-2) with 3D radiative transfer (pCRASH), where the ionizing sources are modelled according to the characteristics of the stellar populations in the hydrodynamical simulation. Following the ionization fractions of hydrogen (HI) and helium (HeII, HeIII), and temperature in our simulation, we find that reionization starts at z~11 and ends at z~6, and high density regions near sources are ionized earlier than low density regions far from sources.
In the third part of this thesis we couple the cosmological SPH simulation and the radiative transfer simulations with a physically motivated, self-consistent model for LAEs, in order to understand the importance of the ionization state of the IGM, the escape fraction of ionizing photons from galaxies and dust in the interstellar medium (ISM) on the visibility of LAEs. Comparison of our models results with the LAE Lyman Alpha (Lya) and UV luminosity functions at z~6.6 reveals a three-dimensional degeneracy between the ionization state of the IGM, the ionizing photons escape fraction and the ISM dust distribution, which implies that LAEs act not only as tracers of reionization but also of the ionizing photon escape fraction and of the ISM dust distribution. This degeneracy does not even break down when we compare simulated with observed clustering of LAEs at z~6.6. However, our results show that reionization has the largest impact on the amplitude of the LAE angular correlation functions, and its imprints are clearly distinguishable from those of properties on galactic scales. These results show that reionization cannot be constrained tightly by exclusively using LAE observations. Further observational constraints, e.g. tomographies of the redshifted hydrogen 21cm line, are required.
In addition we also use our LAE model to probe the question when a galaxy is visible as a LAE or a LBG. Within our model galaxies above a critical stellar mass can produce enough luminosity to be visible as a LBG and/or a LAE. By finding an increasing duty cycle of LBGs with Lya emission as the UV magnitude or stellar mass of the galaxy rises, our model reveals that the brightest (and most massive) LBGs most often show Lya emission.
Predicting the Lya equivalent width (Lya EW) distribution and the fraction of LBGs showing Lya emission at z~6.6, we reproduce the observational trend of the Lya EWs with UV magnitude. However, the Lya EWs of the UV brightest LBGs exceed observations and can only be reconciled by accounting for an increased Lya attenuation of massive galaxies, which implies that the observed Lya brightest LAEs do not necessarily coincide with the UV brightest galaxies. We have analysed the dependencies of LAE observables on the properties of the galactic and intergalactic medium and the LAE-LBG connection, and this enhances our understanding of the nature of LAEs.
The purpose of this thesis is to develop an automated inversion scheme to derive point and finite source parameters for weak earthquakes, here intended with the unusual meaning of earthquakes with magnitudes at the limit or below the bottom magnitude threshold of standard source inversion routines. The adopted inversion approaches entirely rely on existing inversion software, the methodological work mostly targeting the development and tuning of optimized inversion flows. The resulting inversion scheme is tested for very different datasets, and thus allows the discussion on the source inversion problem at different scales. In the first application, dealing with mining induced seismicity, the source parameters determination is addressed at a local scale, with source-sensor distance of less than 3 km. In this context, weak seismicity corresponds to event below magnitude MW 2.0, which are rarely target of automated source inversion routines. The second application considers a regional dataset, namely the aftershock sequence of the 2010 Maule earthquake (Chile), using broadband stations at regional distances, below 300 km. In this case, the magnitude range of the target aftershocks range down to MW 4.0. This dataset is here considered as a weak seismicity case, since the analysis of such moderate seismicity is generally investigated only by moment tensor inversion routines, with no attempt to resolve source duration or finite source parameters. In this work, automated multi-step inversion schemes are applied to both datasets with the aim of resolving point source parameters, both using double couple (DC) and full moment tensor (MT) models, source duration and finite source parameters. A major result of the analysis of weaker events is the increased size of resulting moment tensor catalogues, which interpretation may become not trivial. For this reason, a novel focal mechanism clustering approach is used to automatically classify focal mechanisms, allowing the investigation of the most relevant and repetitive rupture features. The inversion of the mining induced seismicity dataset reveals the repetitive occurrence of similar rupture processes, where the source geometry is controlled by the shape of the mined panel. Moreover, moment tensor solutions indicate a significant contribution of tensile processes. Also the second application highlights some characteristic geometrical features of the fault planes, which show a general consistency with the orientation of the slab. The additional inversion for source duration allowed to verify the empirical correlation for moment normalized earthquakes in subduction zones among a decreasing rupture duration with increasing source depth, which was so far only observed for larger events.
