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As an integral part of ALICE, the dedicated heavy ion experiment at CERN’s Large Hadron Collider, the Transition Radiation Detector (TRD) contributes to the experiment’s tracking, triggering and particle identification. Central element in the TRD’s processing chain is its trigger and readout processor, the Global Tracking Unit (GTU). The GTU implements fast triggers on various signatures, which rely on the reconstruction of up to 20 000 particle track segments to global tracks, and performs the buffering and processing of event raw data as part of a complex detector readout tree.
The high data rates the system has to handle and its dual use as trigger and readout processor with shared resources and interwoven processing paths require the GTU to be a unique, high-performance parallel processing system. To achieve high data taking efficiency, all elements of the GTU are optimized for high running stability and low dead time.
The solutions presented in this thesis for the handling of readout data in the GTU, from the initial reception to the final assembly and transmission to the High-Level Trigger computer farm, address all these aspects. The presented concepts employ multi-event buffering, in-stream data processing, extensive embedded diagnostics, and advanced features of modern FPGAs to build a robust high-performance system that can conduct the high- bandwidth readout of the TRD with maximum stability and minimized dead time. The work summarized here not only includes the complete process from the conceptual layout of the multi-event data handling and segment control, but also its implementation, simulation, verification, operation and commissioning. It also covers the system upgrade for the second data taking period and presents an analysis of the actual system performance.
The presented design of the GTU’s input stage, which is comprised of 90 FPGA-based nodes, is built to support multi-event buffering for the data received from the 18 TRD supermodules on 1080 optical links at the full sender aggregate net bandwidth of 2.16 Tbit/s. With careful design of the control logic and the overall data path, the readout on the 18 concentrator nodes of the supermodule stage can utilize an effective aggregate output bandwidth of initially 3.33 GiB/s, and, after the successful readout bandwidth upgrade, 6.50 GiB/s via 18 optical links. The high possible readout link utilization of more than 99 % and the intermediate buffering of events on the GTU helps to keep the dead time associated with the local event building and readout typically below 10%. The GTU has been used for production data taking since start-up of the experiment and ever since performs the event buffering, local event building and readout for the TRD in a correct, efficient and highly dependable fashion.
Compact objects - black holes and neutron stars - are fascinating objects, not only for the astrophysicists, but for a wide range of researchers, including astronomers, theoretical physicists, particle and nuclear physicists, condensed matter physicists and arguably for the layman as well.
First theorized in the first part of the twentieth century, for a long time these objects have been considered just exotic ideas or mathematical curiosities. Pulsar were however detected in the late 1960s and readily identified as rotating, radiating neutron stars, while the first candidate black hole, Cygnus X-1, was observed in 1972. Since then the interest in these objects has steadily grown.
The reasons behind this interest are easily understood considering that compact object dwell at the intersection of many different areas of physics, and are ideal laboratories to explore the interplay between these areas.
Black holes, which are purely gravitational objects, are perfectly suited to study the nature of gravity, its manifestations such as gravitational waves, and the differences between various theories of gravity in the regime where they are expected to be most relevant, i.e. the strong field regime. However, just like any massive astrophysical object, black holes are interested by accretion phenomena, which are thought to be the power source of some very bright astrophysical emitters of electromagnetic signals, such as active galactic nuclei or X-ray binaries.
At the same time, black holes exist in a variety of different mass scales, from stellar mass to supermassive black holes billions of times heavier. The latter play a very important and yet not fully understood role in the formation and evolution of galaxies, as well as in shaping the large scale structure of the universe, making them relevant to cosmology as well.
Neutron stars share with black holes the characteristic of being gravitationally dominated systems; but because they are composed of baryon matter, they display a much richer behaviour. It has been realized early on that the matter in neutron star cores reaches extreme densities, exceeding the one in atomic nuclei. This means that neutron stars could provide invaluable information on the behaviour of matter in such extreme conditions (which are impossible to achieve in laboratory experiments), such as details of the nucleonic interaction, the properties of hyperons or of quark-gluon plasmas.
