Molekulardynamik-Simulation zur Struktur von SiO 2-Oberflächen mit adsorbiertem Wasser

In der vorliegenden Arbeit werdenMolekulardynamik-Simulationen zur Untersuchung derstatischen Eigenschaften von amorphenSiliziumdioxidoberflächen (Siliziumdioxid) durchgeführt. Da das von van Beest, Kramer und van Santen vorgeschlagene,sogenannte BKS-Potential für Bulksysteme optimiert wurde und an Oberflächen deutlichandere Ladungsverteilungenauftreten als im Bulk, ist die Anwendbarkeit diesesPotentials für Oberflächensystemefraglich. Aus diesem Grund haben wir untersucht, inwieweitsich die Oberflächeneigenschaften von Systemen, die mit Hilfe des BKS-Potentials äquilibriertwurden, durch ein Nachrelaxieren mit einer ab-initio-Simulation (Car-Parrinello-Methode)ändern. Mit Hilfe der Kombination aus BKS- und Car-Parrinello-Methode (CPMD)konnten wir feststellen, daß sich die Systeme aufgrund des Nachrelaxierens in z-Richtungweiter ausdehnen. Desweiteren zeigte sich insbesondere bei kleinen Ringen (kommen nur ander Oberfläche vor), daß es deutliche Abweichungen in den Geometrien (Atomabstände,Winkel usw.) zwischen der reinen BKS- und der kombinierten BKS-CPMD-Methode gibt. Anhand vonCPMD-Simulationen konnten wir zeigen, daß es durch die Wechselwirkung eines Wassermolekülsmit einem 2er-Ring zum Aufbrechen dieser Ringstruktur und zur Bildung von zweiSilanolgruppen (SiOH) kommt. Desweiteren stellten wir fest, daß es sich hierbei um eineexotherme Reaktion (Energiedifferenz 1.6 eV) handelt, für die eineEnergiebarriere von 1.1 eV überwunden werden muß. Ferner ergab sich, daß die an der Bildung des2er-Ringes beteiligten, stark deformierten Tetraeder nach dem Aufbrechen dieserRingstruktur eine nahezu ideale Tetraederform annehmen.

Novel simulation methods for Coulomb and hydrodynamic interactions

This thesis presents new methods to simulate systems with hydrodynamic and electrostatic interactions. Part 1 is devoted to computer simulations of Brownian particles with hydrodynamic interactions. The main influence of the solvent on the dynamics of Brownian particles is that it mediates hydrodynamic interactions. In the method, this is simulated by numerical solution of the Navier--Stokes equation on a lattice. To this end, the Lattice--Boltzmann method is used, namely its D3Q19 version. This model is capable to simulate compressible flow. It gives us the advantage to treat dense systems, in particular away from thermal equilibrium. The Lattice--Boltzmann equation is coupled to the particles via a friction force. In addition to this force, acting on {it point} particles, we construct another coupling force, which comes from the pressure tensor. The coupling is purely local, i.~e. the algorithm scales linearly with the total number of particles. In order to be able to map the physical properties of the Lattice--Boltzmann fluid onto a Molecular Dynamics (MD) fluid, the case of an almost incompressible flow is considered. The Fluctuation--Dissipation theorem for the hybrid coupling is analyzed, and a geometric interpretation of the friction coefficient in terms of a Stokes radius is given. Part 2 is devoted to the simulation of charged particles. We present a novel method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. This algorithm scales linearly, too. We focus on the Molecular Dynamics version of the method and show that it is intimately related to the Car--Parrinello approach, while being equivalent to solving Maxwell's equations with freely adjustable speed of light. The Lagrangian formulation of the coupled particles--fields system is derived. The quasi--Hamiltonian dynamics of the system is studied in great detail. For implementation on the computer, the equations of motion are discretized with respect to both space and time. The discretization of the electromagnetic fields on a lattice, as well as the interpolation of the particle charges on the lattice is given. The algorithm is as local as possible: Only nearest neighbors sites of the lattice are interacting with a charged particle. Unphysical self--energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green's function. The method allows easy parallelization using standard domain decomposition. Some benchmarking results of the algorithm are presented and discussed.

