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Starting from a classical picture of shear viscosity we construct a steady velocity gradient in the partonic cascade BAMPS. Using the Navier-Stokes-equation we calculate the shear viscosity coefficient. For elastic isotropic scatterings we find a very good agreement with the analytic values. For both elastic and inelastic scatterings with pQCD cross sections we find good agreement with previously published calculations.
The goal of this project is to develop a framework for a cell that takes in consideration its internal structure, using an agent-based approach. In this framework, a cell was simulated as many sub-particles interacting to each other. This sub-particles can, in principle, represent any internal structure from the cell (organelles, etc). In the model discussed here, two types of sub-particles were used: membrane sub-particles and cytosolic elements. A kinetic and dynamic Delaunay triangulation was used in order to define the neighborhood relations between the sub-particles. However, it was soon noted that the relations defined by the Delaunay triangulation were not suitable to define the interactions between membrane sub-particles. The cell membrane is a lipid bilayer, and does not present any long range interactions between their sub-particles. This means that the membrane particles should not be able to interact in a long range. Instead, their interactions should be confined to the two-dimensional surface supposedly formed by the membrane. A method to select, from the original three-dimensional triangulations, connections restricted to the two-dimensional surface formed by the cell membrane was then developed. The algorithm uses as starting point the three-dimensional Delaunay triangulation involving both internal and membrane sub-particles. From this triangulation, only the subset of connections between membrane sub-particles was considered. Since the cell is full of internal particles, the collection of the membrane particles' connections will resemble the surface to be obtained, even though it will still have many connections that do not belong to the restricted triangulation on the surface. This "thick surface" was called a quasi-surface. The following step was to refine the quasi-surface, cutting out some of the connections so that the ones left made a proper surface triangulation with the membrane points. For that, the quasi-surface was separated in clusters. Clusters are defined as areas on the quasi-surface that are not yet properly triangulated on a two-dimensional surface. Each of the clusters was then re-triangulated independently, using re-triangulation methods also developed during this work. The interactions between cytosolic elements was given by a Lennard-Jones potential, as well as the interactions between cytosolic elements and membrane particles. Between only membrane particles, the interactions were given by an elastic interaction. For each particle, the equation of motion was written. The algorithm chosen to solve the equations of motion was the Verlet algorithm. Since the cytosol can be approximated as a gel, it is reasonable to suppose that the sub-cellular particles are moving in an overdamped environment. Therefore, an overdamped approximation was used for all interactions. Additionally, an adaptive algorithm was used in order to define the size of the time step used in each interaction. After the method to re-triangulate the membrane points was implemented, the time needed to re-triangulate a single cluster was studied, followed by an analysis on how the time needed to re-triangulate each point in a cluster varied with the cluster size. The frequency of appearance for each cluster size was also compared, as this information is necessary to guarantee that the total time needed by to re-triangulate a cell is convergent. At last, the total time spent re-triangulating a surface was plotted, as well as a scaling for the total re-triangulation time with the variation. Even though there is still a lot to be done, the work presented here is an important step on the way to the main goal of this project: to create an agent-based framework that not only allows the simulation of any sub-cellular structure of interest but also provides meaningful interaction relations to particles belonging to the cell membrane.
In this paper we discuss experimental evidence related to the structure and origin of the bosonic spectral function alpha 2F (omega) in high-temperature superconducting (HTSC) cuprates at and near optimal doping. Global properties of alpha 2F (omega), such as number and positions of peaks, are extracted by combining optics, neutron scattering, ARPES and tunnelling measurements. These methods give evidence for strong electron-phonon interaction (EPI) with 1<lambda ep <~ 3.5 in cuprates near optimal doping. We clarify how these results are in favor of the modified Migdal-Eliashberg (ME) theory for HTSC cuprates near optimal doping. In Section 2 we discuss theoretical ingredients—such as strong EPI, strong correlations—which are necessary to explain the mechanism of d-wave pairing in optimally doped cuprates. These comprise the ME theory for EPI in strongly correlated systems which give rise to the forward scattering peak. The latter is supported by the long-range part of EPI due to the weakly screened Madelung interaction in the ionic-metallic structure of layered HTSC cuprates. In this approach EPI is responsible for the strength of pairing while the residual Coulomb interaction and spin fluctuations trigger the d-wave pairing.