...
The mission of the Compressed Baryonic Matter (CBM) experiment is to investigate the phase diagram of strongly interacting matter in the region of high net-baryon densities and moderate temperatures. According to various transport models, matter densities of more than 5 times saturation density can be reached in collisions between gold nuclei at beam energies between 5 and 11 GeV per nucleon, which will be available at FAIR. The core detector of the CBM experiment is the Silicon Tracking System (STS), which is used to measure the tracks of up to 700 particles per collision with high efficiency (>95%) and good momentum resolution (<1.5%). The technological and experimental challenge is to realize a detector system with very low material budget, in order to reduce multiple scattering of the particles, and a free-streaming data readout chain, in order to achieve reaction rates up to 10 MHz together with an online event reconstruction and selection.
The STS comprises 8 tracking stations positioned between 30 cm and 100 cm downstream the target inside a magnetic field, covering polar emission angles up to 25 degrees. A station consists of vertical structures with increasing number (between 8 and 16, depending on station number), each structure carrying between 2 and 10 double-sided microstrip silicon sensors, which are connected through low-mass microcables to the readout electronics placed at the detector periphery outside the active detector area.
The work presented in this thesis focuses on the detector performance simulation and local hit pattern reconstruction in the STS. For efficient detector design and reconstruction performance, a reliable detector response model is of utmost importance. Within this work, a realistic detector response model was designed and implemented in the CBM software framework. The model includes non-uniform energy loss of an incident particle within a sensor, electric field of a planar p-n junction, Lorentz shift of the charge carriers, their diffusion, and the influence of parasitic capacitances. The developed model has been verified with experimental data from detector tests in a relativistic proton beam. Cluster size distributions at different beam incident angles are sensitive to charge sharing effects and were chosen as an observable for the verification. Taking into account parasitic capacitances further improves the agreement with measured data.
Using the developed detector response model, the cluster position finding algorithm was improved. For two-strip clusters, a new, unbiased algorithm has been developed, which gives smaller residuals than the Centre-Of-Gravity algorithm. For larger clusters, the head-tail algorithm is used as the default one. For an estimate of the track parameters, the Kalman Filter based track fit requires not only hit positions but their uncertainties as an input. A new analytic method to estimate the hit position errors has been designed in this work. It requires as input neither measured spatial resolution nor information about an incident particle track. The method includes all the sources of uncertainties independently, namely: the cluster position finding algorithm itself, the non-uniform energy loss of incident particles, the electronics noise, and the discretisation of charge in the readout chip.
The verification with simulations shows improvements in hit and track pull distributions as well as x²-distributions in comparison to the previous simple approach. The analytic method improves the track parameters reconstruction by 5-10%.
Several STS module prototypes have been tested in a relativistic proton beam. A signal to-noise ratio was obtained at the level of 10-15 for modules made of 30 cm long microcable and of either one or two 6.2 x 6.2 cm² CiS sensors.
First simulations have shown that this signal-to-noise ratio is sufficient to reach the required efficiency and momentum resolution. The high-radiation environment of CBM operation will deteriorate the sensor performance. Radiation hardness of sensors has been studied in the beam with sensors irradiated to 2 x 10[hoch 14] 1MeV [neq/cm²], twice the lifetime dose expected for CBM operation. Charge collection efficiency drops by 17-25%, and simultaneously noise levels increase 1.5-1.75 times. The simulations show that if all sensors in the STS setup are exposed to such a fluence uniformly, the track reconstruction efficiency drops from 95.5% to 93.2% and the momentum resolution degrades from 1.6% to 1.7%.