Development of empirical potentials for amorphous silica

Development of empirical potentials for amorphous silica Amorphous silica (SiO2) is of great importance in geoscience and mineralogy as well as a raw material in glass industry. Its structure is characterized as a disordered continuous network of SiO4 tetrahedra. Many efforts have been undertaken to understand the microscopic properties of silica by classical molecular dynamics (MD) simulations. In this method the interatomic interactions are modeled by an effective potential that does not take explicitely into account the electronic degrees of freedom. In this work, we propose a new methodology to parameterize such a potential for silica using ab initio simulations, namely Car-Parrinello (CP) method [Phys. Rev. Lett. 55, 2471 (1985)]. The new potential proposed is compared to the BKS potential [Phys. Rev. Lett. 64, 1955 (1990)] that is considered as the benchmark potential for silica. First, CP simulations have been performed on a liquid silica sample at 3600 K. The structural features so obtained have been compared to the ones predicted by the classical BKS potential. Regarding the bond lengths the BKS tends to underestimate the Si-O bond whereas the Si-Si bond is overestimated. The inter-tetrahedral angular distribution functions are also not well described by the BKS potential. The corresponding mean value of theSiOSi angle is found to be ≃ 147◦, while the CP yields to aSiOSi angle centered around 135◦. Our aim is to fit a classical Born-Mayer/Coulomb pair potential using ab initio calculations. To this end, we use the force-matching method proposed by Ercolessi and Adams [Europhys. Lett. 26, 583 (1994)]. The CP configurations and their corresponding interatomic forces have been considered for a least square fitting procedure. The classical MD simulations with the resulting potential have lead to a structure that is very different from the CP one. Therefore, a different fitting criterion based on the CP partial pair correlation functions was applied. Using this approach the resulting potential shows a better agreement with the CP data than the BKS ones: pair correlation functions, angular distribution functions, structure factors, density of states and pressure/density were improved. At low temperature, the diffusion coefficients appear to be three times higher than those predicted by the BKS model, however showing a similar temperature dependence. Calculations have also been carried out on crystalline samples in order to check the transferability of the potential. The equilibrium geometry as well as the elastic constants of α-quartz at 0 K are well described by our new potential although the crystalline phases have not been considered for the parameterization. We have developed a new potential for silica which represents an improvement over the pair potentials class proposed so far. Furthermore, the fitting methodology that has been developed in this work can be applied to other network forming systems such as germania as well as mixtures of SiO2 with other oxides (e.g. Al2O3, K2O, Na2O).

Heteroatom containing polycyclic aromatic hydrocarbons with positive charge - synthesis and characterization

The synthesis and characterization of various heteroatom containing PAHs with positive charge were investigated in this work: 1. A series of 2-phenyl-benzo[8,9]quinolizino[4,5,6,7-fed]phenanthridinylium (PQP) salts with different alkyl chains and anions were synthesized. The synthesis of the extended derivates of PQP salts with two fused benzene rings, 2-phenyl-naphthacene[1,2]quinolizino[3,4,5,6-def]benzo[i]phenanthridinium (DBPQP) tetrafluoroborate was also developed. The self-assembly behavior of these amphiphilic PAHs was investigated in methanolic solution as well as in the bulk. Various aggregates with different morphologies such as fibers, tubes and vesicals were obtained from their solution. All of these morphology changes could be ascribed to the changes in intermolecular interactions which resulting from the difference in the molecular structures such as aromatic cores, alkyl chains and counterions. 2. The synthetic strategy of oxygen containing positively charged PAHs, benzo[5,6]naphthaceno[1,12,11,10-jklmna]xanthylium (BNAX) salts and its dibenzo derivates, DBNAX salts were developed. With a similar method, sulfur containing benzo[5,6]naphthaceno[1,12,11,10-jklmna]thioxanthylium (BNATX) salts were also synthesized. Various BNAX salts with different alkyl chains could be obtained and their supramolecular behavior were investigated. A discotic liquid crystalline behavior was observed for di- (3-25) and tridodecyl (3-27) substituted BNAX salts and both compounds exhibited large unit cell in their 2D-WAXS patterns which could be attributed to the formation of dimer structures. By drop casting their methanolic solution on silicon wafers, similar nanoscaled fibers from monododecyl substituted BNAX bromide 3-24 and DBNAX bromide 3-35 could be observed. 3. A novel synthetic method toward nitrogen containing 14-phenyl-dibenzo[jk,mn]naphtho[2,1,8-fgh]thebenidinium (DBNT) salts was also developed. In this method, the undehydrogenated precursor of DBNT, dibenzoacridinium salt could be produced directly from the reaction between dibenzoxanthenylium derivates and amine/aniline in reasonable yields. Various DBNT salts with different alkyl and alkylphenyl chains on their nitrogen atom were synthesized in this two-step method. The self-assembly behavior of two alkylated DBNT salts, 4-15a and 4-18b was also studied in this work. Compound 4-15a formed nanoscaled fibers and helical aggregates were obtained from 4-18b in their methanolic solutions. 4. Various ionic complexes were derived by complexing PQP and DBPQP cations with different sulfate/sulfonate group containing anionic surfactants. The ionic complexes resulting from the ionic self-assembly (ISA) method exhibited self-assembly behavior which was controllable by the species and shape of cations and anions. Various aggregates such as nanofibers and spherical aggregates could be produced from their methanolic solution in a defined manner conveniently.