In the present work, the problem of protein folding is addressed from the point of view of equilibrium thermodynamics. The conformation of a globular protein in solution at common temperatures is quite complicated without any geometrical symmetry, but it is an ordered state in the sense of its biological activity. This complicated conformation of a single protein molecule is destroyed upon increasing the temperature or by the addition of appropriate chemical agents, as is revealed by the loss of its activity and change of the physical properties, and so on. Once the complicated native structures having biological activity are lost, it would be natural to suppose that the native structure could hardly be restored. Nevertheless, pioneers, such as Anson and Mirsky, recognized as early as in 1925 that this was not always the case. If one defines the folded and unfolded states of a protein as two distinct phases of a system, then under the variation of temperature the system is transformed from one phase state into another and vice versa. The process of protein folding is accompanied by the release or absorption of a certain amount of energy, corresponding to the first-oder-type phase transitions in the bulk. Knowing the partition function of the system one can evaluate its energy and heat capacity under different temperatures. This task was performed in this work. The results of the developed statistical mechanics model were compared with the results of molecular dynamic simulations of alanine poylpeptides. In particular, the dependencies on temperature of the total energy of the system and heat capacity were compared for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. The good correspondence of the results of the theoretical model with the results of molecular dynamics simulations allowed to validate the assumptions made about the system and to establish the accuracy range of the theory. In order to perform the comparison of the results of theoretical model and the molecular dynamics simulations it is necessary to perform the efficient analysis of the results of molecular dynamics simulations. This task was also addressed in the present work. In particular, different ways to obtain dependence of the heat capacity on temperature from molecular dynamics simulations are discussed and the most efficient one is proposed. The present thesis reports the result of molecular dynamic simulations for not only alanine polypeptides by also for valine and leucine polypeptides. In valine and leucine polypeptides, it is also possible to observe the helix↔random coil transitions with the increase of temperature. The current thesis presents a work that starts with the investigation of the fundamental degrees of freedom in polypeptides that are responsible for the conformational transitions. Then this knowledge is applied for the statistical mechanics description of helix↔coil transitions in polypeptides. Finally, the theoretical formalism is generalized for the case of proteins in water environment and the comparison of the results of the statistical mechanics model with the experimental measurements of the heat capacity on temperature dependencies for two globular proteins is performed. The presented formalism is based on fundamental physical properties of the system and provides the possibility to describe the folding↔unfolding transitions quantitatively. The combination of these two facts is the major novelty of the presented approach in comparison to the existing ones. The “transparent” physical nature of the formalism provides a possibility to further apply it to a large variety of systems and processes. For instance, it can be used for investigation of the influence of the mutations in the proteins on their stability. This task is of primary importance for design of novel proteins and drug delivering molecules in medicine. It can provide further insights into the problem of protein aggregation and formation of amyloids. The problem of protein aggregation is closely associated with various illnesses such as Alzheimer and mad cow disease. With certain modifications, the presented theoretical method can be applied to the description of the protein crystallization process, which is important for the determination of the structure of proteins with X-Rays. There many other possible applications of the ideas described in the thesis. For instance, the similar formalism can be developed for the description of melting and unzipping of DNA, growth of nanotubes, formation of fullerenes, etc.