The continuous conversion of natural wildlife habitats into agricultural areas, as well as the fragmentation of the last wildlife refuges, is increasing the interface between people and wildlife. When wildlife negatively impacts on people and vice versa, we speak about human-wildlife conflicts (HWCs). This definition includes losses on both sides and takes into consideration the rooting of most of these conflicts between different groups of interest, such as advocates for nature conservation and economic groups. The centres of highest biodiversity are located in developing countries, which are also characterized by poverty. In African and Asian countries, people living in the vicinity of national parks and other conservation areas mostly receive only little support through the government or conservation organisations. Especially for those people who are dependent on agriculture, damage to fields and harvests can have catastrophic consequences. If the species causing damage is protected by national or even international law, the farmer is not allowed to use lethal methods, but has to approach the authority in charge. If this agency, however, cannot offer appropriate support, resentment, anger or even hate develops, and the support for wildlife conservation activities declines. For this reason, HWCs were declared as one of the most important conservation topics today, being particularly relevant for large and threatened species such as the African and Asian elephant, hippopotamus and the greater one-horned rhino, as well as for large predators. Up to today, no general assessment scheme has been recommended for damage caused by protected wildlife species.
In my study, HWCs in Asia and Africa are compared, focussing on all herbivorous species identified which damaged crops. For the French NGO Awely, des animaux et des hommes, I developed a detailed assessment scheme suitable for all terrestrial ecosystems, and any type of HWCs and any species (Chapter 2). This HWC assessment scheme was used in four different study areas located in two African countries (South Luangwa/Zambia (SL), Tarangire/Tanzania (TA)) and two Asian countries (Bardia/Nepal (BA) and Manas/India (MA)). This scheme ran for six consecutive years (2009 to 2014) for Zambia, Nepal and India and two years (2010 to 2011) for Tanzania. To carry out the assessments, I trained local HWC officers (Awely Red Caps) to assess HWCs by field observations (measurement of damage, identification of species through signs of presence, landscape attributes etc.) and interviews with aggrieved parties (socio economic data). Results of this assessment are presented in Chapters 2-4.
To determine whether elephants prefer or avoid specific crop species, two field experiments were carried out, one in SL and one in BA (Chapter 5 and 6). For this, two test plots were set up and damage by elephants (and other herbivores) were quantified.
Within this doctoral thesis, 3306 damage events of 7408 aggrieved parties were analysed. In three out of the four study areas (SL, BA, MA), elephants caused the highest number of damage events compared to all other wildlife species, however, in TA, most fields were damaged by zebra. Furthermore, the greater one-horned rhino, hippopotamus, wild boar, bushpig, deer and antelope, as well as primates, caused damage to fields and harvests. Damage to houses and other property were nearly exclusively caused by elephants.
With this doctoral thesis I was able to show that season, crop availability, type and the phenological stage of the crop played an important role for crop damaging behavior of herbivores (Chapter 2). Elephants especially damaged rice, maize and wheat and preferred all crop types in a mature stage of growth. In contrast, rhinos preferred wheat to rice and similar to antelope and deer, they preferred crops at earlier stages of growth, before ripening. Crop damage by wildlife species varied strongly in size; most damages fell below 40% of the total harvest per farmer, but in several cases (3 to 8% depending on the study area), harvests were completely destroyed. Interestingly, during times of low nutritional availability in the natural habitat (dry season), crop damages in all four study areas were significantly less than during other seasons.
In all four study areas, crop protection strategies, such as active guarding in the fields, chasing wildlife with noise or fire torches or erecting barriers, were used. In some cases protection strategies were combined. Analysis of data revealed that traditional protection strategies did not reduce the costs of damage (Chapter 3). In some cases, costs of damage, on protected fields were even higher than for unprotected fields. Only in MA did strategic and cohesive guarding significantly reduce crop damage by wildlife species.