Entwicklung eines Tests zur Ablösung von Tierversuchen beim Nachweis von Pertussis-Toxin

Weltweit existiert keine zum Tierversuch alternative Methode, um adsorbierte Pertussis-Impfstoffe auf restliche Toxin-Aktivität hin zu untersuchen. Der im Europäischen Arzneibuch vorgeschriebene Tierversuch besitzt nach Erfahrungen der Industrie, internationaler Prüfbehörden sowie des Paul-Ehrlich-Institutes eine schlechte Aussagekraft. Er ist wenig standardisierbar und weist häufig ein zweifelhaftes Ergebnis auf, so dass Wiederholungen und damit einhergehend ein hoher Verbrauch an Versuchstieren unumgänglich sind. Enthält der Impfstoff Reste von nicht-inaktiviertem Pertussis-Toxin (PTx), muss mit schweren und schwersten Nebenwirkungen bei den Impflingen gerechnet werden. In dieser Arbeit wurde ein In vitro-Nachweis für aktives PTx entwickelt. rnAngeregt durch Publikationen, wonach Pertussis-Toxin humane Monozyten aktiviert, wurde zunächst versucht, diesen Effekt zum Toxin-Nachweis auszunutzen. Die vorliegende Arbeit zeigt jedoch eindeutig, dass Pertussis-Toxin selbst nicht zur Stimulation humaner Monozyten führt. Vielmehr konnte nachgewiesen werden, dass die Aktivierung dieser Immunzellen auf Kontaminationen durch Lipopolysaccharide zurückzuführen ist. Damit wurden die Aussagen in den oben erwähnten Veröffentlichungen widerlegt. Dieses Ergebnis wurde bereits zur Publikation eingereicht.rnNunmehr wurden verschiedene Ansätze zum Nachweis von Pertussis-Toxin entwickelt, welche seine enzymatischen Aktivitäten als NAD-Glycohydrolase und ADP-Ribosyltransferase ausnutzen. Zunächst wurde versucht, die Hydrolyse von NAD zu ADP-Ribose und Nicotinamid photometrisch nachzuweisen. Wegen unbefriedigender Sensitivität wurde dieses Verfahren zu einem fluorometrischen Nachweis weiterentwickelt. Verwendet wurde hier fluorogenes etheno-NAD, welches von Pertussis-Toxin als Substrat akzeptiert wird. Letzteres Prinzip ist zum In vitro-Nachweis von Pertussis-Toxin geeignet, wird jedoch durch das in Impfstoffen häufig verwendete Adsorbens Aluminiumhydroxid gestört. Deshalb wurde dieser Ansatz aufgegeben und ein neuer Weg verfolgt, welcher am Energiestoffwechsel von humanen Zellen ansetzt. Eine Konsequenz des Angriffs von Pertussis-Toxin auf seine Zielzellen im Respirationstrakt besteht – nach komplexen Reaktionen des Signaltransduktionsweges – im Absenken des ATP-Gehaltes. Als menschliche Surrogat-Zellen wurden frisch isolierte periphere mononukleäre Zellen (PBMCs) sowie die permanente Lymphozyten-Zelllinie Jurkat eingesetzt und deren ATP-Gehalt mittels Luziferin-Luziferase-Lumineszenz gemessen. Der Test wird nicht durch Lipopolysaccharid gestört und auch Aluminiumhydroxid übt erst nach mehreren Stunden Inkubation einen interferierenden Einfluss aus. Ebenso konnte aktives Pertussis-Toxin mit Hilfe kryokonservierter PBMCs detektiert werden, auch in orientierenden Versuchen mit komplexen Impfstoffen. Der Pertussis-ATP-Test kommt der In vivo-Situation in der Zelle sehr nahe, weil beide Untereinheiten des Toxins in einem Test überprüft werden. Demnach soll er Bestandteil einer geplanten internationalen Studie zu alternativen Pertussis-Toxin-Testungen sein.

Leishmania major parasites and their interaction with human macrophages

First both life stages of Leishmania major (L. major) FEBNI parasites, promastigotes as well as amastigotes, were characterized. We found that the virulence marker GP63 and cysteine peptidase b (Cpb) were higher expressed by axenic amastigotes as compared to promastigotes. In addition to the L. major FEBNI strain, we applied and successfully modified our novel in vitro method to generate axenic amastigotes of the L. major Friedlin and 5ASKH strains. Interestingly, these L. major strains needed another temperature to be transferred into amastigotes in the axenic culture system. Investigating apoptosis mechanisms in both parasite life stages of L. major FEBNI we found both ROS dependent and independent cell death mechanisms. Focusing on promastigote and amastigote interaction with pro-inflammatory (MF I) and anti-inflammatory (MF II) macrophages we found amastigotes to be more infective as compared to promastigotes. Moreover, we could demonstrate that pro-inflammatory MF I were less susceptible to infection than anti-inflammatory MF II. Finally we investigated parasite stage-specific responses of MF I + II and their defense mechanisms against L. major. Using knockdown techniques for primary human macrophages we identified a new mechanism enabling intracellular killing of promastigotes inside MF I. This mechanism depends on the antimicrobial molecule cathelicidin (LL-37).