The Sedimentology, Ichnology and Hydrogeochemistry of the Late Miocene, Marginal Marine, Upper Pebas and Nauta Formations, Amazonian Foreland Basin, Peru

This thesis includes detailed sedimentological and ichnological studies on two geological units: the Pebas Formation, with a special focus in its informal upper member, and the Nauta Formation. Both formations were deposited during the Miocene in Northeastern Peruvian Amazonia, in the Amazon retroarc foreland basin. The Pebas and Nauta successions mainly consist of non-consolidated, clastic sedimentary deposits arranged into sand- to mud-dominated heterolithic successions, which can be upward-coarsening to upward-fining. Sediments in both the Pebas and Nauta successions range from mud to fine- to medium-grained sand. The main facies observed were 1) mud-dominated horizontal heterolithic couplets; 2) rooted brownish mud; 3) lenticular, mud-draped, cross-stratified sand; 4) mud- to sand-dominated, inclined heterolithic stratification; 5) sand-dominated horizontal heterolithic couplets; and 6) mud-draped, trough cross-stratified sand. Locally, tidal rhythmites were documented. The facies are interpreted as: 1) muddy, shallow, subaqueous flats/shoals; 2) palaeosols; 3) secondary tidal channels or run-off creeks; 4) tidally influenced point bars; 5) shoreface deposits; and 6) subtidal compound dunes. Thalassinoides-dominated Glossifungites ichnofacies, low-diversity expressions of the Skolithos ichnofacies and depauperate suites consisting of elements common to the Cruziana ichnofacies strongly indicate brackish-water conditions. However, continental trace fossil assemblages, with possible elements common to the Scoyenia ichnofacies, have also been identified. In addition to the palaeoenvironmental study, a local hydrogeochemical characterisation of the Pebas and Nauta formations was also conducted. The geochemistry of the groundwaters reflects the characteristics and the soil geochemistry of the geological formations studied. The Pebas formation has low hardness, acid to neutral waters, whereas the upper Pebas has high hardness, acid to neutral waters. In both units, the arsenic content is locally high. The Nauta formation has low hardness acid groundwaters. A regional review of the Pebas and Nauta formations placed the local observations into a continental perspective and suggests that the whole Pebas-Nauta system was a probably shallow (some tens of metres at maximum), brackish- to freshwater, tidally-influenced epicontinental embayment with a probable semi-diurnal to mixed tidal regime and a microtidal range, surrounded by continental environments such as forest floors, lagoons, rivers and their flood plains, and lakes.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Modelling Long-Run Relationship between Spot and Future Prices of Different Commodities

The purpose of this study is to investigate whether there exists any kind of relationship between the spot and future prices of the different commodities or not. Commodities like cocoa, coffee, crude oil, gold, natural gas and silver are considered from January 3, 2000 to December 31, 2012. For this purpose, ADF test and KPSS test are used in testing the stationarity whereas Johansen Cointegration test is used in testing the long-run relationship. Johansen co-integration test exhibits that there at least 5 co-integrating pairs out of 6 except crude oil. Moreover, the result of Granger Causality supports the fact that if two or more than two time series tend to be co-integrated there exists either uni-directional or bi-directional relationship. However, our results reveled that although there exists the co-integration between the variable, one might not granger causes another .VAR model is also used to measure the proportion of effects. These findings will help the derivative market and arbitragers in developing the strategies to gain the maximum profit in the financial market.