Besides damage in the fields, elephants also caused damage to properties in the villages. In search for stored staple crops, they damaged houses, grain stores and kitchens. Such damage was analysed in three study areas (SL, BA, MA) (Chapter 4). Although property damage occurred less frequently compared to crop damage in the fields, the mean cost of this damage was found to be double in BA/MA and four times higher in SL, compared to the costs of crop damage in the fields. It is further remarkable that property damage significantly increased towards the dry season, when the harvest was brought into the villages.
The findings of this study underpin the assumption that wildlife herbivores, especially elephants, are lured to fields and crops because the highly nutritional food (crop) being readily available. Traditional crop protection is cost and labour intensive and does not reduce the costs of damage. For this reason, crop types, which are thought to be not consumed by elephants were systematically tested on their attractiveness in field experiments in SL and BA (Chapter 5 and 6). In SL, lemon grass, ginger and garlic were proven to be less attractive to African elephants than maize and in BA, basil, turmeric, chamomile, coriander, mint, citronella and lemon grass were found to be less attractive to Asian elephants than rice.
The results of this doctoral thesis are relevant for the management of wildlife conservation as they can lead to new approaches to the mitigation of HWCs in African and Asian countries. Finally, specific needs for more scientific research in this field have been identified.
Most of the elements in the universe are produced via charged-particle fusion reactions during the primordial nucleosynthesis and different stellar burning stages, as well as via neutron-capture reactions. Around 35 heavy, proton-rich isotopes are bypassed by those reaction paths, the p nuclei. A series of photo-disintegration reactions occurring in supernovae, called the γ process, was suggested as a mechanisms to produce the p nuclei. Numerical simulations of the γ process have been unable to reproduce the observed abundances of the light p isotopes. Recent models showed that a series of proton capture reactions could provide the observed abundances. Hence, the cross sections of the crucial capture reactions have to be measured in order to test those assumptions.
Radiative proton captures in addition to the γ-process could reproduce the observed abundance pattern. This thesis presents preparations of a proton capture measurement on the radioactive 91Nb in standard kinematics with a calorimetric 4π setup. The 91Nb(p,γ)92Mo reaction might be the key to explain the production of one of the most abundant p-nuclei, 92Mo. So far, no experimental data for this reaction is available.
We produced a sample of 91Nb, with a half-life of 680 yr, at the Physikalisch Technische Bundesanstalt in Braunschweig, Germany, by irradiating 92Mo with protons in the energy range of 12 – 20MeV. 91Nb was produced via the reaction 92Mo(p,2p)91Nb and via 92Mo(p,pn)91Mo, where 91Mo decays to 91Nb with a half-life of 15.5min. To predict the amount of produced 91Nb the cross section of 92Mo(p, 2p) was measured. It was found to be higher than the value given by theoretical calculations with TALYS. Finally, 91Nb was chemically separated from the molybdenum carried at Paul-Scherrer- Institut, Villigen, Switzerland.
In-beam total absorption cross-section measurement of the reaction 91Nb(p,γ)92Mo with 2 MeV protons at FRANZ is planed with the produced 91Nb. A 4π BaF2 detector consisting of 41 crystals will be used. During this experiment we will measure the sum energy and the multiplicity of each event. The freshly produced 91Nb constitutes only a minor component of the sample material. The sum energy and multiplicity are crucial to distinguish the desired 91Nb(p,γ) from all the other more dominant reactions. The expected multiplicity and the efficiency of the setup were carefully simulated with DICEBOX and GEANT4. It was possible to show that background reactions can be effectively suppressed. The most important background contributions could be identified and result from 92Mo(p,γ), 19F(p,γ), and 19F(p,α).
In this work the flexibility requirements of a highly renewable European electricity network that has to cover fluctuations of wind and solar power generation on different temporal and spatial scales are studied. Cost optimal ways to do so are analysed that include optimal distribution of the infrastructure, large scale transmission, storage, and dispatchable generators. In order to examine these issues, a model of increasing sophistication is built, first considering different flexibility classes of conventional generation, then adding storage, before finally considering transmission to see the effects of each.
