Electrostatics plays a crucial role in the membrane biology. Negatively charged lipids (such as PS, PA and PIP2) are subject to redistribution under the action of electrostatic forces during various signalling events. Membrane recruitment of multiple signalling proteins (such as MARCKS or Src kinase) is often maintained by positively charged polybasic domains (PD). Even though adsorption of these proteins to the cellular membrane has been extensively investigated, very little is known about how electrostatic interactions contribute to their membrane lateral dynamics. This thesis presents an investigation of the contribution of electrostatic interactions to the membrane lateral dynamics by means of novel computational tools. First, I developed a dynamic Monte-Carlo automaton that faithfully simulates lateral diffusion of the adsorbed positively charged PD of a peripheral membrane protein, as well as the dynamics of mono- (PS, PA) and polyvalent (PIP2) anionic lipids within the bilayer. This model allowed to investigate the major characteristics of protein-membrane diffusion on the uniform membrane. In agreement with earlier results, the simulations revealed the following microscopic phenomena: 1) Electrostatic lipid demixing in the vicinity of the PD; 2) PD interacts with PIP2 stronger than with monovalent lipids. On the spatially heterogeneous membrane the automaton predicted a directional drift of the PD, which was validated by a simple mean-field analytical model. The predicted phenomenon could potentially play a major role in membrane domain formation. To test this hypothesis and to investigate the membrane dynamics on larger scales I developed a continuous model, which was based on the results of the automaton simulations. The results of the continuous model and the Monte-Carlo simulations were shown to be in quantitative agreement. The continuous model allows one to simulate the electrostatic membrane dynamics on micrometer scales and can be used to describe various biologically important processes, such as endocytic cup initiation.

The CEBAF Large Acceptance Spectrometer for the 12 GeV era, known as CLAS12, uses the time of flight (TOF) system to identify charged particles from scattering events between the beam and target. The TOF system is divided into two parts: The Forward time of flight system, and the Central time of flight system. These two sub-systems subtend different polar angles of the detector geometry for wide acceptance of scattered particles. Reconstruction is the service used to identify particles from the interactions between the beam and target, called as a vertex or the point where the interaction occurs. The vertex position is traced back using the tracking system and the TOF system. The resolution of the detector affects the accuracy of the reconstructed vertex location. This paper’s goal will be to develop software for validation suite for CLAS12, which will include central and forward tracking plots. Plots will be developed to check the precision of the reconstructed vertices in both the central and forward detectors. This will be done assuming a target with zero dimension at 𝑣𝑧 = 0, and an extended target of 5 cm at 𝑣𝑧 = 0. This paper will also look at the TOF resolution, and identify particles using the TOF detectors and the effect of the vertex correction on the velocity vs. momentum plots.

<p>Next-to-minimal super-symmetric extensions of the Standard Model (SM) predict the existence of several non-SM like Higgs bosons. The process pp→a₁h^±→4b+W involves the production and the decay of a spin-0 charged Higgs boson and a CP-odd Higgs boson a₁ which can have a sizable cross section in the NMSSM. The invariant masses of these intermediate bosons can be reconstructed from the four momenta of the final state particles using mass minimization algorithms. This thesis presents a cut-based analysis of two mass scenarios and specialized algorithms that are capable of recovering the signal in a large background arising from Standard Model processes such as ttbar. The analysis is tested with a realistic ATLAS detector simulation investigating trigger efficiencies and probing several jet reconstruction algorithms.</p>

<p>A generator-level study of dilepton ttbar events to search for light charged Higgs bosons at the LHC is presented with the aim of finding a new variable to discriminate between charged Higgs signals and Standard Model signatures. The spin effects in leptonic decays of H^± and W bosons are studied and a new angular distribution is identified as a discriminating variable. Studies are performed for different charged Higgs masses at two different center ofmass energies. Monte Carlo samples of Z+jets production are also used to test the analysis.</p>