The adaptation of cell growth and proliferation to environmental changes is essential for the surviving of biological systems. The evolutionary conserved Ser/Thr protein kinase “Target of Rapamycin” (TOR) has emerged as a major signaling node that integrates the sensing of numerous growth signals to the coordinated regulation of cellular metabolism and growth. Although the TOR signaling pathway has been widely studied in heterotrophic organisms, the research on TOR in photosynthetic eukaryotes has been hampered by the reported land plant resistance to rapamycin. Thus, the finding that Chlamydomonas reinhardtii is sensitive to rapamycin, establish this unicellular green alga as a useful model system to investigate TOR signaling in photosynthetic eukaryotes.
The observation that rapamycin does not fully arrest Chlamydomonas growth, which is different from observations made in other organisms, prompted us to investigate the regulatory function of TOR in Chlamydomonas in context of the cell cycle. Therefore, a growth system that allowed synchronously growth under widely unperturbed cultivation in a fermenter system was set up and the synchronized cells were characterized in detail. In a highly resolved kinetic study, the synchronized cells were analyzed for their changes in cytological parameters as cell number and size distribution and their starch content. Furthermore, we applied mass spectrometric analysis for profiling of primary and lipid metabolism. This system was then used to analyze the response dynamics of the Chlamydomonas metabolome and lipidome to TOR-inhibition by rapamycin
The results show that TOR inhibition reduces cell growth, delays cell division and daughter cell release and results in a 50% reduced cell number at the end of the cell cycle. Consistent with the growth phenotype we observed strong changes in carbon and nitrogen partitioning in the direction of rapid conversion into carbon and nitrogen storage through an accumulation of starch, triacylglycerol and arginine. Interestingly, it seems that the conversion of carbon into triacylglycerol occurred faster than into starch after TOR inhibition, which may indicate a more dominant role of TOR in the regulation of TAG biosynthesis than in the regulation of starch.
This study clearly shows, for the first time, a complex picture of metabolic and lipidomic dynamically changes during the cell cycle of Chlamydomonas reinhardtii and furthermore reveals a complex regulation and adjustment of metabolite pools and lipid composition in response to TOR inhibition.
What is a radical? Somebody who goes against mainstream opinions? An agitator who suggests transforming society at the risk of endangering its harmony? In the political context of the British Isles at the end of the eighteenth century, the word radical had a negative connotation. It referred to the Levellers and the English Civil War, it brought back a period of history which was felt as a traumatic experience. Its stigmas were still vivid in the mind of the political leaders of these times. The reign of Cromwell was certainly the main reason for the general aversion of any form of virulent contestation of the power, especially when it contained political claims.
In the English political context, radicalism can be understood as the different campaigns for parliamentary reforms establishing universal suffrage. However, it became evident that not all those who were supporting such a reform originated from the same social class or shared the same ideals. As a matter of fact, the reformist associations and their leaders often disagreed with each other. Edward Royle and Hames Walvin claimed that radicalism could not be analyzed historically as a concept, because it was not a homogeneous movement, nor it had common leaders and a clear ideology. For them, radicalism was merely a loose concept, « a state of mind rather than a plan of action. »
At the beginning of the nineteenth-century, the newspaper The Northern Star used the word radical in a positive way to designate a person or a group of people whose ideas were conform to those of the newspaper. However, an opponent of parliamentary reform will use the same word in a negative way, in this case the word radical will convey a notion of menace. From the very beginning, the term radical covered a large spectrum of ideas and conceptions. In fact, the plurality of what the word conveys is the main characteristic of what a radical is. As a consequence, because the radicals tended to differentiate themselves with their plurality and their differences rather than with common features, it seems impossible to define what radicalism (whose suffix in –ism implies that it designate a doctrine, an ideology) is. Nevertheless, today it is accepted by all historians. From the mid-twentieth century, we could say that it was taken from granted to consider radicalism as a movement that fitted with the democratic precepts (universal suffrage, freedom of speech) of our modern world.