To conclude, in this work it was shown that slowly flexible base load generators can only be used in energy systems with renewable shares of less than 50%, independent of the expansion of an interconnecting transmission network within Europe. Furthermore, for a system with a dominant fraction of renewable generation, highly flexible generators are essentially the only necessary class of backup generators. The total backup capacity can only be decreased significantly if interconnecting transmission is allowed, clearly favouring a European-wide energy network. These results are independent of the complexity level of the cost assumptions used for the models. The use of storage technologies allows to reduce the required conventional backup capacity further. This highlights the importance of including additional technologies into the energy system that provide flexibility to balance fluctuations caused by the renewable energy sources. These technologies could for example be advanced energy storage systems, interconnecting transmission in the electricity network, and hydro power plants.
It was demonstrated that a cost optimal European electricity system with almost 100% renewable generation can have total system costs comparable to today's system cost. However, this requires a very large transmission grid expansion to nine times the line volume of the present-day system. Limiting transmission increases the system cost by up to a third, however, a compromise grid with four times today's line volume already locks in most of the cost benefits. Therefore, it is very clear that by increasing the pan-European network connectivity, a cost efficient inclusion of renewable energies can be achieved, which is strongly needed to reach current climate change prevention goals.
It was also shown that a similarly cost efficient, highly renewable European electricity system can be achieved that considers a wide range of additional policy constraints and plausible changes of economic parameters.
After entorhinal deafferentiation of the hippocampal dentate gyrus a reinnervation of the denervated neurons by axon collaterals can be observed. This process takes place in a matter of weeks. However, the overall functional effect on the hippocampal network is still unclear.
In an effort to investigate this effect of axonal sprouting on the neuronal network of the dentate gyrus we compared the electrophysiological response of the dentate gyrus after electric stimulation in wild-type mice (WT mice) with a normal post-lesion sprouting, with genetically modified mice with an overexpression of the growth-protein CAP23 (cytoskeleton-associated protein 23). CAP23 overexpressing mice (CAP23tg mice) are known to have an enhanced axonal growth and sprouting after lesion.
The mice (both the WT as well as the CAP23tg mice) were deeply anesthetized and a lesion of the perforant path was induced stereotactically with a wire knife. After that the mice were permitted to survive for 4-6 weeks for partial reinnervation of the dentate gyrus before they were again operated and evoked potentials were measured (extracellular recordings of evoked potentials in the dentate gyrus). Non-lesioned litter-mate mice were taken as reference. The sprouting and the correct position of the electrodes was confirmed histologically.
For electrophysiological investigation we assessed laminar profiles and calculated a current-source density (CSD). In lesioned CAP23tg mice compared to lesioned WT mice this CSD-analysis revealed a significant enhancement of the current sink in the area of deafferentiation (outer molecular layer) and a significant excitation in the granule-cell layer.
Our results show that axonal sprouting seems to enhance the excitability of granule-cells. Thus, even if an enhanced axonal sprouting might accelerate the reinnervation of denervated dendrites after lesion, but it also leads to posttraumatic hyperexcitability of the neuronal network. In a therapeutic approach of fascilitating axonal sprouting this hyperexcitability has to be taken into consideration.
This thesis investigates second-order relativistic hydrodynamics and transport coefficients in strongly correlated systems. Our focus is mainly on the physical conditions relevant to heavy-ion collisions, as well as compact dense stellar objects at nonzero temperatures and in strong magnetic fields.
Chapter 1 provides a brief introduction to the area of research covered by this thesis, specifically relativistic hydrodynamics and transport in hot and dense media, which occur in heavy-ion collisions and heated stellar matter.