Eine der Faustregeln der Kolloid- und Oberflächenphysik ist, dass die meisten Oberflächen geladen sind, wenn sie mit einem Lösungsmittel, normalerweise Wasser, in Kontakt treten. Dies ist zum Beispiel bei ladungsstabilisierten Kolloidalen Suspensionen der Fall, bei denen die Oberfläche der Kolloidteilchen geladen ist (gewöhnlich mit einer Ladung von mehreren Hunderttausend Elementarladungen), oder bei Monoschichten ionischer Tenside, die auf einer Luft-Wasser Grenzfläche sitzen (wobei die wasserliebenden Kopfgruppen durch die Freisetzung von Gegenionen geladen werden), sowie bei Doppelschichten, die geladene phospholipide enthalten (wie Zellmembranen). In dieser Arbeit betrachten wir einige Modellsysteme, die zwar eine vereinfachte Fassung der Realität darstellen, von denen wir aber dennoch erwarten koennen, dass wir mit ihrer Hilfe einige physikalische Eigenschaften realer geladener Systeme (Kolloide und Elektrolyte) einfangen können. / One of the rules-of-thumb of colloid and surface physics is that most surfaces are charged when in contact with a solvent, usually water. This is the case, for instance, in charge-stabilized colloidal suspensions, where the surface of the colloidal particles are charged (usually with a charge of hundreds to thousands of e, the elementary charge), monolayers of ionic surfactants sitting at an air-water interface (where the water-loving head groups become charged by releasing counterions), or bilayers containing charged phospholipids (as cell membranes). In this work, we look at some model-systems that, although being a simplified version of reality, are expected to capture some of the physical properties of real charged systems (colloids and electrolytes).<br /> <br /> We initially study the simple double layer, composed by a charged wall in the presence of its counterions. The charges at the wall are smeared out and the dielectric constant is the same everywhere. The Poisson-Boltzmann (PB) approach gives asymptotically exact counterion density profiles around charged objects in the weak-coupling limit of systems with low-valent counterions, surfaces with low charge density and high temperature (or small Bjerrum length). Using Monte Carlo simulations, we obtain the profiles around the charged wall and compare it with both Poisson-Boltzmann (in the low coupling limit) and the novel strong coupling (SC) theory in the opposite limit of high couplings. In the latter limit, the simulations show that the SC leads in fact to asymptotically correct density profiles. We also compare the Monte Carlo data with previously calculated corrections to the Poisson-Boltzmann theory. We also discuss in detail the methods used to perform the computer simulations.<br /> <br /> After studying the simple double layer in detail, we introduce a dielectric jump at the charged wall and investigate its effect on the counterion density distribution. As we will show, the Poisson-Boltzmann description of the double layer remains a good approximation at low coupling values, while the strong coupling theory is shown to lead to the correct density profiles close to the wall (and at all couplings). For very large couplings, only systems where the difference between the dielectric constants of the wall and of the solvent is small are shown to be well described by SC.<br /> <br /> Another experimentally relevant modification to the simple double layer is to make the charges at the plane discrete.<br /> The counterions are still assumed to be point-like, but we constraint the distance of approach between ions in the plane and counterions to a minimum distance D. The ratio between D and the distance between neighboring ions in the plane is, as we will see, one of the important quantities in determining the influence of the discrete nature of the charges at the wall over the density profiles. Another parameter that plays an important role, as in the previous case, is the coupling as we will demonstrate, systems with higher coupling are more subject to discretization effects than systems with low coupling parameter.<br /> <br /> After studying the isolated double layer, we look at the interaction between two double layers. The system is composed by two equally charged walls at distance d, with the counterions confined between them. The charge at the walls is smeared out and the dielectric constant is the same everywhere. Using Monte-Carlo simulations we obtain the inter-plate pressure in the global parameter space, and the pressure is shown to be negative (attraction) at certain conditions. The simulations also show that the equilibrium plate separation (where the pressure changes from attractive to repulsive) exhibits a novel unbinding transition. We compare the Monte Carlo results with the strong-coupling theory, which is shown to describe well the bound states of systems with moderate and high couplings. The regime where the two walls are very close to each other is also shown to be well described by the SC theory.<br /> <br /> Finally, Using a field-theoretic approach, we derive the exact low-density ("virial") expansion of a binary mixture of positively and negatively charged hard spheres (two-component hard-core plasma, TCPHC). The free energy obtained is valid for systems where the diameters d_+ and d_- and the charge valences q_+ and q_- of positive and negative ions are unconstrained, i.e., the same expression can be used to treat dilute salt solutions (where typically d_+ ~ d_- and q_+ ~ q_-) as well as colloidal suspensions (where the difference in size and valence between macroions and counterions can be very large). We also discuss some applications of our results.

A generator-level study of dilepton ttbar events to search for light charged Higgs bosons at the LHC is presented with the aim of finding a new variable to discriminate between charged Higgs signals and Standard Model signatures. The spin effects in leptonic decays of H± and W bosons are studied and a new angular distribution is identified as a discriminating variable. Studies are performed for different charged Higgs masses at two different center ofmass energies. Monte Carlo samples of Z+jets production are also used to test the analysis.

With the depletion of petroleum based fuels and the corresponding concerns of national energy security issues, natural gas as an alternative fuel in IC engine applications has become an attractive option. Natural gas requires minimum mixture preparation, and is chemically stable, both of which make it a suitable fuel for homogeneous charged compression ignition (HCCI) engines. Compared to petroleum based fuels, natural gas produces less green-house emissions. However, natural gas is hard to auto-ignite and therefore requires a higher compression ratio, some amount of intake heating, or some type of pre-ignition. In addition, natural gas usually has large differences in fuel composition from field to field, which adds more uncertainties for engine applications. The current study determines the auto-ignition characteristics, engine performance, and nitric oxides emissions as functions of major operating parameters for a natural gas fueled HCCI engine, and determines differences relative to gasoline fueled HCCI engines which have been studied for many years. These tasks have been done using both zero- and multi-dimensional engine simulations. By zero-dimensional simulation, the effects of varying equivalence ratios, engine speeds, compression ratio, EGR level, intake pressure and fuel compositions are determined and analyzed in detail. To be able to account for the in-cylinder inhomogeneous effect on the HCCI combustion, multi-zone models coupled with cold-flow CFD simulations are employed in addition to the single-zone model. The effects of non-homogeneous temperature and equivalence ratio stratification on the ignition timing, combustion phasing, and emissions formation have been studied and discussed. Finally, the preliminary two-dimensional axial-symmetric CFD simulations have been conducted to study the in-cylinder temperature and the species distributions, which provide better visualization of the natural gas auto-ignition process.