Let us first look at radicalism as a convenient way to designate the different popular movements appealing to universal suffrage during the time period 1792-1848. We could easily observe through the successions of men and associations, a long lasting radical state of mind: Cartwright, Horne Tooke, Thomas Hardy, Francis Burdett, William Cobbett, Henry Hunt, William Lovett, Bronterre O’Brien, Feargus O’Connor, The London Society for Constitutional information (SCI), The London Corresponding Society (LCS), The Hampden Clubs, The Chartists, etc. These organizations and people acknowledged having many things in common and being inspired by one another in carrying out their activities. These influences can be seen in the language and the political ideology that British historians name as "Constitutionalist", but also, in the political organization of extra-parliamentary societies. Most of the radicals were eager to redress injustices and, in practice, they were inspired by a plan of actions drawn on from the pamphlets of the True Whigs of the eighteenth-century. We contest the argument that the radicals lacked coherence and imagination or that they did not know how to put into practice their ambitions. In fact, their innovative forms of protest left a mark on history and found many successors in the twentieth century. Radicals’ prevarications were the result of prohibitive legislation that regulated the life of associations and the refusal of the authorities to cooperate with them.
As mentioned above, the term radical was greatly used and the contemporaries of the period starting from the French Revolution to Chartism never had to quarrel about the notions the word radical covered. However, this does not imply that all radicals were the same or that they belong to the same entity. Equally to Horne Tooke, the Reverend and ultra-Tory Stephens was considered as a radical, it went also with the shoemaker Thomas Hardy and the extravagant aristocrat Francis Burdett. Whether one belonged to the Aristocracy, the middle-class, the lower class or the Church, nothing could prevent him from being a radical. Surely, anybody could be a radical in its own way. Radicalism was wide enough to embrace everybody, from revolutionary reformers to paternalistic Tories.
We were interested to clarify the meaning of the term radical because its inclusive nature was overlooked by historians. That’s why the term radical figures in the original title of our dissertation Les voix/voies radicales (radical voices/ways to radicalism). In the French title, both words voix/voies are homonymous; the first one voix (voice) correspond to people, the second one voies (ways) refers to ideas. By this, we wanted to show that the word radical belongs to the sphere of ideas and common experience but also to the nature of human beings.
Methodoloy
The thesis stresses less on the question of class and its formation than on the circumstances that brought people to change their destiny and those of their fellows or to modernize the whole society. We challenged the work of E.P. Thompson, who in his famous book, The Making of the English Working Class, defined the radical movements in accordance with an idea of class.
How a simple shoe-maker, Thomas Hardy, could become the center of attention during a trial where he was accused of being the mastermind of a modern revolution? What brought William Cobbett, an ultra-Tory, self-taught intellectual, to gradually espouse the cause of universal suffrage at a period where it was unpopular to do so? Why a whole population gathered to hear Henry Hunt, a gentleman farmer whose background did not destine him for becoming the champion of the people? It seemed that the easiest way to answer to these questions and to understand the nature of the popular movements consisted in studying the life of their leaders. We aimed at reconstructing the universe which surrounded the principal actors of the reform movements as if we were a privileged witness of theses times.
This idea to associate the biographies of historical characters for a period of more than fifty years arouse when we realized that key events of the reform movements were echoing each other, such the trial of Thomas Hardy in 1794 and the massacre of Peterloo of 1819. The more we learned about the major events of radicalism and the life of their leaders, the more we were intrigued. Finally, one could ask himself if being a radical was not after all a question of character rather than one of class. The different popular movements in favour of a parliamentary reform were in fact far more inclusive and diversified from what historians traditionally let us to believe. For instance, once he manage to gather a sufficient number of members of the popular classes, Thomas Hardy projected to give the control of his association to an intellectual elite led by Horne Tooke.
Moreover, supporters of the radical reforms followed leaders whose background was completely different as theirs. For example, O’Connor claimed royal descent from the ancient kings of Ireland. William Cobbett, owner of a popular newspaper was proud of his origins as a farmer. William Lovett, close to the liberals and a few members of parliament came from a very poor family of fishermen. We have thus put together the life of these five men, Thomas hardy, William Cobbett, Henry Hunt, William Lovett and Feargus O’Connor in order to compose a sort of a saga of the radicals. This association gives us a better idea of the characteristics of the different movements in which they participated, but also, throw light on the circumstances of their formation and their failures, on the particular atmosphere which prevailed at these times, on the men who influenced these epochs, and finally on the marks they had left. These men were at the heart of a whole network and in contact with other actors of peripheral movements. They gathered around themselves close and loyal fellows with whom they shared many struggles but also quarreled and had strong words.
The original part of our approach is reflected in the choice to not consider studying the fluctuations of the radical movements in a linear fashion where the story follows a strict chronology. We decided to split up the main issue of the thesis through different topics. To do so, we simply have described the life of the people who inspired these movements. Each historical figure covers a chapter, and the general story follows a chronological progression. Sometimes we had to go back through time or discuss the same events in different chapters when the main protagonists lived in the same period of time.