In Chapter 2 we give a new formulation of second-order dissipative hydrodynamics for relativistic systems using Zubarev's non-equilibrium statistical operator approach. We first solve the quantum Liouville equation with an infinitesimal source term to construct a non-equilibrium statistical operator which is a non-local functional of the thermodynamic parameters and their space-time gradients. Exploiting then the gradient expansion of the statistical operator we derive transport equations for the shear stress tensor, the bulk viscous pressure and the flavour diffusion currents up to the second order in hydrodynamic gradients.
We show that the second-order corrections to the dissipative fluxes arise from (i) the quadratic terms of the Taylor expansion of the statistical operator; and (ii) the linear terms which are nonlocal in space and time. These non-local corrections generate finite relaxation time scales in the evolution of the dissipative quantities. We derive the most generic form of the transport equations which involve gradients of the dissipative fluxes, as well as products of two first-order quantities (i.e., either thermodynamic forces or dissipative fluxes). We then go on to express the first- and the second-order transport coefficients, which appear in these equations, via certain two- and three-point equilibrium correlation functions. Finally, we express the relaxation times for the dissipative fluxes via the frequency-derivatives of the corresponding first-order transport coefficients.
In Chapter 3 we compute the transport coefficients of quark matter in the strong coupling regime within the two-flavor Nambu-Jona-Lasinio model. We apply the Kubo-Zubarev formalism to obtain the thermal and the electrical conductivities as well as the shear and the bulk viscosities by evaluating the corresponding equilibrium two-point correlation functions at the leading order in the 1/N_c expansion. In this approximation the conductivities and the shear viscosity are given by single-loop skeleton diagrams, whereas the bulk viscosity includes an infinite geometrical series of multi-loop diagrams. The dispersive effects that lead to nonzero transport coefficients arise from quark-meson fluctuations above the Mott transition temperature T_M, where meson decay into two on-mass-shell quarks is kinematically allowed.
We find that the conductivities and the shear viscosity are decreasing functions of temperature and density above T_M. We also show that the Wiedemann-Franz law does not hold. The ratio of the shear viscosity to the entropy density is larger than unity close to the Mott temperature and approaches the AdS/CFT bound at higher temperatures. We conjecture on the basis of the uncertainty principle that the ratio of the thermal conductivity to the heat capacity per unit volume is bounded from below by 1/18.
The case of the bulk viscosity turns out to be special, because the multi-loop contributions dominate the single-loop contribution close to the Mott line in the case where the chiral symmetry is explicitly broken. We find that in this case only at high temperatures the one-loop contribution becomes dominant. The resulting bulk viscosity exceeds the shear viscosity close to the Mott temperature by factors 5-20 when multi-loop contributions are included. In the high-temperature domain the bulk viscosity is negligible compared to the shear viscosity. For practical applications we provide simple, but accurate fits to the transport coefficients, which can facilitate the implementation of our results in hydrodynamics codes.
In Chapter 4 we compute the electrical conductivity of finite temperature, strongly magnetized crust of a compact star which may be formed in the aftermath of a supernova explosion, binary neutron star merger, or during accretion processes in X-ray binaries. We focus on the temperature-density regime where plasma is in the liquid state and, therefore, the conductivity is dominated by the electron scattering off correlated nuclei. The dynamical screening of electron-ion interaction is implemented in terms of the polarization tensor computed in the hard-thermal-loop (HTL) effective field theory of QED plasma. The correlations of the background ionic component are accounted for via a structure factor derived from Monte Carlo simulations of one-component plasma.
With this input we solve the Boltzmann kinetic equation in relaxation time approximation taking into account the anisotropy of transport due to the magnetic field. The electrical conductivity tensor is studied numerically as a function of temperature, density, magnetic field and the crust composition in a broad parameter range. We find that the conductivity as a function of temperature attains a minimum at the transition from the degenerate to the nondegenerate regime of electrons. We also provide accurate fit formulas to our numerical results for three components of the conductivity tensor. In addition, we provide supplemental tables which can be used in dissipative magneto-hydrodynamics(MHD) simulations of warm compact stars.
We summarize our results and discuss the perspectives in Chapter 5.