Clathrates are candidate materials for thermoelectric applications because of a number of unique properties. The clathrate I phases in the Ba-Ni-Ge ternary system allow controlled variation of the charge carrier concentration by adjusting the Ni content. Depending on the Ni content, the physical properties vary from metal-like to insulator-like and show a transition from p-type to n-type conduction. Here we present first results on the characterization of millimeter-sized single crystals grown by the Bridgman technique. Single crystals with a composition of Ba8Ni3.5Ge42.1h0.4 show metallic behavior (dp/dT > 0) albeit with high resistivity at room temperature [p (300 K) = 1 mOhm cm]. The charge carrier concentration at 300 K, as determined from Hall-effect measurements, is 2.3 e-/unit cell. The dimensionless thermoelectric figure of merit estimated at 680 K is ZT ~ 0.2. Keywords Clathrates - thermoelectric material - intermetallic compound - nickel
Nanocarbon structures, such as fullerenes and nanotubes, have generated considerable interest and research, due to their unique properties and potential applications. In this thesis, we present a study of the phase transition properties of nanocarbon clusters,in particular, we pay special consideration to fullerenes. The work presented in this thesis is largely theoretical and computational in nature, employing as a tool, molecular dynamics simulations to probe the dynamic stability of fullerenes and associated nanocarbon structures such as graphenes and nanotubes.
This work reports on the study of the projectile x-ray emission in relativistic ion-atom collisions. Excitation of K-shell in He-like uranium ions, electron capture into H-like uranium ions and Simultaneous ionization and excitation of initially He-like uranium ions have been studied using the experimental storage ring at GSI. Information about the population of the excited states for the H- and He-like uranium ions, can be obtained by measuring the angular distribution of the decay radiation. Since the Ly_alpha2 transition is isotropic, the intensities of the Ly_alpha1 and K_alpha transitions were normalized to the Ly_alpha2 line. For the K_alpha1 and K_alpha2 transitions originating from the excitation of the He-like uranium ions, no alignment was observed. In contrast, the Ly_alpha1 radiation from the simultaneous ionization-excitation process of the He-like uranium ions shows a clear alignment. It is shown that the alignment of Ly_alpha1 was obtained by the Alignment parameter A_20. The experimental value leads to the inclusion of a magnetic term in the interaction potential. It is interesting to note that in the case of the Ly_alpha1 emission the small M2 contribution added coherently to the E1 transition amplitudes enhances the anisotropy. The capture process of target electrons into the highly-charged heavy ions was studied using H-like uranium ions at an incident energy of 220 MeV/u, impinging on N2 gas-target. It was shown that, the strongly aligned electrons captured in 2p3/2 level will couple with the available 1s1/2 electron which shows no initial directional preference. The magnetic sub-state population of the 2p3/2 electron will be redistributed according to the coupling rules to the magnetic sub-states of the relevant two-electron states. Consequently, the 1^P1 and 3^P2 states are corresponding to the the strongly aligned 2p3/2 state. This leads to the large anisotropy in the corresponding individual ground state transitions contributing to the K_alpha1 emission. Due to the fact that the 1^P1 --> 1^S0 and 3^P2 --> 1^S0 transitions are experimentally not resolved, a more detailed analysis of the angular dependence of the K_alpha1 radiation is required. From the K_alpha1/K_alpha2 ratio, the current results show that the incoherent addition of the E1 and M2 transition components yield to an almost isotropic emission of the total K_alpha1. In contrast to the radiative electron capture, the experimental results for the K-shell single excitation of He-like uranium ions indicate that only the 1^P1 level contributes to the K_alpha1 transition. For this case, the anisotropy parameter beta_20 was found to be -0.20 + 0.03 which is similar to that one calculated for pure E1 transition. This work also reports on the study of a two-electron process: the simultaneous ionization and excitation occurring in relativistic collisions of heavy highly-charged ions with gaseous targets. The investigation was performed on He-like uranium ions impinging upon xenon gas-target at an incident energy of 220 MeV/u. The measurements have been performed at the ESR gas-target using atomic xenon with a typical area density of 10^12 particles/cm^2. In contrast to the solid state target, the use of gas target offers the advantage of clear separation of the one step two-electron process due to the fact that the probability of two consecutive collision in such thin targets is negligible and the double step processes can be excluded. During the process of simultaneous ionization and excitation in He-like uranium ions, one of the ground-state electrons is promoted into the continuum and the other into the L-subshell states of the projectile. To select this process, the Lyman-series radiation has been measured at various observation angles in coincidence with up-charged projectiles (U^91+). From the yields of the Ly_alpha1 and Ly_alpha2 projectile radiation, the relative cross section for the process of simultaneous ionization and excitation was directly determined. The angle dependent measurement of the radiation yields provide information about the angular distributions of the emitted radiation and permits the determination of the alignment parameter A_{20}. This parameter gives information on the level population and the collision impact parameter. The present results (b^exp = 810 fm) show that the simultaneous ionization and excitation is a process which occurs at small impact parameter.
