Modeling and simulation of fibrinogen and its adsorption behavior

In this thesis different approaches for the modeling and simulation of the blood protein fibrinogen are presented. The approaches are meant to systematically connect the multiple time and length scales involved in the dynamics of fibrinogen in solution and at inorganic surfaces. The first part of the thesis will cover simulations of fibrinogen on an all atom level. Simulations of the fibrinogen protomer and dimer are performed in explicit solvent to characterize the dynamics of fibrinogen in solution. These simulations reveal an unexpectedly large and fast bending motion that is facilitated by molecular hinges located in the coiled-coil region of fibrinogen. This behavior is characterized by a bending and a dihedral angle and the distribution of these angles is measured. As a consequence of the atomistic detail of the simulations it is possible to illuminate small scale behavior in the binding pockets of fibrinogen that hints at a previously unknown allosteric effect. In a second step atomistic simulations of the fibrinogen protomer are performed at graphite and mica surfaces to investigate initial adsorption stages. These simulations highlight the different adsorption mechanisms at the hydrophobic graphite surface and the charged, hydrophilic mica surface. It is found that the initial adsorption happens in a preferred orientation on mica. Many effects of practical interest involve aggregates of many fibrinogen molecules. To investigate such systems, time and length scales need to be simulated that are not attainable in atomistic simulations. It is therefore necessary to develop lower resolution models of fibrinogen. This is done in the second part of the thesis. First a systematically coarse grained model is derived and parametrized based on the atomistic simulations of the first part. In this model the fibrinogen molecule is represented by 45 beads instead of nearly 31,000 atoms. The intra-molecular interactions of the beads are modeled as a heterogeneous elastic network while inter-molecular interactions are assumed to be a combination of electrostatic and van der Waals interaction. A method is presented that determines the charges assigned to beads by matching the electrostatic potential in the atomistic simulation. Lastly a phenomenological model is developed that represents fibrinogen by five beads connected by rigid rods with two hinges. This model only captures the large scale dynamics in the atomistic simulations but can shed light on experimental observations of fibrinogen conformations at inorganic surfaces.

Single meson production in proton diffraction at 190 GeV/c at COMPASS

The quark model successfully describes all ground state bary-ons as members of $SU(N)$ flavour multiplets. For excited baryon states the situation is totally different. There are much less states found in the experiment than predicted in most theoretical calculations. This fact has been known for a long time as the 'missing resonance problem'. In addition, many states found in experiments are only poorly measured up to now. Therefore, further experimental efforts are needed to clarify the situation.rnrnAt mbox{COMPASS}, reactions of a $190uskgigaeVperclight$ hadron beam impinging on a liquid hydrogen target are investigated.rnThe hadron beam contains different species of particles ($pi$, $K$, $p$). To distinguish these particles, two Cherenkov detectors are used. In this thesis, a new method for the identification of particles from the detector information is developed. This method is based on statistical approaches and allows a better kaon identification efficiency with a similar purity compared to the method, which was used before.rnrnThe reaction $pprightarrow ppX$ with $X=(pi^0,~eta,~omega,~phi)$ is used to study different production mechanisms. A previous analysis of $omega$ and $phi$ mesons is extended to pseudoscalar mesons. As the resonance contributions in $peta$ are smaller than in $ppi^0$ a different behaviour of these two final states is expected as a function of kinematic variables. The investigation of these differences allows to study different production mechanisms and to estimate the size of the resonant contribution in the different channels.rnrnIn addition, the channel $pprightarrow ppX$ allows to study baryon resonances in the $pX$ system.rnIn the mbox{COMPASS} energy regime, the reaction is dominated by Pomeron exchange. As a Pomeron carries vacuum quantum numbers, no isospin is transferred between the target proton and the beam proton. Therefore, the $pX$ final state has isospin $textstylefrac{1}{2}$ and all baryon resonances in this channel are $N^ast$ baryons. This offers the opportunity to do spectroscopy without taking $Delta$ resonances into account. rnrnTo disentangle the contributions of different resonances a partial wave analysis (PWA) is used. Different resonances have different spin and parity $J^parity$, which results in different angular distributions of the decay particles. These angular distributions can be calculated from models and then be fitted to the data. From the fit the contributions of the single resonances as well as resonance parameters -- namely the mass and the width -- can be extracted. In this thesis, two different approaches for a partial wave analysis of the reaction $pprightarrow pppi^0$ are developed and tested.