The theory of strong interactions — Quantum Chromodynamics (QCD) — is well-defined mathematically. However, direct applications of this theory to experiment are rather limited due to significant technical obstacles. Even some general features of QCD remain unclear to date.
Hence, phenomenological input is important and needed for practical applications, e.g. for theoretical analysis of the heavy-ion collision experiments. In this thesis the role of hadronic interactions is studied in the hadron resonance gas (HRG) model — a popular model for the confined phase of QCD. The description of hadronic interactions is based on the famous van der Waals (VDW) equation and its quantum statistical generalization. While this is not the conventional choice for nuclear/hadronic physicspplications, the simplicity of the VDW approach makes it extremely useful.
In particular, this framework allows to include the two most basic ingredients of hadron-hadron interaction: the short-range repulsion, modeled by excluded-volume (EV) corrections, and the intermediate range attraction. The first part of the thesis considers just the repulsive EV interactions between hadrons. A hitherto unknown, but surprisingly strong sensitivity of the long known thermal fits to heavy-ion hadron yield data to the choice of hadron eigenvolumes is uncovered. It challenges the robustness of the chemical freeze-out temperature and baryochemical potential determination from the thermal fits. However, at the same time, the extracted value of the entropy per baryon is found to be a robust observable which depends weakly on this systematic uncertainty of the HRG model.
A Monte Carlo procedure to treat EV interactions in HRG is also introduced in this thesis. It allows to study simultaneous effects of EV and of exact charge conservation in HRG for the first time. Generalizations of the classical VDW equation are required for its applications in hadronic physics. he grand canonical ensemble (GCE) formulation of the classical VDW equation is presented. Remarkably, this important aspect of the VDW equation was not discovered before. The GCE formulation yields the analytic structure of the critical fluctuations, both in the vicinity of and far off the critical point. These critical fluctuations are presently actively being used as probes for the QCD critical point. Another extension is the hitherto undiscovered generalization of the VDW equation to include quantum Bose-Einstein and Fermi-Dirac statistics. It is performed for both single-component and multi-component fluids. The Fermi-Dirac VDW equation is applied for the first time. It is used to describe nucleons and basic properties of nuclear matter. The quantum statistical generalization of the VDW equation developed in this work is quite general, and can be applied for any fluid. Thus, its applications are not restricted to QCD physics, but may also find themselves in chemistry and/or industry. The quantum statistical VDW equation is used to describe baryonic interactions in full HRG. The VDW parameters $a$ and $b$ are fixed to the nuclear ground state and the predictions of the model are confronted with lattice QCD calculations. The inclusion of baryonic interactions leads to a qualitatively different behavior of the fluctuations of conserved charges in the crossover region. In many cases it resembles the lattice data. These results suggest that hadrons do not melt quickly with increasing temperature, as one could conclude on the basis of the common simple ideal HRG model. Calculations at finite chemical potentials show that the nuclear liquid-gas transition manifests itself by non-trivial fluctuations of the net baryon number in heavy ion collisions. In the final part of the thesis the pure glue initial scenario for high-energy hadron and heavy-ion collisions is explored. This scenario is shown not to spoil the existing agreement of the hadronic and electromagnetic observables description in Pb+Pb collisions at energies available at the CERN Large Hadron Collider. Hydrodynamic calculations suggest that collisions of small-sized nuclei at lower collision energies available at the BNL Relativistic Heavy Ion Collider are promising in the search for the traces of the chemically non-equilibrium gluon-dominated phase transition.