The discovery of a charged Higgs boson (H+) would be an unambiguous sign of physics beyond the Standard Model. This thesis describes preparations for the H+ search with the ATLAS experiment at the Large Hadron Collider at CERN. The H+ discovery potential is evaluated, and tools for H+ searches are developed and refined. The H+→τν decay mode has been known as the most promising H+ discovery channel. Within this thesis, first studies of this channel with realistic detector simulation, trigger simulation and consideration of all dominant systematic uncertainties have been performed. Although, as shown by these studies, the discovery sensitivity is significantly degraded compared to studies using a parametrized detector simulation, this channel remains the most powerful ATLAS H+ discovery mode. Future searches will rely on multivariate analysis techniques like the Iterative Discriminant Analysis (IDA) method. First studies indicate that a significant sensitivity increase can be achieved compared to studies based on sequential cuts. The largest uncertainty in H+ searches is the expected $t\bar{t}$ background contribution. It is shown that numbers obtained from simulated events could be off by a factor of two, decreasing the discovery sensitivity dramatically. In this thesis, the Embedding Method for data-driven background estimation is presented. By replacing the muon signature in $t\bar{t}$ events with a simulated τ, events which allow an estimation of the background contribution at the 10% level are obtained. The ATLAS τ identification focuses on comparably clean environments like Z and W decays. To optimize the performance in high-multiplicity events like H+→τν, tau leptons are studied in $t\bar{t}$ and pile-up events. Variables which do not show discrimination power in high-multiplicity events are identified, and in some cases similar, more powerful variables are found. This allows to recover some of the performance loss and to increase the robustness of the τ identification. For the analysis of large amounts of data produced by the ATLAS detector, seamless interoperability of the various Grid flavors is required. This thesis introduces translators to overcome differences in the information system between a number of Grid projects,and highlights important areas for future standardization.

La production de paires de quarks top se désintégrant en deux leptons dont au moins un lepton tau est étudiée dans le cadre de l'expérience CDF auprès du collisionneur proton-antiproton, Tevatron, a FNAL aux USA. La sélection exige un électron ou un muon produit par désintégration du lepton tau ou par désintégration d'un W. L'analyse utilise toutes les données enregistrées, 9 fb-1, avec un déclenchement basé sur un électron ou muon à faible moment transverse et une trace chargée isolée. La section efficace de production de paires de top a cette énergie obtenue est de 8,2+-1.7(+1.2-1.1)+-0,5 pb, et le rapport de branchement en leptons tau est de 0,120+-0,027(+0,022-0,019)+-0,007 avec erreur statistique, systématique et sur la luminosité respectivement. Ce sont à jour les résultats les plus précis dans ce canal de désintégration du top, en bon accord avec les résultats obtenus au Tevatron avec tous les autres canaux de désintégration du top. Le rapport de branchement est aussi mesuré en séparant les événements tau plus lepton et avec deux leptons tau avec une méthode de maximum de vraisemblance. C'est la première fois que ces modes de désintégration sont identifiés séparément. Par une méthode de maximum de vraisemblance appliquée pour séparer ces deux canaux une mesure alternative du rapport de branchement du top en lepton tau de 0,098+-0,022(stat.)+-0,014(syst.) est obtenue, en bon accord avec les prédictions du Modèle Standard. Une limite supérieure de 0,159 pour ce rapport de branchement, avec 95% de niveau de confiance est extraite donnant un indice de Physique au delà du Modèle Standard en particulier un possible boson de Higgs chargé.

An algorithm for extracting event information from a Coulomb Explosion Imaging (CEI) position sensitive detector (PSD) is developed and compared with previously employed schemes. The PSD is calibrated using a newly designed grid overlay and validates the quality of the described algorithm. Precision calculations are performed to determine how best the CEI apparatus at The University of Waterloo can be improved. An algorithm for optimizing coincidence measurements of polyatomic molecules in CEI experiments is developed. Predictions of improved efficiency based on this algorithm are performed and compared with experiments using a triatomic molecule. Analysis of an OCS targeted CEI experiment using highly charged Argon ions to initiate ionization is performed. The resulting measurements are presented using a variety of visualization tools to reveal asynchronous and sequential fragmentation channels of OCS3+.