Hadronic correlation functions with quark-disconnected contributions in lattice QCD

One of the fundamental interactions in the Standard Model of particle physicsrnis the strong force, which can be formulated as a non-abelian gauge theoryrncalled Quantum Chromodynamics (QCD). rnIn the low-energy regime, where the QCD coupling becomes strong and quarksrnand gluons are confined to hadrons, a perturbativernexpansion in the coupling constant is not possible.rnHowever, the introduction of a four-dimensional Euclidean space-timernlattice allows for an textit{ab initio} treatment of QCD and provides arnpowerful tool to study the low-energy dynamics of hadrons.rnSome hadronic matrix elements of interest receive contributionsrnfrom diagrams including quark-disconnected loops, i.e. disconnected quarkrnlines from one lattice point back to the same point. The calculation of suchrnquark loops is computationally very demanding, because it requires knowledge ofrnthe all-to-all propagator. In this thesis we use stochastic sources and arnhopping parameter expansion to estimate such propagators.rnWe apply this technique to study two problems which relay crucially on therncalculation of quark-disconnected diagrams, namely the scalar form factor ofrnthe pion and the hadronic vacuum polarization contribution to the anomalousrnmagnet moment of the muon.rnThe scalar form factor of the pion describes the coupling of a charged pion torna scalar particle. We calculate the connected and the disconnected contributionrnto the scalar form factor for three different momentum transfers. The scalarrnradius of the pion is extracted from the momentum dependence of the form factor.rnThe use ofrnseveral different pion masses and lattice spacings allows for an extrapolationrnto the physical point. The chiral extrapolation is done using chiralrnperturbation theory ($chi$PT). We find that our pion mass dependence of thernscalar radius is consistent with $chi$PT at next-to-leading order.rnAdditionally, we are able to extract the low energy constant $ell_4$ from thernextrapolation, and ourrnresult is in agreement with results from other lattice determinations.rnFurthermore, our result for the scalar pion radius at the physical point isrnconsistent with a value that was extracted from $pipi$-scattering data. rnThe hadronic vacuum polarization (HVP) is the leading-order hadronicrncontribution to the anomalous magnetic moment $a_mu$ of the muon. The HVP canrnbe estimated from the correlation of two vector currents in the time-momentumrnrepresentation. We explicitly calculate the corresponding disconnectedrncontribution to the vector correlator. We find that the disconnectedrncontribution is consistent with zero within its statistical errors. This resultrncan be converted into an upper limit for the maximum contribution of therndisconnected diagram to $a_mu$ by using the expected time-dependence of therncorrelator and comparing it to the corresponding connected contribution. Wernfind the disconnected contribution to be smaller than $approx5%$ of thernconnected one. This value can be used as an estimate for a systematic errorrnthat arises from neglecting the disconnected contribution.rn

Monte Carlo simulations of nucleation of colloidal crystals

A crystal nucleus in a finite volume may exhibit phase coexistence with a surrounding fluid. The thermodynamic properties of the coexisting fluid (pressure and chemical potential) are enhanced relative to their coexistence values. This enhancement is uniquely related to the surface excess free energy. rnA model for weakly attractive soft colloidal particles is investigated, the so called Asakura-Oosawa model. In simulations, this model allows for the calculation of the pressure in the liquid using the virial formula directly. The phase coexistence pressure in the thermodynamic limit is obtained from the interface velocity method. We introduce a method by which the chemical potential in dense liquids can be measured. There is neither a need to locate the interface nor to compute the anisotropic interfacial tension to obtain nucleation barriers. Therefore, our analysis is appropriate for nuclei of arbitrary shape. Monte Carlo simulations over a wide range of nucleus volumes yield to nucleation barriers independent from the total system volume. The interfacial tension is determined via the ensemble-switch method, hence a detailed test of classical nucleation theory is possible. The anisotropy of the interfacial tension and the resulting non-spherical shape has only a minor effect on the barrier for the Asakura-Oosawa model.