Lattice simulation of a center symmetric three dimensional effective theory for SU(2) Yang-Mills
(2010)
We present lattice simulations of a center symmetric dimensionally reduced effective field theory for SU(2) Yang Mills which employ thermal Wilson lines and three-dimensional magnetic fields as fundamental degrees of freedom. The action is composed of a gauge invariant kinetic term, spatial gauge fields and a potential for the Wilson line which includes a "fuzzy" bag term to generate non-perturbative fluctuations between Z(2) degenerate ground states. The model is studied in the limit where the gauge fields are set to zero as well as the full model with gauge fields. We confirm that, at moderately weak coupling, the "fuzzy" bag term leads to eigenvalue repulsion in a finite region above the deconfining phase transition which shrinks in the extreme weak-coupling limit. A non-trivial Z(N) symmetric vacuum arises in the confined phase. The effective potential for the Polyakov loop in the theory with gauge fields is extracted from the simulations including all modes of the loop as well as for cooled configurations where the hard modes have been averaged out. The former is found to exhibit a non-analytic contribution while the latter can be described by a mean-field like ansatz with quadratic and quartic terms, plus a Vandermonde potential which depends upon the location within the phase diagram. Other results include the exact location of the phase boundary in the plane spanned by the coupling parameters, correlation lengths of several operators in the magnetic and electric sectors and the spatial string tension. We also present results from simulations of the full 4D Yang-Mills theory and attempt to make a qualitative comparison to the 3D effective theory.
In this thesis, we study the properties of excitations in the systems of interacting fermions. These excitations can be bosonic such as collective modes which we handle in the first part of this thesis or fermionic like quasi particles and quasi holes. One of the important points, to investigate the excitations is their damping which corresponds to their life-time in the system. This thesis consists of two parts, where in both parts, we use the field-theoretical methods to examine the problem.
Event-by-event fluctuations of the particle yield ratios in heavy-ion collisions at 20 - 158 AGeV
(2010)
Non-statistical event-by-event fluctuations are considered as an important signal for the critical endpoint of the QCD phase diagram. Event-by-event fluctuations of different observables are thus investigated in detail in current experiments but are also an important observable to be studied at the future CBM experiment at FAIR. In this work we present the energy and centrality dependence of event-by-event fluctuations of particle yield ratios measured by the NA49 experiment in Pb+Pb collisions at 20 - 158 AGeV. Systematic studies of the influence of the dE/dx resolution on the particle identification and the centrality bin size were performed. Results can be compared to event-by-event fluctuations measured by NA49 for different observables such as <pt> or the mean charged particle multiplicity. Main results of these studies are an increase of absolute value of the dynamical particle ratio fluctuations with decreasing centrality for all considered ratios, saturation of the K/Pi and K/p ratio fluctuations for peripheral Pb + Pb collisions at 158A GeV and scaling of the energy and centrality dependences of the p/Pi ratio fluctuations with NpNPi. The measured energy and centrality dependences of the K/Pi and K/p ratio fluctuations scale with NK in a different way. The saturation of the mentioned ratios fluctuations was attributed to the development of pronounced spike at zero in the eventwise ratio distributions, which, as was shown by Monte Carlo simulations, influence the measured fluctuations in the very peripheral Pb + Pb collisions at 158A GeV. In future, the CBM experiment at FAIR will investigate the intermediate region of the QCD phase diagram in great detail searching for the first order phase transition line and the expected critical endpoint. It is therefore important to closely investigate its sensitivity towards particle ratio fluctuations in Au+Au collisions at 10-45 AGeV beam energy. Detailed simulation studies will be presented. As an outcome of these feasibility studies we conclude that the CBM experiment will be able to provide high quality data on the subject of the event-by-event flucutations of particle yield ratios with sensitivity in the order of 1%.