G-protein coupled receptors (GPCRs) are a predominant class of cell-surface receptors in eukaryotic life. They are responsible for the perception of a broad range of ligands and involved in a multitude of physiological functions. GPCRs are therefore of crucial interest for biological and pharmaceutical research. Molecular analysis and functional characterisation of GPCRs is frequently hampered by challenges in efficient large-scale production, non-destructive purification and long-term stability. Cell-free protein synthesis (CFPS) provides new production platforms for GPCRs by extracting the protein synthesis machinery of the cell in an open system that allows target-oriented modulations of the synthesis process and direct access to the nascent polypeptide chain. CFPS is fast, reliable and highly adaptable. Unfortunately, highly productive cell-free synthesis of GPCRs is often opposed by low product quality. This thesis was aimed to adapt and improve some of the new possibilities for the cell-free production of GPCRs in high yield and quality for structural and pharmaceutical analysis. An E. coli based CFPS system was applied to synthesise various turkey and human Beta-adrenergic receptor (Beta1AR) derivatives as well as human Endothelin receptors type A and B (ETA and ETB) constructs. Both receptor families are important drug targets and pharmacologically addressed in the treatment of several cardiovascular diseases. CF-synthesis was mainly performed in presence of nanodiscs (ND), which are reconstituted high density lipoprotein particles forming discoidal bilayer patches with a diameter varyring from 6 to approx. 15 nm. The supplementation of ND in the CF-synthesis reaction caused the co-translational solubilisation of the freshly synthesised GPCRs. The fraction of the solubilised GPCR that was correctly folded was analysed by the competence to bind its ligand alprenolol or Endothelin-1, respectively. Both the solubilisation efficiency and the ability to fold in a ligand binding competent state was strongly affected by the lipid composition of the supplied ND. Best results were generally achieved with lipids having phosphoglycerol headgroups and unsaturated fatty acid chains with 18 carbon atoms. Furthermore, thermostabilisation by introduction of point mutations had a large positive impact on the folding efficiency of both Beta1AR and ETB receptor. Formation of a conserved disulphide bridge in the extracellular region was additionally found to be crucial for the function of the ETB receptor. Disulphide bridge formation could be enhanced by applying a glutathione-based redox system in the CFPS. Further improvements in the quality of ETB receptor could be made by the enrichment of heat-shock chaperones in the CF-reaction. Depending on the receptor type and DNA-template, roughly 10 – 30 nmol (350 – 1500 µg) of protein could be synthesised in 1 ml of CF-reaction mixture. After the applied optimisation steps, the fractions of correctly folded receptor could be improved by several orders of magnitude and were finally in between 35% for the thermostabilised turkey Beta1AR, 9% for the thermostabilised ETB receptor, 6.5% for the non-stabilised ETB receptor, 1 - 5% for non-stabilised turkey Beta1AR and for human Beta1AR isoforms and 0.1% for ETA receptor. Therefore, between 2 and 120 µg of GPCR could be synthesised in a ligand binding competent form, depending on the receptor and its modifications. Correctly folded turkey Beta1AR and ETB receptors were thermostable at 30°C and could be stored at 4°C for several weeks after purification. Yields of the thermostabilised turkey Beta1AR were sufficient to purify the receptor in a two-step process by ligand-binding chromatography to obtain pure and correctly folded receptor in the lipid bilayer of a ND. Furthermore, a lipid dependent ligand screen could be demonstrated with the turkey Beta1AR and significant alterations in binding affinities to currently in-use pharmaceuticals were found. The established protocols are therefore suitable and highly competetive for a variety of applications such as screening of GPCR ligands, analysis of lipid effects on GPCR function or for the systematical biochemical characterisation of GPCRs. Most promising for future approaches appears to address the suspected bottlenecks of intial insertion of the GPCR-polypeptide chain in the ND bilayer and the thermal stability of the receptors. Nevertheless, the estabilised protocols for the analysed targets in this thesis are already highly competitive to previously published production protocols either in cell-based or cell-free systems with regard to yield of functional protein, speediness and costs. Moreover, the direct accessibility and other general characteristics of cell-free synthesis open a large variety of possible applications and this work can therefore contribute to the molecular characterisation of this important receptor type and to the development of new pharmaceuticals.