FaSSIF-C, a Cholesterol containing biorelevant intestinal model medium for development and test of oral drug formulations

Biorelevante Medien sind entwickelt worden, um die Bedingungen im Magen-Darm-Trakt vor und nach der Mahlzeit zu imitieren. Mit FaSSIF und FeSSIF wurden Medien eingeführt, die nicht nur die pH- und Puffer-Kapazität des Dünndarms widerspiegeln, sondern auch Lipid und physiologische Tensid-Arten enthalten. Diese Medien (FaSSIF-V2 und FaSSlFmod6.5) wurden für Bioverfügbarkeitstudien in der Medikamentenentwicklung im Laufe der Jahre kontinuierlich weiterentwickelt. Dennoch sind die auf dem Markt verfügbaren Medien immer noch nicht in der Lage, die realen physiologischen Bedingungen zu simulieren. In der jetzigen Zusammensetzung sind nicht alle Kompetenten enthalten, welche natürlicher Weise im Duodenum vorkommen. Darüber hinaus wird nur eine 1:5 Verdünnung von FeSSIF zu FaSSIF angenommen, die individuelle Wasserzufuhr bei Medikamentengabe wird hierdurch jedoch nur eingeschränkt simuliert, obwohl diese von Patient zu Patient schwanken kann. rnZiel dieser Dissertation war die Verbesserung der Vorhersage der Auflösung und Absorption lipophiler Arzneistoffe durch Simulation der Bedingungen im zweiten Teil des Zwölffingerdarms mit neuen biorelevanten Medien, sowie unter Einwirkung zusätzlicher Detergention als Wirkstoffträger. rnUm den Effekt der Verdünnungsrate und Zeit im Dünndarm zu untersuchen, wurde die Entwicklung der Nanopartikel in der Magen-Darm-Flüssigkeit FaSSIFmod6.5 zu verschiedenen Zeitpunkten und Wassergehalten untersucht. Dafür wurden kinetische Studien an verschieden konzentrierten Modellmedien nach Verdünnungssprung untersucht. Das Modell entspricht der Vermischung der Gallenflüssigkeit mit dem Darminhalt bei variablem Volumen. Die Ergebnisse zeigen, dass Art und Größe der Nanopartikel stark von Verdünnung und Einirkungszeit abhängen. rnrnDie menschliche Darmflüssigkeit enthält Cholesterin, welches in allen früheren Modellmedien fehlt. Daher wurden biokompatible und physiologische Modellflüssigkeiten, FaSSIF-C, entwickelt. Der Cholesteringehalt von FaSSIF - 7C entspricht der Gallenflüssigkeit einer gesunden Frau, FaSSIF - 10C der einer gesunden männlichen Person und FaSSIF - 13C der in einigen Krankheitszuständen. Die intestinale Teilchen-Struktur-Untersuchung mit dynamische Lichtstreuung (DLS) und Neutronen-Kleinwinkelstreuung (SANS) ergab, dass die Korngröße von Vesikeln mit zunehmender Cholesterin-Konzentration abnahm. Zu hohe Cholesterin-Konzentration bewirkte zusätzlich sehr große Partikel, welche vermutlich aus Cholesterin-reichen “Disks“ bestehen. Die Löslichkeiten einiger BCS Klasse II Wirkstoffe (Fenofibrat, Griseofulvin, Carbamazepin, Danazol) in diesen neuen Medien zeigten, dass die Löslichkeit in unterschiedlicher Weise mit der Cholesteringehalt zusammen hing und dieser Effekt selektiv für die Droge war. rnDarüber hinaus wurde die Wirkung von einigen Tensiden auf die kolloidale Struktur und Löslichkeit von Fenofibrat in FaSSIFmod6.5 und FaSSIF -7C untersucht. Struktur und Löslichkeit waren Tensid- und Konzentrations-abhängig. Im Falle von FaSSIFmod6.5 zeigten die Ergebnisse eine dreifache Verzweigung der Lösungswege. Im Bereich mittlerer Tensidkonzentration wurde eine Löslichkeitslücke der Droge zwischen der Zerstörung der Galle-Liposomen und der Bildung von Tensid-reichen Mizellen beobachtet. In FaSSIF - 7C, zerstörten Tenside in höherer Konzentration die Liposomenstruktur trotz der allgemeinen Stabilisierung der Membranen durch Cholesterin. rnDie in dieser Arbeit vorgestellten Ergebnisse ergeben, dass die Anwesenheit von Cholesterin als eine fehlende Komponente der menschlichen Darmflüssigkeit in biorelevanten Medien wichtig ist und dazu beitragen kann, das in vivo Verhalten schwerlöslicher Arzneistoffe im Körper besser vorhersagen zu können. Der Verdünnungsgrad hat einen Einfluss auf die Nanopartikel-Struktur und Tenside beeinflussen die Löslichkeit von Medikamenten in biorelevanten Medien: Dieser Effekt ist sowohl von der Konzentration das Tensids abhängig, als auch dessen Typ.rnrn

[Papers : from Annalen der Physik, ser. 4, Bd. 17-19, 1905].

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