Radical movements were influenced by people of different backgrounds. What united them above all was their wish to obtain a normalization of the political world, to redress injustices and obtain parliamentary reform. We paid particular attention to the moments where the life of these men corresponded to an intense activity of the radical movement or to a transition of its ideas and organization. We were not so much interested in their feelings about secondary topics nor did we about their affective relations. Furthermore, we had little interest in their opinions on things which were not connected to our topic unless it helped us to have a better understanding of their personality. We have purposely reduced the description of our protagonists to their radical sphere. Of course we talked about their background and their intellectual development; people are prone to experience reversals of opinions, the case of Cobbett is the most striking one.
The life of these personalities coincided with particular moments of the radical movement, such as the first popular political associations, the first open-air mass meetings, the first popular newspapers, etc. We wanted to emphasize the personalities of those who addressed speeches and who were present in the radical associations. One could argue that the inconvenience of focusing on a particular person presents a high risk of overlooking events and people who were not part of his world. However, it was essential to differ from an analysis or a chronicle which had prevailed in the studies of the radical movements, as we aimed at offering a point of view that completed the precedents works written on that topic. In order to do so, we have deliberately put the humane character of the radical movement at the center of our work and used the techniques of biography as a narrative thread.
Conclusion
The life of each historical figure that we have portrayed corresponded to a particular epoch of the radical movement. Comparing the speeches of the radical leaders over a long period of time, we noticed that the radical ideology evolved. The principles of the Rights of Men faded away and gave place to more concrete reasoning, such as the right to benefit from one’s own labour. This transition is characterized by the Chartist period of Feargus O’Connor. This does not mean that collective memory and radical tradition ceased to play an important part. The popular classes were always appealed to Constitutional rhetoric and popular myths. Indeed, thanks to them they identified themselves and justified their claims to universal suffrage.
We focused on the life of a few influent leaders of radicalism in order to understand its evolution and its nature. The description of their lives constituted our narrative thread and it enabled us to maintain consistency in our thesis. If the chapters are independent the one from the other, events and speeches are in correspondences. Sometimes we could believe that we were witnessing a repetition of facts and events as if history was repeating itself endlessly. However, like technical progress, the spirit of time, Zeitgeist, experiences changes and mutations. These features are fundamental elements to comprehend historical phenomena; the latter cannot be simplified to philosophical, sociological, or historical concept. History is a science which has this particularity that the physical reality of phenomena has a human dimension. As a consequence, it is essential not to lose touch with the human aspect of history when one pursues studies and intellectual activities on a historical phenomenon.
We decided to take a route opposite to the one taken by many historians. We have first identified influential people from different epochs before entering into concepts analysis. Thanks to this compilation of radical leaders, a new and fresh look to the understanding of radicalism was possible. Of course, we were not the first one to have studied them, but we ordered them following a chronology, like Plutarch enjoyed juxtaposing Greeks and Romans historical figures. Thanks to this technique we wanted to highlight the features of the radical leaders’ speeches, personalities and epochs, but also their differences. At last, we tried to draw the outlines and the heart of different radical movements in order to follow the ways that led to radicalism. We do not pretend to have offered an original and exclusive definition of radicalism, we mainly wanted to understand the nature of what defines somebody as a radical and explain the reasons why thousands of people decided to believe in this man. Moreover, we wanted to distance ourselves from the ideological debate of the Cold War which permeated also the interpretation of past events. Too often, the history of radicalism was either narrated with a form of revolutionary nostalgia or in order to praise the merits of liberalism.
If the great mass meetings ends in the mid-nineteenth-century with the fall of Chartism, this practice spread out in the whole world in the twentieth-century. Incidentally, the Arab Spring of the beginning of the twenty-first-century demonstrated that a popular platform was the best way for the people to claim their rights and destabilize a political system which they found too authoritative. Through protest the people express an essential quality of revolt, which is an expression of emancipation from fear. From then on, a despotic regime loses this psychological terror which helped it to maintain itself into power. The balance of power between the government and its people would also take a new turn. The radicals won this psychological victory more than 150 years ago and yet universal suffrage was obtained only a century later. From the acceptance of the principles of liberties to their cultural practice, a long route has to be taken to change people’s mind. It is a wearisome struggle for the most vulnerable people. In the light of western history, fundamental liberties must be constantly defended. Paradoxically, revolt is an essential and constitutive element of the maintenance of democracy.